@article{Schafer2024-fs, title = {{BioKGrapher}: Initial evaluation of automated knowledge graph construction from biomedical literature}, author = {Sch{\"a}fer, Henning and Idrissi-Yaghir, Ahmad and Arzideh, Kamyar and Damm, Hendrik and Pakull, Tabea M G and Schmidt, Cynthia S and Bahn, Mikel and Lodde, Georg and Livingstone, Elisabeth and Schadendorf, Dirk and Nensa, Felix and Horn, Peter A and Friedrich, Christoph M}, journal = {Comput. Struct. Biotechnol. J.}, publisher = {Elsevier BV}, volume = {24}, pages = {639--660}, month = dec, year = {2024}, keywords = {Clinical guidelines; Entity linking; Knowledge graph; Named entity recognition; Software}, copyright = {http://creativecommons.org/licenses/by-nc-nd/4.0/}, language = {en} }
@article{Hoyer2024-xp, title = {{AI-based} digital histopathology for perihilar cholangiocarcinoma: A step, not a jump}, author = {Hoyer, Dieter P and Ting, Saskia and Rogacka, Nina and Koitka, Sven and Hosch, Ren{\'e} and Flaschel, Nils and Haubold, Johannes and Malamutmann, Eugen and St{\"u}ben, Bj{\"o}rn-Ole and Treckmann, J{\"u}rgen and Nensa, Felix and Baldini, Giulia}, journal = {J. Pathol. Inform.}, publisher = {Elsevier BV}, volume = {15}, number = {100345}, pages = {100345}, month = dec, year = {2024}, keywords = {Artificial intelligence; Cholangiocarcinoma; Digital pathology; Klatskin; Segmentation; Survival analysis}, copyright = {http://creativecommons.org/licenses/by/4.0/}, language = {en} }
@article{Nensa2024-qd, title = {Beyond accuracy: Reproducibility must lead {AI} advances in radiology}, author = {Nensa, Felix and Pinto Dos Santos, Daniel and Dietzel, Mathias}, journal = {Eur. J. Radiol.}, publisher = {Elsevier BV}, volume = {180}, number = {111703}, pages = {111703}, month = nov, year = {2024}, language = {en} }
@article{Brehmer2024-cb, title = {Establishing medical intelligence-leveraging Fast Healthcare Interoperability Resources to improve clinical management: Retrospective cohort and clinical implementation study}, author = {Brehmer, Alexander and Sauer, Christopher Martin and Salazar Rodr{\'\i}guez, Jayson and Herrmann, Kelsey and Kim, Moon and Keyl, Julius and Bahnsen, Fin Hendrik and Frank, Benedikt and K{\"o}hrmann, Martin and Rassaf, Tienush and Mahabadi, Amir-Abbas and Hadaschik, Boris and Darr, Christopher and Herrmann, Ken and Tan, Susanne and Buer, Jan and Brenner, Thorsten and Reinhardt, Hans Christian and Nensa, Felix and Gertz, Michael and Egger, Jan and Kleesiek, Jens}, journal = {J. Med. Internet Res.}, publisher = {JMIR Publications Inc.}, volume = {26}, pages = {e55148}, month = oct, year = {2024}, keywords = {FHIR; clinical decision-making; clinical informatics; clinical management; data exchange; electronic health records; interoperability; medical intelligence; quality improvement; quality of care; real-world evidence}, language = {en} }
@article{Salhofer2024-eq, title = {{CT-based} body composition analysis and pulmonary fat attenuation volume as biomarkers to predict overall survival in patients with non-specific interstitial pneumonia}, author = {Salh{\"o}fer, Luca and Bonella, Francesco and Meetschen, Mathias and Umutlu, Lale and Forsting, Michael and Schaarschmidt, Benedikt M and Opitz, Marcel and Beck, Nikolas and Zensen, Sebastian and Hosch, Ren{\'e} and Parmar, Vicky and Nensa, Felix and Haubold, Johannes}, journal = {Eur. Radiol. Exp.}, publisher = {Springer Science and Business Media LLC}, volume = {8}, number = {1}, pages = {114}, month = oct, year = {2024}, keywords = {Body composition; Deep learning; Lung diseases (interstitial); Survival analysis; Tomography (x-ray computed)}, copyright = {https://creativecommons.org/licenses/by/4.0}, language = {en} }
@article{Welsner2024-yr, title = {Opportunistic screening for low bone mineral density in adults with cystic fibrosis using low-dose computed tomography of the chest with artificial intelligence}, author = {Welsner, Matthias and Navel, Henning and Hosch, Rene and Rathsmann, Peter and Stehling, Florian and Mathew, Annie and Sutharsan, Sivagurunathan and Strassburg, Svenja and Westh{\"o}lter, Dirk and Taube, Christian and Zensen, Sebastian and Schaarschmidt, Benedikt M and Forsting, Michael and Nensa, Felix and Holtkamp, Mathias and Haubold, Johannes and Salh{\"o}fer, Luca and Opitz, Marcel}, journal = {J. Clin. Med.}, volume = {13}, number = {19}, month = oct, year = {2024}, keywords = {DXA; adults; artificial intelligence; bone disease; bone mineral density; computed tomography; cystic fibrosis; opportunistic screening; osteoporosis}, language = {en} }
@article{hanssen_ncbench_2024, title = {{NCBench}: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for {DNA}-sequencing-based variant calling}, volume = {12:1125}, copyright = {https://creativecommons.org/licenses/by/4.0/}, shorttitle = {{NCBench}}, url = {https://f1000research.com/articles/12-1125}, doi = {10.12688/f1000research.140344.2}, language = {en}, urldate = {2024-11-15}, journal = {F1000Research}, author = {Hanssen, Friederike and Gabernet, Gisela and Bäuerle, Famke and Stöcker, Bianca and Wiegand, Felix and Smith, Nicholas H. and Mertes, Christian and Neogi, Avirup Guha and Brandhoff, Leon and Ossowski, Anna and Altmueller, Janine and Becker, Kerstin and Petzold, Andreas and Sturm, Marc and Stöcker, Tyll and Sivalingam, Sugirthan and Brand, Fabian and Schmidt, Axel and Buness, Andreas and Probst, Alexander J. and Motameny, Susanne and Köster, Johannes}, month = sep, year = {2024}, keywords = {benchmarking, continuous, NGS, variant calling}, file = {Full Text PDF:/home/johannes/Zotero/storage/FS6SJ9AJ/Hanssen et al. - 2024 - NCBench providing an open, reproducible, transparent, adaptable, and continuous benchmark approach.pdf:application/pdf} }
@article{Styczen2024-xi, title = {Impact of imaging biomarkers from body composition analysis on outcome of endovascularly treated acute ischemic stroke patients}, author = {Styczen, Hanna and Maus, Volker and Weiss, Daniel and Goertz, Lukas and Hosch, Ren{\'e} and Rubbert, Christian and Beck, Nikolas and Holtkamp, Mathias and Salh{\"o}fer, Luca and Schubert, Rosa and Deuschl, Cornelius and Nensa, Felix and Haubold, Johannes}, journal = {J. Neurointerv. Surg.}, month = sep, year = {2024}, keywords = {CT Angiography; Stroke; Thrombectomy}, language = {en} }
@article{Baldini2024-ei, title = {Addressing the contrast media recognition challenge: A fully automated machine learning approach for predicting contrast phases in {CT} imaging}, author = {Baldini, Giulia and Hosch, Ren{\'e} and Schmidt, Cynthia S and Borys, Katarzyna and Kroll, Lennard and Koitka, Sven and Haubold, Patrizia and Pelka, Obioma and Nensa, Felix and Haubold, Johannes}, journal = {Invest. Radiol.}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {59}, number = {9}, pages = {635--645}, month = sep, year = {2024}, language = {en} }
@article{Klug2024-du, title = {From admission to discharge: a systematic review of clinical natural language processing along the patient journey}, author = {Klug, Katrin and Beckh, Katharina and Antweiler, Dario and Chakraborty, Nilesh and Baldini, Giulia and Laue, Katharina and Hosch, Ren{\'e} and Nensa, Felix and Schuler, Martin and Giesselbach, Sven}, journal = {BMC Med. Inform. Decis. Mak.}, publisher = {Springer Science and Business Media LLC}, volume = {24}, number = {1}, pages = {238}, month = aug, year = {2024}, keywords = {Bias; Clinical natural language processing; Explainable ML; Out-of-distribution generalization; Patient journey}, copyright = {https://creativecommons.org/licenses/by/4.0}, language = {en} }
@article{Muller2024-sm, title = {{AI-derived} body composition parameters as prognostic factors in patients with {HCC} undergoing {TACE} in a multicenter study}, author = {M{\"u}ller, Lukas and M{\"a}hringer-Kunz, Aline and Auer, Timo Alexander and Fehrenbach, Uli and Gebauer, Bernhard and Haubold, Johannes and Schaarschmidt, Benedikt Michael and Kim, Moon-Sung and Hosch, Ren{\'e} and Nensa, Felix and Kleesiek, Jens and Diallo, Thierno D and Eisenbl{\"a}tter, Michel and Kuzior, Hanna and Roehlen, Natascha and Bettinger, Dominik and Steinle, Verena and Mayer, Philipp and Zopfs, David and Pinto Dos Santos, Daniel and Kloeckner, Roman}, journal = {JHEP Rep.}, publisher = {Elsevier BV}, volume = {6}, number = {8}, pages = {101125}, month = aug, year = {2024}, keywords = {Artificial Intelligence; Body Composition; Hepatocellular Carcinoma; Transarterial Chemoembolization}, copyright = {http://creativecommons.org/licenses/by/4.0/}, language = {en} }
@article{uzuner_orthanq_2024, title = {Orthanq: transparent and uncertainty-aware haplotype quantification with application in {HLA}-typing}, volume = {25}, issn = {1471-2105}, shorttitle = {Orthanq}, url = {https://doi.org/10.1186/s12859-024-05832-4}, doi = {10.1186/s12859-024-05832-4}, number = {1}, urldate = {2024-11-15}, journal = {BMC Bioinformatics}, author = {Uzuner, Hamdiye and Paschen, Annette and Schadendorf, Dirk and Köster, Johannes}, month = jul, year = {2024}, keywords = {Bayesian latent variable model, Genomic variants, Haplotype quantification, HLA typing, Uncertainty quantification}, pages = {240}, file = {Full Text PDF:/home/johannes/Zotero/storage/J75FKL4U/Uzuner et al. - 2024 - Orthanq transparent and uncertainty-aware haplotype quantification with application in HLA-typing.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/EALVNGHN/s12859-024-05832-4.html:text/html} }
@article{Kohnke2024-oo, title = {A proof of concept for microcirculation monitoring using machine learning based hyperspectral imaging in critically ill patients: a monocentric observational study}, author = {Kohnke, Judith and Pattberg, Kevin and Nensa, Felix and Kuhlmann, Henning and Brenner, Thorsten and Schmidt, Karsten and Hosch, Ren{\'e} and Espeter, Florian}, journal = {Crit. Care}, publisher = {Springer Science and Business Media LLC}, volume = {28}, number = {1}, pages = {230}, month = jul, year = {2024}, copyright = {https://creativecommons.org/licenses/by/4.0}, language = {en} }
@article{schuler_neoadjuvant_2024, title = {Neoadjuvant nivolumab with or without relatlimab in resectable non-small-cell lung cancer: a randomized phase 2 trial}, volume = {30}, copyright = {2024 The Author(s)}, issn = {1546-170X}, shorttitle = {Neoadjuvant nivolumab with or without relatlimab in resectable non-small-cell lung cancer}, url = {https://www.nature.com/articles/s41591-024-02965-0}, doi = {10.1038/s41591-024-02965-0}, language = {en}, number = {6}, urldate = {2024-11-15}, journal = {Nature Medicine}, author = {Schuler, Martin and Cuppens, Kristof and Plönes, Till and Wiesweg, Marcel and Du Pont, Bert and Hegedus, Balazs and Köster, Johannes and Mairinger, Fabian and Darwiche, Kaid and Paschen, Annette and Maes, Brigitte and Vanbockrijck, Michel and Lähnemann, David and Zhao, Fang and Hautzel, Hubertus and Theegarten, Dirk and Hartemink, Koen and Reis, Henning and Baas, Paul and Schramm, Alexander and Aigner, Clemens}, month = jun, year = {2024}, note = {Publisher: Nature Publishing Group}, keywords = {Drug development, Randomized controlled trials, Translational research}, pages = {1602--1611}, file = {Full Text PDF:/home/johannes/Zotero/storage/NX2KNE42/Schuler et al. - 2024 - Neoadjuvant nivolumab with or without relatlimab in resectable non-small-cell lung cancer a randomi.pdf:application/pdf} }
@article{Ruckert2024-au, title = {{ROCOv2}: Radiology objects in {COntext} version 2, an updated multimodal image dataset}, author = {R{\"u}ckert, Johannes and Bloch, Louise and Br{\"u}ngel, Raphael and Idrissi-Yaghir, Ahmad and Sch{\"a}fer, Henning and Schmidt, Cynthia S and Koitka, Sven and Pelka, Obioma and Abacha, Asma Ben and G Seco de Herrera, Alba and M{\"u}ller, Henning and Horn, Peter A and Nensa, Felix and Friedrich, Christoph M}, journal = {Sci. Data}, publisher = {Springer Science and Business Media LLC}, volume = {11}, number = {1}, pages = {688}, month = jun, year = {2024}, copyright = {https://creativecommons.org/licenses/by/4.0}, language = {en} }
@article{Schuler2024-jz, title = {Early metabolic response by {PET} predicts sensitivity to next-line targeted therapy in {EGFR-mutated} lung cancer with unknown mechanism of acquired resistance}, author = {Schuler, Martin and Hense, J{\"o}rg and Darwiche, Kaid and Michels, Sebastian and Hautzel, Hubertus and Kobe, Carsten and Lueong, Smiths and Metzenmacher, Martin and Herold, Thomas and Zaun, Gregor and Laue, Katharina and Drzezga, Alexander and Theegarten, Dirk and Nensa, Felix and Wolf, J{\"u}rgen and Herrmann, Ken and Wiesweg, Marcel}, journal = {J. Nucl. Med.}, publisher = {Society of Nuclear Medicine}, volume = {65}, number = {6}, pages = {851--855}, month = jun, year = {2024}, keywords = {EGFR TKI; FDG PET/CT; metabolic response; resistance; targeted therapy}, language = {en} }
@article{Haubold2024-ib, title = {{BOA}: A {CT-based} body and organ analysis for radiologists at the Point of care}, author = {Haubold, Johannes and Baldini, Giulia and Parmar, Vicky and Schaarschmidt, Benedikt Michael and Koitka, Sven and Kroll, Lennard and van Landeghem, Natalie and Umutlu, Lale and Forsting, Michael and Nensa, Felix and Hosch, Ren{\'e}}, journal = {Invest. Radiol.}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {59}, number = {6}, pages = {433--441}, month = jun, year = {2024}, language = {en} }
@article{Koitka2024-gg, title = {{SAROS}: A dataset for whole-body region and organ segmentation in {CT} imaging}, author = {Koitka, Sven and Baldini, Giulia and Kroll, Lennard and van Landeghem, Natalie and Pollok, Olivia B and Haubold, Johannes and Pelka, Obioma and Kim, Moon and Kleesiek, Jens and Nensa, Felix and Hosch, Ren{\'e}}, journal = {Sci. Data}, publisher = {Springer Science and Business Media LLC}, volume = {11}, number = {1}, pages = {483}, month = may, year = {2024}, copyright = {https://creativecommons.org/licenses/by/4.0}, language = {en} }
@inproceedings{webetal, author = {Weber, Frank-Andreas and Schoth, J. and Jagemann, P. and Schmidt, T. and Widera, Marek and Wilhelm, Alexander and Meyer, F. and Schmithausen, Ricarda and Kraiselburd, Ivana and Moebus, S. and Schmiege, Dennis and Wintgens, T. and Linnemann, V. and Wolber, J.-L}, year = {2024}, month = apr, pages = {}, title = {WBEready – Wastewater-based epidemiology and preparedness: research needs for an adaptive monitoring in the Public Health Service}, volume = {86}, journal = {Das Gesundheitswesen}, doi = {10.1055/s-0044-1781837} }
@inproceedings{Sachse24, author = {Sachse, S. and Anastasiou, Olympia and Elsner, Carina and Ross, R. and Goretzki, S. and Goer, S. and Nagel, R. and Koldehoff, M. and Savin, Mykhailo and Döhla, Manuel and Mutters, Nico and Thomas, Alexander and Kraiselburd, Ivana and Meyer, F. and Schmithausen, Ricarda and Dittmer, Ulf}, year = {2024}, month = apr, pages = {}, title = {From airport to school to hospital – the story of a rare SARS-CoV-2 virus variant import}, volume = {86}, journal = {Das Gesundheitswesen}, doi = {10.1055/s-0044-1781946} }
@article{Westholter2024-ga, title = {Elexacaftor/tezacaftor/ivacaftor influences body composition in adults with cystic fibrosis: a fully automated {CT-based} analysis}, author = {Westh{\"o}lter, Dirk and Haubold, Johannes and Welsner, Matthias and Salh{\"o}fer, Luca and Wienker, Johannes and Sutharsan, Sivagurunathan and Stra{\ss}burg, Svenja and Taube, Christian and Umutlu, Lale and Schaarschmidt, Benedikt M and Koitka, Sven and Zensen, Sebastian and Forsting, Michael and Nensa, Felix and Hosch, Ren{\'e} and Opitz, Marcel}, journal = {Sci. Rep.}, volume = {14}, number = {1}, pages = {9465}, month = apr, year = {2024}, language = {en} }
@article{Wienker2024-sw, title = {Body composition impacts outcome of bronchoscopic lung volume reduction in patients with severe emphysema: a fully automated {CT-based} analysis}, author = {Wienker, Johannes and Darwiche, Kaid and R{\"u}sche, Nele and B{\"u}scher, Erik and Karpf-Wissel, R{\"u}diger and Winantea, Jane and {\"O}zkan, Filiz and Westh{\"o}lter, Dirk and Taube, Christian and Kersting, David and Hautzel, Hubertus and Salh{\"o}fer, Luca and Hosch, Ren{\'e} and Nensa, Felix and Forsting, Michael and Schaarschmidt, Benedikt M and Zensen, Sebastian and Theysohn, Jens and Umutlu, Lale and Haubold, Johannes and Opitz, Marcel}, journal = {Sci. Rep.}, volume = {14}, number = {1}, pages = {8718}, month = apr, year = {2024}, keywords = {Artificial intelligence; Body composition; Bronchoscopic lung volume reduction; Chronic obstructive pulmonary disease; Computed tomography; Deep learning; Emphysema; Valves}, language = {en} }
@article{Meetschen2024-en, title = {{AI-assisted} X-ray fracture detection in residency training: Evaluation in pediatric and adult trauma patients}, author = {Meetschen, Mathias and Salh{\"o}fer, Luca and Beck, Nikolas and Kroll, Lennard and Ziegenfu{\ss}, Christoph David and Schaarschmidt, Benedikt Michael and Forsting, Michael and Mizan, Shamoun and Umutlu, Lale and Hosch, Ren{\'e} and Nensa, Felix and Haubold, Johannes}, journal = {Diagnostics (Basel)}, publisher = {MDPI AG}, volume = {14}, number = {6}, pages = {596}, month = mar, year = {2024}, keywords = {X-rays; artificial intelligence; bone; diagnostic imaging; fractures; quality improvement}, copyright = {https://creativecommons.org/licenses/by/4.0/}, language = {en} }
@article{Umutlu2024-vg, title = {Radiomics analysis of multiparametric {PET/MRI} for {N-} and M-staging in patients with primary cervical cancer}, author = {Umutlu, Lale and Nensa, Felix and Demircioglu, Aydin and Antoch, Gerald and Herrmann, Ken and Forsting, Michael and Grueneisen, Johannes Stefan}, journal = {Nuklearmedizin}, publisher = {Georg Thieme Verlag KG}, volume = {63}, number = {1}, pages = {34--42}, month = feb, year = {2024}, language = {en} }
@article{Haubold2024-gi, title = {{AI} as a new frontier in contrast media research: Bridging the gap between contrast media reduction, the contrast-free question and new application discoveries}, author = {Haubold, Johannes and Hosch, Ren{\'e} and Jost, Gregor and Kreis, Felix and Forsting, Michael and Pietsch, Hubertus and Nensa, Felix}, journal = {Invest. Radiol.}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {59}, number = {2}, pages = {206--213}, month = feb, year = {2024}, language = {en} }
@article{Fuchs2024-cz, title = {Closing the loop for {AI-ready} radiology}, author = {Fuchs, Moritz and Gonzalez, Camila and Frisch, Yannik and Hahn, Paul and Matthies, Philipp and Gruening, Maximilian and Pinto Dos Santos, Daniel and Dratsch, Thomas and Kim, Moon and Nensa, Felix and Trenz, Manuel and Mukhopadhyay, Anirban}, journal = {Rofo}, volume = {196}, number = {2}, pages = {154--162}, month = feb, year = {2024}, language = {en} }
@article{Parmar2024-hk, title = {Fully automated {MR-based} virtual biopsy of primary {CNS} lymphomas}, author = {Parmar, Vicky and Haubold, Johannes and Salh{\"o}fer, Luca and Meetschen, Mathias and Wrede, Karsten and Glas, Martin and Guberina, Maja and Blau, Tobias and Bos, Denise and Kureishi, Anisa and Hosch, Ren{\'e} and Nensa, Felix and Forsting, Michael and Deuschl, Cornelius and Umutlu, Lale}, journal = {Neurooncol. Adv.}, publisher = {Oxford University Press (OUP)}, volume = {6}, number = {1}, pages = {vdae022}, month = jan, year = {2024}, keywords = {artificial intelligence; central nervous system; glioma; lymphoma; neoplasms magnetic resonance imaging}, language = {en} }
@article{Salhofer2024-xh, title = {The importance of educational tools and a new software solution for visualizing and quantifying report correction in radiology training}, author = {Salh{\"o}fer, Luca and Haubold, Johannes and Gutt, Maurice and Hosch, Ren{\'e} and Umutlu, Lale and Meetschen, Mathias and Schuessler, Maximilian and Forsting, Michael and Nensa, Felix and Schaarschmidt, Benedikt Michael}, journal = {Sci. Rep.}, volume = {14}, number = {1}, pages = {1172}, month = jan, year = {2024}, language = {en} }
@article{Rempe2024-tl, title = {k-strip: A novel segmentation algorithm in k-space for the application of skull stripping}, author = {Rempe, Moritz and Mentzel, Florian and Pomykala, Kelsey L and Haubold, Johannes and Nensa, Felix and Kroeninger, Kevin and Egger, Jan and Kleesiek, Jens}, journal = {Comput. Methods Programs Biomed.}, publisher = {Elsevier BV}, volume = {243}, number = {107912}, pages = {107912}, month = jan, year = {2024}, keywords = {Complex convolutional networks; Deep learning; Magnetic resonance imaging (MRI); Skull stripping; k-space}, copyright = {http://creativecommons.org/licenses/by-nc-nd/4.0/}, language = {en} }
@article{Dada2024-bv, title = {Information extraction from weakly structured radiological reports with natural language queries}, author = {Dada, Amin and Ufer, Tim Leon and Kim, Moon and Hasin, Max and Spieker, Nicola and Forsting, Michael and Nensa, Felix and Egger, Jan and Kleesiek, Jens}, journal = {Eur. Radiol.}, volume = {34}, number = {1}, pages = {330--337}, month = jan, year = {2024}, keywords = {Information extraction; Machine learning; Natural language processing}, language = {en} }
@article{SCHMIEGE2024114379, title = {Small-scale wastewater-based epidemiology (WBE) for infectious diseases and antibiotic resistance: A scoping review}, journal = {International Journal of Hygiene and Environmental Health}, volume = {259}, pages = {114379}, year = {2024}, issn = {1438-4639}, doi = {https://doi.org/10.1016/j.ijheh.2024.114379}, url = {https://www.sciencedirect.com/science/article/pii/S1438463924000609}, author = {Schmiege, Dennis and Haselhoff, Timo and Thomas, Alexander and Kraiselburd, Ivana and Meyer, Folker and Moebus, Susanne}, keywords = {Antimicrobial resistance, Building, Neighborhood, Public health, Virus, Wastewater surveillance} }
@article{RN5113, author = {Thomas, Alexander and Battenfeld, Thomas and Kraiselburd, Ivana and Anastasiou, Olympia and Dittmer, Ulf and Dörr, Ann-Kathrin and Dörr, Adrian and Elsner, Carina and Gosch, Jule and Le-Trilling, Vu Thuy Khanh and Magin, Simon and Scholtysik, René and Yilmaz, Pelin and Trilling, Mirko and Schöler, Lara and Köster, Johannes and Meyer, Folker}, title = {UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example}, journal = {BMC Genomics}, volume = {25}, number = {1}, pages = {647}, issn = {1471-2164}, doi = {10.1186/s12864-024-10539-0}, url = {https://doi.org/10.1186/s12864-024-10539-0}, year = {2024}, type = {Journal Article} }
@article{vaccines12070785, author = {Cherneha, Maxim and Zydek, Isabel and Braß, Peer and Korth, Johannes and Jansen, Sarah and Esser, Stefan and Karsten, Christina B. and Meyer, Folker and Kraiselburd, Ivana and Dittmer, Ulf and Lindemann, Monika and Horn, Peter A. and Witzke, Oliver and Thümmler, Laura and Krawczyk, Adalbert}, title = {Immunogenicity of the Monovalent Omicron XBB.1.5-Adapted BNT162b2 COVID-19 Vaccine in People Living with HIV (PLWH)}, journal = {Vaccines}, volume = {12}, year = {2024}, number = {7}, article-number = {785}, url = {https://www.mdpi.com/2076-393X/12/7/785}, issn = {2076-393X}, doi = {10.3390/vaccines12070785} }
@article{RN174, author = {Shelton, S. D. and House, S. and Martins Nascentes Melo, L. and Ramesh, V. and Chen, Z. and Wei, T. and Wang, X. and Llamas, C. B. and Venigalla, S. S. K. and Menezes, C. J. and Allies, G. and Krystkiewicz, J. and Rosler, J. and Meckelmann, S. W. and Zhao, P. and Rambow, F. and Schadendorf, D. and Zhao, Z. and Gill, J. G. and DeBerardinis, R. J. and Morrison, S. J. and Tasdogan, A. and Mishra, P.}, title = {Pathogenic mitochondrial DNA mutations inhibit melanoma metastasis}, journal = {Sci Adv}, volume = {10}, number = {44}, pages = {eadk8801}, issn = {2375-2548 (Electronic) 2375-2548 (Linking)}, doi = {10.1126/sciadv.adk8801}, url = {https://www.ncbi.nlm.nih.gov/pubmed/39485847}, year = {2024}, type = {Journal Article} }
@article{Hua2024.08.01.606144, author = {Hua, Yichao and Weng, Linqian and Zhao, Fang and Rambow, Florian}, title = {SeuratExtend: Streamlining Single-Cell RNA-Seq Analysis Through an Integrated and Intuitive Framework}, elocation-id = {2024.08.01.606144}, year = {2024}, doi = {10.1101/2024.08.01.606144}, publisher = {Cold Spring Harbor Laboratory}, url = {https://www.biorxiv.org/content/early/2024/08/04/2024.08.01.606144}, eprint = {https://www.biorxiv.org/content/early/2024/08/04/2024.08.01.606144.full.pdf}, journal = {bioRxiv} }
@article{RN262, author = {Dobersalske, C. and Rauschenbach, L. and Hua, Y. and Berliner, C. and Steinbach, A. and Gruneboom, A. and Kokkaliaris, K. D. and Heiland, D. H. and Berger, P. and Langer, S. and Tan, C. L. and Stenzel, M. and Landolsi, S. and Weber, F. and Darkwah Oppong, M. and Werner, R. A. and Gull, H. and Schroder, T. and Linsenmann, T. and Buck, A. K. and Gunzer, M. and Stuschke, M. and Keyvani, K. and Forsting, M. and Glas, M. and Kipnis, J. and Steindler, D. A. and Reinhardt, H. C. and Green, E. W. and Platten, M. and Tasdogan, A. and Herrmann, K. and Rambow, F. and Cima, I. and Sure, U. and Scheffler, B.}, title = {Cranioencephalic functional lymphoid units in glioblastoma}, journal = {Nat Med}, issn = {1546-170X (Electronic) 1078-8956 (Linking)}, doi = {10.1038/s41591-024-03152-x}, url = {https://www.ncbi.nlm.nih.gov/pubmed/39085419}, year = {2024}, type = {Journal Article} }
@article{RN197, author = {Lu, Y. and Travnickova, J. and Badonyi, M. and Rambow, F. and Coates, A. and Khan, Z. and Marques, J. and Murphy, L. C. and Garcia-Martinez, P. and Marais, R. and Louphrasitthiphol, P. and Chan, A. H. Y. and Schofield, C. J. and von Kriegsheim, A. and Marsh, J. A. and Pavet, V. and Sansom, O. J. and Illingworth, R. S. and Patton, E. E.}, title = {ALDH1A3-acetaldehyde metabolism potentiates transcriptional heterogeneity in melanoma}, journal = {Cell Rep}, volume = {43}, number = {7}, pages = {114406}, issn = {2211-1247 (Electronic)}, doi = {10.1016/j.celrep.2024.114406}, url = {https://www.ncbi.nlm.nih.gov/pubmed/38963759}, year = {2024}, type = {Journal Article} }
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@article{Beckmann2023-tr, title = {Semantic integration of {BPMN} models and {FHIR} data to enable personalized decision support for malignant melanoma}, author = {Beckmann, Catharina and Keuchel, Daniel and Soleman, Wa and N{\"u}rnberg, Sylvia and B{\"o}ckmann, Britta}, journal = {Information (Basel)}, publisher = {MDPI AG}, volume = {14}, number = {12}, pages = {649}, month = dec, year = {2023}, copyright = {https://creativecommons.org/licenses/by/4.0/}, language = {en} }
@article{Engelke2023-cr, title = {Optimizing platelet transfusion through a personalized deep learning risk assessment system for demand management}, author = {Engelke, Merlin and Schmidt, Cynthia Sabrina and Baldini, Giulia and Parmar, Vicky and Hosch, Ren{\'e} and Borys, Katarzyna and Koitka, Sven and Turki, Amin T and Haubold, Johannes and Horn, Peter A and Nensa, Felix}, journal = {Blood}, publisher = {American Society of Hematology}, volume = {142}, number = {26}, pages = {2315--2326}, month = dec, year = {2023}, language = {en} }
@article{Sauter2023-lw, title = {A systematic comparison of task adaptation techniques for digital histopathology}, author = {Sauter, Daniel and Lodde, Georg and Nensa, Felix and Schadendorf, Dirk and Livingstone, Elisabeth and Kukuk, Markus}, journal = {Bioengineering (Basel)}, volume = {11}, number = {1}, month = dec, year = {2023}, keywords = {CNN; cancer; computer vision; fine-tuning; transfer learning; whole-slide imaging}, language = {en} }
@article{Rausch2023-fg, title = {Falling off the screening grid-Predictors for postponed utilization of psycho-oncological support in cancer patients and its implications for distress assessment and management}, author = {Rausch, Raya and B{\"a}uerle, Alexander and Rentrop, Vanessa and Jansen, Christoph and Nensa, Felix and Palm, Stefan and Tewes, Mitra and Schadendorf, Dirk and Skoda, Eva-Maria and Teufel, Martin}, journal = {Psychooncology}, publisher = {Wiley}, volume = {32}, number = {11}, pages = {1727--1735}, month = nov, year = {2023}, keywords = {PROM; cancer; distress; electronic screening; intention; oncology; patient journey; psycho-oncology; subjective need; utilization}, copyright = {http://creativecommons.org/licenses/by-nc/4.0/}, language = {en} }
@article{Tamulevicius2023-wv, title = {Preoperative computed tomography volumetry and graft weight estimation of left lateral segment in pediatric living donor liver transplant}, author = {Tamulevicius, Martynas and Oezcelik, Arzu and Koitka, Sven and Theysohn, Jens M and Hoyer, Dieter P and Farzaliyev, Fardad and Haubold, Johannes and Nensa, Felix and Treckmann, J{\"u}rgen and Malamutmann, Eugen}, journal = {Exp. Clin. Transplant.}, volume = {21}, number = {10}, pages = {831--836}, month = oct, year = {2023}, language = {en} }
@article{Sauter2023-ok, title = {Deep learning in computational dermatopathology of melanoma: A technical systematic literature review}, author = {Sauter, Daniel and Lodde, Georg and Nensa, Felix and Schadendorf, Dirk and Livingstone, Elisabeth and Kukuk, Markus}, journal = {Comput. Biol. Med.}, publisher = {Elsevier BV}, volume = {163}, number = {107083}, pages = {107083}, month = sep, year = {2023}, keywords = {Machine learning; Neural network; Survey; Systematic review; Whole slide imaging}, copyright = {http://creativecommons.org/licenses/by/4.0/}, language = {en} }
@article{bergkamp_virally_2023, title = {A virally encoded {GPCR} drives glioblastoma through feed-forward activation of the {SK1}-{S1P1} signaling axis}, volume = {16}, url = {https://www.science.org/doi/10.1126/scisignal.ade6737}, doi = {10.1126/scisignal.ade6737}, number = {798}, urldate = {2023-08-16}, journal = {Science Signaling}, author = {Bergkamp, Nick D. and van Senten, Jeffrey R. and Brink, Hendrik J. and Bebelman, Maarten P. and van den Bor, Jelle and Çobanoğlu, Tuğçe S. and Dinkla, Kasper and Köster, Johannes and Klau, Gunnar and Siderius, Marco and Smit, Martine J.}, month = aug, year = {2023}, note = {Publisher: American Association for the Advancement of Science}, pages = {eade6737} }
@article{Fischer2023-mu, title = {Identification of radiomic biomarkers in a set of four skeletal muscle groups on Dixon {MRI} of the {NAKO} {MR} study}, author = {Fischer, Marc and K{\"u}stner, Thomas and Pappa, Sofia and Niendorf, Thoralf and Pischon, Tobias and Kr{\"o}ncke, Thomas and Bette, Stefanie and Schramm, Sara and Schmidt, B{\"o}rge and Haubold, Johannes and Nensa, Felix and Nonnenmacher, Tobias and Palm, Viktoria and Bamberg, Fabian and Kiefer, Lena and Schick, Fritz and Yang, Bin}, journal = {BMC Med. Imaging}, publisher = {Springer Science and Business Media LLC}, volume = {23}, number = {1}, pages = {104}, month = aug, year = {2023}, keywords = {German national cohort; Magnetic resonance imaging; Radiomics; Texture feature analysis}, copyright = {https://creativecommons.org/licenses/by/4.0}, language = {en} }
@article{Engelke2023-lu, title = {Predicting individual patient platelet demand in a large tertiary care hospital using machine learning}, author = {Engelke, Merlin and Brieske, Christian Martin and Parmar, Vicky and Flaschel, Nils and Kureishi, Anisa and Hosch, Rene and Koitka, Sven and Schmidt, Cynthia Sabrina and Horn, Peter A and Nensa, Felix}, journal = {Transfus. Med. Hemother.}, publisher = {S. Karger AG}, volume = {50}, number = {4}, pages = {277--285}, month = aug, year = {2023}, keywords = {Blood transfusion; Donor management; Machine learning; Patient individual; Platelet; Platelet concentrates; Platelet prediction}, copyright = {https://creativecommons.org/licenses/by-nc/4.0/}, language = {en} }
@article{Hosch2023-yz, title = {{FHIR-PYrate}: a data science friendly Python package to query {FHIR} servers}, author = {Hosch, Ren{\'e} and Baldini, Giulia and Parmar, Vicky and Borys, Katarzyna and Koitka, Sven and Engelke, Merlin and Arzideh, Kamyar and Ulrich, Moritz and Nensa, Felix}, journal = {BMC Health Serv. Res.}, volume = {23}, number = {1}, pages = {734}, month = jul, year = {2023}, keywords = {Dataframe; Dicom; Electronic patient record; FHIR; Information extraction; Python}, language = {en} }
@article{Alatzides2023-ll, title = {Adipopenia in body composition analysis: a promising imaging biomarker and potential predictive factor for patients undergoing transjugular intrahepatic portosystemic shunt placement}, author = {Alatzides, Georgios Luca and Haubold, Johannes and Steinberg, Hannah Luisa and Koitka, Sven and Parmar, Vicky and Grueneisen, Johannes and Zeller, Amos Cornelius and Schmidt, Hartmut and Theysohn, Jens Matthias and Li, Yan and Nensa, Felix and Schaarschmidt, Benedikt Michael}, journal = {Br. J. Radiol.}, volume = {96}, number = {1146}, pages = {20220863}, month = jun, year = {2023}, language = {en} }
@article{Haubold2023-fx, title = {Contrast agent dose reduction in {MRI} utilizing a generative adversarial network in an exploratory animal study}, author = {Haubold, Johannes and Jost, Gregor and Theysohn, Jens Matthias and Ludwig, Johannes Maximilian and Li, Yan and Kleesiek, Jens and Schaarschmidt, Benedikt Michael and Forsting, Michael and Nensa, Felix and Pietsch, Hubertus and Hosch, Ren{\'e}}, journal = {Invest. Radiol.}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {58}, number = {6}, pages = {396--404}, month = jun, year = {2023}, language = {en} }
@article{Borys2023-zs, title = {Explainable {AI} in medical imaging: An overview for clinical practitioners - Beyond saliency-based {XAI} approaches}, author = {Borys, Katarzyna and Schmitt, Yasmin Alyssa and Nauta, Meike and Seifert, Christin and Kr{\"a}mer, Nicole and Friedrich, Christoph M and Nensa, Felix}, journal = {Eur. J. Radiol.}, volume = {162}, pages = {110786}, month = may, year = {2023}, keywords = {Black-Box; Explainability; Explainable AI; Interpretability; Medical imaging; Radiology}, language = {en} }
@article{Haubold2023-mt, title = {Individualized scan protocols for {CT} angiography: an animal study for contrast media or radiation dose optimization}, author = {Haubold, Johannes and Zensen, Sebastian and Hosch, Ren{\'e} and Schaarschmidt, Benedikt Michael and Bos, Denise and Schmidt, Bernhardt and Flohr, Thomas and Li, Yan and Forsting, Michael and Pietsch, Hubertus and Nensa, Felix and Jost, Gregor}, journal = {Eur. Radiol. Exp.}, publisher = {Springer Science and Business Media LLC}, volume = {7}, number = {1}, pages = {24}, month = apr, year = {2023}, keywords = {Animals; Contrast media; Radiation; Tomography (x-ray computed)}, copyright = {https://creativecommons.org/licenses/by/4.0}, language = {en} }
@article{Haubold2023-lx, title = {{AI} co-pilot: content-based image retrieval for the reading of rare diseases in chest {CT}}, author = {Haubold, Johannes and Zeng, Ke and Farhand, Sepehr and Stalke, Sarah and Steinberg, Hannah and Bos, Denise and Meetschen, Mathias and Kureishi, Anisa and Zensen, Sebastian and Goeser, Tim and Maier, Sandra and Forsting, Michael and Nensa, Felix}, journal = {Sci. Rep.}, volume = {13}, number = {1}, pages = {4336}, month = mar, year = {2023}, language = {en} }
@article{Nauta2023_csur_evaluating-xai-survey, author = {Nauta, Meike and Trienes, Jan and Pathak, Shreyasi and Nguyen, Elisa and Peters, Michelle and Schmitt, Yasmin and Schl\"{o}tterer, J\"{o}rg and van Keulen, Maurice and Seifert, Christin}, journal = {ACM Comput. Surv.}, title = {From Anecdotal Evidence to Quantitative Evaluation Methods: A Systematic Review on Evaluating Explainable AI}, year = {2023}, issn = {0360-0300}, month = feb, address = {New York, NY, USA}, doi = {10.1145/3583558}, keywords = {explainability, explainable AI, explainable artificial intelligence, XAI, interpretable machine learning, interpretability, quantitative evaluation methods, evaluation}, publisher = {Association for Computing Machinery}, url = {https://doi.org/10.1145/3583558} }
@article{Okumus2023-rg, title = {Preoperative {PET-SUVmax} and volume based {PET} parameters of the primary tumor fail to predict nodal upstaging in early-stage lung cancer}, author = {Okumus, {\"O}zlem and Mardanzai, Khaled and Pl{\"o}nes, Till and Theegarten, Dirk and Darwiche, Kaid and Schuler, Martin and Nensa, Felix and Hautzel, Hubertus and Hermann, Ken and Stuschke, Martin and Hegedus, Balazs and Aigner, Clemens}, journal = {Lung Cancer}, publisher = {Elsevier BV}, volume = {176}, pages = {82--88}, month = feb, year = {2023}, keywords = {CRP; Lung cancer; MTV; Nodal upstaging; PET-SUVmax; TLG}, language = {en} }
@article{Keyl2023-hq, title = {Deep learning-based assessment of body composition and liver tumour burden for survival modelling in advanced colorectal cancer}, author = {Keyl, Julius and Hosch, Ren{\'e} and Berger, Aaron and Ester, Oliver and Greiner, Tobias and Bogner, Simon and Treckmann, J{\"u}rgen and Ting, Saskia and Schumacher, Brigitte and Albers, David and Markus, Peter and Wiesweg, Marcel and Forsting, Michael and Nensa, Felix and Schuler, Martin and Kasper, Stefan and Kleesiek, Jens}, journal = {J. Cachexia Sarcopenia Muscle}, publisher = {Wiley}, volume = {14}, number = {1}, pages = {545--552}, month = feb, year = {2023}, keywords = {Body composition; Colorectal cancer; Computed tomography; Machine learning; Prognosis}, copyright = {http://creativecommons.org/licenses/by-nc-nd/4.0/}, language = {en} }
@article{hartmann_insane_2023, title = {Insane in the vembrane: filtering and transforming {VCF}/{BCF} files}, volume = {39}, issn = {1367-4811}, shorttitle = {Insane in the vembrane}, url = {https://doi.org/10.1093/bioinformatics/btac810}, doi = {10.1093/bioinformatics/btac810}, number = {1}, urldate = {2023-01-13}, journal = {Bioinformatics}, author = {Hartmann, Till and Schröder, Christopher and Kuthe, Elias and Lähnemann, David and Köster, Johannes}, month = jan, year = {2023}, pages = {btac810}, file = {Full Text PDF:/home/johannes/Zotero/storage/VCTPYA27/Hartmann et al. - 2023 - Insane in the vembrane filtering and transforming.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/UGEMZDUK/6909012.html:text/html} }
@article{Rietberg2023_mdpi_classifying-ms-patient-reports, author = {Rietberg, Max Tigo and Nguyen, Van Bach and Geerdink, Jeroen and Vijlbrief, Onno and Seifert, Christin}, journal = {Diagnostics}, title = {Accurate and Reliable Classification of Unstructured Reports on Their Diagnostic Goal Using BERT Models}, year = {2023}, issn = {2075-4418}, number = {7}, volume = {13}, article-number = {1251}, doi = {10.3390/diagnostics13071251}, url = {https://www.mdpi.com/2075-4418/13/7/1251} }
@article{Borys2023_ejr_xai-in-medical-saliency, author = {Borys, Katarzyna and {Alyssa Schmitt}, Yasmin and Nauta, Meike and Seifert, Christin and Krämer, Nicole and Friedrich, Christoph M. and Nensa, Felix}, journal = {European Journal of Radiology}, title = {Explainable AI in Medical Imaging: An overview for clinical practitioners – Saliency-based XAI approaches}, year = {2023}, issn = {0720-048X}, pages = {110787}, doi = {https://doi.org/10.1016/j.ejrad.2023.110787}, keywords = {Explainable AI, Medical Imaging, Radiology, Black-Box, Explainability, Interpretability}, url = {https://www.sciencedirect.com/science/article/pii/S0720048X23001018} }
@article{Borys2023_ejr_xai-in-medical-beyond-saliency, author = {Borys, Katarzyna and Schmitt, Yasmin Alyssa and Nauta, Meike and Seifert, Christin and Krämer, Nicole and Friedrich, Christoph M. and Nensa, Felix}, journal = {European Journal of Radiology}, title = {Explainable AI in medical imaging: An overview for clinical practitioners – Beyond saliency-based XAI approaches}, year = {2023}, issn = {0720-048X}, pages = {110786}, volume = {162}, doi = {https://doi.org/10.1016/j.ejrad.2023.110786}, keywords = {Explainable AI, Medical imaging, Radiology, Black-Box, Explainability, Interpretability}, url = {https://www.sciencedirect.com/science/article/pii/S0720048X23001006} }
@article{Lu2023_tsnre_channel-contribution-sleep-scoring, author = {Lu, Changqing and Pathak, Shreyasi and Englebienne, Gwenn and Seifert, Christin}, journal = {IEEE Transactions on Neural Systems and Rehabilitation Engineering}, title = {Channel Contribution In Deep Learning Based Automatic Sleep Scoring – How Many Channels Do We Need?}, year = {2023}, pages = {494-505}, doi = {10.1109/TNSRE.2022.3227040} }
@article{SCHMIEGE2023165458, title = {Analyzing community wastewater in sub-sewersheds for the small-scale detection of SARS-CoV-2 variants in a German metropolitan area}, journal = {Science of The Total Environment}, volume = {898}, pages = {165458}, year = {2023}, issn = {0048-9697}, doi = {https://doi.org/10.1016/j.scitotenv.2023.165458}, url = {https://www.sciencedirect.com/science/article/pii/S0048969723040810}, author = {Schmiege, Dennis and Kraiselburd, Ivana and Haselhoff, Timo and Thomas, Alexander and Doerr, Adrian and Gosch, Jule and Schoth, Jens and Teichgräber, Burkhard and Moebus, Susanne and Meyer, Folker}, keywords = {COVID-19, Public health, Small-scale, Single nucleotide variants (SNVs), Wastewater surveillance, Whole genome sequencing} }
@article{10.3389/fimmu.2023.1150667, author = {Bormann, Maren and Brochhagen, Leonie and Alt, Mira and Otte, Mona and Thümmler, Laura and van de Sand, Lukas and Kraiselburd, Ivana and Thomas, Alexander and Gosch, Jule and Braß, Peer and Ciesek, Sandra and Widera, Marek and Dolff, Sebastian and Dittmer, Ulf and Witzke, Oliver and Meyer, Folker and Lindemann, Monika and Schönfeld, Andreas and Rohn, Hana and Krawczyk, Adalbert}, title = {Immune responses in COVID-19 patients during breakthrough infection with SARS-CoV-2 variants Delta, Omicron-BA.1 and Omicron-BA.5}, journal = {Frontiers in Immunology}, volume = {14}, year = {2023}, url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.1150667}, doi = {10.3389/fimmu.2023.1150667}, issn = {1664-3224} }
@article{10.3389/fmicb.2023.1267270, author = {Hartmann, Martin and Herzog, Claude and Brunner, Ivano and Stierli, Beat and Meyer, Folker and Buchmann, Nina and Frey, Beat}, title = {Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition}, journal = {Frontiers in Microbiology}, volume = {14}, year = {2023}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1267270}, doi = {10.3389/fmicb.2023.1267270}, issn = {1664-302X} }
@article{https://doi.org/10.1002/mbo3.1347, author = {Stach, Tom L. and Sieber, Guido and Shah, Manan and Simon, Sophie A. and Soares, André and Bornemann, Till L. V. and Plewka, Julia and Künkel, Julian and Becker, Christian and Meyer, Folker and Boenigk, Jens and Probst, Alexander J.}, title = {Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater}, journal = {MicrobiologyOpen}, volume = {12}, number = {2}, pages = {e1347}, keywords = {ARG, freshwater, mesocosm, metagenomics, microbiome, stressor}, doi = {https://doi.org/10.1002/mbo3.1347}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/mbo3.1347}, eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/mbo3.1347}, year = {2023} }
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@article{RN63, author = {Martins Nascentes Melo, L. and Herrera-Rios, D. and Hinze, D. and Loffek, S. and Oezel, I. and Turiello, R. and Klein, J. and Leonardelli, S. and Westedt, I. V. and Al-Matary, Y. and Egea-Rodriguez, S. and Brenzel, A. and Bau, M. and Sucker, A. and Hadaschik, E. and Wirsdorfer, F. and Hanenberg, H. and Uhlenbrock, N. and Rauh, D. and Pozniak, J. and Rambow, F. and Marine, J. C. and Effern, M. and Glodde, N. and Schadendorf, D. and Jablonska, J. and Holzel, M. and Helfrich, I.}, title = {Glucocorticoid activation by HSD11B1 limits T cell-driven interferon signaling and response to PD-1 blockade in melanoma}, journal = {J Immunother Cancer}, volume = {11}, number = {4}, issn = {2051-1426 (Electronic) 2051-1426 (Linking)}, doi = {10.1136/jitc-2021-004150}, url = {https://www.ncbi.nlm.nih.gov/pubmed/37028818}, year = {2023}, type = {Journal Article} }
@article{RN64, author = {Shoji, K. F. and Bayet, E. and Leverrier-Penna, S. and Le Devedec, D. and Mallavialle, A. and Marionneau-Lambot, S. and Rambow, F. and Perret, R. and Joussaume, A. and Viel, R. and Fautrel, A. and Khammari, A. and Constantin, B. and Tartare-Deckert, S. and Penna, A.}, title = {The mechanosensitive TRPV2 calcium channel promotes human melanoma invasiveness and metastatic potential}, journal = {EMBO Rep}, volume = {24}, number = {4}, pages = {e55069}, issn = {1469-3178 (Electronic) 1469-221X (Print) 1469-221X (Linking)}, doi = {10.15252/embr.202255069}, url = {https://www.ncbi.nlm.nih.gov/pubmed/36744297}, year = {2023}, type = {Journal Article} }
@article{RN65, author = {Hua, Y. and Vella, G. and Rambow, F. and Allen, E. and Martinez, A. A. and Duhamel, M. and Takeda, A. and Jalkanen, S. and Junius, S. and Smeets, A. and Nittner, D. and Dimmeler, S. and Hehlgans, T. and Liston, A. and Bosisio, F. M. and Floris, G. and Laoui, D. and Hollmen, M. and Lambrechts, D. and Merchiers, P. and Marine, J. C. and Schlenner, S. and Bergers, G.}, title = {Cancer immunotherapies transition endothelial cells into HEVs that generate TCF1(+) T lymphocyte niches through a feed-forward loop}, journal = {Cancer Cell}, volume = {41}, number = {1}, pages = {226}, issn = {1878-3686 (Electronic) 1535-6108 (Linking)}, doi = {10.1016/j.ccell.2022.12.006}, url = {https://www.ncbi.nlm.nih.gov/pubmed/36626867}, year = {2023}, type = {Journal Article} }
@article{Theysohn2022-xo, title = {Prediction of left lobe hypertrophy after right lobe radioembolization of the liver using a clinical data model with external validation}, author = {Theysohn, Jens M and Demircioglu, Aydin and Kleditzsch, Malte and Ludwig, Johannes M and Weber, Manuel and Umutlu, Lale and Li, Yan and Kircher, Malte and Lapa, Constantin and Buck, Andreas and Koehler, Michael and Wildgruber, Moritz and Lange, Christian M and Palard, Xavier and Garin, Etienne and Herrmann, Ken and Forsting, Michael and Nensa, Felix}, journal = {Sci. Rep.}, publisher = {Springer Science and Business Media LLC}, volume = {12}, number = {1}, pages = {20718}, month = dec, year = {2022}, copyright = {https://creativecommons.org/licenses/by/4.0}, language = {en} }
@article{Jonske2022-wy, title = {Deep Learning-driven classification of external {DICOM} studies for {PACS} archiving}, author = {Jonske, Frederic and Dederichs, Maximilian and Kim, Moon-Sung and Keyl, Julius and Egger, Jan and Umutlu, Lale and Forsting, Michael and Nensa, Felix and Kleesiek, Jens}, journal = {Eur. Radiol.}, publisher = {Springer Science and Business Media LLC}, volume = {32}, number = {12}, pages = {8769--8776}, month = dec, year = {2022}, keywords = {Artificial intelligence; Machine learning; Radiology information systems}, copyright = {https://creativecommons.org/licenses/by/4.0}, language = {en} }
@article{Hosch2022-up, title = {Artificial intelligence guided enhancement of digital {PET}: scans as fast as {CT}?}, author = {Hosch, Ren{\'e} and Weber, Manuel and Sraieb, Miriam and Flaschel, Nils and Haubold, Johannes and Kim, Moon-Sung and Umutlu, Lale and Kleesiek, Jens and Herrmann, Ken and Nensa, Felix and Rischpler, Christoph and Koitka, Sven and Seifert, Robert and Kersting, David}, journal = {Eur. J. Nucl. Med. Mol. Imaging}, publisher = {Springer Science and Business Media LLC}, volume = {49}, number = {13}, pages = {4503--4515}, month = nov, year = {2022}, keywords = {Artificial intelligence; CT; Digital PET; Image post-reconstruction; Low-count PET; PET}, copyright = {https://creativecommons.org/licenses/by/4.0}, language = {en} }
@article{imangaliyevDiagnosisInflammatoryBowel2022, title = {Diagnosis of {{Inflammatory Bowel Disease}} and {{Colorectal Cancer}} through {{Multi-View Stacked Generalization Applied}} on {{Gut Microbiome Data}}}, author = {Imangaliyev, Sultan and Schl{\"o}tterer, J{\"o}rg and Meyer, Folker and Seifert, Christin}, year = {2022}, month = oct, journal = {Diagnostics}, volume = {12}, number = {10}, pages = {2514}, issn = {2075-4418}, doi = {10.3390/diagnostics12102514}, langid = {english} }
@article{Koitka2022-zj, title = {Fully automated preoperative liver volumetry incorporating the anatomical location of the central hepatic vein}, author = {Koitka, Sven and Gudlin, Phillip and Theysohn, Jens M and Oezcelik, Arzu and Hoyer, Dieter P and Dayangac, Murat and Hosch, Ren{\'e} and Haubold, Johannes and Flaschel, Nils and Nensa, Felix and Malamutmann, Eugen}, journal = {Sci. Rep.}, volume = {12}, number = {1}, pages = {16479}, month = oct, year = {2022}, language = {en} }
@article{Haubold2022-oo, title = {Contrast media reduction in computed tomography with deep learning using a generative adversarial network in an experimental animal study}, author = {Haubold, Johannes and Jost, Gregor and Theysohn, Jens Matthias and Ludwig, Johannes Maximilian and Li, Yan and Kleesiek, Jens and Schaarschmidt, Benedikt Michael and Forsting, Michael and Nensa, Felix and Pietsch, Hubertus and Hosch, Ren{\'e}}, journal = {Invest. Radiol.}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {57}, number = {10}, pages = {696--703}, month = oct, year = {2022}, language = {en} }
@article{Hosch2022-aj, title = {Biomarkers extracted by fully automated body composition analysis from chest {CT} correlate with {SARS-CoV-2} outcome severity}, author = {Hosch, Ren{\'e} and Kattner, Simone and Berger, Marc Moritz and Brenner, Thorsten and Haubold, Johannes and Kleesiek, Jens and Koitka, Sven and Kroll, Lennard and Kureishi, Anisa and Flaschel, Nils and Nensa, Felix}, journal = {Sci. Rep.}, volume = {12}, number = {1}, pages = {16411}, month = sep, year = {2022}, language = {en} }
@incollection{Beckmann2022-fg, title = {Guideline-based context-sensitive decision modeling for melanoma patients}, booktitle = {Studies in Health Technology and Informatics}, author = {Beckmann, Catharina Lena and Lodde, Georg and Livingstone, Elisabeth and Schadendorf, Dirk and B{\"o}ckmann, Britta}, publisher = {IOS Press}, series = {Studies in health technology and informatics}, month = aug, year = {2022} }
@article{cernavaMetadataHarmonizationStandards2022, title = {Metadata Harmonization\textendash{{Standards}} Are the Key for a Better Usage of Omics Data for Integrative Microbiome Analysis}, author = {Cernava, Tomislav and Rybakova, Daria and Buscot, Fran{\c c}ois and Clavel, Thomas and McHardy, Alice Carolyn and Meyer, Fernando and Meyer, Folker and Overmann, J{\"o}rg and Stecher, B{\"a}rbel and Sessitsch, Angela and Schloter, Michael and Berg, Gabriele and Arruda, Paulo and Bartzanas, Thomas and Kostic, Tanja and Brennan, Paula Iara and Biazotti, B{\'a}rbara Bort and {Champomier-Verges}, Marie-Christine and Charles, Trevor and Coakley, Mairead and Cotter, Paul and Cowan, Don and D'Hondt, Kathleen and Ferrocino, Ilario and Foterek, Kristina and {Herrero-Corral}, Gema and Huitema, Carly and Jansson, Janet and Liu, Shuang-Jiang and Malloy, Paula and Maguin, Emmanuelle and Markiewicz, Lidia and Mcclure, Ryan and Moser, Andreas and Roovers, Jolien and Ryan, Matthew and Sarand, Inga and Schelkle, Bettina and Meisner, Annelein and Schurr, Ulrich and Selvin, Joseph and Tsakalidou, Effie and Wagner, Martin and Wakelin, Steve and Wiczkowski, Wies{\l}aw and Winkler, Hanna and Xiao, Juanjuan and Bunthof, Christine J. and {de Souza}, Rafael Soares Correa and Sanz, Yolanda and Lange, Lene and Smidt, Hauke and {The MicrobiomeSupport Team}}, year = {2022}, month = jun, journal = {Environmental Microbiome}, volume = {17}, number = {1}, pages = {33}, issn = {2524-6372}, doi = {10.1186/s40793-022-00425-1} }
@article{tuns_detection_2022, title = {Detection and {Validation} of {Circular} {DNA} {Fragments} {Using} {Nanopore} {Sequencing}}, volume = {13}, issn = {1664-8021}, url = {https://www.frontiersin.org/articles/10.3389/fgene.2022.867018}, urldate = {2023-10-03}, journal = {Frontiers in Genetics}, author = {Tüns, Alicia Isabell and Hartmann, Till and Magin, Simon and González, Rocío Chamorro and Henssen, Anton George and Rahmann, Sven and Schramm, Alexander and Köster, Johannes}, year = {2022}, file = {Full Text PDF:/home/johannes/Zotero/storage/3TUXUXEW/Tüns et al. - 2022 - Detection and Validation of Circular DNA Fragments.pdf:application/pdf} }
@misc{Haller2022_preprints_short-answare-grading-survey, title = {Survey on Automated Short Answer Grading with Deep Learning: From Word Embeddings to Transformers}, author = {Haller, Stefan and Aldea, Adina and Seifert, Christin and Strisciuglio, Nicola}, year = {2022}, publisher = {{arXiv}}, doi = {10.48550/ARXIV.2204.03503}, copyright = {Creative Commons Attribution 4.0 International}, keywords = {Artificial Intelligence (cs.AI),Computation and Language (cs.CL),FOS: Computer and information sciences,Machine Learning (cs.LG)} }
@article{nautaUncoveringCorrectingShortcut2022, title = {Uncovering and {{Correcting Shortcut Learning}} in {{Machine Learning Models}} for {{Skin Cancer Diagnosis}}}, author = {Nauta, Meike and Walsh, Ricky and Dubowski, Adam and Seifert, Christin}, year = {2022}, journal = {Diagnostics}, volume = {12}, number = {1}, issn = {2075-4418}, doi = {10.3390/diagnostics12010040} }
@inproceedings{Nguyen2022_iclr-blog_pplmrevisiteds-mammoth, title = {{{PPLM}} Revisited: {{Steering}} and Beaming a Lumbering Mammoth to Control Text Generation}, booktitle = {{{ICLR}} Blog Track}, author = {Nguyen, Van Bach and Trienes, Jan and Nauta, Meike and Pathak, Shreyasi and Youssef, Paul and Imangaliyev, Sultan and Schl{\"o}tterer, J{\"o}rg and Seifert, Christin}, url = {https://iclr-blog-track.github.io/2022/03/25/PPLM/}, year = {2022} }
@misc{Nguyen2022_preprints_conversational-xai, title = {Explaining Machine Learning Models in Natural Conversations: {{Towards}} a Conversational {{XAI}} Agent}, author = {Nguyen, Van Bach and Schl{\"o}tterer, J{\"o}rg and Seifert, Christin}, year = {2022}, publisher = {{arXiv}}, doi = {10.48550/ARXIV.2209.02552}, copyright = {Creative Commons Attribution Non Commercial No Derivatives 4.0 International}, keywords = {Artificial Intelligence (cs.AI),Computation and Language (cs.CL),FOS: Computer and information sciences} }
@inproceedings{papenmeierHowAccurateDoes2022, title = {How {{Accurate Does It Feel}}? \textendash{} {{Human Perception}} of {{Different Types}} of {{Classification Mistakes}}}, booktitle = {Proceedings of the 2022 {{CHI Conference}} on {{Human Factors}} in {{Computing Systems}}}, author = {Papenmeier, Andrea and Kern, Dagmar and Hienert, Daniel and Kammerer, Yvonne and Seifert, Christin}, year = {2022}, series = {{{CHI}} '22}, publisher = {{Association for Computing Machinery}}, address = {{New York, NY, USA}}, doi = {10.1145/3491102.3501915} }
@article{papenmeierItComplicatedRelationship2022, title = {It's {{Complicated}}: {{The Relationship}} between {{User Trust}}, {{Model Accuracy}} and {{Explanations}} in {{AI}}}, author = {Papenmeier, Andrea and Kern, Dagmar and Englebienne, Gwenn and Seifert, Christin}, year = {2022}, journal = {ACM Trans. Comput.-Hum. Interact.}, publisher = {{Association for Computing Machinery}}, address = {{New York, NY, USA}}, doi = {10.1145/3495013} }
@inproceedings{Trienes2022_tsar_patient-friendly-clinical-notes, title = {Patient-Friendly Clinical Notes: {{Towards}} a New Text Simplification Dataset}, booktitle = {Proc. {{EMNLP}} Workshop on Text Simplification, Accessibility, and Readability ({{TSAR}})}, author = {Trienes, Jan and Schl{\"o}tterer, J{\"o}rg and Schildhaus, Hans-Ulrich and Seifert, Christin}, year = {2022} }
@inproceedings{Youssef2022_dmbih_model-personalizaton-patient-data, title = {Model Personalization with Static and Dynamic Patients' Data}, booktitle = {Proc. {{ICDM}} Workshop on Data Mining in Biomedical Informatics and Healthcare ({{DMBIH}})}, author = {Youssef, Paul and Schl{\"o}tterer, J{\"o}rg and Imangaliyev, Sultan and Seifert, Christin}, year = {2022} }
@inproceedings{Zerhoudi2022_cikm_simiir20-framework, title = {The {{SimIIR}} 2.0 Framework: {{User}} Types, Markov Model-Based Interaction Simulation, and Advanced Query Generation}, booktitle = {31st {{ACM}} International Conference on Information and Knowledge Management ({{CIKM}} 2022)}, author = {Zerhoudi, Saber and G{\"u}nther, Sebastian and Plassmeier, Kim and Borst, Timo and Seifert, Christin and Hagen, Matthias and Granitzer, Michael}, year = {2022}, publisher = {{ACM}}, site = {Atlanta, Georgia, USA} }
@inproceedings{zerhoudiEvaluatingSimulatedUser2022, title = {Evaluating {{Simulated User Interaction}} and {{Search Behaviour}}}, booktitle = {Advances in {{Information Retrieval}}}, author = {Zerhoudi, Saber and Granitzer, Michael and Seifert, Christin and Schl{\"o}tterer, J{\"o}rg}, year = {2022}, publisher = {{Springer International Publishing}}, address = {{Cham}}, doi = {DOI: 10.1007/978-3-030-99739-7_28} }
@inproceedings{zerhoudiSimulatingUserInteraction2022, title = {Simulating {{User Interaction}} and {{Search Behaviour}} in {{Digital Libraries}}}, booktitle = {Proc. {{Italian Research Conference}} on {{Digital Libraries}}}, author = {Zerhoudi, Saber and Granitzer, Michael and Seifert, Christin and Schl{\"o}tterer, J{\"o}rg}, year = {2022}, series = {{{IRCDL}}} }
@article{RN1743, author = {Tuns, A. I. and Hartmann, T. and Magin, S. and Gonzalez, R. C. and Henssen, A. G. and Rahmann, S. and Schramm, A. and Koster, J.}, title = {Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing}, journal = {Front Genet}, volume = {13}, pages = {867018}, note = {Tuns, Alicia Isabell Hartmann, Till Magin, Simon Gonzalez, Rocio Chamorro Henssen, Anton George Rahmann, Sven Schramm, Alexander Koster, Johannes eng Switzerland 2022/06/18 Front Genet. 2022 May 30;13:867018. doi: 10.3389/fgene.2022.867018. eCollection 2022.}, keywords = {algorithm cancer circular DNA nanopore sequencing snakemake}, issn = {1664-8021 (Print) 1664-8021 (Linking)}, doi = {10.3389/fgene.2022.867018}, url = {https://www.ncbi.nlm.nih.gov/pubmed/35711922}, year = {2022}, type = {Journal Article} }
@article{dohla2022sars, title = {SARS-CoV-2 in environmental samples of quarantined households}, author = {D{\"o}hla, Manuel and Schulte, Bianca and Wilbring, Gero and K{\"u}mmerer, Beate Mareike and D{\"o}hla, Christin and Sib, Esther and Richter, Enrico and Ottensmeyer, Patrick Frank and Haag, Alexandra and Engelhart, Steffen and others}, journal = {Viruses}, volume = {14}, year = {2022}, publisher = {MDPI} }
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@article{wessendorf2022dynamics, title = {Dynamics, outcomes and prerequisites of the first SARS-CoV-2 superspreading event in Germany in February 2020: a cross-sectional epidemiological study}, author = {Wessendorf, Lukas and Richter, Enrico and Schulte, Bianca and Schmithausen, Ricarda Maria and Exner, Martin and Lehmann, Nils and Coenen, Martin and Fuhrmann, Christine and Kellings, Angelika and H{\"u}sing, Anika and others}, journal = {BMJ open}, volume = {12}, year = {2022}, publisher = {British Medical Journal Publishing Group} }
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@article{hackstein2022suppression, title = {Suppression of systemic T cell immunity to viral infection during liver injury is prevented by inhibition of interferon and IL-10 signaling}, author = {Hackstein, Philipp Carl and Spitzer, Jasper and Symeonidis, Konstantinos and Horvatic, Helena and Bedke, Tanja and Steglich, Babett and Assmus, Lisa and Odainic, Alexandru and Kessler, Nina and Klein, Sabine and others}, journal = {bioRxiv}, year = {2022}, publisher = {Cold Spring Harbor Laboratory} }
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@article{le2022identification, title = {Identification of herbal teas and their compounds eliciting antiviral activity against SARS-CoV-2 in vitro}, author = {Le-Trilling, Vu Thuy Khanh and Mennerich, Denise and Schuler, Corinna and Sakson, Roman and Lill, Julia K. and Kasarla, Siva Swapna and Kopczynski, Dominik and Loroch, Stefan and Flores-Martinez, Yulia and Katschinski, Benjamin and Wohlgemuth, Kerstin and Gunzer, Matthias and Meyer, Folker and Phapale, Prasad and Dittmer, Ulf and Sickmann, Albert and Trilling, Mirko}, journal = {BMC Biology}, volume = {20}, number = {264}, year = {2022}, doi = {https://doi.org/10.1186/s12915-022-01468-z}, url = {https://www.sciencedirect.com/science/article/pii/S0048969723040810} }
@article{mahgoub2022iris, title = {IRIS: Online Reconfiguration of Distributed NoSQL Databases for Dynamic Workloads}, author = {Mahgoub, Ashraf and Wood, Paul C and Mitra, Subrata and Meyer, Folker and Chaterji, Somali and Bagchi, Saurabh}, year = {2022} }
@article{DBLP:journals/corr/abs-2205-09706, title = {K-Strip: {{A}} Novel Segmentation Algorithm in k-Space for the Application of Skull Stripping}, author = {Rempe, Moritz and Mentzel, Florian and Pomykala, Kelsey L. and Haubold, Johannes and Nensa, Felix and Kr{\"o}ninger, Kevin and Egger, Jan and Kleesiek, Jens}, year = {2022}, journal = {CoRR}, volume = {abs/2205.09706}, eprint = {2205.09706}, eprinttype = {arxiv}, doi = {10.48550/arXiv.2205.09706}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2205-09706.bib}, timestamp = {Tue, 24 May 2022 01:00:00 +0200} }
@inproceedings{DBLP:conf/bildmed/FischerSBGMWSKS22, title = {{{DICOM}} Whole Slide Imaging for Computational Pathology Research in Kaapana and the Joint Imaging Platform}, booktitle = {Bildverarbeitung F\"ur Die Medizin 2022 - Proceedings, German Workshop on Medical Image Computing, Heidelberg, June 26-28, 2022}, author = {Fischer, Maximilian and Schader, Philipp and Braren, Rickmer and G{\"o}tz, Michael and Muckenhuber, Alexander and Weichert, Wilko and Sch{\"u}ffler, Peter and Kleesiek, Jens and Scherer, Jonas and Kades, Klaus and {Maier-Hein}, Klaus H. and Nolden, Marco}, editor = {{Maier-Hein}, Klaus H. and Deserno, Thomas M. and Handels, Heinz and Maier, Andreas and Palm, Christoph and Tolxdorff, Thomas}, year = {2022}, series = {Informatik Aktuell}, pages = {273--278}, publisher = {{Springer}}, doi = {10.1007/978-3-658-36932-3\_58}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/bildmed/FischerSBGMWSKS22.bib}, timestamp = {Fri, 08 Apr 2022 08:58:58 +0200} }
@article{DBLP:journals/corr/abs-2203-11132, title = {Review of Disentanglement Approaches for Medical Applications - towards Solving the Gordian Knot of Generative Models in Healthcare}, author = {Fragemann, Jana and Ardizzone, Lynton and Egger, Jan and Kleesiek, Jens}, year = {2022}, journal = {CoRR}, volume = {abs/2203.11132}, eprint = {2203.11132}, eprinttype = {arxiv}, doi = {10.48550/arXiv.2203.11132}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2203-11132.bib}, timestamp = {Tue, 29 Mar 2022 01:00:00 +0200} }
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@article{DBLP:journals/corr/abs-2205-07139, title = {Breaking with Fixed Set Pathology Recognition through Report-Guided Contrastive Training}, author = {Seibold, Constantin and Rei{\ss}, Simon and Sarfraz, M. Saquib and Stiefelhagen, Rainer and Kleesiek, Jens}, year = {2022}, journal = {CoRR}, volume = {abs/2205.07139}, eprint = {2205.07139}, eprinttype = {arxiv}, doi = {10.48550/arXiv.2205.07139}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2205-07139.bib}, timestamp = {Tue, 17 May 2022 01:00:00 +0200} }
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@misc{nauta2022, title = {From Anecdotal Evidence to Quantitative Evaluation Methods: {{A}} Systematic Review on Evaluating Explainable {{AI}}}, author = {Nauta, Meike and Trienes, Jan and Pathak, Shreyasi and Nguyen, Elisa and Peters, Michelle and Schmitt, Yasmin and Schl{\"o}tterer, J{\"o}rg and {van Keulen}, Maurice and Seifert, Christin}, year = {2022}, publisher = {{arXiv}}, doi = {10.48550/ARXIV.2201.08164}, copyright = {arXiv.org perpetual, non-exclusive license} }
@article{DBLP:journals/corr/abs-2202-10244, title = {Stochastic Modeling of Inhomogeneities in the Aortic Wall and Uncertainty Quantification Using a Bayesian Encoder-Decoder Surrogate}, author = {Ranftl, Sascha and {Rolf-Pissarczyk}, Malte and Wolkerstorfer, Gloria and Pepe, Antonio and Egger, Jan and {von der Linden}, Wolfgang and Holzapfel, Gerhard A.}, year = {2022}, journal = {CoRR}, volume = {abs/2202.10244}, eprint = {2202.10244}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2202.10244}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2202-10244.bib}, timestamp = {Thu, 03 Mar 2022 00:00:00 +0100} }
@article{DBLP:journals/jdi/EggerWWBKPSDKJG22, title = {Studierfenster: An Open Science Cloud-Based Medical Imaging Analysis Platform}, author = {Egger, Jan and Wild, Daniel and Weber, Maximilian and Bedoya, Christopher A. Ramirez and Karner, Florian and Prutsch, Alexander and Schmied, Michael and Dionysio, Christina and Krobath, Dominik and Jin, Yuan and Gsaxner, Christina and Li, Jianning and Pepe, Antonio}, year = {2022}, journal = {Journal of Digital Imaging}, volume = {35}, number = {2}, pages = {340--355}, doi = {10.1007/s10278-021-00574-8}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/jdi/EggerWWBKPSDKJG22.bib}, timestamp = {Wed, 23 Mar 2022 00:00:00 +0100} }
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@article{RN99, author = {Karras, P. and Bordeu, I. and Pozniak, J. and Nowosad, A. and Pazzi, C. and Van Raemdonck, N. and Landeloos, E. and Van Herck, Y. and Pedri, D. and Bervoets, G. and Makhzami, S. and Khoo, J. H. and Pavie, B. and Lamote, J. and Marin-Bejar, O. and Dewaele, M. and Liang, H. and Zhang, X. and Hua, Y. and Wouters, J. and Browaeys, R. and Bergers, G. and Saeys, Y. and Bosisio, F. and van den Oord, J. and Lambrechts, D. and Rustgi, A. K. and Bechter, O. and Blanpain, C. and Simons, B. D. and Rambow, F. and Marine, J. C.}, title = {A cellular hierarchy in melanoma uncouples growth and metastasis}, journal = {Nature}, volume = {610}, number = {7930}, pages = {190-198}, issn = {1476-4687 (Electronic) 0028-0836 (Linking)}, doi = {10.1038/s41586-022-05242-7}, url = {https://www.ncbi.nlm.nih.gov/pubmed/36131018}, year = {2022}, type = {Journal Article} }
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@inproceedings{nautaIntrinsicallyInterpretableImage2021, title = {Intrinsically {{Interpretable Image Recognition}} with {{Neural Prototype Trees}}}, booktitle = {Beyond {{Fairness}}: {{Towards}} a {{Just}}, {{Equitable}}, and {{Accountable Computer Vision}}: {{CVPR}} 2021 {{Workshop}}}, author = {Nauta, Meike and van Bree, Ron and Seifert, Christin}, year = {2021} }
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@inproceedings{nautaThisLooksThat2021, title = {This {{Looks Like That}}, {{Because}} ... {{Explaining Prototypes}} for {{Interpretable Image Recognition}}}, booktitle = {Proc. {{ECML PKDD International Workshop}} on {{eXplainable Knowledge Discovery}} in {{Data Mining}} ({{XKDD}})}, author = {Nauta, Meike and Jutte, Annemarie and Provoost, Jesper and Seifert, Christin}, year = {2021} }
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@inproceedings{DBLP:conf/bildmed/SchererNKMKSGNF21, title = {Abstract: {{Joint}} Imaging Platform for Federated Clinical Data Analytics}, booktitle = {Bildverarbeitung F\"ur Die Medizin 2021 - Proceedings, German Workshop on Medical Image Computing, Regensburg, March 7-9, 2021}, author = {Scherer, Jonas and Nolden, Marco and Kleesiek, Jens and Metzger, Jasmin and Kades, Klaus and Schneider, Verena and Gao, Hanno and Neher, Peter F. and Floca, Ralf and Schlemmer, Heinz-Peter and {Maier-Hein}, Klaus H.}, editor = {Palm, Christoph and Deserno, Thomas M. and Handels, Heinz and Maier, Andreas and {Maier-Hein}, Klaus H. and Tolxdorff, Thomas}, year = {2021}, series = {Informatik Aktuell}, pages = {127}, publisher = {{Springer}}, doi = {10.1007/978-3-658-33198-6\_31}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/bildmed/SchererNKMKSGNF21.bib}, timestamp = {Wed, 03 Mar 2021 16:00:48 +0100} }
@inproceedings{DBLP:conf/isbi/SeiboldFGKSSK21, title = {Prediction of Low-Kev Monochromatic Images from Polyenergetic {{CT}} Scans for Improved Automatic Detection of Pulmonary Embolism}, booktitle = {18th {{IEEE}} International Symposium on Biomedical Imaging, {{ISBI}} 2021, Nice, France, April 13-16, 2021}, author = {Seibold, Constantin and Fink, Matthias A. and Goos, Charlotte and Kauczor, Hans-Ulrich and Schlemmer, Heinz-Peter and Stiefelhagen, Rainer and Kleesiek, Jens}, year = {2021}, pages = {1017--1020}, publisher = {{IEEE}}, doi = {10.1109/ISBI48211.2021.9433966}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/isbi/SeiboldFGKSSK21.bib}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200} }
@inproceedings{DBLP:conf/isbi/SekuboyinaOKM21, title = {A Relational-Learning Perspective to Multi-Label Chest {{X-ray}} Classification}, booktitle = {18th {{IEEE}} International Symposium on Biomedical Imaging, {{ISBI}} 2021, Nice, France, April 13-16, 2021}, author = {Sekuboyina, Anjany and {O{\~n}oro-Rubio}, Daniel and Kleesiek, Jens and Malone, Brandon}, year = {2021}, pages = {1618--1622}, publisher = {{IEEE}}, doi = {10.1109/ISBI48211.2021.9433786}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/isbi/SekuboyinaOKM21.bib}, timestamp = {Mon, 31 May 2021 01:00:00 +0200} }
@article{DBLP:journals/corr/abs-2102-01445, title = {Prediction of Low-{{keV}} Monochromatic Images from Polyenergetic {{CT}} Scans for Improved Automatic Detection of Pulmonary Embolism}, author = {Seibold, Constantin and Fink, Matthias A. and Goos, Charlotte and Kauczor, Hans-Ulrich and Schlemmer, Heinz-Peter and Stiefelhagen, Rainer and Kleesiek, Jens}, year = {2021}, journal = {CoRR}, volume = {abs/2102.01445}, eprint = {2102.01445}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2102.01445}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2102-01445.bib}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200} }
@article{DBLP:journals/corr/abs-2103-06220, title = {A Relational-Learning Perspective to Multi-Label Chest {{X-ray}} Classification}, author = {Sekuboyina, Anjany and {O{\~n}oro-Rubio}, Daniel and Kleesiek, Jens and Malone, Brandon}, year = {2021}, journal = {CoRR}, volume = {abs/2103.06220}, eprint = {2103.06220}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2103.06220}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2103-06220.bib}, timestamp = {Tue, 16 Mar 2021 00:00:00 +0100} }
@article{DBLP:journals/corr/abs-2104-05642, title = {Common Limitations of Image Processing Metrics: {{A}} Picture Story}, author = {Reinke, Annika and Eisenmann, Matthias and Tizabi, Minu Dietlinde and Sudre, Carole H. and R{\"a}dsch, Tim and Antonelli, Michela and Arbel, Tal and Bakas, Spyridon and Cardoso, M. Jorge and Cheplygina, Veronika and Farahani, Keyvan and Glocker, Ben and {Heckmann-N{\"o}tzel}, Doreen and Isensee, Fabian and Jannin, Pierre and Kahn, Charles E. and Kleesiek, Jens and Kur{\c c}, Tahsin M. and Kozubek, Michal and Landman, Bennett A. and Litjens, Geert and {Maier-Hein}, Klaus H. and Menze, Bjoern H. and M{\"u}ller, Henning and Petersen, Jens and Reyes, Mauricio and Rieke, Nicola and Stieltjes, Bram and Summers, Ronald M. and Tsaftaris, Sotirios A. and {van Ginneken}, Bram and {Kopp-Schneider}, Annette and J{\"a}ger, Paul and {Maier-Hein}, Lena}, year = {2021}, journal = {CoRR}, volume = {abs/2104.05642}, eprint = {2104.05642}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2104.05642}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2104-05642.bib}, timestamp = {Fri, 04 Mar 2022 00:00:00 +0100} }
@article{DBLP:journals/corr/abs-2105-05874, title = {The Federated Tumor Segmentation ({{FeTS}}) Challenge}, author = {Pati, Sarthak and Baid, Ujjwal and Zenk, Maximilian and Edwards, Brandon and Sheller, Micah J. and Reina, G. Anthony and Foley, Patrick and Gruzdev, Alexey and Martin, Jason and Albarqouni, Shadi and Chen, Yong and Shinohara, Russell Taki and Reinke, Annika and Zimmerer, David and Freymann, John B. and Kirby, Justin S. and Davatzikos, Christos and Colen, Rivka R. and Kotrotsou, Aikaterini and Marcus, Daniel S. and Milchenko, Mikhail and Nazeri, Arash and {Fathallah-Shaykh}, Hassan M. and Wiest, Roland and Jakab, Andr{\'a}s and Weber, Marc-Andr{\'e} and Mahajan, Abhishek and {Maier-Hein}, Lena and Kleesiek, Jens and Menze, Bjoern H. and {Maier-Hein}, Klaus H. and Bakas, Spyridon}, year = {2021}, journal = {CoRR}, volume = {abs/2105.05874}, eprint = {2105.05874}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2105.05874}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2105-05874.bib}, timestamp = {Tue, 18 May 2021 01:00:00 +0200} }
@article{DBLP:journals/corr/abs-2108-02998, title = {{{AI-based}} Aortic Vessel Tree Segmentation for Cardiovascular Diseases Treatment: {{Status}} Quo}, author = {Jin, Yuan and Pepe, Antonio and Li, Jianning and Gsaxner, Christina and Zhao, Fen-hua and Kleesiek, Jens and Frangi, Alejandro F. and Egger, Jan}, year = {2021}, journal = {CoRR}, volume = {abs/2108.02998}, eprint = {2108.02998}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2108.02998}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2108-02998.bib}, timestamp = {Wed, 11 Aug 2021 01:00:00 +0200} }
@article{DBLP:journals/corr/abs-2112-00735, title = {Reference-Guided Pseudo-Label Generation for Medical Semantic Segmentation}, author = {Seibold, Constantin and Rei{\ss}, Simon and Kleesiek, Jens and Stiefelhagen, Rainer}, year = {2021}, journal = {CoRR}, volume = {abs/2112.00735}, eprint = {2112.00735}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2112.00735}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2112-00735.bib}, timestamp = {Wed, 08 Dec 2021 00:00:00 +0100} }
@inproceedings{DBLP:conf/dsn/MedeirosGKF21, title = {Third International Workshop on Data-Centric Dependability and Security ({{DCDS}})}, booktitle = {51st Annual {{IEEE}}/{{IFIP}} International Conference on Dependable Systems and Networks Workshops, {{DSN}} Workshops 2021, Taipei, Taiwan, June 21-24, 2021}, author = {Medeiros, Ib{\'e}ria and Gashi, Ilir and Kamp, Michael and Ferreira, Pedro}, year = {2021}, pages = {xii}, publisher = {{IEEE}}, doi = {10.1109/DSN-W52860.2021.00006}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/dsn/MedeirosGKF21.bib}, timestamp = {Sat, 09 Apr 2022 01:00:00 +0200} }
@inproceedings{DBLP:conf/iclr/LiJZKD21, title = {{{FedBN}}: {{Federated}} Learning on Non-{{IID}} Features via Local Batch Normalization}, booktitle = {9th International Conference on Learning Representations, {{ICLR}} 2021, Virtual Event, Austria, May 3-7, 2021}, author = {Li, Xiaoxiao and Jiang, Meirui and Zhang, Xiaofei and Kamp, Michael and Dou, Qi}, year = {2021}, publisher = {{OpenReview.net}}, url = {https://openreview.net/forum?id=6YEQUn0QICG}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/iclr/LiJZKD21.bib}, timestamp = {Wed, 23 Jun 2021 17:36:39 +0200} }
@inproceedings{DBLP:conf/nips/PetzkaKASB21, title = {Relative Flatness and Generalization}, booktitle = {Advances in Neural Information Processing Systems 34: {{Annual}} Conference on Neural Information Processing Systems 2021, {{NeurIPS}} 2021, December 6-14, 2021, Virtual}, author = {Petzka, Henning and Kamp, Michael and Adilova, Linara and Sminchisescu, Cristian and Boley, Mario}, editor = {Ranzato, Marc'Aurelio and Beygelzimer, Alina and Dauphin, Yann N. and Liang, Percy and Vaughan, Jennifer Wortman}, year = {2021}, pages = {18420--18432}, url = {https://proceedings.neurips.cc/paper/2021/hash/995f5e03890b029865f402e83a81c29d-Abstract.html}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/nips/PetzkaKASB21.bib}, timestamp = {Tue, 03 May 2022 01:00:00 +0200} }
@book{DBLP:conf/pkdd/2021-w1, title = {Machine Learning and Principles and Practice of Knowledge Discovery in Databases - International Workshops of {{ECML PKDD}} 2021, Virtual Event, September 13-17, 2021, Proceedings, Part {{I}}}, editor = {Kamp, Michael and Koprinska, Irena and Bibal, Adrien and Bouadi, Tassadit and Fr{\'e}nay, Beno{\^i}t and Gal{\'a}rraga, Luis and Oramas, Jos{\'e} and Adilova, Linara and Krishnamurthy, Yamuna and Kang, Bo and Largeron, Christine and Lijffijt, Jefrey and Viard, Tiphaine and Welke, Pascal and Ruocco, Massimiliano and Aune, Erlend and Gallicchio, Claudio and Schiele, Gregor and Pernkopf, Franz and Blott, Michaela and Fr{\"o}ning, Holger and Schindler, G{\"u}nther and Guidotti, Riccardo and Monreale, Anna and Rinzivillo, Salvatore and Biecek, Przemyslaw and Ntoutsi, Eirini and Pechenizkiy, Mykola and Rosenhahn, Bodo and Buckley, Christopher L. and Cialfi, Daniela and Lanillos, Pablo and Ramstead, Maxwell and Verbelen, Tim and Ferreira, Pedro M. and Andresini, Giuseppina and Malerba, Donato and Medeiros, Ib{\'e}ria and {Fournier-Viger}, Philippe and Nawaz, M. Saqib and Ventura, Sebasti{\'a}n and Sun, Meng and Zhou, Min and Bitetta, Valerio and Bordino, Ilaria and Ferretti, Andrea and Gullo, Francesco and Ponti, Giovanni and Severini, Lorenzo and Ribeiro, Rita P. and Gama, Jo{\~a}o and Gavald{\`a}, Ricard and Cooper, Lee A. D. and Ghazaleh, Naghmeh and Richiardi, Jonas and Roqueiro, Damian and Miranda, Diego Saldana and Sechidis, Konstantinos and Gra{\c c}a, Guilherme}, year = {2021}, series = {Communications in Computer and Information Science}, volume = {1524}, publisher = {{Springer}}, doi = {10.1007/978-3-030-93736-2}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/pkdd/2021-w1.bib}, isbn = {978-3-030-93735-5}, timestamp = {Sat, 12 Mar 2022 00:00:00 +0100} }
@book{DBLP:conf/pkdd/2021-w2, title = {Machine Learning and Principles and Practice of Knowledge Discovery in Databases - International Workshops of {{ECML PKDD}} 2021, Virtual Event, September 13-17, 2021, Proceedings, Part {{II}}}, editor = {Kamp, Michael and Koprinska, Irena and Bibal, Adrien and Bouadi, Tassadit and Fr{\'e}nay, Beno{\^i}t and Gal{\'a}rraga, Luis and Oramas, Jos{\'e} and Adilova, Linara and Krishnamurthy, Yamuna and Kang, Bo and Largeron, Christine and Lijffijt, Jefrey and Viard, Tiphaine and Welke, Pascal and Ruocco, Massimiliano and Aune, Erlend and Gallicchio, Claudio and Schiele, Gregor and Pernkopf, Franz and Blott, Michaela and Fr{\"o}ning, Holger and Schindler, G{\"u}nther and Guidotti, Riccardo and Monreale, Anna and Rinzivillo, Salvatore and Biecek, Przemyslaw and Ntoutsi, Eirini and Pechenizkiy, Mykola and Rosenhahn, Bodo and Buckley, Christopher L. and Cialfi, Daniela and Lanillos, Pablo and Ramstead, Maxwell and Verbelen, Tim and Ferreira, Pedro M. and Andresini, Giuseppina and Malerba, Donato and Medeiros, Ib{\'e}ria and {Fournier-Viger}, Philippe and Nawaz, M. Saqib and Ventura, Sebasti{\'a}n and Sun, Meng and Zhou, Min and Bitetta, Valerio and Bordino, Ilaria and Ferretti, Andrea and Gullo, Francesco and Ponti, Giovanni and Severini, Lorenzo and Ribeiro, Rita P. and Gama, Jo{\~a}o and Gavald{\`a}, Ricard and Cooper, Lee A. D. and Ghazaleh, Naghmeh and Richiardi, Jonas and Roqueiro, Damian and Miranda, Diego Saldana and Sechidis, Konstantinos and Gra{\c c}a, Guilherme}, year = {2021}, series = {Communications in Computer and Information Science}, volume = {1525}, publisher = {{Springer}}, doi = {10.1007/978-3-030-93733-1}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/pkdd/2021-w2.bib}, isbn = {978-3-030-93732-4}, timestamp = {Sat, 12 Mar 2022 00:00:00 +0100} }
@inproceedings{DBLP:conf/pkdd/LinsnerADKF21, title = {Approaches to Uncertainty Quantification in Federated Deep Learning}, booktitle = {Machine Learning and Principles and Practice of Knowledge Discovery in Databases - International Workshops of {{ECML PKDD}} 2021, Virtual Event, September 13-17, 2021, Proceedings, Part {{I}}}, author = {Linsner, Florian and Adilova, Linara and D{\"a}ubener, Sina and Kamp, Michael and Fischer, Asja}, editor = {Kamp, Michael and Koprinska, Irena and Bibal, Adrien and Bouadi, Tassadit and Fr{\'e}nay, Beno{\^i}t and Gal{\'a}rraga, Luis and Oramas, Jos{\'e} and Adilova, Linara and Krishnamurthy, Yamuna and Kang, Bo and Largeron, Christine and Lijffijt, Jefrey and Viard, Tiphaine and Welke, Pascal and Ruocco, Massimiliano and Aune, Erlend and Gallicchio, Claudio and Schiele, Gregor and Pernkopf, Franz and Blott, Michaela and Fr{\"o}ning, Holger and Schindler, G{\"u}nther and Guidotti, Riccardo and Monreale, Anna and Rinzivillo, Salvatore and Biecek, Przemyslaw and Ntoutsi, Eirini and Pechenizkiy, Mykola and Rosenhahn, Bodo and Buckley, Christopher L. and Cialfi, Daniela and Lanillos, Pablo and Ramstead, Maxwell and Verbelen, Tim and Ferreira, Pedro M. and Andresini, Giuseppina and Malerba, Donato and Medeiros, Ib{\'e}ria and {Fournier-Viger}, Philippe and Nawaz, M. Saqib and Ventura, Sebasti{\'a}n and Sun, Meng and Zhou, Min and Bitetta, Valerio and Bordino, Ilaria and Ferretti, Andrea and Gullo, Francesco and Ponti, Giovanni and Severini, Lorenzo and Ribeiro, Rita P. and Gama, Jo{\~a}o and Gavald{\`a}, Ricard and Cooper, Lee A. D. and Ghazaleh, Naghmeh and Richiardi, Jonas and Roqueiro, Damian and Miranda, Diego Saldana and Sechidis, Konstantinos and Gra{\c c}a, Guilherme}, year = {2021}, series = {Communications in Computer and Information Science}, volume = {1524}, pages = {128--145}, publisher = {{Springer}}, doi = {10.1007/978-3-030-93736-2\_12}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/pkdd/LinsnerADKF21.bib}, timestamp = {Sat, 12 Mar 2022 14:00:32 +0100} }
@article{DBLP:journals/corr/abs-2102-07623, title = {{{FedBN}}: {{Federated}} Learning on Non-{{IID}} Features via Local Batch Normalization}, author = {Li, Xiaoxiao and Jiang, Meirui and Zhang, Xiaofei and Kamp, Michael and Dou, Qi}, year = {2021}, journal = {CoRR}, volume = {abs/2102.07623}, eprint = {2102.07623}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2102.07623}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2102-07623.bib}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200} }
@article{DBLP:journals/corr/abs-2103-03943, title = {Novelty Detection in Sequential Data by Informed Clustering and Modeling}, author = {Adilova, Linara and Chen, Siming and Kamp, Michael}, year = {2021}, journal = {CoRR}, volume = {abs/2103.03943}, eprint = {2103.03943}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2103.03943}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2103-03943.bib}, timestamp = {Mon, 15 Mar 2021 00:00:00 +0100} }
@article{DBLP:journals/corr/abs-2110-03469, title = {Federated Learning from Small Datasets}, author = {Kamp, Michael and Fischer, Jonas and Vreeken, Jilles}, year = {2021}, journal = {CoRR}, volume = {abs/2110.03469}, eprint = {2110.03469}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2110.03469}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2110-03469.bib}, timestamp = {Thu, 21 Oct 2021 01:00:00 +0200} }
@article{DBLP:journals/corr/abs-2110-09974, title = {{{TsmoBN}}: {{Interventional}} Generalization for Unseen Clients in Federated Learning}, author = {Jiang, Meirui and Zhang, Xiaofei and Kamp, Michael and Li, Xiaoxiao and Dou, Qi}, year = {2021}, journal = {CoRR}, volume = {abs/2110.09974}, eprint = {2110.09974}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2110.09974}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2110-09974.bib}, timestamp = {Mon, 25 Oct 2021 01:00:00 +0200} }
@inproceedings{Julka2022, title = {Conditional Generative Adversarial Networks for Speed Control in Trajectory Simulation}, booktitle = {Machine Learning, Optimization, and Data Science}, author = {Julka, Sahib and Sowrirajan, Vishal and Schl{\"o}tterer, J{\"o}rg and Granitzer, Michael}, editor = {Nicosia, Giuseppe and Ojha, Varun and La Malfa, Emanuele and La Malfa, Gabriele and Jansen, Giorgio and Pardalos, Panos M. and Giuffrida, Giovanni and Umeton, Renato}, year = {2021}, pages = {436--450}, publisher = {{Springer International Publishing}}, address = {{Cham}}, doi = {10.1007/978-3-030-95470-3_33}, isbn = {978-3-030-95470-3} }
@inproceedings{Schmidt2021, title = {Towards a Trustworthy, Secure and Reliable Enclave for Machine Learning in a Hospital Setting: {{The Essen Medical Computing Platform}} ({{EMCP}})}, booktitle = {2021 {{IEEE}} Third International Conference on Cognitive Machine Intelligence ({{CogMI}})}, author = {Schmidt, Hendrik F.R. and Schl{\"o}tterer, J{\"o}rg and Bargull, Marcel and Nasca, Enrico and Aydelott, Ryan and Seifert, Christin and Meyer, Folker}, year = {2021}, pages = {116--123}, doi = {10.1109/CogMI52975.2021.00023} }
@book{DBLP:conf/miccai/2021autoimplant, title = {Towards the Automatization of Cranial Implant Design in Cranioplasty {{II}} - Second Challenge, {{AutoImplant}} 2021, Held in Conjunction with {{MICCAI}} 2021, Strasbourg, France, October 1, 2021, Proceedings}, editor = {Li, Jianning and Egger, Jan}, year = {2021}, series = {Lecture Notes in Computer Science}, volume = {13123}, publisher = {{Springer}}, doi = {10.1007/978-3-030-92652-6}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/miccai/2021autoimplant.bib}, isbn = {978-3-030-92651-9}, timestamp = {Thu, 09 Dec 2021 00:00:00 +0100} }
@inproceedings{DBLP:conf/miccai/KroviakovLE21, title = {Sparse Convolutional Neural Network for Skull Reconstruction}, booktitle = {Towards the Automatization of Cranial Implant Design in Cranioplasty {{II}} - Second Challenge, {{AutoImplant}} 2021, Held in Conjunction with {{MICCAI}} 2021, Strasbourg, France, October 1, 2021, Proceedings}, author = {Kroviakov, Artem and Li, Jianning and Egger, Jan}, editor = {Li, Jianning and Egger, Jan}, year = {2021}, series = {Lecture Notes in Computer Science}, volume = {13123}, pages = {80--94}, publisher = {{Springer}}, doi = {10.1007/978-3-030-92652-6\_7}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/miccai/KroviakovLE21.bib}, timestamp = {Thu, 09 Dec 2021 00:00:00 +0100} }
@inproceedings{DBLP:conf/miccai/LiPGJE21, title = {Learning to Rearrange Voxels in Binary Segmentation Masks for Smooth Manifold Triangulation}, booktitle = {Towards the Automatization of Cranial Implant Design in Cranioplasty {{II}} - Second Challenge, {{AutoImplant}} 2021, Held in Conjunction with {{MICCAI}} 2021, Strasbourg, France, October 1, 2021, Proceedings}, author = {Li, Jianning and Pepe, Antonio and Gsaxner, Christina and Jin, Yuan and Egger, Jan}, editor = {Li, Jianning and Egger, Jan}, year = {2021}, series = {Lecture Notes in Computer Science}, volume = {13123}, pages = {45--62}, publisher = {{Springer}}, doi = {10.1007/978-3-030-92652-6\_5}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/miccai/LiPGJE21.bib}, timestamp = {Sat, 09 Apr 2022 01:00:00 +0200} }
@inproceedings{DBLP:conf/miccai/YuLE21, title = {{{PCA-Skull}}: {{3D}} Skull Shape Modelling Using Principal Component Analysis}, booktitle = {Towards the Automatization of Cranial Implant Design in Cranioplasty {{II}} - Second Challenge, {{AutoImplant}} 2021, Held in Conjunction with {{MICCAI}} 2021, Strasbourg, France, October 1, 2021, Proceedings}, author = {Yu, Lei and Li, Jianning and Egger, Jan}, editor = {Li, Jianning and Egger, Jan}, year = {2021}, series = {Lecture Notes in Computer Science}, volume = {13123}, pages = {105--115}, publisher = {{Springer}}, doi = {10.1007/978-3-030-92652-6\_9}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/miccai/YuLE21.bib}, timestamp = {Thu, 09 Dec 2021 00:00:00 +0100} }
@inproceedings{DBLP:conf/vrst/GsaxnerL0SE21, title = {Inside-out Instrument Tracking for Surgical Navigation in Augmented Reality}, booktitle = {{{VRST}} '21: 27th {{ACM}} Symposium on Virtual Reality Software and Technology, Virtual Event / Osaka, Japan, December 8 - 10, 2021}, author = {Gsaxner, Christina and Li, Jianning and Pepe, Antonio and Schmalstieg, Dieter and Egger, Jan}, editor = {Itoh, Yuichi and Takashima, Kazuki and Punpongsanon, Parinya and Sra, Misha and Fujita, Kazuyuki and Yoshida, Shigeo and Piumsomboon, Tham}, year = {2021}, pages = {4:1--4:11}, publisher = {{ACM}}, doi = {10.1145/3489849.3489863}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/vrst/GsaxnerL0SE21.bib}, timestamp = {Sat, 09 Apr 2022 01:00:00 +0200} }
@article{DBLP:journals/cmpb/GsaxnerPLIWSE21, title = {Augmented Reality for Head and Neck Carcinoma Imaging: {{Description}} and Feasibility of an Instant Calibration, Markerless Approach}, author = {Gsaxner, Christina and Pepe, Antonio and Li, Jianning and Ibrahimpasic, Una and Wallner, J{\"u}rgen and Schmalstieg, Dieter and Egger, Jan}, year = {2021}, journal = {Computer Methods and Programs in Biomedicine}, volume = {200}, pages = {105854}, doi = {10.1016/j.cmpb.2020.105854}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/cmpb/GsaxnerPLIWSE21.bib}, timestamp = {Tue, 01 Jun 2021 01:00:00 +0200} }
@article{DBLP:journals/corr/abs-2108-05269, title = {Learning to Rearrange Voxels in Binary Segmentation Masks for Smooth Manifold Triangulation}, author = {Li, Jianning and Pepe, Antonio and Gsaxner, Christina and Jin, Yuan and Egger, Jan}, year = {2021}, journal = {CoRR}, volume = {abs/2108.05269}, eprint = {2108.05269}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2108.05269}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2108-05269.bib}, timestamp = {Wed, 18 Aug 2021 01:00:00 +0200} }
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@article{heinemann2020research, title = {Research note: tracing pathways of entry and persistence of facultative pathogenic and antibiotic-resistant bacteria in a commercial broiler farm with substantial health problems}, author = {Heinemann, C{\'e}line and Leubner, Caroline D and Savin, Mykhailo and Sib, Esther and Schmithausen, Ricarda M and Steinhoff-Wagner, Julia}, journal = {Poultry science}, volume = {99}, year = {2020}, publisher = {Elsevier} }
@article{streeck2020infectioo, title = {Infection fatality rate of SARS-CoV-2 infection in a German community with a super-spreading event. 2020}, author = {Streeck, Hendrik and Schulte, Bianca and K{\"u}mmerer, Beate M and Richter, Enrico and H{\"o}ller, Tobias and Fuhrmann, Christine and Bartok, Eva and Dolscheid, Ramona and Berger, Moritz and Wessendorf, Lukas and others}, journal = {Nat Commun}, volume = {11}, year = {2020} }
@article{savin2020colistin, title = {Colistin-resistant enterobacteriaceae isolated from process waters and wastewater from German poultry and pig slaughterhouses}, author = {Savin, Mykhailo and Bierbaum, Gabriele and Blau, Khald and Parcina, Marijo and Sib, Esther and Smalla, Kornelia and Schmithausen, Ricarda and Heinemann, C{\'e}line and Hammerl, Jens A and Kreyenschmidt, Judith}, journal = {Frontiers in Microbiology}, volume = {11}, year = {2020}, publisher = {Frontiers Media SA} }
@article{streeck2020infectiop, title = {Infection fatality rate of SARS-CoV2 in a super-spreading event in Germany}, author = {Streeck, Hendrik and Schulte, Bianca and K{\"u}mmerer, Beate M and Richter, Enrico and H{\"o}ller, Tobias and Fuhrmann, Christine and Bartok, Eva and Dolscheid-Pommerich, Ramona and Berger, Moritz and Wessendorf, Lukas and others}, journal = {Nature communications}, volume = {11}, year = {2020}, publisher = {Nature Publishing Group} }
@article{exner2020chemical, title = {Chemical disinfection in healthcare settings: critical aspects for the development of global strategies}, author = {Exner, Martin and Bhattacharya, Sanjay and Gebel, J{\"u}rgen and Goroncy-Bermes, Peter and Hartemann, Philippe and Heeg, Peter and Ilschner, Carola and Kramer, Axel and Ling, Moi Lin and Merkens, Wolfgang and others}, journal = {GMS hygiene and infection control}, volume = {15}, year = {2020}, publisher = {German Medical Science} }
@article{streeck2020infectioq, title = {Infection fatality rate of SARS-CoV-2 infection in a German community with a super-spreading event. medRxiv}, author = {Streeck, Hendrik and Schulte, Bianca and Kuemmerer, B and Richter, Enrico and H{\"o}ller, Tobias and Fuhrmann, Christine and Bartok, Eva and Dolscheid, R and Berger, M and Wessendorf, L and others}, journal = {Preprint posted online June}, volume = {2}, year = {2020} }
@article{schloter_mikrobiomeforschung_2020, title = {Mikrobiome—{Forschung} zwischen {Theorie} und praktischer {Anwendung}}, volume = {26}, journal = {BIOspektrum}, author = {Schloter, Michael and Meyer, Folker and Berg, Gabriele}, year = {2020}, note = {Publisher: Springer Berlin Heidelberg} }
@article{schriml_covid-19_2020-1, title = {{COVID}-19 pandemic reveals the peril of ignoring metadata standards}, volume = {7}, url = {https://www.ncbi.nlm.nih.gov/pubmed/32561801}, doi = {10.1038/s41597-020-0524-5}, journal = {Sci Data}, author = {Schriml, L. M. and Chuvochina, M. and Davies, N. and Eloe-Fadrosh, E. A. and Finn, R. D. and Hugenholtz, P. and Hunter, C. I. and Hurwitz, B. L. and Kyrpides, N. C. and Meyer, Folker and Mizrachi, I. K. and Sansone, S. A. and Sutton, G. and Tighe, S. and Walls, R.}, year = {2020}, note = {Type: Journal Article} }
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@inproceedings{DBLP:conf/accv/SeiboldKSS20, title = {Self-Guided Multiple Instance Learning for Weakly Supervised Disease Classification and Localization in Chest Radiographs}, booktitle = {Computer Vision - {{ACCV}} 2020 - 15th Asian Conference on Computer Vision, Kyoto, Japan, November 30 - December 4, 2020, Revised Selected Papers, Part {{V}}}, author = {Seibold, Constantin and Kleesiek, Jens and Schlemmer, Heinz-Peter and Stiefelhagen, Rainer}, editor = {Ishikawa, Hiroshi and Liu, Cheng-Lin and Pajdla, Tom{\'a}s and Shi, Jianbo}, year = {2020}, series = {Lecture Notes in Computer Science}, volume = {12626}, pages = {617--634}, publisher = {{Springer}}, doi = {10.1007/978-3-030-69541-5\_37}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/accv/SeiboldKSS20.bib}, timestamp = {Tue, 02 Mar 2021 08:39:11 +0100} }
@article{DBLP:journals/corr/abs-2010-00127, title = {Self-Guided Multiple Instance Learning for Weakly Supervised Disease Classification and Localization in Chest Radiographs}, author = {Seibold, Constantin and Kleesiek, Jens and Schlemmer, Heinz-Peter and Stiefelhagen, Rainer}, year = {2020}, journal = {CoRR}, volume = {abs/2010.00127}, eprint = {2010.00127}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2010.00127}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2010-00127.bib}, timestamp = {Mon, 12 Oct 2020 01:00:00 +0200} }
@inproceedings{DBLP:conf/dsn/MedeirosGKF20, title = {Second International Workshop on Data-Centric Dependability and Security ({{DCDS}})}, booktitle = {50th Annual {{IEEE}}/{{IFIP}} International Conference on Dependable Systems and Networks Workshops, {{DSN}} Workshops 2020, Valencia, Spain, June 29 - July 2, 2020}, author = {Medeiros, Ib{\'e}ria and Gashi, Ilir and Kamp, Michael and Ferreira, Pedro}, year = {2020}, pages = {xi}, publisher = {{IEEE}}, doi = {10.1109/DSN-W50199.2020.00007}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/dsn/MedeirosGKF20.bib}, timestamp = {Tue, 19 Apr 2022 01:00:00 +0200} }
@inproceedings{DBLP:conf/kdd/WelkeSKW20, title = {{{HOPS}}: {{Probabilistic}} Subtree Mining for Small and Large Graphs}, booktitle = {{{KDD}} '20: {{The}} 26th {{ACM SIGKDD}} Conference on Knowledge Discovery and Data Mining, Virtual Event, {{CA}}, {{USA}}, August 23-27, 2020}, author = {Welke, Pascal and Seiffarth, Florian and Kamp, Michael and Wrobel, Stefan}, editor = {Gupta, Rajesh and Liu, Yan and Tang, Jiliang and Prakash, B. Aditya}, year = {2020}, pages = {1275--1284}, publisher = {{ACM}}, doi = {10.1145/3394486.3403180}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/kdd/WelkeSKW20.bib}, timestamp = {Tue, 09 Mar 2021 00:00:00 +0100} }
@book{DBLP:conf/pkdd/2020-w, title = {{{ECML PKDD}} 2020 Workshops - Workshops of the European Conference on Machine Learning and Knowledge Discovery in Databases ({{ECML PKDD}} 2020): {{SoGood}} 2020, {{PDFL}} 2020, {{MLCS}} 2020, {{NFMCP}} 2020, {{DINA}} 2020, {{EDML}} 2020, {{XKDD}} 2020 and {{INRA}} 2020, Ghent, Belgium, September 14-18, 2020, Proceedings}, editor = {Koprinska, Irena and Kamp, Michael and Appice, Annalisa and Loglisci, Corrado and Antonie, Luiza and Zimmermann, Albrecht and Guidotti, Riccardo and {\"O}zg{\"o}bek, {\"O}zlem and Ribeiro, Rita P. and Gavald{\`a}, Ricard and Gama, Jo{\~a}o and Adilova, Linara and Krishnamurthy, Yamuna and Ferreira, Pedro M. and Malerba, Donato and Medeiros, Ib{\'e}ria and Ceci, Michelangelo and Manco, Giuseppe and Masciari, Elio and Ras, Zbigniew W. and Christen, Peter and Ntoutsi, Eirini and Schubert, Erich and Zimek, Arthur and Monreale, Anna and Biecek, Przemyslaw and Rinzivillo, Salvatore and Kille, Benjamin and Lommatzsch, Andreas and Gulla, Jon Atle}, year = {2020}, series = {Communications in Computer and Information Science}, volume = {1323}, publisher = {{Springer}}, doi = {10.1007/978-3-030-65965-3}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/pkdd/2020-w.bib}, isbn = {978-3-030-65964-6}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200} }
@inproceedings{DBLP:conf/pkdd/HeppeKAHPM20, title = {Resource-Constrained on-Device Learning by Dynamic Averaging}, booktitle = {{{ECML PKDD}} 2020 Workshops - Workshops of the European Conference on Machine Learning and Knowledge Discovery in Databases ({{ECML PKDD}} 2020): {{SoGood}} 2020, {{PDFL}} 2020, {{MLCS}} 2020, {{NFMCP}} 2020, {{DINA}} 2020, {{EDML}} 2020, {{XKDD}} 2020 and {{INRA}} 2020, Ghent, Belgium, September 14-18, 2020, Proceedings}, author = {Heppe, Lukas and Kamp, Michael and Adilova, Linara and Heinrich, Danny and Piatkowski, Nico and Morik, Katharina}, editor = {Koprinska, Irena and Kamp, Michael and Appice, Annalisa and Loglisci, Corrado and Antonie, Luiza and Zimmermann, Albrecht and Guidotti, Riccardo and {\"O}zg{\"o}bek, {\"O}zlem and Ribeiro, Rita P. and Gavald{\`a}, Ricard and Gama, Jo{\~a}o and Adilova, Linara and Krishnamurthy, Yamuna and Ferreira, Pedro M. and Malerba, Donato and Medeiros, Ib{\'e}ria and Ceci, Michelangelo and Manco, Giuseppe and Masciari, Elio and Ras, Zbigniew W. and Christen, Peter and Ntoutsi, Eirini and Schubert, Erich and Zimek, Arthur and Monreale, Anna and Biecek, Przemyslaw and Rinzivillo, Salvatore and Kille, Benjamin and Lommatzsch, Andreas and Gulla, Jon Atle}, year = {2020}, series = {Communications in Computer and Information Science}, volume = {1323}, pages = {129--144}, publisher = {{Springer}}, doi = {10.1007/978-3-030-65965-3\_9}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/pkdd/HeppeKAHPM20.bib}, timestamp = {Thu, 23 Jun 2022 19:56:56 +0200} }
@article{DBLP:journals/corr/abs-2001-00939, title = {Feature-Robustness, Flatness and Generalization Error for Deep Neural Networks}, author = {Petzka, Henning and Adilova, Linara and Kamp, Michael and Sminchisescu, Cristian}, year = {2020}, journal = {CoRR}, volume = {abs/2001.00939}, eprint = {2001.00939}, eprinttype = {arxiv}, url = {http://arxiv.org/abs/2001.00939}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2001-00939.bib}, timestamp = {Fri, 10 Jan 2020 00:00:00 +0100} }
@article{DBLP:journals/corr/abs-2009-12098, title = {Resource-Constrained on-Device Learning by Dynamic Averaging}, author = {Heppe, Lukas and Kamp, Michael and Adilova, Linara and Heinrich, Danny and Piatkowski, Nico and Morik, Katharina}, year = {2020}, journal = {CoRR}, volume = {abs/2009.12098}, eprint = {2009.12098}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2009.12098}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2009-12098.bib}, timestamp = {Wed, 30 Sep 2020 01:00:00 +0200} }
@inproceedings{schliski2020ecir, title = {Influence of Random Walk Parametrization on Graph Embeddings}, booktitle = {Advances in Information Retrieval}, author = {Schliski, Fabian and Schl{\"o}tterer, J{\"o}rg and Granitzer, Michael}, editor = {Jose, Joemon M. and Yilmaz, Emine and Magalh{\~a}es, Jo{\~a}o and Castells, Pablo and Ferro, Nicola and Silva, M{\'a}rio J. and Martins, Fl{\'a}vio}, year = {2020}, series = {{{ECIR}} 2020}, pages = {58--65}, publisher = {{Springer International Publishing}}, address = {{Cham}}, isbn = {978-3-030-45442-5} }
@article{schloetterer2020cola, title = {{{QueryCrumbs}} Search Query History Visualization \textendash{} {{Usability}}, Transparency and Long-Term Usage}, author = {Schl{\"o}tterer, J{\"o}rg and Seifert, Christin and Satchell, Christopher and Granitzer, Michael}, year = {2020}, journal = {Journal of Computer Languages}, volume = {57}, pages = {100941}, issn = {2590-1184}, doi = {10.1016/j.cola.2020.100941}, keywords = {Information refinding,Information retrieval,Queryhistory visualization,Search experts,Search history} }
@phdthesis{schlotterer2020supporting, title = {Supporting the Discovery of Long-Tail Resources on the Web}, author = {Schl{\"o}tterer, J{\"o}rg}, year = {2020}, eprint = {urn:nbn:de:bvb:739-opus4-8539}, eprinttype = {urn}, school = {University of Passau}, keywords = {peer-other} }
@inproceedings{DBLP:conf/mibam/PepeSLGCFE20, title = {{{IRIS}}: Interactive Real-Time Feedback Image Segmentation with Deep Learning}, booktitle = {Medical Imaging 2020: {{Biomedical}} Applications in Molecular, Structural, and Functional Imaging, Houston, {{TX}}, {{USA}}, February 15-20, 2020}, author = {Pepe, Antonio and Schussnig, Richard and Li, Jianning and Gsaxner, Christina and Chen, Xiaojun and Fries, Thomas-Peter and Egger, Jan}, editor = {Kr{\'o}l, Andrzej and Gimi, Barjor S.}, year = {2020}, series = {{{SPIE}} Proceedings}, volume = {11317}, pages = {113170R}, publisher = {{SPIE}}, doi = {10.1117/12.2551354}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/mibam/PepeSLGCFE20.bib}, timestamp = {Thu, 23 Jul 2020 19:19:00 +0200} }
@book{DBLP:conf/miccai/2020autoimplant, title = {Towards the Automatization of Cranial Implant Design in Cranioplasty - First Challenge, {{AutoImplant}} 2020, Held in Conjunction with {{MICCAI}} 2020, Lima, Peru, October 8, 2020, Proceedings}, editor = {Li, Jianning and Egger, Jan}, year = {2020}, series = {Lecture Notes in Computer Science}, volume = {12439}, publisher = {{Springer}}, doi = {10.1007/978-3-030-64327-0}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/miccai/2020autoimplant.bib}, isbn = {978-3-030-64326-3}, timestamp = {Thu, 10 Dec 2020 00:00:00 +0100} }
@inproceedings{DBLP:conf/miccai/EderLE20, title = {Learning Volumetric Shape Super-Resolution for Cranial Implant Design}, booktitle = {Towards the Automatization of Cranial Implant Design in Cranioplasty - First Challenge, {{AutoImplant}} 2020, Held in Conjunction with {{MICCAI}} 2020, Lima, Peru, October 8, 2020, Proceedings}, author = {Eder, Matthias and Li, Jianning and Egger, Jan}, editor = {Li, Jianning and Egger, Jan}, year = {2020}, series = {Lecture Notes in Computer Science}, volume = {12439}, pages = {104--113}, publisher = {{Springer}}, doi = {10.1007/978-3-030-64327-0\_12}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/miccai/EderLE20.bib}, timestamp = {Thu, 17 Dec 2020 00:00:00 +0100} }
@inproceedings{DBLP:conf/miccai/JinLE20, title = {High-Resolution Cranial Implant Prediction via Patch-Wise Training}, booktitle = {Towards the Automatization of Cranial Implant Design in Cranioplasty - First Challenge, {{AutoImplant}} 2020, Held in Conjunction with {{MICCAI}} 2020, Lima, Peru, October 8, 2020, Proceedings}, author = {Jin, Yuan and Li, Jianning and Egger, Jan}, editor = {Li, Jianning and Egger, Jan}, year = {2020}, series = {Lecture Notes in Computer Science}, volume = {12439}, pages = {94--103}, publisher = {{Springer}}, doi = {10.1007/978-3-030-64327-0\_11}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/miccai/JinLE20.bib}, timestamp = {Thu, 17 Dec 2020 00:00:00 +0100} }
@inproceedings{DBLP:conf/miccai/KarnerGPLFAWE20, title = {Single-Shot Deep Volumetric Regression for Mobile Medical Augmented Reality}, booktitle = {Multimodal Learning for Clinical Decision Support and Clinical Image-Based Procedures - 10th International Workshop, {{ML-CDS}} 2020, and 9th International Workshop, {{CLIP}} 2020, Held in Conjunction with {{MICCAI}} 2020, Lima, Peru, October 4-8, 2020, Proceedings}, author = {Karner, Florian and Gsaxner, Christina and Pepe, Antonio and Li, Jianning and Fleck, Philipp and Arth, Clemens and Wallner, J{\"u}rgen and Egger, Jan}, editor = {{Syeda-Mahmood}, Tanveer F. and Drechsler, Klaus and Greenspan, Hayit and Madabhushi, Anant and Karargyris, Alexandros and Linguraru, Marius George and Laura, Cristina Oyarzun and Shekhar, Raj and Wesarg, Stefan and Ballester, Miguel {\'A}ngel Gonz{\'a}lez and Erdt, Marius}, year = {2020}, series = {Lecture Notes in Computer Science}, volume = {12445}, pages = {64--74}, publisher = {{Springer}}, doi = {10.1007/978-3-030-60946-7\_7}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/miccai/KarnerGPLFAWE20.bib}, timestamp = {Tue, 17 May 2022 16:11:27 +0200} }
@inproceedings{DBLP:conf/miccai/LiE20, title = {Dataset Descriptor for the {{AutoImplant}} Cranial Implant Design Challenge}, booktitle = {Towards the Automatization of Cranial Implant Design in Cranioplasty - First Challenge, {{AutoImplant}} 2020, Held in Conjunction with {{MICCAI}} 2020, Lima, Peru, October 8, 2020, Proceedings}, author = {Li, Jianning and Egger, Jan}, editor = {Li, Jianning and Egger, Jan}, year = {2020}, series = {Lecture Notes in Computer Science}, volume = {12439}, pages = {10--15}, publisher = {{Springer}}, doi = {10.1007/978-3-030-64327-0\_2}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/miccai/LiE20.bib}, timestamp = {Thu, 17 Dec 2020 00:00:00 +0100} }
@inproceedings{DBLP:conf/miccai/LiPGCE20, title = {A Baseline Approach for {{AutoImplant}}: {{The MICCAI}} 2020 Cranial Implant Design Challenge}, booktitle = {Multimodal Learning for Clinical Decision Support and Clinical Image-Based Procedures - 10th International Workshop, {{ML-CDS}} 2020, and 9th International Workshop, {{CLIP}} 2020, Held in Conjunction with {{MICCAI}} 2020, Lima, Peru, October 4-8, 2020, Proceedings}, author = {Li, Jianning and Pepe, Antonio and Gsaxner, Christina and {von Campe}, Gord and Egger, Jan}, editor = {{Syeda-Mahmood}, Tanveer F. and Drechsler, Klaus and Greenspan, Hayit and Madabhushi, Anant and Karargyris, Alexandros and Linguraru, Marius George and Laura, Cristina Oyarzun and Shekhar, Raj and Wesarg, Stefan and Ballester, Miguel {\'A}ngel Gonz{\'a}lez and Erdt, Marius}, year = {2020}, series = {Lecture Notes in Computer Science}, volume = {12445}, pages = {75--84}, publisher = {{Springer}}, doi = {10.1007/978-3-030-60946-7\_8}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/miccai/LiPGCE20.bib}, timestamp = {Wed, 07 Apr 2021 01:00:00 +0200} }
@inproceedings{DBLP:conf/miccai/PepeMGLFSE20, title = {Semi-Supervised Virtual Regression of Aortic Dissections Using {{3D}} Generative Inpainting}, booktitle = {Thoracic Image Analysis - Second International Workshop, {{TIA}} 2020, Held in Conjunction with {{MICCAI}} 2020, Lima, Peru, October 8, 2020, Proceedings}, author = {Pepe, Antonio and Mistelbauer, Gabriel and Gsaxner, Christina and Li, Jianning and Fleischmann, Dominik and Schmalstieg, Dieter and Egger, Jan}, editor = {Petersen, Jens and Est{\'e}par, Ra{\'u}l San Jos{\'e} and {Schmidt-Richberg}, Alexander and Gerard, Sarah E. and {Lassen-Schmidt}, Bianca and Jacobs, Colin and Beichel, Reinhard and Mori, Kensaku}, year = {2020}, series = {Lecture Notes in Computer Science}, volume = {12502}, pages = {130--140}, publisher = {{Springer}}, doi = {10.1007/978-3-030-62469-9\_12}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/miccai/PepeMGLFSE20.bib}, timestamp = {Sat, 14 Nov 2020 00:00:00 +0100} }
@inproceedings{DBLP:conf/miigp/EggerGPMGLEC20, title = {A Comprehensive Workflow and Framework for Immersive Virtual Endoscopy of Dissected Aortae from {{CTA}} Data}, booktitle = {Medical Imaging 2020: {{Image-guided}} Procedures, Robotic Interventions, and Modeling, Houston, {{TX}}, {{USA}}, February 15-20, 2020}, author = {Egger, Jan and Gunacker, Simon and Pepe, Antonio and Melito, Gian Marco and Gsaxner, Christina and Li, Jianning and Ellermann, Katrin and Chen, Xiaojun}, editor = {Fei, Baowei and Linte, Cristian A.}, year = {2020}, series = {{{SPIE}} Proceedings}, volume = {11315}, pages = {1131531}, publisher = {{SPIE}}, doi = {10.1117/12.2559239}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/conf/miigp/EggerGPMGLEC20.bib}, timestamp = {Tue, 11 Jan 2022 00:00:00 +0100} }
@article{DBLP:journals/corr/abs-2005-02760, title = {Design and Development of a Web-Based Tool for Inpainting of Dissected Aortae in Angiography Images}, author = {Prutsch, Alexander and Pepe, Antonio and Egger, Jan}, year = {2020}, journal = {CoRR}, volume = {abs/2005.02760}, eprint = {2005.02760}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2005.02760}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2005-02760.bib}, timestamp = {Sat, 09 May 2020 01:00:00 +0200} }
@article{DBLP:journals/corr/abs-2006-00980, title = {An Online Platform for Automatic Skull Defect Restoration and Cranial Implant Design}, author = {Li, Jianning and Pepe, Antonio and Gsaxner, Christina and Egger, Jan}, year = {2020}, journal = {CoRR}, volume = {abs/2006.00980}, eprint = {2006.00980}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2006.00980}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2006-00980.bib}, timestamp = {Tue, 09 Jun 2020 01:00:00 +0200} }
@article{DBLP:journals/corr/abs-2006-12449, title = {A Baseline Approach for {{AutoImplant}}: The {{MICCAI}} 2020 Cranial Implant Design Challenge}, author = {Li, Jianning and Pepe, Antonio and Gsaxner, Christina and {von Campe}, Gord and Egger, Jan}, year = {2020}, journal = {CoRR}, volume = {abs/2006.12449}, eprint = {2006.12449}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2006.12449}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2006-12449.bib}, timestamp = {Tue, 23 Jun 2020 01:00:00 +0200} }
@article{DBLP:journals/corr/abs-2010-14881, title = {Medical Deep Learning - {{A}} Systematic Meta-Review}, author = {Egger, Jan and Gsaxner, Christina and Pepe, Antonio and Li, Jianning}, year = {2020}, journal = {CoRR}, volume = {abs/2010.14881}, eprint = {2010.14881}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2010.14881}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2010-14881.bib}, timestamp = {Tue, 03 Nov 2020 00:00:00 +0100} }
@article{DBLP:journals/corr/abs-2011-08184, title = {Deep Learning - {{A}} First Meta-Survey of Selected Reviews across Scientific Disciplines and Their Research Impact}, author = {Egger, Jan and Pepe, Antonio and Gsaxner, Christina and Li, Jianning}, year = {2020}, journal = {CoRR}, volume = {abs/2011.08184}, eprint = {2011.08184}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2011.08184}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2011-08184.bib}, timestamp = {Wed, 18 Nov 2020 00:00:00 +0100} }
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@article{RN40, author = {Scortegagna, M. and Hockemeyer, K. and Dolgalev, I. and Pozniak, J. and Rambow, F. and Li, Y. and Feng, Y. and Tinoco, R. and Otero, D. C. and Zhang, T. and Brown, K. and Bosenberg, M. and Bradley, L. M. and Marine, J. C. and Aifantis, I. and Ronai, Z. A.}, title = {Siah2 control of T-regulatory cells limits anti-tumor immunity}, journal = {Nat Commun}, volume = {11}, number = {1}, pages = {99}, issn = {2041-1723 (Electronic) 2041-1723 (Linking)}, doi = {10.1038/s41467-019-13826-7}, url = {https://www.ncbi.nlm.nih.gov/pubmed/31911617}, year = {2020}, type = {Journal Article} }
@article{RN21, author = {Li, X. and Karras, P. and Torres, R. and Rambow, F. and van den Oord, J. and Marine, J. C. and Kos, L.}, title = {Disseminated Melanoma Cells Transdifferentiate into Endothelial Cells in Intravascular Niches at Metastatic Sites}, journal = {Cell Rep}, volume = {31}, number = {11}, pages = {107765}, issn = {2211-1247 (Electronic)}, doi = {10.1016/j.celrep.2020.107765}, url = {https://www.ncbi.nlm.nih.gov/pubmed/32553158}, year = {2020}, type = {Journal Article} }
@article{baaijens_full-length_2019, title = {Full-length de novo viral quasispecies assembly through variation graph construction}, volume = {35}, issn = {1367-4803}, url = {https://doi.org/10.1093/bioinformatics/btz443}, doi = {10.1093/bioinformatics/btz443}, number = {24}, urldate = {2021-06-30}, journal = {Bioinformatics}, author = {Baaijens, Jasmijn A and Van der Roest, Bastiaan and Köster, Johannes and Stougie, Leen and Schönhuth, Alexander}, month = dec, year = {2019}, pages = {5086--5094}, file = {Full Text PDF:/home/johannes/Zotero/storage/53D5FAFU/Baaijens et al. - 2019 - Full-length de novo viral quasispecies assembly th.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/Y99JV9A7/5506652.html:text/html} }
@article{koster_enhancing_2019, title = {Enhancing sensitivity and controlling false discovery rate in somatic indel discovery}, copyright = {© 2019, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, url = {https://www.biorxiv.org/content/10.1101/741256v1}, doi = {10.1101/741256}, language = {en}, urldate = {2019-08-23}, journal = {bioRxiv}, author = {Köster, Johannes and Dijkstra, Louis and Marschall, Tobias and Schönhuth, Alexander}, month = aug, year = {2019}, pages = {741256}, file = {Full Text PDF:/home/johannes/Zotero/storage/XG5KEZLC/Köster et al. - 2019 - Enhancing sensitivity and controlling false discov.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/R2MFI7X2/741256v1.html:text/html} }
@article{Becker2019-du, title = {Natural language processing of German clinical colorectal cancer notes for guideline-based treatment evaluation}, author = {Becker, Matthias and Kasper, Stefan and B{\"o}ckmann, Britta and J{\"o}ckel, Karl-Heinz and Virchow, Isabel}, journal = {Int. J. Med. Inform.}, publisher = {Elsevier BV}, volume = {127}, pages = {141--146}, month = jul, year = {2019}, keywords = {Electronic health records; Information extraction; Knowledge management; Natural language processing}, copyright = {http://creativecommons.org/licenses/by-nc-nd/4.0/}, language = {en} }
@article{koster_bayesian_2019, title = {A {Bayesian} model for single cell transcript expression analysis on {MERFISH} data}, volume = {35}, issn = {1367-4803}, url = {https://academic.oup.com/bioinformatics/article/35/6/995/5078469}, doi = {10.1093/bioinformatics/bty718}, language = {en}, number = {6}, urldate = {2019-05-03}, journal = {Bioinformatics}, author = {Köster, Johannes and Brown, Myles and Liu, X. Shirley}, month = mar, year = {2019}, pages = {995--1001}, file = {Full Text:/home/johannes/Zotero/storage/7I6XXAEP/Köster et al. - 2019 - A Bayesian model for single cell transcript expres.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/ICTS5ZQ5/5078469.html:text/html} }
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@inproceedings{stocker_protein_2019, series = {Lecture {Notes} in {Computer} {Science}}, title = {Protein {Complex} {Similarity} {Based} on {Weisfeiler}-{Lehman} {Labeling}}, isbn = {978-3-030-32047-8}, language = {en}, booktitle = {Similarity {Search} and {Applications}}, publisher = {Springer International Publishing}, author = {Stöcker, Bianca K. and Schäfer, Till and Mutzel, Petra and Köster, Johannes and Kriege, Nils and Rahmann, Sven}, editor = {Amato, Giuseppe and Gennaro, Claudio and Oria, Vincent and Radovanović, Miloš}, year = {2019}, keywords = {Constrained protein interaction networks, Jaccard similarity, Protein complexes, Similarity measure, Weisfeiler-Lehman labeling}, pages = {308--322}, file = {Springer Full Text PDF:/home/johannes/Zotero/storage/R3TECB2Y/Stöcker et al. - 2019 - Protein Complex Similarity Based on Weisfeiler-Leh.pdf:application/pdf} }
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@article{Kraiselburd2019MetabolicRO, title = {Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP\_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation}, author = {Kraiselburd, Ivana and Br{\"u}ls, Thomas and Heilmann, Geronimo and Kaschani, Farnusch and Kaiser, Markus and Meckenstock, Rainer U.}, journal = {Environmental Microbiology}, year = {2019}, volume = {21}, pages = {1267 - 1286} }
@article{voigt2019occurrence, title = {The occurrence of antimicrobial substances in toilet, sink and shower drainpipes of clinical units: a neglected source of antibiotic residues}, author = {Voigt, AM and Faerber, HA and Wilbring, G and Skutlarek, D and Felder, C and Mahn, R and Wolf, D and Brossart, P and Hornung, T and Engelhart, S and others}, journal = {International journal of hygiene and environmental health}, volume = {222}, year = {2019}, publisher = {Urban \& Fischer} }
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@article{niebel2019faziale, title = {Faziale Nekrose durch Orthopoxviren}, author = {Niebel, Dennis and Hornung, Thorsten and Schmithausen, Ricarda and Rothe, Hanna and Parcina, Marijo and Wenzel, J{\"o}rg and Exner, Martin and Bieber, Thomas}, journal = {Der Hautarzt}, volume = {70}, year = {2019}, publisher = {Springer Medizin} }
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@phdthesis{schmithausen2019one, title = {One health-antibiotic resistance in human, animal and environmental hygiene}, author = {Schmithausen, Ricarda}, year = {2019}, school = {Rheinische Friedrich-Wilhelms-Universit{\"a}t Bonn} }
@article{niebel2019facial, title = {Facial necrosis caused by orthopoxvirus: Differential diagnosis and dermatohistopathological correlation of infectious facial ulcers}, author = {Niebel, Dennis and Hornung, Thorsten and Schmithausen, Ricarda and Rothe, Hanna and Parcina, Marijo and Wenzel, Joerg and Exner, Martin and Bieber, Thomas}, journal = {Der Hautarzt; Zeitschrift fur Dermatologie, Venerologie, und Verwandte Gebiete}, volume = {70}, year = {2019} }
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@article{kampfer2018lelliottia, title = {Lelliottia aquatilis sp. nov., isolated from drinking water}, author = {K{\"a}mpfer, Peter and Glaeser, Stefanie P and Packroff, Gabriele and Behringer, Katja and Exner, Martin and Chakraborty, Trinad and Schmithausen, Ricarda M and Doijad, Swapnil}, journal = {International Journal of Systematic and Evolutionary Microbiology}, volume = {68}, year = {2018}, publisher = {Microbiology Society} }
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@article{westphal2018environment, title = {The environment as a reservoir for antimicrobial resistance: A growing problem for public health?}, author = {Westphal-Settele, Kathi and Konradi, Sabine and Balzer, Frederike and Sch{\"o}nfeld, Jens and Schmithausen, Ricarda}, journal = {Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz}, volume = {61}, year = {2018} }
@article{el2018esbl, title = {ESBL Detection: Comparison of a Commercially Available Chromogenic Test for Third Generation Cephalosporine Resistance and Automated Susceptibility Testing in Enterobactericeae (vol 11, e0160203, 2016)}, author = {El-Jade, Mohamed Ramadan and Parcina, Marijo and Schmithausen, Ricarda Maria and Stein, Christoph and Meilaender, Aline and Hoerauf, Achim and Molitor, Ernst and Bekeredjian-Ding, Isabelle}, journal = {PLOS ONE}, volume = {13}, year = {2018}, publisher = {PUBLIC LIBRARY SCIENCE 1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA} }
@article{schmithausen2018reservoirs, title = {Reservoirs and transmission pathways of resistant indicator bacteria in the biotope pig stable and along the food chain: a review from a one health perspective}, author = {Schmithausen, Ricarda Maria and Schulze-Geisthoevel, Sophia Veronika and Heinemann, C{\'e}line and Bierbaum, Gabriele and Exner, Martin and Petersen, Brigitte and Steinhoff-Wagner, Julia}, journal = {Sustainability}, volume = {10}, year = {2018}, publisher = {MDPI} }
@article{heudorf2018klebsiella, title = {Klebsiella pneumoniae KPC-3 Ausbruch am Universit{\"a}tsklinikum Frankfurt am Main--Teil II: weitere umwelthygienische Erkenntnisse}, author = {Heudorf, U and Kempf, V and Reinheimer, C and Exner, M and Schmithausen, Ricarda and Imirzalioglu, C and Chakraborty, T}, journal = {Das Gesundheitswesen}, volume = {80}, year = {2018}, publisher = {Georg Thieme Verlag KG} }
@inproceedings{exner2018trinkwasserhygiene, title = {Trinkwasserhygiene--unverzichtbare S{\"a}ule des {\"o}ffentlichen Gesundheitsschutzes--R{\"u}ckblick und Ausblick}, author = {Exner, Martin and Schmithausen, Ricarda and Nissing, Werner}, booktitle = {Public Health Forum}, volume = {26}, year = {2018}, organization = {De Gruyter} }
@article{exner2018preliminary, title = {Preliminary risk assessment from a hygienic me-dical perspective concerning antibiotic-resistant bacteria in water bodies, wastewater, bathing wa-ter and possible consequences for drinking water hygiene}, author = {Exner, Martin and Schmithausen, Ricarda and Schreiber, Christiane and Bierbaum, Gabriele and Parcina, Marijo and Engelhart, Steffen and Kistemann, Thomas and Sib, Esther and Walger, Peter and Schwartz, Thomas}, journal = {Hyg Med}, volume = {43}, year = {2018} }
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@article{exner2018vorkommen, title = {Zum Vorkommen und zur vorl{\"a}ufigen hygienisch-medizinischen Bewertung von Antibiotika-resistenten Bakterien mit humanmedizinischer Bedeutung in Gew{\"a}ssern, Abw{\"a}ssern, Badegew{\"a}ssern sowie zu m{\"o}glichen Konsequenzen f{\"u}r die Trinkwasserversorgung}, author = {Exner, Martin and Schmithausen, Ricarda and Schreiber, Christiane and Bierbaum, Gabriele and Parcina, Marijo and Engelhart, Steffen and Kistemann, Thomas and Sib, Esther and Walger, Peter and Schwartz, Thomas}, journal = {Hyg Med}, volume = {43}, year = {2018} }
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@article{arkin_kbase_2018-1, title = {{KBase}: {The} {United} {States} {Department} of {Energy} {Systems} {Biology} {Knowledgebase}}, volume = {36}, url = {https://www.ncbi.nlm.nih.gov/pubmed/29979655}, doi = {10.1038/nbt.4163}, journal = {Nat Biotechnol}, author = {Arkin, A. P. and Cottingham, R. W. and Henry, C. S. and Harris, N. L. and Stevens, R. L. and Maslov, S. and Dehal, P. and Ware, D. and Perez, F. and Canon, S. and Sneddon, M. W. and Henderson, M. L. and Riehl, W. J. and Murphy-Olson, D. and Chan, S. Y. and Kamimura, R. T. and Kumari, S. and Drake, M. M. and Brettin, T. S. and Glass, E. M. and Chivian, D. and Gunter, D. and Weston, D. J. and Allen, B. H. and Baumohl, J. and Best, A. A. and Bowen, B. and Brenner, S. E. and Bun, C. C. and Chandonia, J. M. and Chia, J. M. and Colasanti, R. and Conrad, N. and Davis, J. J. and Davison, B. H. and DeJongh, M. and Devoid, S. and Dietrich, E. and Dubchak, I. and Edirisinghe, J. N. and Fang, G. and Faria, J. P. and Frybarger, P. M. and Gerlach, W. and Gerstein, M. and Greiner, A. and Gurtowski, J. and Haun, H. L. and He, F. and Jain, R. and Joachimiak, M. P. and Keegan, K. P. and Kondo, S. and Kumar, V. and Land, M. L. and Meyer, Folker and Mills, M. and Novichkov, P. S. and Oh, T. and Olsen, G. J. and Olson, R. and Parrello, B. and Pasternak, S. and Pearson, E. and Poon, S. S. and Price, G. A. and Ramakrishnan, S. and Ranjan, P. and Ronald, P. C. and Schatz, M. C. and Seaver, S. M. D. and Shukla, M. and Sutormin, R. A. and Syed, M. H. and Thomason, J. and Tintle, N. L. and Wang, D. and Xia, F. and Yoo, H. and Yoo, S. and Yu, D.}, year = {2018}, note = {Type: Journal Article}, keywords = {Computational Biology/*methods Database Management Systems/*trends Humans *Knowledge Bases Systems Biology/*trends United States} }
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@article{ma_crispr-for_2016, title = {{CRISPR}-{DO} for genome-wide {CRISPR} design and optimization}, volume = {32}, issn = {1367-4803}, url = {https://doi.org/10.1093/bioinformatics/btw476}, doi = {10.1093/bioinformatics/btw476}, number = {21}, urldate = {2021-06-30}, journal = {Bioinformatics}, author = {Ma, Jian and Köster, Johannes and Qin, Qian and Hu, Shengen and Li, Wei and Chen, Chenhao and Cao, Qingyi and Wang, Jinzeng and Mei, Shenglin and Liu, Qi and Xu, Han and Liu, Xiaole Shirley}, month = nov, year = {2016}, pages = {3336--3338}, file = {Full Text PDF:/home/johannes/Zotero/storage/M6ULLHXC/Ma et al. - 2016 - CRISPR-DO for genome-wide CRISPR design and optimi.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/A7TYLUJQ/2415354.html:text/html} }
@article{Bockmann2016-ti, title = {Mobile {IT}: Possibilities and barriers of mHealth}, author = {B{\"o}ckmann, B}, journal = {Radiologe}, publisher = {Springer Science and Business Media LLC}, volume = {56}, number = {4}, pages = {371--374}, month = apr, year = {2016}, keywords = {MHealth; Medical informatics applications; Start-up scene; Strategy; Teleradiology}, language = {de} }
@article{townsend_public_2016, title = {The {Public} {Repository} of {Xenografts} {Enables} {Discovery} and {Randomized} {Phase} {II}-like {Trials} in {Mice}}, volume = {29}, issn = {1535-6108, 1878-3686}, url = {https://www.cell.com/cancer-cell/abstract/S1535-6108(16)30090-3}, doi = {10.1016/j.ccell.2016.03.008}, language = {English}, number = {4}, urldate = {2019-05-03}, journal = {Cancer Cell}, author = {Townsend, Elizabeth C. and Murakami, Mark A. and Christodoulou, Alexandra and Christie, Amanda L. and Köster, Johannes and DeSouza, Tiffany A. and Morgan, Elizabeth A. and Kallgren, Scott P. and Liu, Huiyun and Wu, Shuo-Chieh and Plana, Olivia and Montero, Joan and Stevenson, Kristen E. and Rao, Prakash and Vadhi, Raga and Andreeff, Michael and Armand, Philippe and Ballen, Karen K. and Barzaghi-Rinaudo, Patrizia and Cahill, Sarah and Clark, Rachael A. and Cooke, Vesselina G. and Davids, Matthew S. and DeAngelo, Daniel J. and Dorfman, David M. and Eaton, Hilary and Ebert, Benjamin L. and Etchin, Julia and Firestone, Brant and Fisher, David C. and Freedman, Arnold S. and Galinsky, Ilene A. and Gao, Hui and Garcia, Jacqueline S. and Garnache-Ottou, Francine and Graubert, Timothy A. and Gutierrez, Alejandro and Halilovic, Ensar and Harris, Marian H. and Herbert, Zachary T. and Horwitz, Steven M. and Inghirami, Giorgio and Intlekofer, Andrew M. and Ito, Moriko and Izraeli, Shai and Jacobsen, Eric D. and Jacobson, Caron A. and Jeay, Sébastien and Jeremias, Irmela and Kelliher, Michelle A. and Koch, Raphael and Konopleva, Marina and Kopp, Nadja and Kornblau, Steven M. and Kung, Andrew L. and Kupper, Thomas S. and LeBoeuf, Nicole R. and LaCasce, Ann S. and Lees, Emma and Li, Loretta S. and Look, A. Thomas and Murakami, Masato and Muschen, Markus and Neuberg, Donna and Ng, Samuel Y. and Odejide, Oreofe O. and Orkin, Stuart H. and Paquette, Rachel R. and Place, Andrew E. and Roderick, Justine E. and Ryan, Jeremy A. and Sallan, Stephen E. and Shoji, Brent and Silverman, Lewis B. and Soiffer, Robert J. and Steensma, David P. and Stegmaier, Kimberly and Stone, Richard M. and Tamburini, Jerome and Thorner, Aaron R. and Hummelen, Paul van and Wadleigh, Martha and Wiesmann, Marion and Weng, Andrew P. and Wuerthner, Jens U. and Williams, David A. and Wollison, Bruce M. and Lane, Andrew A. and Letai, Anthony and Bertagnolli, Monica M. and Ritz, Jerome and Brown, Myles and Long, Henry and Aster, Jon C. and Shipp, Margaret A. and Griffin, James D. and Weinstock, David M.}, month = apr, year = {2016}, pmid = {27070704}, pages = {574--586}, file = {Full Text PDF:/home/johannes/Zotero/storage/ZFL85YFX/Townsend et al. - 2016 - The Public Repository of Xenografts Enables Discov.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/GEDHSXW2/S1535-6108(16)30090-3.html:text/html} }
@article{koster_rust-bio_2016, title = {Rust-{Bio}: a fast and safe bioinformatics library}, volume = {32}, issn = {1367-4803}, shorttitle = {Rust-{Bio}}, url = {https://doi.org/10.1093/bioinformatics/btv573}, doi = {10.1093/bioinformatics/btv573}, number = {3}, urldate = {2021-06-30}, journal = {Bioinformatics}, author = {Köster, Johannes}, month = feb, year = {2016}, pages = {444--446}, file = {Full Text PDF:/home/johannes/Zotero/storage/SJDTSN7Q/Köster - 2016 - Rust-Bio a fast and safe bioinformatics library.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/LGEQSUYW/1743419.html:text/html} }
@article{RN1739, author = {Mladenov, E. and Magin, S. and Soni, A. and Iliakis, G.}, title = {DNA double-strand-break repair in higher eukaryotes and its role in genomic instability and cancer: Cell cycle and proliferation-dependent regulation}, journal = {Semin Cancer Biol}, volume = {37-38}, pages = {51-64}, note = {Mladenov, Emil Magin, Simon Soni, Aashish Iliakis, George eng Review Research Support, Non-U.S. Gov't England 2016/03/27 Semin Cancer Biol. 2016 Jun;37-38:51-64. doi: 10.1016/j.semcancer.2016.03.003. Epub 2016 Mar 22.}, keywords = {Cell Cycle/genetics Cell Proliferation/genetics *DNA Breaks, Double-Stranded *DNA Repair *Genomic Instability Humans Neoplasms/*genetics/immunology/*pathology Recombinational DNA Repair *Cell cycle regulation *Cell growth regulation *DNA end resection *Double strand break repair *hrr *Pathway choice *ssa *alt-EJ *c-NHEJ}, issn = {1096-3650 (Electronic) 1044-579X (Linking)}, doi = {10.1016/j.semcancer.2016.03.003}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27016036}, year = {2016}, type = {Journal Article} }
@article{Tondo2016KatGTB, title = {KatG, the Bifunctional Catalase of Xanthomonas citri subsp. citri, Responds to Hydrogen Peroxide and Contributes to Epiphytic Survival on Citrus Leaves}, author = {Tondo, Mar{\'i}a Laura and Delprato, Mar{\'i}a Laura and Kraiselburd, Ivana and Zenoff, Mar{\'i}a Ver{\'o}nica Fern{\'a}ndez and Far{\'i}as, Mar{\'i}a Eugenia and Orellano, Elena G}, journal = {PLoS ONE}, year = {2016}, volume = {11} }
@article{Albarracn2016FunctionalGP, title = {Functional Green-Tuned Proteorhodopsin from Modern Stromatolites}, author = {Albarrac{\'i}n, Virginia Helena and Kraiselburd, Ivana and Bamann, Christian and Wood, Phillip G. and Bamberg, Ernst and Far{\'i}as, Mar{\'i}a Eugenia and G{\"a}rtner, Wolfgang}, journal = {PLoS ONE}, year = {2016}, volume = {11} }
@article{el2016esbl, title = {ESBL detection: comparison of a commercially available chromogenic test for third generation cephalosporine resistance and automated susceptibility testing in Enterobactericeae}, author = {El-Jade, Mohamed Ramadan and Parcina, Marijo and Schmithausen, Ricarda Maria and Stein, Christoph and Meilaender, Alina and Hoerauf, Achim and Molitor, Ernst and Bekeredjian-Ding, Isabelle}, journal = {PloS one}, volume = {11}, year = {2016}, publisher = {Public Library of Science San Francisco, CA USA} }
@article{schulze2016survey, title = {Survey on the risk awareness of german pig and cattle farmers in relation to dealing with MRSA and antibiotics}, author = {Schulze-Geisth{\"o}vel, Sophia Veronika and Tappe, Elisa-Valerie and Schmithausen, Ricarda Maria and Lepkojis, Jan and R{\"o}ttgen, Katharina and Petersen, Brigitte}, journal = {Infection Ecology \& Epidemiology}, volume = {6}, year = {2016}, publisher = {Taylor \& Francis} }
@article{schmithausen2016mrsa, title = {MRSA und ESBL-E in der Schweineproduktion}, author = {Schmithausen, RM and Schulze-Geisth{\"o}vel, SV and Hoerauf, A and Exner, M and Bierbaum, G and Bekeredjian-Ding, I and Petersen, B}, journal = {Zuchtungskunde}, volume = {88}, year = {2016} }
@article{wilke_mg-rast_2016-1, title = {The {MG}-{RAST} metagenomics database and portal in 2015}, volume = {44}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26656948}, doi = {10.1093/nar/gkv1322}, journal = {Nucleic Acids Res}, author = {Wilke, A. and Bischof, J. and Gerlach, W. and Glass, E. and Harrison, T. and Keegan, K. P. and Paczian, T. and Trimble, W. L. and Bagchi, S. and Grama, A. and Chaterji, S. and Meyer, Folker}, year = {2016} }
@article{obrien_spatial_2016, title = {Spatial scale drives patterns in soil bacterial diversity}, volume = {18}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26914164}, doi = {10.1111/1462-2920.13231}, journal = {Environ Microbiol}, author = {O'Brien, S. L. and Gibbons, S. M. and Owens, S. M. and Hampton-Marcell, J. and Johnston, E. R. and Jastrow, J. D. and Gilbert, J. A. and Meyer, Folker and Antonopoulos, D. A.}, year = {2016}, note = {Type: Journal Article} }
@article{keegan_mg-rast_2016, title = {{MG}-{RAST}, a {Metagenomics} {Service} for {Analysis} of {Microbial} {Community} {Structure} and {Function}}, volume = {1399}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26791506}, doi = {10.1007/978-1-4939-3369-3_13}, journal = {Methods Mol Biol}, author = {Keegan, K. P. and Glass, E. M. and Meyer, Folker}, year = {2016}, note = {Type: Journal Article} }
@article{howe_divergent_2016, title = {Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice}, volume = {10}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26473721}, doi = {10.1038/ismej.2015.183}, journal = {ISME J}, author = {Howe, A. and Ringus, D. L. and Williams, R. J. and Choo, Z. N. and Greenwald, S. M. and Owens, S. M. and Coleman, M. L. and Meyer, Folker and Chang, E. B.}, year = {2016}, note = {Type: Journal Article} }
@inproceedings{ross_case_2016, title = {A case study in using discrete-event simulation to improve the scalability of {MG}-{RAST}}, booktitle = {Proceedings of the 2016 {ACM} {SIGSIM} {Conference} on {Principles} of {Advanced} {Discrete} {Simulation}}, author = {Ross, Caitlin and Mubarak, Misbah and Jenkins, John and Carns, Philip and Carothers, Christopher D and Ross, Robert and Tang, Wei and Gerlach, Wolfgang and Meyer, Folker}, year = {2016} }
@article{howe_identification_2016, title = {Identification of the core set of carbon-associated genes in a bioenergy grassland soil}, volume = {11}, journal = {PLoS One}, author = {Howe, Adina and Yang, Fan and Williams, Ryan J and Meyer, Folker and Hofmockel, Kirsten S}, year = {2016}, note = {Publisher: Public Library of Science San Francisco, CA USA} }
@incollection{trimble_metagenomic_2016, title = {Metagenomic design and sequencing}, booktitle = {Field {Guidelines} for {Genetic} {Experimental} {Designs} in {High}-{Throughput} {Sequencing}}, publisher = {Springer, Cham}, author = {Trimble, William L and Greenwald, Stephanie M and Owens, Sarah and Glass, Elizabeth M and Meyer, Folker}, year = {2016} }
@incollection{keegan_mg-rast_2016-1, title = {{MG}-{RAST}, a metagenomics service for analysis of microbial community structure and function}, booktitle = {Microbial environmental genomics ({MEG})}, publisher = {Humana Press, New York, NY}, author = {Keegan, Kevin P and Glass, Elizabeth M and Meyer, Folker}, year = {2016} }
@article{RN38, author = {Riscal, R. and Schrepfer, E. and Arena, G. and Cisse, M. Y. and Bellvert, F. and Heuillet, M. and Rambow, F. and Bonneil, E. and Sabourdy, F. and Vincent, C. and Ait-Arsa, I. and Levade, T. and Thibaut, P. and Marine, J. C. and Portais, J. C. and Sarry, J. E. and Le Cam, L. and Linares, L. K.}, title = {Chromatin-Bound MDM2 Regulates Serine Metabolism and Redox Homeostasis Independently of p53}, journal = {Mol Cell}, volume = {62}, number = {6}, pages = {890-902}, issn = {1097-4164 (Electronic) 1097-2765 (Linking)}, doi = {10.1016/j.molcel.2016.04.033}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27264869}, year = {2016}, type = {Journal Article} }
@article{RN29, author = {Rambow, F. and Bechadergue, A. and Luciani, F. and Gros, G. and Domingues, M. and Bonaventure, J. and Meurice, G. and Marine, J. C. and Larue, L.}, title = {Regulation of Melanoma Progression through the TCF4/miR-125b/NEDD9 Cascade}, journal = {J Invest Dermatol}, volume = {136}, number = {6}, pages = {1229-1237}, issn = {1523-1747 (Electronic) 0022-202X (Linking)}, doi = {10.1016/j.jid.2016.02.803}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26968260}, year = {2016}, type = {Journal Article} }
@article{RN25, author = {Mrad, M. and Imbert, C. and Garcia, V. and Rambow, F. and Therville, N. and Carpentier, S. and Segui, B. and Levade, T. and Azar, R. and Marine, J. C. and Diab-Assaf, M. and Colacios, C. and Andrieu-Abadie, N.}, title = {Downregulation of sphingosine kinase-1 induces protective tumor immunity by promoting M1 macrophage response in melanoma}, journal = {Oncotarget}, volume = {7}, number = {44}, pages = {71873-71886}, issn = {1949-2553 (Electronic) 1949-2553 (Linking)}, doi = {10.18632/oncotarget.12380}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27708249}, year = {2016}, type = {Journal Article} }
@article{RN10, author = {Dewaele, M. and Tabaglio, T. and Willekens, K. and Bezzi, M. and Teo, S. X. and Low, D. H. and Koh, C. M. and Rambow, F. and Fiers, M. and Rogiers, A. and Radaelli, E. and Al-Haddawi, M. and Tan, S. Y. and Hermans, E. and Amant, F. and Yan, H. and Lakshmanan, M. and Koumar, R. C. and Lim, S. T. and Derheimer, F. A. and Campbell, R. M. and Bonday, Z. and Tergaonkar, V. and Shackleton, M. and Blattner, C. and Marine, J. C. and Guccione, E.}, title = {Antisense oligonucleotide-mediated MDM4 exon 6 skipping impairs tumor growth}, journal = {J Clin Invest}, volume = {126}, number = {1}, pages = {68-84}, issn = {1558-8238 (Electronic) 0021-9738 (Linking)}, doi = {10.1172/JCI82534}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26595814}, year = {2016}, type = {Journal Article} }
@article{li_quality_2015, title = {Quality control, modeling, and visualization of {CRISPR} screens with {MAGeCK}-{VISPR}}, volume = {16}, issn = {1474-760X}, url = {https://doi.org/10.1186/s13059-015-0843-6}, doi = {10.1186/s13059-015-0843-6}, number = {1}, urldate = {2019-08-23}, journal = {Genome Biology}, author = {Li, Wei and Köster, Johannes and Xu, Han and Chen, Chen-Hao and Xiao, Tengfei and Liu, Jun S. and Brown, Myles and Liu, X. Shirley}, month = dec, year = {2015}, pages = {281}, file = {Full Text:/home/johannes/Zotero/storage/TGGBQHGJ/Li et al. - 2015 - Quality control, modeling, and visualization of CR.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/QGDV65UK/s13059-015-0843-6.html:text/html} }
@article{schramm_mutational_2015, title = {Mutational dynamics between primary and relapse neuroblastomas}, volume = {47}, copyright = {2015 Nature Publishing Group}, issn = {1546-1718}, url = {https://www.nature.com/articles/ng.3349}, doi = {10.1038/ng.3349}, language = {en}, number = {8}, urldate = {2019-05-03}, journal = {Nature Genetics}, author = {Schramm, Alexander and Köster, Johannes and Assenov, Yassen and Althoff, Kristina and Peifer, Martin and Mahlow, Ellen and Odersky, Andrea and Beisser, Daniela and Ernst, Corinna and Henssen, Anton G. and Stephan, Harald and Schröder, Christopher and Heukamp, Lukas and Engesser, Anne and Kahlert, Yvonne and Theissen, Jessica and Hero, Barbara and Roels, Frederik and Altmüller, Janine and Nürnberg, Peter and Astrahantseff, Kathy and Gloeckner, Christian and De Preter, Katleen and Plass, Christoph and Lee, Sangkyun and Lode, Holger N. and Henrich, Kai-Oliver and Gartlgruber, Moritz and Speleman, Frank and Schmezer, Peter and Westermann, Frank and Rahmann, Sven and Fischer, Matthias and Eggert, Angelika and Schulte, Johannes H.}, month = aug, year = {2015}, pages = {872--877}, file = {Snapshot:/home/johannes/Zotero/storage/BTUWYTFW/ng.html:text/html} }
@article{Heiden2015-da, title = {Virtual Oncological {Networks--IT} support for an evidence-based, oncological health care management}, author = {Heiden, Katja and Sinha, Monika and B{\"o}ckmann, Britta}, journal = {Stud. Health Technol. Inform.}, volume = {216}, pages = {953}, year = {2015}, language = {en} }
@article{RN1738, author = {Magin, Simon. and Papaioannou, M. and Saha, J. and Staudt, C. and Iliakis, G.}, title = {Inhibition of Homologous Recombination and Promotion of Mutagenic Repair of DNA Double-Strand Breaks Underpins Arabinoside-Nucleoside Analogue Radiosensitization}, journal = {Mol Cancer Ther}, volume = {14}, number = {6}, pages = {1424-33}, note = {Magin, Simon Papaioannou, Maria Saha, Janapriya Staudt, Christian Iliakis, George eng Research Support, Non-U.S. Gov't 2015/04/05 Mol Cancer Ther. 2015 Jun;14(6):1424-33. doi: 10.1158/1535-7163.MCT-14-0682. Epub 2015 Apr 3.}, keywords = {Blotting, Western Cell Line, Tumor Cell Proliferation/drug effects/radiation effects Cytarabine/*pharmacology DNA Breaks, Double-Stranded/*drug effects/radiation effects DNA Repair/*drug effects/radiation effects Dose-Response Relationship, Drug Dose-Response Relationship, Radiation Green Fluorescent Proteins/genetics/metabolism Homologous Recombination/*drug effects/radiation effects Humans Microscopy, Confocal RNA Interference Rad51 Recombinase/genetics/metabolism Radiation-Sensitizing Agents/pharmacology Vidarabine/*analogs & derivatives/*pharmacology X-Rays}, issn = {1538-8514 (Electronic) 1535-7163 (Linking)}, doi = {10.1158/1535-7163.MCT-14-0682}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25840584}, year = {2015}, type = {Journal Article} }
@article{Kraiselburd2015FunctionalCO, title = {Functional Characterization of a LOV‐Histidine Kinase Photoreceptor from Xanthomonas citri subsp. citri}, author = {Kraiselburd, Ivana and Gutt, Alexander and Losi, Aba and G{\"a}rtner, Wolfgang and Orellano, Elena G}, journal = {Photochemistry and Photobiology}, year = {2015}, volume = {91} }
@article{schmithausen2015analysis, title = {Analysis of transmission of MRSA and ESBL-E among pigs and farm personnel}, author = {Schmithausen, Ricarda Maria and Schulze-Geisthoevel, Sophia Veronika and Stemmer, Franziska and El-Jade, Mohamed and Reif, Marion and Hack, Sylvia and Meilaender, Alina and Montabauer, Gabriele and Fimmers, Rolf and Parcina, Marijo and others}, journal = {PloS one}, volume = {10}, year = {2015}, publisher = {Public Library of Science} }
@article{schmithausen2015eradication, title = {Eradication of methicillin-resistant Staphylococcus aureus and of Enterobacteriaceae expressing extended-spectrum beta-lactamases on a model pig farm}, author = {Schmithausen, Ricarda Maria and Kellner, Sophia Ricarda and Schulze-Geisthoevel, Sophia Veronika and Hack, Sylvia and Engelhart, Steffen and Bodenstein, Isabel and Al-Sabti, Nahed and Reif, Marion and Fimmers, Rolf and K{\"o}rber-Irrgang, Barbara and others}, journal = {Applied and environmental microbiology}, volume = {81}, year = {2015}, publisher = {American Society for Microbiology} }
@article{wilke_restful_2015, title = {A {RESTful} {API} for accessing microbial community data for {MG}-{RAST}}, volume = {11}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25569221}, doi = {10.1371/journal.pcbi.1004008}, journal = {PLoS Comput Biol}, author = {Wilke, A. and Bischof, J. and Harrison, T. and Brettin, T. and D'Souza, M. and Gerlach, W. and Matthews, H. and Paczian, T. and Wilkening, J. and Glass, E. M. and Desai, N. and Meyer, Folker}, year = {2015}, note = {Type: Journal Article} }
@inproceedings{gerlach_skyport, title = {Skyport: container-based execution environment management for multi-cloud scientific workflows}, booktitle = {Proceedings of the 5th {International} {Workshop} on {Data}-{Intensive} {Computing} in the {Clouds}}, publisher = {IEEE Press}, author = {Gerlach, Wolfgang and Tang, Wei and Keegan, Kevin and Harrison, Travis and Wilke, Andreas and Bischof, Jared and D'Souza, Mark and Devoid, Scott and Murphy-Olson, Daniel and Desai, Narayan}, note = {Type: Conference Proceedings}, year = {2015} }
@misc{wilke_mg-rast_2015, title = {{MG}-{RAST} {Manural} for version 3.6, revision 3}, publisher = {MGRAST}, author = {Wilke, Andreas and Glass, Elizabeth M and Bischof, Jared and Braithwaite, Daniel and Gerlach, W and Harrison, T and Keegan, K and Paczian, T and Trimble, WL and Meyer, F}, year = {2015} }
@article{wilke_a_restful_2015, title = {A {RESTful} {API} for {Accessing} {Microbial} {Community} {Data} for {MG}-{RAST}}, volume = {11}, journal = {PLoS Computational Biology}, author = {Wilke, Andreas and Bischof, Jared and Harrison, Travis and Brettin, Tom and D'Souza, Mark and Gerlach, Wolfgang and Matthews, Hunter and Paczian, Tobias and Wilkening, Jared and Glass, Elizabeth M. and Desai, Narayan Meyer, Folker}, year = {2015} }
@inproceedings{gerlach_container_2015, title = {Container orchestration for scientific workflows}, booktitle = {2015 {IEEE} {International} conference on cloud engineering}, publisher = {IEEE}, author = {Gerlach, Wolfgang and Tang, Wei and Wilke, Andreas and Olson, Dan and Meyer, Folker}, year = {2015} }
@article{xue_eco-evolutionary_2015, title = {Eco-evolutionary dynamics of episomes among ecologically cohesive bacterial populations}, volume = {6}, journal = {MBio}, author = {Xue, Hong and Cordero, Otto X and Camas, Francisco M and Trimble, William and Meyer, Folker and Guglielmini, Julien and Rocha, Eduardo PC and Polz, Martin F}, year = {2015}, note = {Publisher: American Society for Microbiology 1752 N St., NW, Washington, DC} }
@inproceedings{mahadik_specialized_2015, title = {Do specialized distributed frameworks for bioinformatics applications obtain better performance over generic ones?}, booktitle = {Proceedings of the 6th {ACM} {Conference} on {Bioinformatics}, {Computational} {Biology} and {Health} {Informatics}}, author = {Mahadik, Kanak and Tang, Wei and Bagchi, Saurabh and Meyer, Folker}, year = {2015} }
@inproceedings{bischof_shock_2015, title = {Shock: {Active} {Storage} for {Multicloud} {Streaming} {Data} {Analysis}}, volume = {1}, booktitle = {2015 {IEEE}/{ACM} 2nd {International} {Symposium} on {Big} {Data} {Computing} ({BDC})}, publisher = {IEEE}, author = {Bischof, Jared and Wilke, Andreas and Gerlach, Wolfgang and Harrison, Travis and Paczian, Tobias and Tang, Wei and Trimble, William and Wilkening, Jared and Desai, Narayan and Meyer, Folker}, year = {2015}, note = {Issue: 1} }
@incollection{glass_mg-rast_2015, title = {{MG}-{RAST}, a metagenomics service for the analysis of microbial community structure and function}, booktitle = {Hydrocarbon and {Lipid} {Microbiology} {Protocols}}, publisher = {Springer, Berlin, Heidelberg}, author = {Glass, Elizabeth M and Meyer, Folker}, year = {2015} }
@inproceedings{aronson_barriers_2015, title = {Barriers and potential solutions for {Critical} {Zone} data integration between environmental genomics and the geosciences}, volume = {2015}, booktitle = {{AGU} {Fall} {Meeting} {Abstracts}}, author = {Aronson, Emma L and Meyer, Folker and Packman, Aaron Ian and Mayorga, Emilio}, year = {2015} }
@article{hirschman_meeting_2015-1, title = {Meeting {Report}:“{Metagenomics}, {Metadata} and {Meta}-analysis”({M3}) {Special} {Interest} {Group} at {ISMB} 2009}, volume = {2}, journal = {Standards in Genomic Sciences}, author = {Hirschman, Lynette and Sterk, Peter and Field, Dawn and Wooley, John and Cochrane, Guy and Gilbert, Jack and Kolker, Eugene and Kyrpides, Nikos and Meyer, Folker and Mizrachi, Ilene and Meyer, Folker and {others}}, year = {2015} }
@article{RN46, author = {Verfaillie, A. and Imrichova, H. and Atak, Z. K. and Dewaele, M. and Rambow, F. and Hulselmans, G. and Christiaens, V. and Svetlichnyy, D. and Luciani, F. and Van den Mooter, L. and Claerhout, S. and Fiers, M. and Journe, F. and Ghanem, G. E. and Herrmann, C. and Halder, G. and Marine, J. C. and Aerts, S.}, title = {Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state}, journal = {Nat Commun}, volume = {6}, pages = {6683}, issn = {2041-1723 (Electronic) 2041-1723 (Linking)}, doi = {10.1038/ncomms7683}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25865119}, year = {2015}, type = {Journal Article} }
@article{RN31, author = {Rambow, F. and Job, B. and Petit, V. and Gesbert, F. and Delmas, V. and Seberg, H. and Meurice, G. and Van Otterloo, E. and Dessen, P. and Robert, C. and Gautheret, D. and Cornell, R. A. and Sarasin, A. and Larue, L.}, title = {New Functional Signatures for Understanding Melanoma Biology from Tumor Cell Lineage-Specific Analysis}, journal = {Cell Rep}, volume = {13}, number = {4}, pages = {840-853}, issn = {2211-1247 (Electronic)}, doi = {10.1016/j.celrep.2015.09.037}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26489459}, year = {2015}, type = {Journal Article} }
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The complete genome sequence for putative H(2)- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome. Environ Microbiol. 2014. [doi] [url] BibTeX @article{handley_complete_2014, title = {The complete genome sequence for putative {H}(2)- and {S}-oxidizer {Candidatus} {Sulfuricurvum} sp., assembled de novo from an aquifer-derived metagenome}, volume = {16}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24628880}, doi = {10.1111/1462-2920.12453}, journal = {Environ Microbiol}, author = {Handley, K. M. and Bartels, D. and O'Loughlin, E. J. and Williams, K. H. and Trimble, W. L. and Skinner, K. and Gilbert, J. A. and Desai, N. and Glass, E. M. and Paczian, T. and Wilke, A. and Antonopoulos, D. and Kemner, K. M. and Meyer, Folker}, year = {2014}, note = {Type: Journal Article} } E. M. Glass, Y. Dribinsky, P. Yilmaz, H. Levin, R. Van Pelt, D. Wendel, A. Wilke, J. A. Eisen, S. Huse, A. Shipanova, M. Sogin, J. Stajich, R. Knight, Folker Meyer, and L. M. Schriml. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME J. 2014. [doi] [url] BibTeX @article{glass_mixs-be_2014, title = {{MIxS}-{BE}: a {MIxS} extension defining a minimum information standard for sequence data from the built environment}, volume = {8}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24152717}, doi = {10.1038/ismej.2013.176}, journal = {ISME J}, author = {Glass, E. M. and Dribinsky, Y. and Yilmaz, P. and Levin, H. and Van Pelt, R. and Wendel, D. and Wilke, A. and Eisen, J. A. and Huse, S. and Shipanova, A. and Sogin, M. and Stajich, J. and Knight, R. and Meyer, Folker and Schriml, L. M.}, year = {2014}, note = {Type: Journal Article} } D. Field, P. Sterk, R. Kottmann, J. W. De Smet, L. Amaral-Zettler, G. Cochrane, J. R. Cole, N. Davies, P. Dawyndt, G. M. Garrity, J. A. Gilbert, F. O. Glockner, L. Hirschman, H. P. Klenk, R. Knight, N. Kyrpides, Folker Meyer, I. Karsch-Mizrachi, N. Morrison, R. Robbins, I. San Gil, S. Sansone, L. Schriml, T. Tatusova, D. Ussery, P. Yilmaz, O. White, J. Wooley, and G. Caporaso. Genomic standards consortium projects. Stand Genomic Sci. 2014. [doi] [url] BibTeX @article{field_genomic_2014, title = {Genomic standards consortium projects}, volume = {9}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25197446}, doi = {10.4056/sigs.5559680}, journal = {Stand Genomic Sci}, author = {Field, D. and Sterk, P. and Kottmann, R. and De Smet, J. W. and Amaral-Zettler, L. and Cochrane, G. and Cole, J. R. and Davies, N. and Dawyndt, P. and Garrity, G. M. and Gilbert, J. A. and Glockner, F. O. and Hirschman, L. and Klenk, H. P. and Knight, R. and Kyrpides, N. and Meyer, Folker and Karsch-Mizrachi, I. and Morrison, N. and Robbins, R. and San Gil, I. and Sansone, S. and Schriml, L. and Tatusova, T. and Ussery, D. and Yilmaz, P. and White, O. and Wooley, J. and Caporaso, G.}, year = {2014}, note = {Type: Journal Article} } J. Bischof, T. Harrison, T. Paczian, E. Glass, A. Wilke, and Folker Meyer. Metazen - metadata capture for metagenomes. Stand Genomic Sci. 2014. [doi] [url] BibTeX @article{bischof_metazen_2014, title = {Metazen - metadata capture for metagenomes}, volume = {9}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25780508}, doi = {10.1186/1944-3277-9-18}, journal = {Stand Genomic Sci}, author = {Bischof, J. and Harrison, T. and Paczian, T. and Glass, E. and Wilke, A. and Meyer, Folker}, year = {2014}, note = {Type: Journal Article} } T. Thomas, J. Gilbert, and Folker Meyer. 123 of Metagenomics. Encyclopedia of Metagenomics. 2014. Springer New York. BibTeX @incollection{thomas_123_2014, title = {123 of {Metagenomics}}, booktitle = {Encyclopedia of {Metagenomics}}, publisher = {Springer New York}, author = {Thomas, T. and Gilbert, J. and Meyer, Folker}, year = {2014} } Sarah Owens, Kevin Keegan, Folker Meyer, and William Trimble. Characterizing Sequencing Samples with k-mer Spectra for Good and Evil. Journal of biomolecular techniques: JBT. 2014. BibTeX @article{owens_characterizing_2014, title = {Characterizing {Sequencing} {Samples} with k-mer {Spectra} for {Good} and {Evil}}, volume = {25}, journal = {Journal of biomolecular techniques: JBT}, author = {Owens, Sarah and Keegan, Kevin and Meyer, Folker and Trimble, William}, year = {2014}, note = {Publisher: The Association of Biomolecular Resource Facilities} } Wei Tang, Jared Bischof, Narayan Desai, Kanak Mahadik, Wolfgang Gerlach, Travis Harrison, Andreas Wilke, and Folker Meyer. Workload characterization for MG-RAST metagenomic data analytics service in the cloud. 2014 IEEE International Conference on Big Data (Big Data). 2014. IEEE. BibTeX @inproceedings{tang_workload_2014, title = {Workload characterization for {MG}-{RAST} metagenomic data analytics service in the cloud}, booktitle = {2014 {IEEE} {International} {Conference} on {Big} {Data} ({Big} {Data})}, publisher = {IEEE}, author = {Tang, Wei and Bischof, Jared and Desai, Narayan and Mahadik, Kanak and Gerlach, Wolfgang and Harrison, Travis and Wilke, Andreas and Meyer, Folker}, year = {2014} } Wei Tang, Jonathan Jenkins, Folker Meyer, Robert Ross, Rajkumar Kettimuthu, Linda Winkler, Xi Yang, Thomas Lehman, and Narayan Desai. Data-aware resource scheduling for multicloud workflows: A fine-grained simulation approach. 2014 IEEE 6th International Conference on Cloud Computing Technology and Science. 2014. IEEE. BibTeX @inproceedings{tang_data-aware_2014, title = {Data-aware resource scheduling for multicloud workflows: {A} fine-grained simulation approach}, booktitle = {2014 {IEEE} 6th {International} {Conference} on {Cloud} {Computing} {Technology} and {Science}}, publisher = {IEEE}, author = {Tang, Wei and Jenkins, Jonathan and Meyer, Folker and Ross, Robert and Kettimuthu, Rajkumar and Winkler, Linda and Yang, Xi and Lehman, Thomas and Desai, Narayan}, year = {2014} } Wolfgang Gerlach, Wei Tang, Kevin Keegan, Travis Harrison, Andreas Wilke, Jared Bischof, Mark D’Souza, Scott Devoid, Daniel Murphy-Olson, Narayan Desai, and Folker Meyer. Skyport-container-based execution environment management for multi-cloud scientific workflows. 2014 5th International Workshop on Data-Intensive Computing in the Clouds. 2014. IEEE. BibTeX @inproceedings{gerlach_skyport-container-based_2014, title = {Skyport-container-based execution environment management for multi-cloud scientific workflows}, booktitle = {2014 5th {International} {Workshop} on {Data}-{Intensive} {Computing} in the {Clouds}}, publisher = {IEEE}, author = {Gerlach, Wolfgang and Tang, Wei and Keegan, Kevin and Harrison, Travis and Wilke, Andreas and Bischof, Jared and D'Souza, Mark and Devoid, Scott and Murphy-Olson, Daniel and Desai, Narayan and Meyer, Folker}, year = {2014} } Jared Bischof, Travis Harrison, Tobias Paczian, Elizabeth Glass, Andreas Wilke, and Folker Meyer. Metazen - Metadata Capture for Metagenomes. Standards in Genomic Science. 2014. BibTeX @article{bischof_metazen_2014-1, title = {Metazen - {Metadata} {Capture} for {Metagenomes}}, volume = {9}, journal = {Standards in Genomic Science}, author = {Bischof, Jared and Harrison, Travis and Paczian, Tobias and Glass, Elizabeth and Wilke, Andreas and Meyer, Folker}, year = {2014} } Kim M Handley, Daniela Bartels, Edward J O’Loughlin, Kenneth H Williams, William L Trimble, Kelly Skinner, Jack A Gilbert, Narayan Desai, Elizabeth M Glass, Tobias Paczian, and others. The complete genome sequence for putative H 2-and S-oxidizer C andidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome. Environmental microbiology. 2014. BibTeX @article{handley_complete_2014-2, title = {The complete genome sequence for putative {H} 2-and {S}-oxidizer {C} andidatus {Sulfuricurvum} sp., assembled de novo from an aquifer-derived metagenome}, volume = {16}, journal = {Environmental microbiology}, author = {Handley, Kim M and Bartels, Daniela and O'Loughlin, Edward J and Williams, Kenneth H and Trimble, William L and Skinner, Kelly and Gilbert, Jack A and Desai, Narayan and Glass, Elizabeth M and Paczian, Tobias and {others}}, year = {2014} } N. Davies, D. Field, L. Amaral-Zettler, M. S. Clark, J. Deck, A. Drummond, D. P. Faith, J. Geller, J. Gilbert, F. O. Glockner, P. R. Hirsch, J. A. Leong, C. Meyer, M. Obst, S. Planes, C. Scholin, A. P. Vogler, R. D. Gates, R. Toonen, V. Berteaux-Lecellier, M. Barbier, K. Barker, S. Bertilsson, M. Bicak, M. J. Bietz, J. Bobe, L. Bodrossy, A. Borja, J. Coddington, J. Fuhrman, G. Gerdts, R. Gillespie, K. Goodwin, P. C. Hanson, J. M. Hero, D. Hoekman, J. Jansson, C. Jeanthon, R. Kao, A. Klindworth, R. Knight, R. Kottmann, M. S. Koo, G. Kotoulas, A. J. Lowe, V. T. Marteinsson, Folker Meyer, N. Morrison, D. D. Myrold, E. Pafilis, S. Parker, J. J. Parnell, P. N. Polymenakou, S. Ratnasingham, G. K. Roderick, N. Rodriguez-Ezpeleta, K. Schonrogge, N. Simon, N. J. Valette-Silver, Y. P. Springer, G. N. Stone, S. Stones-Havas, S. A. Sansone, K. M. Thibault, P. Wecker, A. Wichels, J. C. Wooley, T. Yahara, A. Zingone, and G. Os COS. The founding charter of the Genomic Observatories Network. Gigascience. 2014. [doi] [url] BibTeX @article{davies_founding_2014-1, title = {The founding charter of the {Genomic} {Observatories} {Network}}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24606731}, doi = {10.1186/2047-217X-3-2}, journal = {Gigascience}, author = {Davies, N. and Field, D. and Amaral-Zettler, L. and Clark, M. S. and Deck, J. and Drummond, A. and Faith, D. P. and Geller, J. and Gilbert, J. and Glockner, F. O. and Hirsch, P. R. and Leong, J. A. and Meyer, C. and Obst, M. and Planes, S. and Scholin, C. and Vogler, A. P. and Gates, R. D. and Toonen, R. and Berteaux-Lecellier, V. and Barbier, M. and Barker, K. and Bertilsson, S. and Bicak, M. and Bietz, M. J. and Bobe, J. and Bodrossy, L. and Borja, A. and Coddington, J. and Fuhrman, J. and Gerdts, G. and Gillespie, R. and Goodwin, K. and Hanson, P. C. and Hero, J. M. and Hoekman, D. and Jansson, J. and Jeanthon, C. and Kao, R. and Klindworth, A. and Knight, R. and Kottmann, R. and Koo, M. S. and Kotoulas, G. and Lowe, A. J. and Marteinsson, V. T. and Meyer, Folker and Morrison, N. and Myrold, D. D. and Pafilis, E. and Parker, S. and Parnell, J. J. and Polymenakou, P. N. and Ratnasingham, S. and Roderick, G. K. and Rodriguez-Ezpeleta, N. and Schonrogge, K. and Simon, N. and Valette-Silver, N. J. and Springer, Y. P. and Stone, G. N. and Stones-Havas, S. and Sansone, S. A. and Thibault, K. M. and Wecker, P. and Wichels, A. and Wooley, J. C. and Yahara, T. and Zingone, A. and COS, G. Os}, year = {2014}, note = {Type: Journal Article} } N. C. Kyrpides, P. Hugenholtz, J. A. Eisen, T. Woyke, M. Goker, C. T. Parker, R. Amann, B. J. Beck, P. S. Chain, J. Chun, R. R. Colwell, A. Danchin, P. Dawyndt, T. Dedeurwaerdere, E. F. DeLong, J. C. Detter, P. De Vos, T. J. Donohue, X. Z. Dong, D. S. Ehrlich, C. Fraser, R. Gibbs, J. Gilbert, P. Gilna, F. O. Glockner, J. K. Jansson, J. D. Keasling, R. Knight, D. Labeda, A. Lapidus, J. S. Lee, W. J. Li, J. Ma, V. Markowitz, E. R. Moore, M. Morrison, Folker Meyer, K. E. Nelson, M. Ohkuma, C. A. Ouzounis, N. Pace, J. Parkhill, N. Qin, R. Rossello-Mora, J. Sikorski, D. Smith, M. Sogin, R. Stevens, U. Stingl, K. Suzuki, D. Taylor, J. M. Tiedje, B. Tindall, M. Wagner, G. Weinstock, J. Weissenbach, O. White, J. Wang, L. Zhang, Y. G. Zhou, D. Field, W. B. Whitman, G. M. Garrity, and H. P. Klenk. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol. 2014. [doi] [url] BibTeX @article{kyrpides_genomic_2014-1, title = {Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains}, volume = {12}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25093819}, doi = {10.1371/journal.pbio.1001920}, journal = {PLoS Biol}, author = {Kyrpides, N. C. and Hugenholtz, P. and Eisen, J. A. and Woyke, T. and Goker, M. and Parker, C. T. and Amann, R. and Beck, B. J. and Chain, P. S. and Chun, J. and Colwell, R. R. and Danchin, A. and Dawyndt, P. and Dedeurwaerdere, T. and DeLong, E. F. and Detter, J. C. and De Vos, P. and Donohue, T. J. and Dong, X. Z. and Ehrlich, D. S. and Fraser, C. and Gibbs, R. and Gilbert, J. and Gilna, P. and Glockner, F. O. and Jansson, J. K. and Keasling, J. D. and Knight, R. and Labeda, D. and Lapidus, A. and Lee, J. S. and Li, W. J. and Ma, J. and Markowitz, V. and Moore, E. R. and Morrison, M. and Meyer, Folker and Nelson, K. E. and Ohkuma, M. and Ouzounis, C. A. and Pace, N. and Parkhill, J. and Qin, N. and Rossello-Mora, R. and Sikorski, J. and Smith, D. and Sogin, M. and Stevens, R. and Stingl, U. and Suzuki, K. and Taylor, D. and Tiedje, J. M. and Tindall, B. and Wagner, M. and Weinstock, G. and Weissenbach, J. and White, O. and Wang, J. and Zhang, L. and Zhou, Y. G. and Field, D. and Whitman, W. B. and Garrity, G. M. and Klenk, H. P.}, year = {2014}, note = {Type: Journal Article}, keywords = {DNA, Archaea/classification/genetics Bacteria/classification/genetics Databases, Archaeal/*genetics Genome, Bacterial/*genetics *Genomics Phylogeny *Sequence Analysis, Genetic Genome} } David Myrold, Mark Bailey, Janet Jansson, Folker Meyer, James Tiedje, Eric Triplett, and Timothy Vogel. Terragenome-The Soil Metagenome Network. 2014. BibTeX @article{myrold_terragenome-soil_2014-1, title = {Terragenome-{The} {Soil} {Metagenome} {Network}}, author = {Myrold, David and Bailey, Mark and Jansson, Janet and Meyer, Folker and Tiedje, James and Triplett, Eric and Vogel, Timothy}, year = {2014} } A. K. Aufdenkampe, E. Mayorga, J. S. Horsburgh, K. A. Lehnert, I. Zaslavsky, Jr. D. W. Valentine, S. M. Richard, R. Cheetham, Folker Meyer, C. Henry, G. Berg-Cross, A. I. Packman, and E. L. Aronson. The community-driven BiG CZ software system for integration and analysis of bio- and geoscience data in the critical zone. AGU Fall Meeting Abstracts. 2014. BibTeX @inproceedings{aufdenkampe_community-driven_2014-1, title = {The community-driven {BiG} {CZ} software system for integration and analysis of bio- and geoscience data in the critical zone}, volume = {2014}, booktitle = {{AGU} {Fall} {Meeting} {Abstracts}}, author = {Aufdenkampe, A. K. and Mayorga, E. and Horsburgh, J. S. and Lehnert, K. A. and Zaslavsky, I. and Valentine, D. W., Jr. and Richard, S. M. and Cheetham, R. and Meyer, Folker and Henry, C. and Berg-Cross, G. and Packman, A. I. and Aronson, E. L.}, year = {2014}, keywords = {1904 Community standards, 1908 Cyberinfrastructure, 1972 Sensor web, 9805 Instruments useful in three or more fields} } Folker Meyer. METAGENOMICS: A GUIDE FROM SAMPLING TO DATA ANALYSIS. The Role of Bioinformatics in Agriculture. 2014. Apple Academic Press. BibTeX @incollection{meyer_metagenomics_2014-1, title = {{METAGENOMICS}: {A} {GUIDE} {FROM} {SAMPLING} {TO} {DATA} {ANALYSIS}}, booktitle = {The {Role} of {Bioinformatics} in {Agriculture}}, publisher = {Apple Academic Press}, author = {Meyer, Folker}, year = {2014} } F. Rambow, A. Bechadergue, G. Saintigny, F. Morizot, C. Mahe, and L. Larue. miR-330-5p targets tyrosinase and induces depigmentation. J Invest Dermatol. 2014. [doi] [url] BibTeX @article{RN30, author = {Rambow, F. and Bechadergue, A. and Saintigny, G. and Morizot, F. and Mahe, C. and Larue, L.}, title = {miR-330-5p targets tyrosinase and induces depigmentation}, journal = {J Invest Dermatol}, volume = {134}, number = {11}, pages = {2846-2849}, issn = {1523-1747 (Electronic) 0022-202X (Linking)}, doi = {10.1038/jid.2014.231}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24862846}, year = {2014}, type = {Journal Article} } M. J. Domingues, F. Rambow, B. Job, L. Papon, W. Liu, L. Larue, and J. Bonaventure. beta-catenin inhibitor ICAT modulates the invasive motility of melanoma cells. Cancer Res. 2014. [doi] [url] BibTeX @article{RN11, author = {Domingues, M. J. and Rambow, F. and Job, B. and Papon, L. and Liu, W. and Larue, L. and Bonaventure, J.}, title = {beta-catenin inhibitor ICAT modulates the invasive motility of melanoma cells}, journal = {Cancer Res}, volume = {74}, number = {7}, pages = {1983-95}, issn = {1538-7445 (Electronic) 0008-5472 (Linking)}, doi = {10.1158/0008-5472.CAN-13-0920}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24514042}, year = {2014}, type = {Journal Article} } </ol> 2013 Kristina Althoff, Anneleen Beckers, Andrea Odersky, Pieter Mestdagh, Johannes Köster, Isabella M. Bray, Kenneth Bryan, Jo Vandesompele, Frank Speleman, Raymond L. Stallings, Alexander Schramm, Angelika Eggert, Annika Sprüssel, and Johannes H. Schulte. MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A. International Journal of Cancer. 2013. [doi] [url] BibTeX @article{althoff_mir-137_2013, title = {{MiR}-137 functions as a tumor suppressor in neuroblastoma by downregulating {KDM1A}}, volume = {133}, copyright = {Copyright © 2013 UICC}, issn = {1097-0215}, url = {http://onlinelibrary.wiley.com/doi/10.1002/ijc.28091/abstract}, doi = {10.1002/ijc.28091}, language = {en}, number = {5}, urldate = {2013-09-19}, journal = {International Journal of Cancer}, author = {Althoff, Kristina and Beckers, Anneleen and Odersky, Andrea and Mestdagh, Pieter and Köster, Johannes and Bray, Isabella M. and Bryan, Kenneth and Vandesompele, Jo and Speleman, Frank and Stallings, Raymond L. and Schramm, Alexander and Eggert, Angelika and Sprüssel, Annika and Schulte, Johannes H.}, year = {2013}, keywords = {Epigenetics, LSD1, miR-137, neuroblastoma}, pages = {1064--1073}, file = {Althoff et al_2013_MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A.pdf:/vol/home/koester/Dropbox/xpapers/Althoff et al_2013_MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/53ZUJG3J/abstract.html:text/html} } Alexander Schramm, Johannes Köster, Tobias Marschall, Marcel Martin, Melanie Schwermer, Kathrin Fielitz, Gabriele Büchel, Matthias Barann, Daniela Esser, Philip Rosenstiel, Sven Rahmann, Angelika Eggert, and Johannes H. Schulte. Next-generation RNA sequencing reveals differential expression of MYCN target genes and suggests the mTOR pathway as a promising therapy target in MYCN-amplified neuroblastoma. International Journal of Cancer. 2013. [doi] [url] BibTeX @article{schramm_next-generation_2013, title = {Next-generation {RNA} sequencing reveals differential expression of {MYCN} target genes and suggests the {mTOR} pathway as a promising therapy target in {MYCN}-amplified neuroblastoma}, volume = {132}, copyright = {Copyright © 2012 UICC}, issn = {1097-0215}, url = {http://onlinelibrary.wiley.com/doi/10.1002/ijc.27787/abstract}, doi = {10.1002/ijc.27787}, language = {en}, number = {3}, urldate = {2013-09-19}, journal = {International Journal of Cancer}, author = {Schramm, Alexander and Köster, Johannes and Marschall, Tobias and Martin, Marcel and Schwermer, Melanie and Fielitz, Kathrin and Büchel, Gabriele and Barann, Matthias and Esser, Daniela and Rosenstiel, Philip and Rahmann, Sven and Eggert, Angelika and Schulte, Johannes H.}, year = {2013}, keywords = {next-generation sequencing, neuroblastoma, mTOR pathway, MYCN}, pages = {E106--E115}, file = {Schramm et al_2013_Next-generation RNA sequencing reveals differential expression of MYCN target.pdf:/vol/home/koester/Dropbox/xpapers/Schramm et al_2013_Next-generation RNA sequencing reveals differential expression of MYCN target.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/AVDZP6HP/abstract\;jsessionid=4DCF5E43C6EE4F573A82C5543C1AE118.html:text/html} } Simon. Magin, J. Saha, M. Wang, V. Mladenova, N. Coym, and G. Iliakis. Lipofection and nucleofection of substrate plasmid can generate widely different readings of DNA end-joining efficiency in different cell lines. DNA repair. 2013. [doi] [url] BibTeX @article{RN301, author = {Magin, Simon. and Saha, J. and Wang, M. and Mladenova, V. and Coym, N. and Iliakis, G.}, title = {Lipofection and nucleofection of substrate plasmid can generate widely different readings of DNA end-joining efficiency in different cell lines}, journal = {DNA repair}, volume = {12}, number = {2}, pages = {148-60}, note = {Magin, Simon Saha, Janapriya Wang, Minli Mladenova, Veronika Coym, Nadine Iliakis, George Netherlands DNA Repair (Amst). 2013 Feb 1;12(2):148-60. doi: 10.1016/j.dnarep.2012.11.008. Epub 2013 Jan 1.}, issn = {1568-7856 (Electronic) 1568-7856 (Linking)}, doi = {10.1016/j.dnarep.2012.11.008}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23286905}, year = {2013}, type = {Journal Article} } E. Mladenov, Simon. Magin, A. Soni, and G. Iliakis. DNA double-strand break repair as determinant of cellular radiosensitivity to killing and target in radiation therapy. Frontiers in oncology. 2013. [doi] [url] BibTeX @article{RN318, author = {Mladenov, E. and Magin, Simon. and Soni, A. and Iliakis, G.}, title = {DNA double-strand break repair as determinant of cellular radiosensitivity to killing and target in radiation therapy}, journal = {Frontiers in oncology}, volume = {3}, pages = {113}, note = {Mladenov, Emil Magin, Simon Soni, Aashish Iliakis, George Switzerland Front Oncol. 2013 May 10;3:113. doi: 10.3389/fonc.2013.00113. Print 2013.}, issn = {2234-943X (Electronic) 2234-943X (Linking)}, doi = {10.3389/fonc.2013.00113}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23675572}, year = {2013}, type = {Journal Article} } Ivana Kraiselburd, Lucas Damián Daurelio, María Laura Tondo, Paz Merelo, Adriana A. Cortadi, Manuel Talón, Francisco R Tadeo, and Elena G Orellano. The LOV Protein of Xanthomonas citri subsp. citri Plays a Significant Role in the Counteraction of Plant Immune Responses during Citrus Canker. PLoS ONE. 2013. BibTeX @article{Kraiselburd2013TheLP, title = {The LOV Protein of Xanthomonas citri subsp. citri Plays a Significant Role in the Counteraction of Plant Immune Responses during Citrus Canker}, author = {Kraiselburd, Ivana and Daurelio, Lucas Dami{\'a}n and Tondo, Mar{\'i}a Laura and Merelo, Paz and Cortadi, Adriana A. and Tal{\'o}n, Manuel and Tadeo, Francisco R and Orellano, Elena G}, journal = {PLoS ONE}, year = {2013}, volume = {8} } Ricarda M. Schmithausen, S Schulze-Geisthoevel, F Stemmer, G Bierbaum, A Hoerauf, M Exner, I Bekeredjian-Ding, and B Petersen. Association of antibiotic usage with MRSA and ESBL prevalence in pig farms. INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY. 2013. BibTeX @inproceedings{schmithausen2013association, title = {Association of antibiotic usage with MRSA and ESBL prevalence in pig farms}, author = {Schmithausen, Ricarda M. and Schulze-Geisthoevel, S and Stemmer, F and Bierbaum, G and Hoerauf, A and Exner, M and Bekeredjian-Ding, I and Petersen, B}, booktitle = {INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY}, volume = {303}, year = {2013}, organization = {ELSEVIER GMBH, URBAN \& FISCHER VERLAG OFFICE JENA, PO BOX 100537, 07705 JENA~…} } D. Williams, W. L. Trimble, M. Shilts, Folker Meyer, and H. Ochman. Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes. BMC Genomics. 2013. [doi] [url] BibTeX @article{williams_rapid_2013, title = {Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes}, volume = {14}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23924250}, doi = {10.1186/1471-2164-14-537}, journal = {BMC Genomics}, author = {Williams, D. and Trimble, W. L. and Shilts, M. and Meyer, Folker and Ochman, H.}, year = {2013}, note = {Type: Journal Article} } E. C. Claud, K. P. Keegan, J. M. Brulc, L. Lu, D. Bartels, E. Glass, E. B. Chang, Folker Meyer, and D. A. Antonopoulos. Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants. Microbiome. 2013. [doi] [url] BibTeX @article{claud_bacterial_2013, title = {Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants}, volume = {1}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24450928}, doi = {10.1186/2049-2618-1-20}, journal = {Microbiome}, author = {Claud, E. C. and Keegan, K. P. and Brulc, J. M. and Lu, L. and Bartels, D. and Glass, E. and Chang, E. B. and Meyer, Folker and Antonopoulos, D. A.}, year = {2013}, note = {Type: Journal Article} } James Vincent, A Wilke, J Bischof, N Desai, M D’Souza, E Glass, K Handley, T Harrison, A Howe, K Keegan, and Folker Meyer. Analysis of Shotgun Metagenomes with MG-RAST. Journal of Biomolecular Techniques: JBT. 2013. BibTeX @article{vincent_analysis_2013, title = {Analysis of {Shotgun} {Metagenomes} with {MG}-{RAST}}, volume = {24}, journal = {Journal of Biomolecular Techniques: JBT}, author = {Vincent, James and Wilke, A and Bischof, J and Desai, N and D'Souza, M and Glass, E and Handley, K and Harrison, T and Howe, A and Keegan, K and Meyer, Folker}, year = {2013}, note = {Publisher: The Association of Biomolecular Resource Facilities} } Andreas Wilke, E Glass, Jared Bischof, Daniel Braithwaite, M Souza, and Wolfgang Gerlach. MG-RAST technical report and manual for version 3.3. 6–Rev 1. Lemont, IL: Argonne National Laboratory. 2013. BibTeX @article{wilke_mg-rast_2013, title = {{MG}-{RAST} technical report and manual for version 3.3. 6–{Rev} 1}, journal = {Lemont, IL: Argonne National Laboratory}, author = {Wilke, Andreas and Glass, E and Bischof, Jared and Braithwaite, Daniel and Souza, M and Gerlach, Wolfgang}, year = {2013} } Andreas Wilke, Elizabeth M Glass, Daniela Bartels, Jared Bischof, Daniel Braithwaite, Mark D’Souza, Wolfgang Gerlach, Travis Harrison, Kevin Keegan, Hunter Matthews, and Folker Meyer. A metagenomics portal for a democratized sequencing world. Methods in Enzymology. 2013. Academic Press. BibTeX @incollection{wilke_metagenomics_2013, title = {A metagenomics portal for a democratized sequencing world}, volume = {531}, booktitle = {Methods in {Enzymology}}, publisher = {Academic Press}, author = {Wilke, Andreas and Glass, Elizabeth M and Bartels, Daniela and Bischof, Jared and Braithwaite, Daniel and D’Souza, Mark and Gerlach, Wolfgang and Harrison, Travis and Keegan, Kevin and Matthews, Hunter and Meyer, Folker}, year = {2013} } Elizabeth M. Glass, Yekaterina Dribinsky, Pelin Yilamz, Folker Meyer, and Lynn M. Schriml. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME. 2013. BibTeX @inproceedings{elizabeth_m_glass_mixs-be_2013, title = {{MIxS}-{BE}: a {MIxS} extension defining a minimum information standard for sequence data from the built environment}, booktitle = {{ISME}}, author = {Glass, Elizabeth M. and Dribinsky, Yekaterina and Yilamz, Pelin and Meyer, Folker and Schriml, Lynn M.}, year = {2013} } Wei Tang, Jared Wilkening, Narayan Desai, Wolfgang Gerlach, Andreas Wilke, and Folker Meyer. A Scalable Data Analysis Platform for Metagenomics. 2013 IEEE International Conference on Big Data. 2013. BibTeX @inproceedings{tang_scalable_2013, title = {A {Scalable} {Data} {Analysis} {Platform} for {Metagenomics}}, booktitle = {2013 {IEEE} {International} {Conference} on {Big} {Data}}, author = {Tang, Wei and Wilkening, Jared and Desai, Narayan and Gerlach, Wolfgang and Wilke, Andreas and Meyer, Folker}, year = {2013} } Wei Tang, Jared Wilkening, Jared Bischof, Wolfgang Gerlach, Andreas Wilke, Narayan Desai, and Folker Meyer. Building Scalable Data Management and Analysis Infrastructure for Metagenomics. 2013. BibTeX @article{tang_building_2013, title = {Building {Scalable} {Data} {Management} and {Analysis} {Infrastructure} for {Metagenomics}}, author = {Tang, Wei and Wilkening, Jared and Bischof, Jared and Gerlach, Wolfgang and Wilke, Andreas and Desai, Narayan and Meyer, Folker}, year = {2013} } Folker Meyer30. BIG DATA IN BIOLOGY: PITFALLS WHEN USING SHOTGUN METAGENOMICS TO DEFINE HYPOTHESES ABOUT MICROBIAL COMMUNITIES. The Science and Applications of Microbial Genomics: Workshop Summary. 2013. National Academies Press. BibTeX @inproceedings{meyer30_big_2013, title = {{BIG} {DATA} {IN} {BIOLOGY}: {PITFALLS} {WHEN} {USING} {SHOTGUN} {METAGENOMICS} {TO} {DEFINE} {HYPOTHESES} {ABOUT} {MICROBIAL} {COMMUNITIES}}, booktitle = {The {Science} and {Applications} of {Microbial} {Genomics}: {Workshop} {Summary}}, publisher = {National Academies Press}, author = {Meyer30, Folker}, year = {2013} } V. B. Young, L. H. Raffals, S. M. Huse, M. Vital, D. Dai, P. D. Schloss, J. M. Brulc, D. A. Antonopoulos, R. L. Arrieta, J. H. Kwon, K. G. Reddy, N. A. Hubert, S. L. Grim, J. H. Vineis, S. Dalal, H. G. Morrison, A. M. Eren, Folker Meyer, T. M. Schmidt, J. M. Tiedje, E. B. Chang, and M. L. Sogin. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome. 2013. [doi] [url] BibTeX @article{young_multiphasic_2013-1, title = {Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis}, volume = {1}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24451366}, doi = {10.1186/2049-2618-1-9}, journal = {Microbiome}, author = {Young, V. B. and Raffals, L. H. and Huse, S. M. and Vital, M. and Dai, D. and Schloss, P. D. and Brulc, J. M. and Antonopoulos, D. A. and Arrieta, R. L. and Kwon, J. H. and Reddy, K. G. and Hubert, N. A. and Grim, S. L. and Vineis, J. H. and Dalal, S. and Morrison, H. G. and Eren, A. M. and Meyer, Folker and Schmidt, T. M. and Tiedje, J. M. and Chang, E. B. and Sogin, M. L.}, year = {2013}, note = {Type: Journal Article} } S. J. Gallagher, F. Rambow, M. Kumasaka, D. Champeval, A. Bellacosa, V. Delmas, and L. Larue. Beta-catenin inhibits melanocyte migration but induces melanoma metastasis. Oncogene. 2013. [doi] [url] BibTeX @article{RN14, author = {Gallagher, S. J. and Rambow, F. and Kumasaka, M. and Champeval, D. and Bellacosa, A. and Delmas, V. and Larue, L.}, title = {Beta-catenin inhibits melanocyte migration but induces melanoma metastasis}, journal = {Oncogene}, volume = {32}, number = {17}, pages = {2230-8}, issn = {1476-5594 (Electronic) 0950-9232 (Linking)}, doi = {10.1038/onc.2012.229}, url = {https://www.ncbi.nlm.nih.gov/pubmed/22665063}, year = {2013}, type = {Journal Article} } 2012 Johannes Köster and Sven Rahmann. Snakemake—a scalable bioinformatics workflow engine. Bioinformatics. 2012. [doi] [url] BibTeX @article{koster_snakemakescalable_2012, title = {Snakemake—a scalable bioinformatics workflow engine}, volume = {28}, issn = {1367-4803}, url = {https://academic.oup.com/bioinformatics/article/28/19/2520/290322}, doi = {10.1093/bioinformatics/bts480}, language = {en}, number = {19}, urldate = {2019-05-03}, journal = {Bioinformatics}, author = {Köster, Johannes and Rahmann, Sven}, month = oct, year = {2012}, pages = {2520--2522}, file = {Full Text PDF:/home/johannes/Zotero/storage/88LHZAD5/Köster and Rahmann - 2012 - Snakemake—a scalable bioinformatics workflow engin.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/GCC3G4A6/290322.html:text/html} } Johannes Köster and Sven Rahmann. Building and Documenting Workflows with Python-Based Snakemake. German Conference on Bioinformatics 2012. 2012. Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik. [doi] [url] BibTeX @inproceedings{koster_building_2012, address = {Dagstuhl, Germany}, series = {{OpenAccess} {Series} in {Informatics} ({OASIcs})}, title = {Building and {Documenting} {Workflows} with {Python}-{Based} {Snakemake}}, volume = {26}, copyright = {All rights reserved}, isbn = {978-3-939897-44-6}, url = {http://drops.dagstuhl.de/opus/volltexte/2012/3717}, doi = {http://dx.doi.org/10.4230/OASIcs.GCB.2012.49}, booktitle = {German {Conference} on {Bioinformatics} 2012}, publisher = {Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik}, author = {Köster, Johannes and Rahmann, Sven}, editor = {Böcker, Sebastian and Hufsky, Franziska and Scheubert, Kerstin and Schleicher, Jana and Schuster, Stefan}, year = {2012}, pages = {49--56}, annote = {Keywords: workflow engine, dependency graph, knapsack problem, Python, high-throughput sequencing, next-generation sequencing} } Ivana Kraiselburd, Analía I. Alet, María Laura Tondo, Silvana Petrocelli, Lucas Damián Daurelio, Jesica Monzón, Oscar Adolfo Ruiz, Aba Losi, and Elena G Orellano. A LOV Protein Modulates the Physiological Attributes of Xanthomonas axonopodis pv. citri Relevant for Host Plant Colonization. PLoS ONE. 2012. BibTeX @article{Kraiselburd2012ALP, title = {A LOV Protein Modulates the Physiological Attributes of Xanthomonas axonopodis pv. citri Relevant for Host Plant Colonization}, author = {Kraiselburd, Ivana and Alet, Anal{\'i}a I. and Tondo, Mar{\'i}a Laura and Petrocelli, Silvana and Daurelio, Lucas Dami{\'a}n and Monz{\'o}n, Jesica and Ruiz, Oscar Adolfo and Losi, Aba and Orellano, Elena G}, journal = {PLoS ONE}, year = {2012}, volume = {7} } Ricarda M. Schmithausen, V Raab, and B Petersen. MRSA in Mensch, Tier und Lebensmitteln–Eine Übersicht. Aktuelle Ernährungsmedizin. 2012. BibTeX @article{schmithausen2012mrsa, title = {MRSA in Mensch, Tier und Lebensmitteln--Eine {\"U}bersicht}, author = {Schmithausen, Ricarda M. and Raab, V and Petersen, B}, journal = {Aktuelle Ern{\"a}hrungsmedizin}, volume = {37}, year = {2012} } A. Wilke, T. Harrison, J. Wilkening, D. Field, E. M. Glass, N. Kyrpides, K. Mavrommatis, and Folker Meyer. The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics. 2012. [doi] [url] BibTeX @article{wilke_m5nr_2012, title = {The {M5nr}: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools}, volume = {13}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22720753}, doi = {10.1186/1471-2105-13-141}, journal = {BMC Bioinformatics}, author = {Wilke, A. and Harrison, T. and Wilkening, J. and Field, D. and Glass, E. M. and Kyrpides, N. and Mavrommatis, K. and Meyer, Folker}, year = {2012}, note = {Type: Journal Article} } W. L. Trimble, K. P. Keegan, M. D’Souza, A. Wilke, J. Wilkening, J. Gilbert, and Folker Meyer. Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. BMC Bioinformatics. 2012. [doi] [url] BibTeX @article{trimble_short-read_2012, title = {Short-read reading-frame predictors are not created equal: sequence error causes loss of signal}, volume = {13}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22839106}, doi = {10.1186/1471-2105-13-183}, journal = {BMC Bioinformatics}, author = {Trimble, W. L. and Keegan, K. P. and D'Souza, M. and Wilke, A. and Wilkening, J. and Gilbert, J. and Meyer, Folker}, year = {2012}, note = {Type: Journal Article} } T. Thomas, J. Gilbert, and Folker Meyer. Metagenomics - a guide from sampling to data analysis. Microb Inform Exp. 2012. [doi] [url] BibTeX @article{thomas_metagenomics_2012, title = {Metagenomics - a guide from sampling to data analysis}, volume = {2}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22587947}, doi = {10.1186/2042-5783-2-3}, journal = {Microb Inform Exp}, author = {Thomas, T. and Gilbert, J. and Meyer, Folker}, year = {2012}, note = {Type: Journal Article} } D. McDonald, J. C. Clemente, J. Kuczynski, J. R. Rideout, J. Stombaugh, D. Wendel, A. Wilke, S. Huse, J. Hufnagle, Folker Meyer, R. Knight, and J. G. Caporaso. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience. 2012. [doi] [url] BibTeX @article{mcdonald_biological_2012, title = {The {Biological} {Observation} {Matrix} ({BIOM}) format or: how {I} learned to stop worrying and love the ome-ome}, volume = {1}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23587224}, doi = {10.1186/2047-217X-1-7}, journal = {Gigascience}, author = {McDonald, D. and Clemente, J. C. and Kuczynski, J. and Rideout, J. R. and Stombaugh, J. and Wendel, D. and Wilke, A. and Huse, S. and Hufnagle, J. and Meyer, Folker and Knight, R. and Caporaso, J. G.}, year = {2012}, note = {Type: Journal Article} } R. Knight, J. Jansson, D. Field, N. Fierer, N. Desai, J. A. Fuhrman, P. Hugenholtz, D. van der Lelie, Folker Meyer, R. Stevens, M. J. Bailey, J. I. Gordon, G. A. Kowalchuk, and J. A. Gilbert. Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol. 2012. [doi] [url] BibTeX @article{knight_unlocking_2012, title = {Unlocking the potential of metagenomics through replicated experimental design}, volume = {30}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22678395}, doi = {10.1038/nbt.2235}, journal = {Nat Biotechnol}, author = {Knight, R. and Jansson, J. and Field, D. and Fierer, N. and Desai, N. and Fuhrman, J. A. and Hugenholtz, P. and van der Lelie, D. and Meyer, Folker and Stevens, R. and Bailey, M. J. and Gordon, J. I. and Kowalchuk, G. A. and Gilbert, J. A.}, year = {2012}, note = {Type: Journal Article} } K. P. Keegan, W. L. Trimble, J. Wilkening, A. Wilke, T. Harrison, M. D’Souza, and Folker Meyer. A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE. PLoS Comput Biol. 2012. [doi] [url] BibTeX @article{keegan_platform-independent_2012, title = {A platform-independent method for detecting errors in metagenomic sequencing data: {DRISEE}}, volume = {8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22685393}, doi = {10.1371/journal.pcbi.1002541}, journal = {PLoS Comput Biol}, author = {Keegan, K. P. and Trimble, W. L. and Wilkening, J. and Wilke, A. and Harrison, T. and D'Souza, M. and Meyer, Folker}, year = {2012}, note = {Type: Journal Article} } J. A. Gilbert, Y. Bao, H. Wang, S. A. Sansone, S. C. Edmunds, N. Morrison, Folker Meyer, L. M. Schriml, N. Davies, P. Sterk, J. Wilkening, G. M. Garrity, D. Field, R. Robbins, D. P. Smith, I. Mizrachi, and C. Moreau. Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012. Stand Genomic Sci. 2012. [doi] [url] BibTeX @article{gilbert_report_2012, title = {Report of the 13(th) {Genomic} {Standards} {Consortium} {Meeting}, {Shenzhen}, {China}, {March} 4-7, 2012}, volume = {6}, url = {https://www.ncbi.nlm.nih.gov/pubmed/22768370}, doi = {10.4056/sigs.2876184}, journal = {Stand Genomic Sci}, author = {Gilbert, J. A. and Bao, Y. and Wang, H. and Sansone, S. A. and Edmunds, S. C. and Morrison, N. and Meyer, Folker and Schriml, L. M. and Davies, N. and Sterk, P. and Wilkening, J. and Garrity, G. M. and Field, D. and Robbins, R. and Smith, D. P. and Mizrachi, I. and Moreau, C.}, year = {2012}, note = {Type: Journal Article} } N. Desai, D. Antonopoulos, J. A. Gilbert, E. M. Glass, and Folker Meyer. From genomics to metagenomics. Curr Opin Biotechnol. 2012. [doi] [url] BibTeX @article{desai_genomics_2012, title = {From genomics to metagenomics}, volume = {23}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22227326}, doi = {10.1016/j.copbio.2011.12.017}, journal = {Curr Opin Biotechnol}, author = {Desai, N. and Antonopoulos, D. and Gilbert, J. A. and Glass, E. M. and Meyer, Folker}, year = {2012}, note = {Type: Journal Article} } T. O. Delmont, E. Prestat, K. P. Keegan, M. Faubladier, P. Robe, I. M. Clark, E. Pelletier, P. R. Hirsch, Folker Meyer, J. A. Gilbert, D. Le Paslier, P. Simonet, and T. M. Vogel. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J. 2012. [doi] [url] BibTeX @article{delmont_structure_2012, title = {Structure, fluctuation and magnitude of a natural grassland soil metagenome}, volume = {6}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22297556}, doi = {10.1038/ismej.2011.197}, journal = {ISME J}, author = {Delmont, T. O. and Prestat, E. and Keegan, K. P. and Faubladier, M. and Robe, P. and Clark, I. M. and Pelletier, E. and Hirsch, P. R. and Meyer, Folker and Gilbert, J. A. and Le Paslier, D. and Simonet, P. and Vogel, T. M.}, year = {2012}, note = {Type: Journal Article} } Elizabeth M Glass and Folker Meyer. Analysis of metagenomics data. Bioinformatics for High Throughput Sequencing. 2012. Springer, New York, NY. BibTeX @incollection{glass_analysis_2012, title = {Analysis of metagenomics data}, booktitle = {Bioinformatics for {High} {Throughput} {Sequencing}}, publisher = {Springer, New York, NY}, author = {Glass, Elizabeth M and Meyer, Folker}, year = {2012} } Torsten Thomas, Jack Gilbert, and Folker Meyer. Metagenomics-a guide from sampling to data analysis. Microbial informatics and experimentation. 2012. BibTeX @article{thomas_metagenomics-guide_2012, title = {Metagenomics-a guide from sampling to data analysis}, volume = {2}, journal = {Microbial informatics and experimentation}, author = {Thomas, Torsten and Gilbert, Jack and Meyer, Folker}, year = {2012}, note = {Publisher: BioMed Central} } J Gilbert and Folker Meyer. Modeling the Earth Microbiome – Careful planning can reduce sampling and measurement biases while building data sets describing microbes across multiple ecosystems. ASM Microbe. 2012. BibTeX @article{gilbert_modeling_2012, title = {Modeling the {Earth} {Microbiome} – {Careful} planning can reduce sampling and measurement biases while building data sets describing microbes across multiple ecosystems}, journal = {ASM Microbe}, author = {Gilbert, J and Meyer, Folker}, year = {2012} } Jack A Gilbert, Charlie Catlett, Narayan Desai, Rob Knight, Owen White, Robert Robbins, Rajesh Sankaran, Susanna-Assunta Sansone, Dawn Field, and Folker Meyer. Conceptualizing a Genomics Software Institute (GSI). Standards in genomic sciences. 2012. BibTeX @article{gilbert_conceptualizing_2012, title = {Conceptualizing a {Genomics} {Software} {Institute} ({GSI})}, volume = {6}, journal = {Standards in genomic sciences}, author = {Gilbert, Jack A and Catlett, Charlie and Desai, Narayan and Knight, Rob and White, Owen and Robbins, Robert and Sankaran, Rajesh and Sansone, Susanna-Assunta and Field, Dawn and Meyer, Folker}, year = {2012}, note = {Publisher: BioMed Central} } Le T Phung, William L Trimble, Folker Meyer, Jack A Gilbert, and Simon Silver. Draft genome sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071). 2012. American Society for Microbiology 1752 N St., NW, Washington, DC. BibTeX @misc{phung_draft_2012, title = {Draft genome sequence of {Alcaligenes} faecalis subsp. faecalis {NCIB} 8687 ({CCUG} 2071)}, publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC}, author = {Phung, Le T and Trimble, William L and Meyer, Folker and Gilbert, Jack A and Silver, Simon}, year = {2012} } Andrea D Olivas, Benjamin D Shogan, Vesta Valuckaite, Alexander Zaborin, Natalya Belogortseva, Mark Musch, Folker Meyer, William L. Trimble, Gary An, Jack Gilbert, and John Alverdy. Intestinal tissues induce an SNP mutation in Pseudomonas aeruginosa that enhances its virulence: possible role in anastomotic leak. 2012. BibTeX @article{olivas_intestinal_2012, title = {Intestinal tissues induce an {SNP} mutation in {Pseudomonas} aeruginosa that enhances its virulence: possible role in anastomotic leak}, author = {Olivas, Andrea D and Shogan, Benjamin D and Valuckaite, Vesta and Zaborin, Alexander and Belogortseva, Natalya and Musch, Mark and Meyer, Folker and L. Trimble, William and An, Gary and Gilbert, Jack and Alverdy, John}, year = {2012}, note = {Publisher: Public Library of Science San Francisco, USA} } F Meyer, WL Trimble, EB Chang, and KM Handley. Functional predictions from inference and observation in sequence-based inflammatory bowel disease research. Genome Biology. 2012. BibTeX @article{meyer_functional_2012, title = {Functional predictions from inference and observation in sequence-based inflammatory bowel disease research}, volume = {13}, journal = {Genome Biology}, author = {Meyer, F and Trimble, WL and Chang, EB and Handley, KM}, year = {2012} } William L Trimble, Le T Phung, Folker Meyer, Simon Silver, and Jack A Gilbert. Draft genome sequence of Achromobacter piechaudii strain HLE. 2012. American Society for Microbiology 1752 N St., NW, Washington, DC. BibTeX @misc{trimble_draft_2012, title = {Draft genome sequence of {Achromobacter} piechaudii strain {HLE}}, publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC}, author = {Trimble, William L and Phung, Le T and Meyer, Folker and Silver, Simon and Gilbert, Jack A}, year = {2012} } William L Trimble, Le T Phung, Folker Meyer, Jack A Gilbert, and Simon Silver. Draft genome sequence of Agrobacterium albertimagni strain AOL15. 2012. American Society for Microbiology 1752 N St., NW, Washington, DC. BibTeX @misc{trimble_draft_2012-1, title = {Draft genome sequence of {Agrobacterium} albertimagni strain {AOL15}}, publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC}, author = {Trimble, William L and Phung, Le T and Meyer, Folker and Gilbert, Jack A and Silver, Simon}, year = {2012} } Jack A Gilbert, William L Trimble, Le T Phung, Folker Meyer, and Simon Silver. Draft Genome Sequence of Achromobacter. J. Bacteriol. 2012. BibTeX @article{gilbert_draft_2012, title = {Draft {Genome} {Sequence} of {Achromobacter}}, volume = {194}, journal = {J. Bacteriol}, author = {Gilbert, Jack A and Trimble, William L and Phung, Le T and Meyer, Folker and Silver, Simon}, year = {2012} } S. Makhzami, F. Rambow, V. Delmas, and L. Larue. Efficient gene expression profiling of laser-microdissected melanoma metastases. Pigment Cell Melanoma Res. 2012. [doi] [url] BibTeX @article{RN23, author = {Makhzami, S. and Rambow, F. and Delmas, V. and Larue, L.}, title = {Efficient gene expression profiling of laser-microdissected melanoma metastases}, journal = {Pigment Cell Melanoma Res}, volume = {25}, number = {6}, pages = {783-91}, issn = {1755-148X (Electronic) 1755-1471 (Linking)}, doi = {10.1111/pcmr.12013}, url = {https://www.ncbi.nlm.nih.gov/pubmed/22934821}, year = {2012}, type = {Journal Article} } S. Colombo, D. Champeval, F. Rambow, and L. Larue. Transcriptomic analysis of mouse embryonic skin cells reveals previously unreported genes expressed in melanoblasts. J Invest Dermatol. 2012. [doi] [url] BibTeX @article{RN6, author = {Colombo, S. and Champeval, D. and Rambow, F. and Larue, L.}, title = {Transcriptomic analysis of mouse embryonic skin cells reveals previously unreported genes expressed in melanoblasts}, journal = {J Invest Dermatol}, volume = {132}, number = {1}, pages = {170-8}, issn = {1523-1747 (Electronic) 0022-202X (Linking)}, doi = {10.1038/jid.2011.252}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21850021}, year = {2012}, type = {Journal Article} } I. Berlin, F. Luciani, S. J. Gallagher, F. Rambow, A. Conde-Perez, S. Colombo, D. Champeval, V. Delmas, and L. Larue. General strategy to analyse coat colour phenotypes in mice. Pigment Cell Melanoma Res. 2012. [doi] [url] BibTeX @article{RN5, author = {Berlin, I. and Luciani, F. and Gallagher, S. J. and Rambow, F. and Conde-Perez, A. and Colombo, S. and Champeval, D. and Delmas, V. and Larue, L.}, title = {General strategy to analyse coat colour phenotypes in mice}, journal = {Pigment Cell Melanoma Res}, volume = {25}, number = {1}, pages = {117-9}, issn = {1755-148X (Electronic) 1755-1471 (Linking)}, doi = {10.1111/j.1755-148X.2011.00912.x}, url = {https://www.ncbi.nlm.nih.gov/pubmed/22085368}, year = {2012}, type = {Journal Article} } 2011 Johannes Köster, Eli Zamir, and Sven Rahmann. Protein Hypernetworks: a Logic Framework for Interaction Dependencies and Perturbation Effects in Protein Networks. 2011. [url] BibTeX @techreport{koster_protein_2011, type = {{arXiv} e-print}, title = {Protein {Hypernetworks}: a {Logic} {Framework} for {Interaction} {Dependencies} and {Perturbation} {Effects} in {Protein} {Networks}}, copyright = {All rights reserved}, shorttitle = {Protein {Hypernetworks}}, url = {http://arxiv.org/abs/1106.2562}, number = {1106.2562}, urldate = {2013-10-08}, author = {Köster, Johannes and Zamir, Eli and Rahmann, Sven}, month = jun, year = {2011}, keywords = {Quantitative Biology - Molecular Networks}, annote = {Comment: Preprint, submitted to Bioinformatics; 7 pages, 5 figures, 4 pages supplement For further information, see http://www.rahmannlab.de/research/hypernetworks}, file = {arXiv.org Snapshot:/home/johannes/Zotero/storage/SNEFRU2G/1106.html:text/html;Köster et al_2011_Protein Hypernetworks.pdf:/vol/home/koester/Dropbox/xpapers/Köster et al_2011_Protein Hypernetworks.pdf:application/pdf} } Katrin M Kirschbaum, Frank Musshoff, Ricarda Schmithausen, Sarah Stockhausen, and Burkhard Madea. Optimization and validation of CEDIA drugs of abuse immunoassay tests in serum on Hitachi 912. Forensic science international. 2011. Elsevier. BibTeX @article{kirschbaum2011optimization, title = {Optimization and validation of CEDIA drugs of abuse immunoassay tests in serum on Hitachi 912}, author = {Kirschbaum, Katrin M and Musshoff, Frank and Schmithausen, Ricarda and Stockhausen, Sarah and Madea, Burkhard}, journal = {Forensic science international}, volume = {212}, year = {2011}, publisher = {Elsevier} } Ricarda Maria Schmithausen. Optinierung laborinterner Cut-off-Werte fur die immunchemische Vortestung auf Amphetamine und Cannabinoide im forensischen Labor. Rheinische Friedrich-Wilhelms-Universität in Bonn. 2011. BibTeX @phdthesis{schmithausen2011optinierung, title = {Optinierung laborinterner Cut-off-Werte fur die immunchemische Vortestung auf Amphetamine und Cannabinoide im forensischen Labor}, author = {Schmithausen, Ricarda Maria}, year = {2011}, school = {Rheinische Friedrich-Wilhelms-Universit{\"a}t in Bonn} } P. Yilmaz, R. Kottmann, D. Field, R. Knight, J. R. Cole, L. Amaral-Zettler, J. A. Gilbert, I. Karsch-Mizrachi, A. Johnston, G. Cochrane, R. Vaughan, C. Hunter, J. Park, N. Morrison, P. Rocca-Serra, P. Sterk, M. Arumugam, M. Bailey, L. Baumgartner, B. W. Birren, M. J. Blaser, V. Bonazzi, T. Booth, P. Bork, F. D. Bushman, P. L. Buttigieg, P. S. Chain, E. Charlson, E. K. Costello, H. Huot-Creasy, P. Dawyndt, T. DeSantis, N. Fierer, J. A. Fuhrman, R. E. Gallery, D. Gevers, R. A. Gibbs, I. San Gil, A. Gonzalez, J. I. Gordon, R. Guralnick, W. Hankeln, S. Highlander, P. Hugenholtz, J. Jansson, A. L. Kau, S. T. Kelley, J. Kennedy, D. Knights, O. Koren, J. Kuczynski, N. Kyrpides, R. Larsen, C. L. Lauber, T. Legg, R. E. Ley, C. A. Lozupone, W. Ludwig, D. Lyons, E. Maguire, B. A. Methe, Folker Meyer, B. Muegge, S. Nakielny, K. E. Nelson, D. Nemergut, J. D. Neufeld, L. K. Newbold, A. E. Oliver, N. R. Pace, G. Palanisamy, J. Peplies, J. Petrosino, L. Proctor, E. Pruesse, C. Quast, J. Raes, S. Ratnasingham, J. Ravel, D. A. Relman, S. Assunta-Sansone, P. D. Schloss, L. Schriml, R. Sinha, M. I. Smith, E. Sodergren, A. Spo, J. Stombaugh, J. M. Tiedje, D. V. Ward, G. M. Weinstock, D. Wendel, O. White, A. Whiteley, A. Wilke, J. R. Wortman, T. Yatsunenko, and F. O. Glockner. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 2011. [doi] [url] BibTeX @article{yilmaz_minimum_2011, title = {Minimum information about a marker gene sequence ({MIMARKS}) and minimum information about any (x) sequence ({MIxS}) specifications}, volume = {29}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21552244}, doi = {10.1038/nbt.1823}, journal = {Nat Biotechnol}, author = {Yilmaz, P. and Kottmann, R. and Field, D. and Knight, R. and Cole, J. R. and Amaral-Zettler, L. and Gilbert, J. A. and Karsch-Mizrachi, I. and Johnston, A. and Cochrane, G. and Vaughan, R. and Hunter, C. and Park, J. and Morrison, N. and Rocca-Serra, P. and Sterk, P. and Arumugam, M. and Bailey, M. and Baumgartner, L. and Birren, B. W. and Blaser, M. J. and Bonazzi, V. and Booth, T. and Bork, P. and Bushman, F. D. and Buttigieg, P. L. and Chain, P. S. and Charlson, E. and Costello, E. K. and Huot-Creasy, H. and Dawyndt, P. and DeSantis, T. and Fierer, N. and Fuhrman, J. A. and Gallery, R. E. and Gevers, D. and Gibbs, R. A. and San Gil, I. and Gonzalez, A. and Gordon, J. I. and Guralnick, R. and Hankeln, W. and Highlander, S. and Hugenholtz, P. and Jansson, J. and Kau, A. L. and Kelley, S. T. and Kennedy, J. and Knights, D. and Koren, O. and Kuczynski, J. and Kyrpides, N. and Larsen, R. and Lauber, C. L. and Legg, T. and Ley, R. E. and Lozupone, C. A. and Ludwig, W. and Lyons, D. and Maguire, E. and Methe, B. A. and Meyer, Folker and Muegge, B. and Nakielny, S. and Nelson, K. E. and Nemergut, D. and Neufeld, J. D. and Newbold, L. K. and Oliver, A. E. and Pace, N. R. and Palanisamy, G. and Peplies, J. and Petrosino, J. and Proctor, L. and Pruesse, E. and Quast, C. and Raes, J. and Ratnasingham, S. and Ravel, J. and Relman, D. A. and Assunta-Sansone, S. and Schloss, P. D. and Schriml, L. and Sinha, R. and Smith, M. I. and Sodergren, E. and Spo, A. and Stombaugh, J. and Tiedje, J. M. and Ward, D. V. and Weinstock, G. M. and Wendel, D. and White, O. and Whiteley, A. and Wilke, A. and Wortman, J. R. and Yatsunenko, T. and Glockner, F. O.}, year = {2011}, note = {Type: Journal Article} } A. Wilke, J. Wilkening, E. M. Glass, N. Desai, and Folker Meyer. An experience report: porting the MG‐RAST rapid metagenomics analysis pipeline to the cloud.. Concurrency and Computation: Practice and Experience. 2011. BibTeX @article{wilke_experience_2011, title = {An experience report: porting the {MG}‐{RAST} rapid metagenomics analysis pipeline to the cloud.}, volume = {23}, journal = {Concurrency and Computation: Practice and Experience}, author = {Wilke, A. and Wilkening, J. and Glass, E. M. and Desai, N. and Meyer, Folker}, year = {2011}, note = {Type: Journal Article} } A. Wilke, J. Wilkening, E.M. Glass, N. Desai, and Folker Meyer. An experience report: porting the MG-RAST rapid metagenomics analysis pipeline to the cloud. Concurrency and Computation: Practice and Experience. 2011. BibTeX @article{wilke_experience_2011-1, title = {An experience report: porting the {MG}-{RAST} rapid metagenomics analysis pipeline to the cloud}, volume = {23}, journal = {Concurrency and Computation: Practice and Experience}, author = {Wilke, A. and Wilkening, J. and Glass, E.M. and Desai, N. and Meyer, Folker}, year = {2011}, note = {Type: Journal Article} } Suparna Mitra, Paul Rupek, Daniel C Richter, Tim Urich, Jack A Gilbert, Folker Meyer, Andreas Wilke, and Daniel H Huson. Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC bioinformatics. 2011. BibTeX @article{mitra_functional_2011, title = {Functional analysis of metagenomes and metatranscriptomes using {SEED} and {KEGG}}, volume = {12}, journal = {BMC bioinformatics}, author = {Mitra, Suparna and Rupek, Paul and Richter, Daniel C and Urich, Tim and Gilbert, Jack A and Meyer, Folker and Wilke, Andreas and Huson, Daniel H}, year = {2011}, note = {Publisher: BioMed Central} } Steffen Lemke, Dionysios A Antonopoulos, Folker Meyer, Marc H Domanus, and Urs Schmidt-Ott. BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae). Bmc Genomics. 2011. BibTeX @article{lemke_bmp_2011, title = {{BMP} signaling components in embryonic transcriptomes of the hover fly {Episyrphus} balteatus ({Syrphidae})}, volume = {12}, journal = {Bmc Genomics}, author = {Lemke, Steffen and Antonopoulos, Dionysios A and Meyer, Folker and Domanus, Marc H and Schmidt-Ott, Urs}, year = {2011}, note = {Publisher: BioMed Central} } Christopher S Henry, Ross Overbeek, Fangfang Xia, Aaron A Best, Elizabeth Glass, Jack Gilbert, Peter Larsen, Rob Edwards, Terry Disz, Folker Meyer, and Rick Stevens. Connecting genotype to phenotype in the era of high-throughput sequencing. Biochimica et Biophysica Acta (BBA)-General Subjects. 2011. BibTeX @article{henry_connecting_2011, title = {Connecting genotype to phenotype in the era of high-throughput sequencing}, volume = {1810}, journal = {Biochimica et Biophysica Acta (BBA)-General Subjects}, author = {Henry, Christopher S and Overbeek, Ross and Xia, Fangfang and Best, Aaron A and Glass, Elizabeth and Gilbert, Jack and Larsen, Peter and Edwards, Rob and Disz, Terry and Meyer, Folker and Stevens, Rick}, year = {2011}, note = {Publisher: Elsevier} } Andreas Wilke, Jared Wilkening, Elizabeth M Glass, Narayan L Desai, and Folker Meyer. Porting the MG-RAST metagenomic data analysis pipeline to the cloud. Concurrency and Computation: Practice & Experience. 2011. BibTeX @article{wilke_porting_2011, title = {Porting the {MG}-{RAST} metagenomic data analysis pipeline to the cloud}, volume = {23}, journal = {Concurrency and Computation: Practice \& Experience}, author = {Wilke, Andreas and Wilkening, Jared and Glass, Elizabeth M and Desai, Narayan L and Meyer, Folker}, year = {2011}, note = {Publisher: John Wiley and Sons Ltd.} } Peter E Larsen, Frank R Collart, Dawn Field, Folker Meyer, Kevin P Keegan, Christopher S Henry, John McGrath, John Quinn, and Jack A Gilbert. Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. Microbial informatics and experimentation. 2011. BibTeX @article{larsen_predicted_2011, title = {Predicted {Relative} {Metabolomic} {Turnover} ({PRMT}): determining metabolic turnover from a coastal marine metagenomic dataset}, volume = {1}, journal = {Microbial informatics and experimentation}, author = {Larsen, Peter E and Collart, Frank R and Field, Dawn and Meyer, Folker and Keegan, Kevin P and Henry, Christopher S and McGrath, John and Quinn, John and Gilbert, Jack A}, year = {2011}, note = {Publisher: BioMed Central} } D. A. Antonopoulos, E. M. Glass, and Folker Meyer. Analyzing Metagenomic data: inferring microbial community function with MG-RAST. Metagenomics and its applications in agriculture, biomedicine, and environmental studies publisher. 2011. Nova Science Publishers. BibTeX @incollection{antonopoulos_analyzing_2011, title = {Analyzing {Metagenomic} data: inferring microbial community function with {MG}-{RAST}}, booktitle = {Metagenomics and its applications in agriculture, biomedicine, and environmental studies publisher}, publisher = {Nova Science Publishers}, author = {Antonopoulos, D. A. and Glass, E. M. and Meyer, Folker}, year = {2011} } Folker Meyer and Nikos Kyrpides. Proposal for Open Discussion-Informatics Challenges for Next Generation Sequencing Metagenomics Experiments.. BIOINFORMATICS. 2011. BibTeX @inproceedings{meyer_proposal_2011, title = {Proposal for {Open} {Discussion}-{Informatics} {Challenges} for {Next} {Generation} {Sequencing} {Metagenomics} {Experiments}.}, booktitle = {{BIOINFORMATICS}}, author = {Meyer, Folker and Kyrpides, Nikos}, year = {2011} } Peter E Larsen, Frank Collart, Folker Meyer, and Jack A Gilbert. PREDICTED RELATIVE METABOLOMIC TURNOVER-Predicting Changes in the Environmental Metabolome from the Metagenome. International Joint Conference on Biomedical Engineering Systems and Technologies. 2011. SCITEPRESS. BibTeX @inproceedings{larsen_predicted_2011-1, title = {{PREDICTED} {RELATIVE} {METABOLOMIC} {TURNOVER}-{Predicting} {Changes} in the {Environmental} {Metabolome} from the {Metagenome}}, volume = {2}, booktitle = {International {Joint} {Conference} on {Biomedical} {Engineering} {Systems} and {Technologies}}, publisher = {SCITEPRESS}, author = {Larsen, Peter E and Collart, Frank and Meyer, Folker and Gilbert, Jack A}, year = {2011} } Peter E Larsen, Frank Collart, Folker Meyer, and Jack A Gilbert. PREDICTED RELATIVE METABOLOMIC TURNOVER. 2011. BibTeX @article{larsen_predicted_2011-2, title = {{PREDICTED} {RELATIVE} {METABOLOMIC} {TURNOVER}}, author = {Larsen, Peter E and Collart, Frank and Meyer, Folker and Gilbert, Jack A}, year = {2011} } Folker Meyer and Nikos Kyrpides. PROPOSAL FOR OPEN DISCUSSION. 2011. BibTeX @article{meyer_proposal_2011-1, title = {{PROPOSAL} {FOR} {OPEN} {DISCUSSION}}, author = {Meyer, Folker and Kyrpides, Nikos}, year = {2011} } Peter E Larsen, Frank R Collart, Dawn Field, Folker Meyer, Kevin P Keegan, Christopher S Henry, John McGrath, John Quinn, and Jack A Gilbert. Relative metabolomic flux: Predicting changes in the environmental metabolome from the metagenome. Microbial Informatics and Experimentation. 2011. BibTeX @article{larsen_relative_2011, title = {Relative metabolomic flux: {Predicting} changes in the environmental metabolome from the metagenome}, volume = {1}, journal = {Microbial Informatics and Experimentation}, author = {Larsen, Peter E and Collart, Frank R and Field, Dawn and Meyer, Folker and Keegan, Kevin P and Henry, Christopher S and McGrath, John and Quinn, John and Gilbert, Jack A}, year = {2011}, note = {Publisher: BioMed Central Ltd.} } A. Birmingham, J. C. Clemente, N. Desai, J. Gilbert, A. Gonzalez, N. Kyrpides, Folker Meyer, E. Nawrocki, P. Sterk, J. Stombaugh, Z. Weinberg, D. Wendel, N. B. Leontis, C. Zirbel, R. Knight, and A. Laederach. Meeting report of the RNA Ontology Consortium January 8-9, 2011. Stand Genomic Sci. 2011. [doi] [url] BibTeX @article{birmingham_meeting_2011-1, title = {Meeting report of the {RNA} {Ontology} {Consortium} {January} 8-9, 2011}, volume = {4}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21677862}, doi = {10.4056/sigs.1724282}, journal = {Stand Genomic Sci}, author = {Birmingham, A. and Clemente, J. C. and Desai, N. and Gilbert, J. and Gonzalez, A. and Kyrpides, N. and Meyer, Folker and Nawrocki, E. and Sterk, P. and Stombaugh, J. and Weinberg, Z. and Wendel, D. and Leontis, N. B. and Zirbel, C. and Knight, R. and Laederach, A.}, year = {2011}, note = {Type: Journal Article} } C. R. Lindsay, S. Lawn, A. D. Campbell, W. J. Faller, F. Rambow, R. L. Mort, P. Timpson, A. Li, P. Cammareri, R. A. Ridgway, J. P. Morton, B. Doyle, S. Hegarty, M. Rafferty, I. G. Murphy, E. W. McDermott, K. Sheahan, K. Pedone, A. J. Finn, P. A. Groben, N. E. Thomas, H. Hao, C. Carson, J. C. Norman, L. M. Machesky, W. M. Gallagher, I. J. Jackson, L. Van Kempen, F. Beermann, C. Der, L. Larue, H. C. Welch, B. W. Ozanne, and O. J. Sansom. P-Rex1 is required for efficient melanoblast migration and melanoma metastasis. Nat Commun. 2011. [doi] [url] BibTeX @article{RN22, author = {Lindsay, C. R. and Lawn, S. and Campbell, A. D. and Faller, W. J. and Rambow, F. and Mort, R. L. and Timpson, P. and Li, A. and Cammareri, P. and Ridgway, R. A. and Morton, J. P. and Doyle, B. and Hegarty, S. and Rafferty, M. and Murphy, I. G. and McDermott, E. W. and Sheahan, K. and Pedone, K. and Finn, A. J. and Groben, P. A. and Thomas, N. E. and Hao, H. and Carson, C. and Norman, J. C. and Machesky, L. M. and Gallagher, W. M. and Jackson, I. J. and Van Kempen, L. and Beermann, F. and Der, C. and Larue, L. and Welch, H. C. and Ozanne, B. W. and Sansom, O. J.}, title = {P-Rex1 is required for efficient melanoblast migration and melanoma metastasis}, journal = {Nat Commun}, volume = {2}, pages = {555}, issn = {2041-1723 (Electronic) 2041-1723 (Linking)}, doi = {10.1038/ncomms1560}, url = {https://www.ncbi.nlm.nih.gov/pubmed/22109529}, year = {2011}, type = {Journal Article} } S. J. Gallagher, F. Luciani, I. Berlin, F. Rambow, G. Gros, D. Champeval, V. Delmas, and L. Larue. General strategy to analyse melanoma in mice. Pigment Cell Melanoma Res. 2011. [doi] [url] BibTeX @article{RN13, author = {Gallagher, S. J. and Luciani, F. and Berlin, I. and Rambow, F. and Gros, G. and Champeval, D. and Delmas, V. and Larue, L.}, title = {General strategy to analyse melanoma in mice}, journal = {Pigment Cell Melanoma Res}, volume = {24}, number = {5}, pages = {987-8}, issn = {1755-148X (Electronic) 1755-1471 (Linking)}, doi = {10.1111/j.1755-148X.2011.00907.x}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21955491}, year = {2011}, type = {Journal Article} } S. Cortellino, J. Xu, M. Sannai, R. Moore, E. Caretti, A. Cigliano, M. Le Coz, K. Devarajan, A. Wessels, D. Soprano, L. K. Abramowitz, M. S. Bartolomei, F. Rambow, M. R. Bassi, T. Bruno, M. Fanciulli, C. Renner, A. J. Klein-Szanto, Y. Matsumoto, D. Kobi, I. Davidson, C. Alberti, L. Larue, and A. Bellacosa. Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell. 2011. [doi] [url] BibTeX @article{RN9, author = {Cortellino, S. and Xu, J. and Sannai, M. and Moore, R. and Caretti, E. and Cigliano, A. and Le Coz, M. and Devarajan, K. and Wessels, A. and Soprano, D. and Abramowitz, L. K. and Bartolomei, M. S. and Rambow, F. and Bassi, M. R. and Bruno, T. and Fanciulli, M. and Renner, C. and Klein-Szanto, A. J. and Matsumoto, Y. and Kobi, D. and Davidson, I. and Alberti, C. and Larue, L. and Bellacosa, A.}, title = {Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair}, journal = {Cell}, volume = {146}, number = {1}, pages = {67-79}, issn = {1097-4172 (Electronic) 0092-8674 (Linking)}, doi = {10.1016/j.cell.2011.06.020}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21722948}, year = {2011}, type = {Journal Article} } 2010 N. Kyrpides, D. Field, P. Sterk, R. Kottmann, F. O. Glockner, L. Hirschman, G. M. Garrity, G. Cochrane, and J. Wooley. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 8. Stand Genomic Sci. 2010. [doi] [url] BibTeX @article{kyrpides_meeting_2010, title = {Meeting {Report} from the {Genomic} {Standards} {Consortium} ({GSC}) {Workshop} 8}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304696}, doi = {10.4056/sigs.1022942}, journal = {Stand Genomic Sci}, author = {Kyrpides, N. and Field, D. and Sterk, P. and Kottmann, R. and Glockner, F. O. and Hirschman, L. and Garrity, G. M. and Cochrane, G. and Wooley, J.}, year = {2010}, note = {Type: Journal Article} } E. Glass, Folker Meyer, J. A. Gilbert, D. Field, S. Hunter, R. Kottmann, N. Kyrpides, S. Sansone, L. Schriml, P. Sterk, O. White, and J. Wooley. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10. Stand Genomic Sci. 2010. [doi] [url] BibTeX @article{glass_meeting_2010, title = {Meeting {Report} from the {Genomic} {Standards} {Consortium} ({GSC}) {Workshop} 10}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304723}, doi = {10.4056/sigs.1423520}, journal = {Stand Genomic Sci}, author = {Glass, E. and Meyer, Folker and Gilbert, J. A. and Field, D. and Hunter, S. and Kottmann, R. and Kyrpides, N. and Sansone, S. and Schriml, L. and Sterk, P. and White, O. and Wooley, J.}, year = {2010}, note = {Type: Journal Article} } J. A. Gilbert, Folker Meyer, R. Knight, D. Field, N. Kyrpides, P. Yilmaz, and J. Wooley. Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010. Stand Genomic Sci. 2010. [doi] BibTeX @article{gilbert_meeting_2010, title = {Meeting report: {GSC} {M5} roundtable at the 13th {International} {Society} for {Microbial} {Ecology} meeting in {Seattle}, {WA}, {USA} {August} 22-27, 2010}, volume = {3}, doi = {10.4056/sigs.1333437}, journal = {Stand Genomic Sci}, author = {Gilbert, J. A. and Meyer, Folker and Knight, R. and Field, D. and Kyrpides, N. and Yilmaz, P. and Wooley, J.}, year = {2010}, note = {Type: Journal Article} } Vincent B Young, Eugene B Chang, Folker Meyer, Mitchell L Sogin, Thomas M Schmidt, and James Tiedje. The Role of the Gut Microbiota in Ulcerative Colitis. 2010. BibTeX @article{young_role_2010, title = {The {Role} of the {Gut} {Microbiota} in {Ulcerative} {Colitis}}, author = {Young, Vincent B and Chang, Eugene B and Meyer, Folker and Sogin, Mitchell L and Schmidt, Thomas M and Tiedje, James}, year = {2010}, note = {Publisher: Nature Publishing Group} } Elizabeth M Glass, Jared Wilkening, Andreas Wilke, Dionysios Antonopoulos, and Folker Meyer. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harbor Protocols. 2010. BibTeX @article{glass_using_2010, title = {Using the metagenomics {RAST} server ({MG}-{RAST}) for analyzing shotgun metagenomes}, volume = {2010}, journal = {Cold Spring Harbor Protocols}, author = {Glass, Elizabeth M and Wilkening, Jared and Wilke, Andreas and Antonopoulos, Dionysios and Meyer, Folker}, year = {2010}, note = {Publisher: Cold Spring Harbor Laboratory Press} } Steffen Lemke, Stephanie E Busch, Dionysios A Antonopoulos, Folker Meyer, Marc H Domanus, and Urs Schmidt-Ott. Maternal activation of gap genes in the hover fly Episyrphus. Development. 2010. BibTeX @article{lemke_maternal_2010, title = {Maternal activation of gap genes in the hover fly {Episyrphus}}, volume = {137}, journal = {Development}, author = {Lemke, Steffen and Busch, Stephanie E and Antonopoulos, Dionysios A and Meyer, Folker and Domanus, Marc H and Schmidt-Ott, Urs}, year = {2010}, note = {Publisher: Company of Biologists} } Yunwei Wang, Dionysios A Antonopoulos, Xiaorong Zhu, Laura Harrell, Ira Hanan, John C Alverdy, Folker Meyer, Mark W Musch, Vincent B Young, and Eugene B Chang. Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Applied microbiology and biotechnology. 2010. BibTeX @article{wang_laser_2010-1, title = {Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon}, volume = {88}, journal = {Applied microbiology and biotechnology}, author = {Wang, Yunwei and Antonopoulos, Dionysios A and Zhu, Xiaorong and Harrell, Laura and Hanan, Ira and Alverdy, John C and Meyer, Folker and Musch, Mark W and Young, Vincent B and Chang, Eugene B}, year = {2010}, note = {Publisher: Springer-Verlag} } Catherine A Pfister, Folker Meyer, and Dionysios A Antonopoulos. Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling. PLoS One. 2010. BibTeX @article{pfister_metagenomic_2010, title = {Metagenomic profiling of a microbial assemblage associated with the {California} mussel: a node in networks of carbon and nitrogen cycling}, volume = {5}, journal = {PLoS One}, author = {Pfister, Catherine A and Meyer, Folker and Antonopoulos, Dionysios A}, year = {2010}, note = {Publisher: Public Library of Science} } Jack A Gilbert, Folker Meyer, and Mark J Bailey. The Future of microbial metagenomics (or is ignorance bliss?). The ISME Journal. 2010. BibTeX @article{gilbert_future_2010, title = {The {Future} of microbial metagenomics (or is ignorance bliss?)}, volume = {5}, journal = {The ISME Journal}, author = {Gilbert, Jack A and Meyer, Folker and Bailey, Mark J}, year = {2010}, note = {Publisher: Nature Publishing Group} } Jack A Gilbert, Folker Meyer, Rob Knight, Dawn Field, Nikos Kyrpides, Pelin Yilmaz, and John Wooley. Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22–27, 2010. Standards in genomic sciences. 2010. BibTeX @article{gilbert_meeting_2010-2, title = {Meeting report: {GSC} {M5} roundtable at the 13th {International} {Society} for {Microbial} {Ecology} meeting in {Seattle}, {WA}, {USA} {August} 22–27, 2010}, volume = {3}, journal = {Standards in genomic sciences}, author = {Gilbert, Jack A and Meyer, Folker and Knight, Rob and Field, Dawn and Kyrpides, Nikos and Yilmaz, Pelin and Wooley, John}, year = {2010}, note = {Publisher: BioMed Central} } Sarah L O’Brien, Elizabeth M Glass, Jennifer M Brulc, Jack A Gilbert, Dionysios A Antonopoulos, and Folker Meyer. Meeting Report: The 2nd Annual Argonne Soils Workshop, Argonne National Laboratory, Chicago USA, October 6-8, 2010. 2010. BibTeX @article{obrien_meeting_2010, title = {Meeting {Report}: {The} 2nd {Annual} {Argonne} {Soils} {Workshop}, {Argonne} {National} {Laboratory}, {Chicago} {USA}, {October} 6-8, 2010}, author = {O’Brien, Sarah L and Glass, Elizabeth M and Brulc, Jennifer M and Gilbert, Jack A and Antonopoulos, Dionysios A and Meyer, Folker}, year = {2010} } Jack A Gilbert, Folker Meyer, Lynn Schriml, Ian R Joint, Martin Mühling, and Dawn Field. Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel. Standards in genomic sciences. 2010. BibTeX @article{gilbert_metagenomes_2010, title = {Metagenomes and metatranscriptomes from the {L4} long-term coastal monitoring station in the {Western} {English} {Channel}}, volume = {3}, journal = {Standards in genomic sciences}, author = {Gilbert, Jack A and Meyer, Folker and Schriml, Lynn and Joint, Ian R and Mühling, Martin and Field, Dawn}, year = {2010}, note = {Publisher: BioMed Central} } Jack A Gilbert, Folker Meyer, Dawn Field, Lynn M Schriml, and George M Garrity. Metagenomics: A foundling finds its feet. Standards in genomic sciences. 2010. BibTeX @article{gilbert_metagenomics_2010, title = {Metagenomics: {A} foundling finds its feet}, volume = {3}, journal = {Standards in genomic sciences}, author = {Gilbert, Jack A and Meyer, Folker and Field, Dawn and Schriml, Lynn M and Garrity, George M}, year = {2010}, note = {Publisher: BioMed Central} } Folker Meyer. Casting a Wider Net: Distributed Resources for Metagenomics (2010 JGI/ANL HPC Workshop). DOE Joint Genome Institute (JGI), LBNL (Lawrence Berkeley National …. 2010. BibTeX @techreport{meyer_casting_2010, title = {Casting a {Wider} {Net}: {Distributed} {Resources} for {Metagenomics} (2010 {JGI}/{ANL} {HPC} {Workshop})}, institution = {DOE Joint Genome Institute (JGI), LBNL (Lawrence Berkeley National …}, author = {Meyer, Folker}, year = {2010} } Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James Cole, Linda Amaral-Zettler, Jack Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane, and Folker Meyer. The “minimum information about an environmental sequence”(MIENS) specification. Nature Precedings. 2010. [url] BibTeX @article{yilmaz_minimum_2010-1, title = {The “minimum information about an environmental sequence”({MIENS}) specification}, url = {https://www.nature.com/articles/npre.2010.5252.1.pdf?proof=t}, journal = {Nature Precedings}, author = {Yilmaz, Pelin and Kottmann, Renzo and Field, Dawn and Knight, Rob and Cole, James and Amaral-Zettler, Linda and Gilbert, Jack and Karsch-Mizrachi, Ilene and Johnston, Anjanette and Cochrane, Guy and Meyer, Folker}, year = {2010} } J. A. Gilbert, Folker Meyer, J. Jansson, J. Gordon, N. Pace, J. Tiedje, R. Ley, N. Fierer, D. Field, N. Kyrpides, F. O. Glockner, H. P. Klenk, K. E. Wommack, E. Glass, K. Docherty, R. Gallery, R. Stevens, and R. Knight. The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. Stand Genomic Sci. 2010. [doi] [url] BibTeX @article{gilbert_earth_2010-1, title = {The {Earth} {Microbiome} {Project}: {Meeting} report of the "1 {EMP} meeting on sample selection and acquisition" at {Argonne} {National} {Laboratory} {October} 6 2010}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304728}, doi = {10.4056/aigs.1443528}, journal = {Stand Genomic Sci}, author = {Gilbert, J. A. and Meyer, Folker and Jansson, J. and Gordon, J. and Pace, N. and Tiedje, J. and Ley, R. and Fierer, N. and Field, D. and Kyrpides, N. and Glockner, F. O. and Klenk, H. P. and Wommack, K. E. and Glass, E. and Docherty, K. and Gallery, R. and Stevens, R. and Knight, R.}, year = {2010}, note = {Type: Journal Article} } J. A. Gilbert, Folker Meyer, D. Antonopoulos, P. Balaji, C. T. Brown, C. T. Brown, N. Desai, J. A. Eisen, D. Evers, D. Field, W. Feng, D. Huson, J. Jansson, R. Knight, J. Knight, E. Kolker, K. Konstantindis, J. Kostka, N. Kyrpides, R. Mackelprang, A. McHardy, C. Quince, J. Raes, A. Sczyrba, A. Shade, and R. Stevens. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci. 2010. [doi] [url] BibTeX @article{gilbert_meeting_2010-3, title = {Meeting report: the terabase metagenomics workshop and the vision of an {Earth} microbiome project}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304727}, doi = {10.4056/sigs.1433550}, journal = {Stand Genomic Sci}, author = {Gilbert, J. A. and Meyer, Folker and Antonopoulos, D. and Balaji, P. and Brown, C. T. and Brown, C. T. and Desai, N. and Eisen, J. A. and Evers, D. and Field, D. and Feng, W. and Huson, D. and Jansson, J. and Knight, R. and Knight, J. and Kolker, E. and Konstantindis, K. and Kostka, J. and Kyrpides, N. and Mackelprang, R. and McHardy, A. and Quince, C. and Raes, J. and Sczyrba, A. and Shade, A. and Stevens, R.}, year = {2010}, note = {Type: Journal Article} } D. Field, S. Sansone, E. F. Delong, P. Sterk, I. Friedberg, P. Gaudet, S. Lewis, R. Kottmann, L. Hirschman, G. Garrity, G. Cochrane, J. Wooley, Folker Meyer, S. Hunter, O. White, B. Bramlett, S. Gregurick, H. Lapp, S. Orchard, P. Rocca-Serra, A. Ruttenberg, N. Shah, C. Taylor, and A. Thessen. Meeting Report: BioSharing at ISMB 2010. Stand Genomic Sci. 2010. [doi] [url] BibTeX @article{field_meeting_2010-2, title = {Meeting {Report}: {BioSharing} at {ISMB} 2010}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304729}, doi = {10.4056/sigs/1403501}, journal = {Stand Genomic Sci}, author = {Field, D. and Sansone, S. and Delong, E. F. and Sterk, P. and Friedberg, I. and Gaudet, P. and Lewis, S. and Kottmann, R. and Hirschman, L. and Garrity, G. and Cochrane, G. and Wooley, J. and Meyer, Folker and Hunter, S. and White, O. and Bramlett, B. and Gregurick, S. and Lapp, H. and Orchard, S. and Rocca-Serra, P. and Ruttenberg, A. and Shah, N. and Taylor, C. and Thessen, A.}, year = {2010}, note = {Type: Journal Article} } G. J. Hather, W. Haynes, R. Higdon, N. Kolker, E. A. Stewart, P. Arzberger, P. Chain, D. Field, B. R. Franza, B. Lin, Folker Meyer, V. Ozdemir, C. V. Smith, G. van Belle, J. Wooley, and E. Kolker. The United States of America and scientific research. PLoS One. 2010. [doi] [url] BibTeX @article{hather_united_2010-1, title = {The {United} {States} of {America} and scientific research}, volume = {5}, url = {https://www.ncbi.nlm.nih.gov/pubmed/20808949}, doi = {10.1371/journal.pone.0012203}, journal = {PLoS One}, author = {Hather, G. J. and Haynes, W. and Higdon, R. and Kolker, N. and Stewart, E. A. and Arzberger, P. and Chain, P. and Field, D. and Franza, B. R. and Lin, B. and Meyer, Folker and Ozdemir, V. and Smith, C. V. and van Belle, G. and Wooley, J. and Kolker, E.}, year = {2010}, note = {Type: Journal Article} } D. Field, S. Sansone, E. F. Delong, P. Sterk, I. Friedberg, R. Kottmann, L. Hirschman, G. Garrity, G. Cochrane, J. Wooley, Folker Meyer, S. Hunter, and O. White. Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010. Stand Genomic Sci. 2010. [doi] [url] BibTeX @article{field_meeting_2010-3, title = {Meeting {Report}: {Metagenomics}, {Metadata} and {MetaAnalysis} ({M3}) at {ISMB} 2010}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304724}, doi = {10.4056/sigs.1383476}, journal = {Stand Genomic Sci}, author = {Field, D. and Sansone, S. and Delong, E. F. and Sterk, P. and Friedberg, I. and Kottmann, R. and Hirschman, L. and Garrity, G. and Cochrane, G. and Wooley, J. and Meyer, Folker and Hunter, S. and White, O.}, year = {2010}, note = {Type: Journal Article} } L. Hirschman, P. Sterk, D. Field, J. Wooley, G. Cochrane, J. Gilbert, E. Kolker, N. Kyrpides, Folker Meyer, I. Mizrachi, Y. Nakamura, S. A. Sansone, L. Schriml, T. Tatusova, O. White, and P. Yilmaz. Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010. Stand Genomic Sci. 2010. [doi] [url] BibTeX @article{hirschman_meeting_2010-1, title = {Meeting {Report}: "{Metagenomics}, {Metadata} and {Meta}-analysis" ({M3}) {Workshop} at the {Pacific} {Symposium} on {Biocomputing} 2010}, volume = {2}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304719}, doi = {10.4056/sigs.802738}, journal = {Stand Genomic Sci}, author = {Hirschman, L. and Sterk, P. and Field, D. and Wooley, J. and Cochrane, G. and Gilbert, J. and Kolker, E. and Kyrpides, N. and Meyer, Folker and Mizrachi, I. and Nakamura, Y. and Sansone, S. A. and Schriml, L. and Tatusova, T. and White, O. and Yilmaz, P.}, year = {2010}, note = {Type: Journal Article} } T. Davidsen, R. Madupu, P. Sterk, D. Field, G. Garrity, J. Gilbert, F. O. Glockner, L. Hirschman, E. Kolker, R. Kottmann, N. Kyrpides, Folker Meyer, N. Morrison, L. Schriml, T. Tatusova, and J. Wooley. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9. Stand Genomic Sci. 2010. [doi] [url] BibTeX @article{davidsen_meeting_2010-3, title = {Meeting {Report} from the {Genomic} {Standards} {Consortium} ({GSC}) {Workshop} 9}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304722}, doi = {10.4056/sigs.1353455}, journal = {Stand Genomic Sci}, author = {Davidsen, T. and Madupu, R. and Sterk, P. and Field, D. and Garrity, G. and Gilbert, J. and Glockner, F. O. and Hirschman, L. and Kolker, E. and Kottmann, R. and Kyrpides, N. and Meyer, Folker and Morrison, N. and Schriml, L. and Tatusova, T. and Wooley, J.}, year = {2010}, note = {Type: Journal Article} } F. Rambow and L. Larue. The quest for the melanoma stem cell: still more questions than answers. Pigment Cell Melanoma Res. 2010. [doi] [url] BibTeX @article{RN32, author = {Rambow, F. and Larue, L.}, title = {The quest for the melanoma stem cell: still more questions than answers}, journal = {Pigment Cell Melanoma Res}, volume = {23}, number = {3}, pages = {307-9}, issn = {1755-148X (Electronic) 1755-1471 (Linking)}, doi = {10.1111/j.1755-148X.2010.00713.x}, url = {https://www.ncbi.nlm.nih.gov/pubmed/20444202}, year = {2010}, type = {Journal Article} } 2009 Folker Meyer, R. Overbeek, and A. Rodriguez. FIGfams: yet another set of protein families. Nucleic Acids Res. 2009. [doi] BibTeX @article{meyer_figfams_2009, title = {{FIGfams}: yet another set of protein families}, volume = {37}, doi = {10.1093/nar/gkp698}, journal = {Nucleic Acids Res}, author = {Meyer, Folker and Overbeek, R. and Rodriguez, A.}, year = {2009}, note = {Type: Journal Article} } T. Bekel, K. Henckel, H. Kuster, Folker Meyer, V. M. Runte, H. Neuweger, D. Paarmann, O. Rupp, M. Zakrzewski, A. Puehler, J. Stoye, and A. Goesmann. The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. Journal of Biotechnology. 2009. [doi] BibTeX @article{bekel_sequence_2009, title = {The {Sequence} {Analysis} and {Management} {System} - {SAMS}-2.0: {Data} management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies}, volume = {140}, doi = {10.1016/j.jbiotec.2009.01.006}, journal = {Journal of Biotechnology}, author = {Bekel, T. and Henckel, K. and Kuster, H. and Meyer, Folker and Runte, V. M. and Neuweger, H. and Paarmann, D. and Rupp, O. and Zakrzewski, M. and Puehler, A. and Stoye, J. and Goesmann, A.}, year = {2009}, note = {Type: Journal Article} } Jared Wilkening, Andreas Wilke, Narayan Desai, and Folker Meyer. Using clouds for metagenomics: a case study. 2009 IEEE International Conference on Cluster Computing and Workshops. 2009. IEEE. BibTeX @inproceedings{wilkening_using_2009, title = {Using clouds for metagenomics: a case study}, booktitle = {2009 {IEEE} {International} {Conference} on {Cluster} {Computing} and {Workshops}}, publisher = {IEEE}, author = {Wilkening, Jared and Wilke, Andreas and Desai, Narayan and Meyer, Folker}, year = {2009} } Yunwei Wang, Dionysios Antonopoulos, Xiaorong Zhu, Lev Lichtenstein, Kenneth Drabik, John C Alverdy, Folker Meyer, Vincent Young, and Eugene B Chang. W1622 Metagenomic Analysis of Intact Mucosa-Associated Microbial Communities of the Human Colon. Gastroenterology. 2009. BibTeX @article{wang_w1622_2009, title = {W1622 {Metagenomic} {Analysis} of {Intact} {Mucosa}-{Associated} {Microbial} {Communities} of the {Human} {Colon}}, volume = {5}, journal = {Gastroenterology}, author = {Wang, Yunwei and Antonopoulos, Dionysios and Zhu, Xiaorong and Lichtenstein, Lev and Drabik, Kenneth and Alverdy, John C and Meyer, Folker and Young, Vincent and Chang, Eugene B}, year = {2009} } Frank Oliver Glockner, Victor Markowitz, Nikos Kyrpides, Folker Meyer, Linda Amaral-Zettler, and James Cole. Flash Updates of GSC projects (GSC8 Meeting). DOE Joint Genome Institute (JGI), LBNL (Lawrence Berkeley National …. 2009. BibTeX @techreport{glockner_flash_2009, title = {Flash {Updates} of {GSC} projects ({GSC8} {Meeting})}, institution = {DOE Joint Genome Institute (JGI), LBNL (Lawrence Berkeley National …}, author = {Glockner, Frank Oliver and Markowitz, Victor and Kyrpides, Nikos and Meyer, Folker and Amaral-Zettler, Linda and Cole, James}, year = {2009} } Dawn Field, Iddo Friedberg, Peter Sterk, Renzo Kottmann, Frank Oliver Glöckner, Lynette Hirschman, George M Garrity, Guy Cochrane, John Wooley, and Jack Gilbert. Meeting Report:“Metagenomics, Metadata and Meta-analysis”(M3) Special Interest Group at ISMB 2009. Standards in genomic sciences. 2009. BibTeX @article{field_meeting_2009-5, title = {Meeting {Report}:“{Metagenomics}, {Metadata} and {Meta}-analysis”({M3}) {Special} {Interest} {Group} at {ISMB} 2009}, volume = {1}, journal = {Standards in genomic sciences}, author = {Field, Dawn and Friedberg, Iddo and Sterk, Peter and Kottmann, Renzo and Glöckner, Frank Oliver and Hirschman, Lynette and Garrity, George M and Cochrane, Guy and Wooley, John and Gilbert, Jack}, year = {2009}, note = {Publisher: BioMed Central} } F. E. Angly, D. Willner, A. Prieto-Davo, R. A. Edwards, R. Schmieder, R. Vega-Thurber, D. A. Antonopoulos, K. Barott, M. T. Cottrell, C. Desnues, E. A. Dinsdale, M. Furlan, M. Haynes, M. R. Henn, Y. Hu, D. L. Kirchman, T. McDole, J. D. McPherson, Folker Meyer, R. M. Miller, E. Mundt, R. K. Naviaux, B. Rodriguez-Mueller, R. Stevens, L. Wegley, L. Zhang, B. Zhu, and F. Rohwer. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol. 2009. [doi] [url] BibTeX @article{angly_gaas_2009-2, title = {The {GAAS} metagenomic tool and its estimations of viral and microbial average genome size in four major biomes}, volume = {5}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20011103}, doi = {10.1371/journal.pcbi.1000593}, journal = {PLoS Comput Biol}, author = {Angly, F. E. and Willner, D. and Prieto-Davo, A. and Edwards, R. A. and Schmieder, R. and Vega-Thurber, R. and Antonopoulos, D. A. and Barott, K. and Cottrell, M. T. and Desnues, C. and Dinsdale, E. A. and Furlan, M. and Haynes, M. and Henn, M. R. and Hu, Y. and Kirchman, D. L. and McDole, T. and McPherson, J. D. and Meyer, Folker and Miller, R. M. and Mundt, E. and Naviaux, R. K. and Rodriguez-Mueller, B. and Stevens, R. and Wegley, L. and Zhang, L. and Zhu, B. and Rohwer, F.}, year = {2009}, note = {Type: Journal Article} } T. Bekel, K. Henckel, H. Kuster, Folker Meyer, V. Mittard Runte, H. Neuweger, D. Paarmann, O. Rupp, M. Zakrzewski, A. Puhler, J. Stoye, and A. Goesmann. The Sequence Analysis and Management System – SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. J Biotechnol. 2009. [doi] [url] BibTeX @article{bekel_sequence_2009-2, title = {The {Sequence} {Analysis} and {Management} {System} – {SAMS}-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies}, volume = {140}, url = {https://www.ncbi.nlm.nih.gov/pubmed/19297685}, doi = {10.1016/j.jbiotec.2009.01.006}, journal = {J Biotechnol}, author = {Bekel, T. and Henckel, K. and Kuster, H. and Meyer, Folker and Mittard Runte, V. and Neuweger, H. and Paarmann, D. and Rupp, O. and Zakrzewski, M. and Puhler, A. and Stoye, J. and Goesmann, A.}, year = {2009}, note = {Type: Journal Article}, keywords = {Bacterial Genomics Information Management/*methods Information Storage and Retrieval/*methods Oligonucleotide Array Sequence Analysis Sequence Analysis, Cluster Analysis Computational Biology Databases, DNA/*methods *Software User-Computer Interface, Genetic Expressed Sequence Tags Gene Library *Genome} } 2008 S. M. Sievert, K. A. Scott, M. G. Klotz, P. S. G. Chain, L. J. Hauser, J. Hemp, M. Hugler, M. Land, A. Lapidus, F. W. Larimer, S. Lucas, S. A. Malfatti, Folker Meyer, I. T. Paulsen, Q. Ren, J. Simon, and U. S. F. Genom Class. Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Applied and Environmental Microbiology. 2008. [doi] BibTeX @article{sievert_genome_2008, title = {Genome of the epsilonproteobacterial chemolithoautotroph {Sulfurimonas} denitrificans}, volume = {74}, doi = {10.1128/aem.01844-07}, journal = {Applied and Environmental Microbiology}, author = {Sievert, S. M. and Scott, K. A. and Klotz, M. G. and Chain, P. S. G. and Hauser, L. J. and Hemp, J. and Hugler, M. and Land, M. and Lapidus, A. and Larimer, F. W. and Lucas, S. and Malfatti, S. A. and Meyer, Folker and Paulsen, I. T. and Ren, Q. and Simon, J. and Class, U. S. F. Genom}, year = {2008}, note = {Type: Journal Article} } Folker Meyer, D. Paarmann, M. D’Souza, R. Olson, E. M. Glass, M. Kubal, T. Paczian, A. Rodriguez, R. Stevens, A. Wilke, J. Wilkening, and R. A. Edwards. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008. [doi] [url] BibTeX @article{meyer_metagenomics_2008, title = {The metagenomics {RAST} server - a public resource for the automatic phylogenetic and functional analysis of metagenomes}, volume = {9}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18803844}, doi = {10.1186/1471-2105-9-386}, journal = {BMC Bioinformatics}, author = {Meyer, Folker and Paarmann, D. and D'Souza, M. and Olson, R. and Glass, E. M. and Kubal, M. and Paczian, T. and Rodriguez, A. and Stevens, R. and Wilke, A. and Wilkening, J. and Edwards, R. A.}, year = {2008}, note = {Type: Journal Article} } G. M. Garrity, D. Field, N. Kyrpides, L. Hirschman, S. A. Sansone, S. Angiuoli, J. R. Cole, F. O. Glockner, E. Kolker, G. Kowalchuk, M. A. Moran, D. Ussery, and O. White. Toward a standards-compliant genomic and metagenomic publication record. Omics. 2008. [doi] [url] BibTeX @article{garrity_toward_2008, title = {Toward a standards-compliant genomic and metagenomic publication record}, volume = {12}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18564916}, doi = {10.1089/omi.2008.A2B2}, journal = {Omics}, author = {Garrity, G. M. and Field, D. and Kyrpides, N. and Hirschman, L. and Sansone, S. A. and Angiuoli, S. and Cole, J. R. and Glockner, F. O. and Kolker, E. and Kowalchuk, G. and Moran, M. A. and Ussery, D. and White, O.}, year = {2008}, note = {Type: Journal Article} } D. Field, G. Garrity, T. Gray, N. Morrison, J. Selengut, P. Sterk, T. Tatusova, N. Thomson, M. J. Allen, S. V. Angiuoli, M. Ashburner, N. Axelrod, S. Baldauf, S. Ballard, J. Boore, G. Cochrane, J. Cole, P. Dawyndt, P. De Vos, C. DePamphilis, R. Edwards, N. Faruque, R. Feldman, J. Gilbert, P. Gilna, F. O. Glockner, P. Goldstein, R. Guralnick, D. Haft, D. Hancock, H. Hermjakob, C. Hertz-Fowler, P. Hugenholtz, I. Joint, L. Kagan, M. Kane, J. Kennedy, G. Kowalchuk, R. Kottmann, E. Kolker, S. Kravitz, N. Kyrpides, J. Leebens-Mack, S. E. Lewis, K. Li, A. L. Lister, P. Lord, N. Maltsev, V. Markowitz, J. Martiny, B. Methe, I. Mizrachi, R. Moxon, K. Nelson, J. Parkhill, L. Proctor, O. White, S. A. Sansone, A. Spiers, R. Stevens, P. Swift, C. Taylor, Y. Tateno, A. Tett, S. Turner, D. Ussery, B. Vaughan, N. Ward, T. Whetzel, I. San Gil, G. Wilson, and A. Wipat. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008. [doi] [url] BibTeX @article{field_minimum_2008, title = {The minimum information about a genome sequence ({MIGS}) specification}, volume = {26}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18464787}, doi = {10.1038/nbt1360}, journal = {Nat Biotechnol}, author = {Field, D. and Garrity, G. and Gray, T. and Morrison, N. and Selengut, J. and Sterk, P. and Tatusova, T. and Thomson, N. and Allen, M. J. and Angiuoli, S. V. and Ashburner, M. and Axelrod, N. and Baldauf, S. and Ballard, S. and Boore, J. and Cochrane, G. and Cole, J. and Dawyndt, P. and De Vos, P. and DePamphilis, C. and Edwards, R. and Faruque, N. and Feldman, R. and Gilbert, J. and Gilna, P. and Glockner, F. O. and Goldstein, P. and Guralnick, R. and Haft, D. and Hancock, D. and Hermjakob, H. and Hertz-Fowler, C. and Hugenholtz, P. and Joint, I. and Kagan, L. and Kane, M. and Kennedy, J. and Kowalchuk, G. and Kottmann, R. and Kolker, E. and Kravitz, S. and Kyrpides, N. and Leebens-Mack, J. and Lewis, S. E. and Li, K. and Lister, A. L. and Lord, P. and Maltsev, N. and Markowitz, V. and Martiny, J. and Methe, B. and Mizrachi, I. and Moxon, R. and Nelson, K. and Parkhill, J. and Proctor, L. and White, O. and Sansone, S. A. and Spiers, A. and Stevens, R. and Swift, P. and Taylor, C. and Tateno, Y. and Tett, A. and Turner, S. and Ussery, D. and Vaughan, B. and Ward, N. and Whetzel, T. and San Gil, I. and Wilson, G. and Wipat, A.}, year = {2008}, note = {Type: Journal Article} } R. K. Aziz, D. Bartels, A. A. Best, M. DeJongh, T. Disz, R. A. Edwards, K. Formsma, S. Gerdes, E. M. Glass, M. Kubal, Folker Meyer, G. J. Olsen, R. Olson, A. L. Osterman, R. A. Overbeek, L. K. McNeil, D. Paarmann, T. Paczian, B. Parrello, G. D. Pusch, C. Reich, R. Stevens, O. Vassieva, V. Vonstein, A. Wilke, and O. Zagnitko. The RAST server: Rapid annotations using subsystems technology. BMC Genomics. 2008. [doi] BibTeX @article{aziz_rast_2008, title = {The {RAST} server: {Rapid} annotations using subsystems technology}, volume = {9}, doi = {10.1186/1471-2164-9-75}, journal = {BMC Genomics}, author = {Aziz, R. K. and Bartels, D. and Best, A. A. and DeJongh, M. and Disz, T. and Edwards, R. A. and Formsma, K. and Gerdes, S. and Glass, E. M. and Kubal, M. and Meyer, Folker and Olsen, G. J. and Olson, R. and Osterman, A. L. and Overbeek, R. A. and McNeil, L. K. and Paarmann, D. and Paczian, T. and Parrello, B. and Pusch, G. D. and Reich, C. and Stevens, R. and Vassieva, O. and Vonstein, V. and Wilke, A. and Zagnitko, O.}, year = {2008}, note = {Type: Journal Article} } R. K. Aziz, D. Bartels, A. A. Best, M. DeJongh, T. Disz, R. A. Edwards, K. Formsma, S. Gerdes, E. M. Glass, M. Kubal, Folker Meyer, G. J. Olsen, R. Olson, A. L. Osterman, R. A. Overbeek, L. K. McNeil, D. Paarmann, T. Paczian, B. Parrello, G. D. Pusch, C. Reich, R. Stevens, O. Vassieva, V. Vonstein, A. Wilke, and O. Zagnitko. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics. 2008. BibTeX @article{aziz_rast_2008-1, title = {The {RAST} {Server}: {Rapid} {Annotations} using {Subsystems} {Technology}}, journal = {BMC Genomics}, author = {Aziz, R. K. and Bartels, D. and Best, A. A. and DeJongh, M. and Disz, T. and Edwards, R. A. and Formsma, K. and Gerdes, S. and Glass, E. M. and Kubal, M. and Meyer, Folker and Olsen, G. J. and Olson, R. and Osterman, A. L. and Overbeek, R. A. and McNeil, L. K. and Paarmann, D. and Paczian, T. and Parrello, B. and Pusch, G. D. and Reich, C. and Stevens, R. and Vassieva, O. and Vonstein, V. and Wilke, A. and Zagnitko, O.}, year = {2008}, note = {Type: Journal Article} } Scott E Battle, Folker Meyer, Jordi Rello, Vanderlene L Kung, and Alan R Hauser. Hybrid pathogenicity island PAGI-5 contributes to the highly virulent phenotype of a Pseudomonas aeruginosa isolate in mammals. Journal of bacteriology. 2008. BibTeX @article{battle_hybrid_2008-1, title = {Hybrid pathogenicity island {PAGI}-5 contributes to the highly virulent phenotype of a {Pseudomonas} aeruginosa isolate in mammals}, volume = {190}, journal = {Journal of bacteriology}, author = {Battle, Scott E and Meyer, Folker and Rello, Jordi and Kung, Vanderlene L and Hauser, Alan R}, year = {2008}, note = {Publisher: American Society for Microbiology} } Francesca Mela, Kathrin Fritsche, Hidde Boersma, Jan D Van Elsas, Daniela Bartels, Folker Meyer, Wietse De Boer, Johannes A Van Veen, and Johan HJ Leveau. Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331. FEMS microbiology ecology. 2008. BibTeX @article{mela_comparative_2008-1, title = {Comparative genomics of the {pIPO2}/{pSB102} family of environmental plasmids: sequence, evolution, and ecology of {pTer331} isolated from {Collimonas} fungivorans {Ter331}}, volume = {66}, journal = {FEMS microbiology ecology}, author = {Mela, Francesca and Fritsche, Kathrin and Boersma, Hidde and Van Elsas, Jan D and Bartels, Daniela and Meyer, Folker and De Boer, Wietse and Van Veen, Johannes A and Leveau, Johan HJ}, year = {2008}, note = {Publisher: Blackwell Publishing Ltd Oxford, UK} } Renzo Kottmann, Tanya Gray, Sean Murphy, Leonid Kagan, Saul Kravitz, Thierry Lombardot, Dawn Field, Frank Oliver Glöckner, and Genomic Standards Consortium. A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). Omics a journal of integrative biology. 2008. BibTeX @article{kottmann_standard_2008-1, title = {A standard {MIGS}/{MIMS} compliant {XML} {Schema}: toward the development of the {Genomic} {Contextual} {Data} {Markup} {Language} ({GCDML})}, volume = {12}, journal = {Omics a journal of integrative biology}, author = {Kottmann, Renzo and Gray, Tanya and Murphy, Sean and Kagan, Leonid and Kravitz, Saul and Lombardot, Thierry and Field, Dawn and Glöckner, Frank Oliver and Consortium, Genomic Standards}, year = {2008}, note = {Publisher: Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 …} } Francesca Mela, Kathrin Fritsche, Hidde Boersma, Jan D van Elsas, Daniela Bartels, Folker Meyer, Wietse de Boer, Johannes A van Veen, and Johan HJ Leveau. Collimonas fungivorans Ter331. 2008. BibTeX @article{mela_collimonas_2008, title = {Collimonas fungivorans {Ter331}}, author = {Mela, Francesca and Fritsche, Kathrin and Boersma, Hidde and van Elsas, Jan D and Bartels, Daniela and Meyer, Folker and de Boer, Wietse and van Veen, Johannes A and Leveau, Johan HJ}, year = {2008} } K. H. Gartemann, B. Abt, T. Bekel, A. Burger, J. Engemann, M. Flugel, L. Gaigalat, A. Goesmann, I. Grafen, J. Kalinowski, O. Kaup, O. Kirchner, L. Krause, B. Linke, A. McHardy, Folker Meyer, S. Pohle, C. Ruckert, S. Schneiker, E. M. Zellermann, A. Puhler, R. Eichenlaub, O. Kaiser, and D. Bartels. The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity. J Bacteriol. 2008. [doi] [url] BibTeX @article{gartemann_genome_2008-2, title = {The genome sequence of the tomato-pathogenic actinomycete {Clavibacter} michiganensis subsp. michiganensis {NCPPB382} reveals a large island involved in pathogenicity}, volume = {190}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18192381}, doi = {10.1128/JB.01595-07}, journal = {J Bacteriol}, author = {Gartemann, K. H. and Abt, B. and Bekel, T. and Burger, A. and Engemann, J. and Flugel, M. and Gaigalat, L. and Goesmann, A. and Grafen, I. and Kalinowski, J. and Kaup, O. and Kirchner, O. and Krause, L. and Linke, B. and McHardy, A. and Meyer, Folker and Pohle, S. and Ruckert, C. and Schneiker, S. and Zellermann, E. M. and Puhler, A. and Eichenlaub, R. and Kaiser, O. and Bartels, D.}, year = {2008}, note = {Type: Journal Article}, keywords = {Bacterial/genetics *Genome, Actinobacteria/*genetics/pathogenicity Base Composition/genetics DNA, Bacterial Genomic Islands/genetics Lycopersicon esculentum/*microbiology Models, Bacterial/chemistry/*genetics Electrophoresis, DNA Serine Endopeptidases/genetics, Gel, Genetic Molecular Sequence Data Operon/genetics Plasmids/genetics Sequence Analysis, Pulsed-Field Genes} } R. Gross, C. A. Guzman, M. Sebaihia, Vapm dos Santos, D. H. Pieper, R. Koebnik, M. Lechner, D. Bartels, J. Buhrmester, J. V. Choudhuri, T. Ebensen, L. Gaigalat, S. Herrmann, A. N. Khachane, C. Larisch, S. Link, B. Linke, Folker Meyer, S. Mormann, D. Nakunst, C. Rukert, S. Schneiker-Bekel, K. Schulze, F. J. Vorholter, T. Yevsa, J. T. Engle, W. E. Goldman, A. Puhler, U. B. Gobel, A. Goesmann, H. Blocker, O. Kaiser, and R. Martinez-Arias. The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics. 2008. [doi] BibTeX @article{gross_missing_2008-2, title = {The missing link: {Bordetella} petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic {Bordetellae}}, volume = {9}, doi = {10.1186/1471-2164-9-449}, journal = {BMC Genomics}, author = {Gross, R. and Guzman, C. A. and Sebaihia, M. and dos Santos, Vapm and Pieper, D. H. and Koebnik, R. and Lechner, M. and Bartels, D. and Buhrmester, J. and Choudhuri, J. V. and Ebensen, T. and Gaigalat, L. and Herrmann, S. and Khachane, A. N. and Larisch, C. and Link, S. and Linke, B. and Meyer, Folker and Mormann, S. and Nakunst, D. and Rukert, C. and Schneiker-Bekel, S. and Schulze, K. and Vorholter, F. J. and Yevsa, T. and Engle, J. T. and Goldman, W. E. and Puhler, A. and Gobel, U. B. and Goesmann, A. and Blocker, H. and Kaiser, O. and Martinez-Arias, R.}, year = {2008}, note = {Type: Journal Article} } F. Rambow, G. Piton, S. Bouet, J. J. Leplat, S. Baulande, A. Marrau, M. Stam, V. Horak, and S. Vincent-Naulleau. Gene expression signature for spontaneous cancer regression in melanoma pigs. Neoplasia. 2008. [doi] [url] BibTeX @article{RN35, author = {Rambow, F. and Piton, G. and Bouet, S. and Leplat, J. J. and Baulande, S. and Marrau, A. and Stam, M. and Horak, V. and Vincent-Naulleau, S.}, title = {Gene expression signature for spontaneous cancer regression in melanoma pigs}, journal = {Neoplasia}, volume = {10}, number = {7}, pages = {714-26, 1 p following 726}, issn = {1476-5586 (Electronic) 1476-5586 (Linking)}, doi = {10.1593/neo.08344}, url = {https://www.ncbi.nlm.nih.gov/pubmed/18592010}, year = {2008}, type = {Journal Article} } F. Rambow, O. Malek, C. Geffrotin, J. J. Leplat, S. Bouet, G. Piton, K. Hugot, C. Bevilacqua, V. Horak, and S. Vincent-Naulleau. Identification of differentially expressed genes in spontaneously regressing melanoma using the MeLiM swine model. Pigment Cell Melanoma Res. 2008. [doi] [url] BibTeX @article{RN33, author = {Rambow, F. and Malek, O. and Geffrotin, C. and Leplat, J. J. and Bouet, S. and Piton, G. and Hugot, K. and Bevilacqua, C. and Horak, V. and Vincent-Naulleau, S.}, title = {Identification of differentially expressed genes in spontaneously regressing melanoma using the MeLiM swine model}, journal = {Pigment Cell Melanoma Res}, volume = {21}, number = {2}, pages = {147-61}, issn = {1755-1471 (Print) 1755-1471 (Linking)}, doi = {10.1111/j.1755-148X.2008.00442.x}, url = {https://www.ncbi.nlm.nih.gov/pubmed/18426408}, year = {2008}, type = {Journal Article} } 2007 S. Schneiker, O. Perlova, O. Kaiser, K. Gerth, A. Alici, M. O. Altmeyer, D. Bartels, T. Bekel, S. Beyer, E. Bode, H. B. Bode, C. J. Bolten, J. V. Choudhuri, S. Doss, Y. A. Elnakady, B. Frank, L. Gaigalat, A. Goesmann, C. Groeger, F. Gross, L. Jelsbak, J. Kalinowski, C. Kegler, T. Knauber, S. Konietzny, M. Kopp, L. Krause, D. Krug, B. Linke, T. Mahmud, R. Martinez-Arias, A. C. McHardy, M. Merai, Folker Meyer, S. Mormann, J. Munoz-Dorado, J. Perez, S. Pradella, S. Rachid, G. Raddatz, F. Rosenau, C. Rueckert, F. Sasse, M. Scharfe, S. C. Schuster, G. Suen, A. Treuner-Lange, G. J. Velicer, F. J. Vorholter, K. J. Weissman, R. Dwelch, S. C. Wenzel, D. E. Whitworth, S. Wilhelm, C. Wittmann, H. Blocker, A. Puhler, and R. Mueller. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol. 2007. [doi] BibTeX @article{schneiker_complete_2007, title = {Complete genome sequence of the myxobacterium {Sorangium} cellulosum}, volume = {25}, doi = {10.1038/nbt1354}, journal = {Nat Biotechnol}, author = {Schneiker, S. and Perlova, O. and Kaiser, O. and Gerth, K. and Alici, A. and Altmeyer, M. O. and Bartels, D. and Bekel, T. and Beyer, S. and Bode, E. and Bode, H. B. and Bolten, C. J. and Choudhuri, J. V. and Doss, S. and Elnakady, Y. A. and Frank, B. and Gaigalat, L. and Goesmann, A. and Groeger, C. and Gross, F. and Jelsbak, L. and Kalinowski, J. and Kegler, C. and Knauber, T. and Konietzny, S. and Kopp, M. and Krause, L. and Krug, D. and Linke, B. and Mahmud, T. and Martinez-Arias, R. and McHardy, A. C. and Merai, M. and Meyer, Folker and Mormann, S. and Munoz-Dorado, J. and Perez, J. and Pradella, S. and Rachid, S. and Raddatz, G. and Rosenau, F. and Rueckert, C. and Sasse, F. and Scharfe, M. and Schuster, S. C. and Suen, G. and Treuner-Lange, A. and Velicer, G. J. and Vorholter, F. J. and Weissman, K. J. and Dwelch, R. and Wenzel, S. C. and Whitworth, D. E. and Wilhelm, S. and Wittmann, C. and Blocker, H. and Puhler, A. and Mueller, R.}, year = {2007}, note = {Type: Journal Article} } R. Overbeek, D. Bartels, V. Vonstein, and Folker Meyer. Annotation of Bacterial and Archaeal Genomes: Improving Accuracy and Consistency. Chemical Reviews. 2007. BibTeX @article{overbeek_annotation_2007, title = {Annotation of {Bacterial} and {Archaeal} {Genomes}: {Improving} {Accuracy} and {Consistency}}, journal = {Chemical Reviews}, author = {Overbeek, R. and Bartels, D. and Vonstein, V. and Meyer, Folker}, year = {2007}, note = {Type: Journal Article} } L. K. McNeil, C. Reich, R. K. Aziz, D. Bartels, M. Cohoon, T. Disz, R. A. Edwards, S. Gerdes, K. Hwang, M. Kubal, G. R. Margaryan, Folker Meyer, W. Mihalo, G. J. Olsen, R. Olson, A. Osterman, D. Paarmann, T. Paczian, B. Parrello, G. D. Pusch, D. A. Rodionov, X. H. Shi, O. Vassieva, V. Vonstein, O. Zagnitko, F. F. Xia, J. Zinner, R. Overbeek, and R. Stevens. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Research. 2007. [doi] BibTeX @article{mcneil_national_2007, title = {The {National} {Microbial} {Pathogen} {Database} {Resource} ({NMPDR}): a genomics platform based on subsystem annotation}, volume = {35}, doi = {10.1093/nar/gkl947}, journal = {Nucleic Acids Research}, author = {McNeil, L. K. and Reich, C. and Aziz, R. K. and Bartels, D. and Cohoon, M. and Disz, T. and Edwards, R. A. and Gerdes, S. and Hwang, K. and Kubal, M. and Margaryan, G. R. and Meyer, Folker and Mihalo, W. and Olsen, G. J. and Olson, R. and Osterman, A. and Paarmann, D. and Paczian, T. and Parrello, B. and Pusch, G. D. and Rodionov, D. A. and Shi, X. H. and Vassieva, O. and Vonstein, V. and Zagnitko, O. and Xia, F. F. and Zinner, J. and Overbeek, R. and Stevens, R.}, year = {2007}, note = {Type: Journal Article} } L. Krause, A. C. McHardy, T. W. Nattkemper, A. Puhler, J. Stoye, and Folker Meyer. GISMO - gene identification using a support vector machine for ORF classification. Nucleic Acids Research. 2007. [doi] BibTeX @article{krause_gismo_2007, title = {{GISMO} - gene identification using a support vector machine for {ORF} classification}, volume = {35}, doi = {10.1093/nar/gkl1083}, journal = {Nucleic Acids Research}, author = {Krause, L. and McHardy, A. C. and Nattkemper, T. W. and Puhler, A. and Stoye, J. and Meyer, Folker}, year = {2007}, note = {Type: Journal Article} } Lutz Krause, Alice C McHardy, Tim W Nattkemper, Alfred Pühler, Jens Stoye, and Folker Meyer. GISMO—gene identification using a support vector machine for ORF classification. Nucleic acids research. 2007. BibTeX @article{krause_gismogene_2007, title = {{GISMO}—gene identification using a support vector machine for {ORF} classification}, volume = {35}, journal = {Nucleic acids research}, author = {Krause, Lutz and McHardy, Alice C and Nattkemper, Tim W and Pühler, Alfred and Stoye, Jens and Meyer, Folker}, year = {2007}, note = {Publisher: Oxford University Press} } Ross Overbeek, Daniela Bartels, Veronika Vonstein, and Folker Meyer. Annotation of bacterial and archaeal genomes: improving accuracy and consistency. Chemical reviews. 2007. BibTeX @article{overbeek_annotation_2007-1, title = {Annotation of bacterial and archaeal genomes: improving accuracy and consistency}, volume = {107}, journal = {Chemical reviews}, author = {Overbeek, Ross and Bartels, Daniela and Vonstein, Veronika and Meyer, Folker}, year = {2007}, note = {Publisher: American Chemical Society} } H. Kuster, A. Becker, C. Firnhaber, N. Hohnjec, K. Manthey, A. M. Perlick, T. Bekel, M. Dondrup, K. Henckel, A. Goesmann, Folker Meyer, D. Wipf, N. Requena, U. Hildebrandt, R. Hampp, U. Nehls, F. Krajinski, P. Franken, and A. Puhler. Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses. Phytochemistry. 2007. [doi] [url] BibTeX @article{kuster_development_2007-2, title = {Development of bioinformatic tools to support {EST}-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses}, volume = {68}, url = {https://www.ncbi.nlm.nih.gov/pubmed/17081576}, doi = {10.1016/j.phytochem.2006.09.026}, journal = {Phytochemistry}, author = {Kuster, H. and Becker, A. and Firnhaber, C. and Hohnjec, N. and Manthey, K. and Perlick, A. M. and Bekel, T. and Dondrup, M. and Henckel, K. and Goesmann, A. and Meyer, Folker and Wipf, D. and Requena, N. and Hildebrandt, U. and Hampp, R. and Nehls, U. and Krajinski, F. and Franken, P. and Puhler, A.}, year = {2007}, note = {Type: Journal Article}, keywords = {Computational Biology/*methods *Expressed Sequence Tags Mycorrhizae/*genetics Oligonucleotide Array Sequence Analysis/*methods Symbiosis/*genetics Transcription, Genetic/*genetics} } F. W. Velten, F. Rambow, P. Metharom, and S. Goerdt. Enhanced T-cell activation and T-cell-dependent IL-2 production by CD83+, CD25high, CD43high human monocyte-derived dendritic cells. Mol Immunol. 2007. [doi] [url] BibTeX @article{RN45, author = {Velten, F. W. and Rambow, F. and Metharom, P. and Goerdt, S.}, title = {Enhanced T-cell activation and T-cell-dependent IL-2 production by CD83+, CD25high, CD43high human monocyte-derived dendritic cells}, journal = {Mol Immunol}, volume = {44}, number = {7}, pages = {1544-50}, issn = {0161-5890 (Print) 0161-5890 (Linking)}, doi = {10.1016/j.molimm.2006.08.020}, url = {https://www.ncbi.nlm.nih.gov/pubmed/17023048}, year = {2007}, type = {Journal Article} } 2006 K. M. Scott, S. M. Sievert, F. N. Abril, L. A. Ball, C. J. Barrett, R. A. Blake, A. J. Boller, P. S. G. Chain, J. A. Clark, C. R. Davis, C. Detter, K. F. Do, K. P. Dobrinski, B. I. Faza, K. A. Fitzpatrick, S. K. Freyermuth, T. L. Harmer, L. J. Hauser, M. Hugler, C. A. Kerfeld, M. G. Klotz, W. W. Kong, M. Land, A. Lapidus, F. W. Larimer, D. L. Longo, S. Lucas, S. A. Malfatti, S. E. Massey, D. D. Martin, Z. McCuddin, Folker Meyer, J. L. Moore, L. H. Ocampo, J. H. Paul, I. T. Paulsen, D. K. Reep, Q. H. Ren, R. L. Ross, P. Y. Sato, P. Thomas, L. E. Tinkham, and G. T. Zeruth. The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. Plos Biology. 2006. [doi] BibTeX @article{scott_genome_2006, title = {The genome of deep-sea vent chemolithoautotroph {Thiomicrospira} crunogena {XCL}-2}, volume = {4}, doi = {10.1371/journal.pbio.0040383}, journal = {Plos Biology}, author = {Scott, K. M. and Sievert, S. M. and Abril, F. N. and Ball, L. A. and Barrett, C. J. and Blake, R. A. and Boller, A. J. and Chain, P. S. G. and Clark, J. A. and Davis, C. R. and Detter, C. and Do, K. F. and Dobrinski, K. P. and Faza, B. I. and Fitzpatrick, K. A. and Freyermuth, S. K. and Harmer, T. L. and Hauser, L. J. and Hugler, M. and Kerfeld, C. A. and Klotz, M. G. and Kong, W. W. and Land, M. and Lapidus, A. and Larimer, F. W. and Longo, D. L. and Lucas, S. and Malfatti, S. A. and Massey, S. E. and Martin, D. D. and McCuddin, Z. and Meyer, Folker and Moore, J. L. and Ocampo, L. H. and Paul, J. H. and Paulsen, I. T. and Reep, D. K. and Ren, Q. H. and Ross, R. L. and Sato, P. Y. and Thomas, P. and Tinkham, L. E. and Zeruth, G. T.}, year = {2006}, note = {Type: Journal Article} } S. Schneiker, Vapm dos Santos, D. Bartels, T. Bekel, M. Brecht, J. Buhrmester, T. N. Chernikova, R. Denaro, M. Ferrer, C. Gertler, A. Goesmann, O. V. Golyshina, F. Kaminski, A. N. Khachane, S. Lang, B. Linke, A. C. McHardy, Folker Meyer, T. Nechitaylo, A. Puhler, D. Regenhardt, O. Rupp, J. S. Sabirova, W. Selbitschka, M. M. Yakimov, K. N. Timmis, F. J. Vorholter, S. Weidner, O. Kaiser, and P. N. Golyshin. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol. 2006. [doi] BibTeX @article{schneiker_genome_2006, title = {Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium {Alcanivorax} borkumensis}, volume = {24}, doi = {10.1038/nbt1232}, journal = {Nat Biotechnol}, author = {Schneiker, S. and dos Santos, Vapm and Bartels, D. and Bekel, T. and Brecht, M. and Buhrmester, J. and Chernikova, T. N. and Denaro, R. and Ferrer, M. and Gertler, C. and Goesmann, A. and Golyshina, O. V. and Kaminski, F. and Khachane, A. N. and Lang, S. and Linke, B. and McHardy, A. C. and Meyer, Folker and Nechitaylo, T. and Puhler, A. and Regenhardt, D. and Rupp, O. and Sabirova, J. S. and Selbitschka, W. and Yakimov, M. M. and Timmis, K. N. and Vorholter, F. J. and Weidner, S. and Kaiser, O. and Golyshin, P. N.}, year = {2006}, note = {Type: Journal Article} } N. Pobigaylo, D. Wetter, S. Szymczak, U. Schiller, S. Kurtz, Folker Meyer, T. W. Nattkemper, and A. Becker. Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti. Applied and Environmental Microbiology. 2006. [doi] BibTeX @article{pobigaylo_construction_2006, title = {Construction of a large signature-tagged mini-{Tn5} transposon library and its application to mutagenesis of {Sinorhizobium} meliloti}, volume = {72}, doi = {10.1128/aem.03072-05}, journal = {Applied and Environmental Microbiology}, author = {Pobigaylo, N. and Wetter, D. and Szymczak, S. and Schiller, U. and Kurtz, S. and Meyer, Folker and Nattkemper, T. W. and Becker, A.}, year = {2006}, note = {Type: Journal Article} } B. Linke, A. C. McHardy, H. Neuweger, L. Krause, and Folker Meyer. REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes. Appl Bioinformatics. 2006. [url] BibTeX @article{linke_reganor_2006, title = {{REGANOR}: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes}, volume = {5}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16922601}, journal = {Appl Bioinformatics}, author = {Linke, B. and McHardy, A. C. and Neuweger, H. and Krause, L. and Meyer, Folker}, year = {2006}, note = {Type: Journal Article} } L. Krause, N. N. Diaz, D. Bartels, R. A. Edwards, A. Puhler, F. Rohwer, Folker Meyer, and J. Stoye. Finding novel genes in bacterial communities isolated from the environment. Bioinformatics. 2006. [url] BibTeX @article{krause_finding_2006, title = {Finding novel genes in bacterial communities isolated from the environment}, volume = {22}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16873483}, journal = {Bioinformatics}, author = {Krause, L. and Diaz, N. N. and Bartels, D. and Edwards, R. A. and Puhler, A. and Rohwer, F. and Meyer, Folker and Stoye, J.}, year = {2006}, note = {Type: Journal Article} } T. Hain, C. Steinweg, C. T. Kuenne, A. Billion, R. Ghai, S. S. Chatterjee, E. Domann, U. Karst, A. Goesmann, T. Bekel, D. Bartels, O. Kaiser, Folker Meyer, A. Puhler, B. Weisshaar, J. Wehland, C. Liang, T. Dandekar, R. Lampidis, J. Kreft, W. Goebel, and T. Chakraborty. Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes. J Bacteriol. 2006. [doi] [url] BibTeX @article{hain_whole-genome_2006, title = {Whole-genome sequence of {Listeria} welshimeri reveals common steps in genome reduction with {Listeria} innocua as compared to {Listeria} monocytogenes}, volume = {188}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16936040}, doi = {10.1128/JB.00758-06}, journal = {J Bacteriol}, author = {Hain, T. and Steinweg, C. and Kuenne, C. T. and Billion, A. and Ghai, R. and Chatterjee, S. S. and Domann, E. and Karst, U. and Goesmann, A. and Bekel, T. and Bartels, D. and Kaiser, O. and Meyer, Folker and Puhler, A. and Weisshaar, B. and Wehland, J. and Liang, C. and Dandekar, T. and Lampidis, R. and Kreft, J. and Goebel, W. and Chakraborty, T.}, year = {2006}, note = {Type: Journal Article} } M. Bauer, M. Kube, H. Teeling, M. Richter, T. Lombardot, E. Allers, C. A. Wurdemann, C. Quast, H. Kuhl, F. Knaust, D. Woebken, K. Bischof, M. Mussmann, J. V. Choudhuri, Folker Meyer, R. Reinhardt, R. I. Amann, and F. O. Glockner. Whole genome analysis of the marine Bacteroidetes ’Gramella forsetii’ reveals adaptations to degradation of polymeric organic matter. Environ Microbiol. 2006. [doi] BibTeX @article{bauer_whole_2006, title = {Whole genome analysis of the marine {Bacteroidetes} '{Gramella} forsetii' reveals adaptations to degradation of polymeric organic matter}, volume = {8}, doi = {10.1111/j.1462-2920.2006.01152.x}, journal = {Environ Microbiol}, author = {Bauer, M. and Kube, M. and Teeling, H. and Richter, M. and Lombardot, T. and Allers, E. and Wurdemann, C. A. and Quast, C. and Kuhl, H. and Knaust, F. and Woebken, D. and Bischof, K. and Mussmann, M. and Choudhuri, J. V. and Meyer, Folker and Reinhardt, R. and Amann, R. I. and Glockner, F. O.}, year = {2006}, note = {Type: Journal Article} } Nataliya Pobigaylo, Danijel Wetter, Silke Szymczak, Ulf Schiller, Stefan Kurtz, Folker Meyer, Tim W Nattkemper, and Anke Becker. Construction of a large signature-tagged mini-Tn 5 transposon library and its application to mutagenesis of Sinorhizobium meliloti. Applied and environmental microbiology. 2006. BibTeX @article{pobigaylo_construction_2006-1, title = {Construction of a large signature-tagged mini-{Tn} 5 transposon library and its application to mutagenesis of {Sinorhizobium} meliloti}, volume = {72}, journal = {Applied and environmental microbiology}, author = {Pobigaylo, Nataliya and Wetter, Danijel and Szymczak, Silke and Schiller, Ulf and Kurtz, Stefan and Meyer, Folker and Nattkemper, Tim W and Becker, Anke}, year = {2006}, note = {Publisher: American Society for Microbiology} } Burkhard Linke, Alice C McHardy, Heiko Neuweger, Lutz Krause, and Folker Meyer. Reganor. Applied bioinformatics. 2006. BibTeX @article{linke_reganor_2006-1, title = {Reganor}, volume = {5}, journal = {Applied bioinformatics}, author = {Linke, Burkhard and McHardy, Alice C and Neuweger, Heiko and Krause, Lutz and Meyer, Folker}, year = {2006}, note = {Publisher: Springer International Publishing} } Folker Meyer. Genome sequencing vs. moore’s law: Cyber challenges for the next decade. CTWatch Quarterly. 2006. BibTeX @article{meyer_genome_2006, title = {Genome sequencing vs. moore’s law: {Cyber} challenges for the next decade}, volume = {2}, journal = {CTWatch Quarterly}, author = {Meyer, Folker}, year = {2006} } 2005 A. Tauch, O. Kaiser, T. Hain, A. Goesmann, B. Weisshaar, A. Albersmeier, T. Bekel, N. Bischoff, I. Brune, T. Chakraborty, J. Kalinowski, Folker Meyer, O. Rupp, S. Schneiker, P. Viehoever, and A. Puhler. Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora. J Bacteriol. 2005. [doi] [url] BibTeX @article{tauch_complete_2005, title = {Complete genome sequence and analysis of the multiresistant nosocomial pathogen {Corynebacterium} jeikeium {K411}, a lipid-requiring bacterium of the human skin flora}, volume = {187}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15968079}, doi = {10.1128/JB.187.13.4671-4682.2005}, journal = {J Bacteriol}, author = {Tauch, A. and Kaiser, O. and Hain, T. and Goesmann, A. and Weisshaar, B. and Albersmeier, A. and Bekel, T. and Bischoff, N. and Brune, I. and Chakraborty, T. and Kalinowski, J. and Meyer, Folker and Rupp, O. and Schneiker, S. and Viehoever, P. and Puhler, A.}, year = {2005}, note = {Type: Journal Article} } R. Overbeek, T. Begley, R.M. Butler, J.V. Choudhuri, N. Diaz, H.-Y. Chuang, M. Cohoon, V. de Crécy-Lagard, T. Disz, R Edwards, M Fonstein, E.D. Frank, S. Gerdes, E.M. Glass, A. Goesmann, L. Krause, B. Linke, A.C. McHardy, Folker Meyer, A. Hanson, D. Iwata-Reuyl, R. Jensen, N. Jamshidi, M. Kubal, N. Larsen, H. Neuweger, C. Rückert, G. J. Olsen, R. Olson, A. Osterman, V. Portnoy, G.D. Pusch, D.A. Rodionov, J. Steiner, R. Stevens, I. Thiele, O. Vassieva, Y. Ye, O. Zagnitko, and V. Vonstein. The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes. Nucleic Acids Res. 2005. BibTeX @article{overbeek_subsystems_2005, title = {The {Subsystems} {Approach} to {Genome} {Annotation} and its {Use} in the {Project} to {Annotate} 1000 {Genomes}}, volume = {33}, journal = {Nucleic Acids Res}, author = {Overbeek, R. and Begley, T. and Butler, R.M. and Choudhuri, J.V. and Diaz, N. and Chuang, H.-Y. and Cohoon, M. and de Crécy-Lagard, V. and Disz, T. and Edwards, R and Fonstein, M and Frank, E.D. and Gerdes, S. and Glass, E.M. and Goesmann, A. and Krause, L. and Linke, B. and McHardy, A.C. and Meyer, Folker and Hanson, A. and Iwata-Reuyl, D. and Jensen, R. and Jamshidi, N. and Kubal, M. and Larsen, N. and Neuweger, H. and Rückert, C. and Olsen, G. J. and Olson, R. and Osterman, A. and Portnoy, V. and Pusch, G.D. and Rodionov, D.A. and Steiner, J. and Stevens, R. and Thiele, I. and Vassieva, O. and Ye, Y. and Zagnitko, O. and Vonstein, V.}, year = {2005}, note = {Type: Journal Article} } A. Goesmann, B. Linke, D. Bartels, M. Dondrup, L. Krause, H. Neuweger, S. Oehm, T. Paczian, A. Wilke, and Folker Meyer. BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser. Nucleic Acids Research. 2005. [doi] BibTeX @article{goesmann_brigep_2005, title = {{BRIGEP} - the {BRIDGE}-based genome-transcriptome-proteome browser}, volume = {33}, doi = {10.1093/nar/gki400}, journal = {Nucleic Acids Research}, author = {Goesmann, A. and Linke, B. and Bartels, D. and Dondrup, M. and Krause, L. and Neuweger, H. and Oehm, S. and Paczian, T. and Wilke, A. and Meyer, Folker}, year = {2005}, note = {Type: Journal Article} } André Frenzel, Katja Manthey, Andreas M Perlick, Folker Meyer, Alfred Pühler, Helge Küster, and Franziska Krajinski. Combined transcriptome profiling reveals a novel family of arbuscular mycorrhizal-specific Medicago truncatula lectin genes. Molecular plant-microbe interactions. 2005. BibTeX @article{frenzel_combined_2005-1, title = {Combined transcriptome profiling reveals a novel family of arbuscular mycorrhizal-specific {Medicago} truncatula lectin genes}, volume = {18}, journal = {Molecular plant-microbe interactions}, author = {Frenzel, André and Manthey, Katja and Perlick, Andreas M and Meyer, Folker and Pühler, Alfred and Küster, Helge and Krajinski, Franziska}, year = {2005}, note = {Publisher: Am Phytopath Society} } Daniela Bartels, Sebastian Kespohl, Stefan Albaum, Tanja Drüke, Alexander Goesmann, Julia Herold, Olaf Kaiser, Alfred Pühler, Friedhelm Pfeiffer, Günter Raddatz, and Folker Meyer. BACCardI—a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics. 2005. BibTeX @article{bartels_baccarditool_2005, title = {{BACCardI}—a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison}, volume = {21}, journal = {Bioinformatics}, author = {Bartels, Daniela and Kespohl, Sebastian and Albaum, Stefan and Drüke, Tanja and Goesmann, Alexander and Herold, Julia and Kaiser, Olaf and Pühler, Alfred and Pfeiffer, Friedhelm and Raddatz, Günter and Meyer, Folker}, year = {2005}, note = {Publisher: Oxford University Press} } Alexander Goesmann, Burkhard Linke, Daniela Bartels, Michael Dondrup, Lutz Krause, Heiko Neuweger, Sebastian Oehm, Tobias Paczian, Andreas Wilke, and Folker Meyer. BRIGEP—the BRIDGE-based genome–transcriptome–proteome browser. Nucleic acids research. 2005. BibTeX @article{goesmann_brigepbridge-based_2005, title = {{BRIGEP}—the {BRIDGE}-based genome–transcriptome–proteome browser}, volume = {33}, journal = {Nucleic acids research}, author = {Goesmann, Alexander and Linke, Burkhard and Bartels, Daniela and Dondrup, Michael and Krause, Lutz and Neuweger, Heiko and Oehm, Sebastian and Paczian, Tobias and Wilke, Andreas and Meyer, Folker}, year = {2005}, note = {Publisher: Oxford University Press} } R. Overbeek, T. Begley, R. M. Butler, J. V. Choudhuri, H. Y. Chuang, M. Cohoon, V. de Crecy-Lagard, N. Diaz, T. Disz, R. Edwards, M. Fonstein, E. D. Frank, S. Gerdes, E. M. Glass, A. Goesmann, A. Hanson, D. Iwata-Reuyl, R. Jensen, N. Jamshidi, L. Krause, M. Kubal, N. Larsen, B. Linke, A. C. McHardy, Folker Meyer, H. Neuweger, G. Olsen, R. Olson, A. Osterman, V. Portnoy, G. D. Pusch, D. A. Rodionov, C. Ruckert, J. Steiner, R. Stevens, I. Thiele, O. Vassieva, Y. Ye, O. Zagnitko, and V. Vonstein. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005. [doi] BibTeX @article{overbeek_subsystems_2006, title = {The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes}, volume = {33}, doi = {10.1093/nar/gki866}, journal = {Nucleic Acids Res}, author = {Overbeek, R. and Begley, T. and Butler, R. M. and Choudhuri, J. V. and Chuang, H. Y. and Cohoon, M. and de Crecy-Lagard, V. and Diaz, N. and Disz, T. and Edwards, R. and Fonstein, M. and Frank, E. D. and Gerdes, S. and Glass, E. M. and Goesmann, A. and Hanson, A. and Iwata-Reuyl, D. and Jensen, R. and Jamshidi, N. and Krause, L. and Kubal, M. and Larsen, N. and Linke, B. and McHardy, A. C. and Meyer, Folker and Neuweger, H. and Olsen, G. and Olson, R. and Osterman, A. and Portnoy, V. and Pusch, G. D. and Rodionov, D. A. and Ruckert, C. and Steiner, J. and Stevens, R. and Thiele, I. and Vassieva, O. and Ye, Y. and Zagnitko, O. and Vonstein, V.}, year = {2005}, note = {Type: Journal Article}, keywords = {Acyl Coenzyme A/metabolism Coenzyme A/biosynthesis Computational Biology *Genome, Archaeal *Genome, Bacterial Genomics/*methods Internet Leucine/metabolism Ribosomal Proteins/classification *Software Terminology as Topic Vocabulary, Controlled} } F. Thieme, R. Koebnik, T. Bekel, C. Berger, J. Boch, D. Buttner, C. Caldana, L. Gaigalat, A. Goesmann, S. Kay, O. Kirchner, C. Lanz, B. Linke, A. C. McHardy, Folker Meyer, G. Mittenhuber, D. H. Nies, U. Niesbach-Klosgen, T. Patschkowski, C. Ruckert, O. Rupp, S. Schneiker, S. C. Schuster, F. J. Vorholter, E. Weber, A. Puhler, U. Bonas, D. Bartels, and O. Kaiser. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol. 2005. [doi] [url] BibTeX @article{thieme_insights_2005-2, title = {Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium {Xanthomonas} campestris pv. vesicatoria revealed by the complete genome sequence}, volume = {187}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16237009}, doi = {10.1128/JB.187.21.7254-7266.2005}, journal = {J Bacteriol}, author = {Thieme, F. and Koebnik, R. and Bekel, T. and Berger, C. and Boch, J. and Buttner, D. and Caldana, C. and Gaigalat, L. and Goesmann, A. and Kay, S. and Kirchner, O. and Lanz, C. and Linke, B. and McHardy, A. C. and Meyer, Folker and Mittenhuber, G. and Nies, D. H. and Niesbach-Klosgen, U. and Patschkowski, T. and Ruckert, C. and Rupp, O. and Schneiker, S. and Schuster, S. C. and Vorholter, F. J. and Weber, E. and Puhler, A. and Bonas, U. and Bartels, D. and Kaiser, O.}, year = {2005}, note = {Type: Journal Article}, keywords = {Adhesins, Bacterial Legionella pneumophila/genetics Molecular Sequence Data Plasmids/genetics Polysaccharides, Bacterial/*chemistry/*genetics Gene Order *Genome, Bacterial/genetics Base Composition Chromosomes, Bacterial/genetics Coxiella burnetii/genetics DNA, Bacterial/genetics Protein Transport/genetics *Sequence Analysis, DNA Synteny Virulence/genetics Virulence Factors/genetics Xanthomonas campestris/*genetics/physiology} } 2004 S. Rendulic, P. Jagtap, A. Rosinus, M. Eppinger, C. Baar, C. Lanz, H. Keller, C. Lambert, K. J. Evans, A. Goesmann, Folker Meyer, R. E. Sockett, and S. C. Schuster. A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science. 2004. [url] BibTeX @article{rendulic_predator_2004, title = {A predator unmasked: life cycle of {Bdellovibrio} bacteriovorus from a genomic perspective}, volume = {303}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14752164}, journal = {Science}, author = {Rendulic, S. and Jagtap, P. and Rosinus, A. and Eppinger, M. and Baar, C. and Lanz, C. and Keller, H. and Lambert, C. and Evans, K. J. and Goesmann, A. and Meyer, Folker and Sockett, R. E. and Schuster, S. C.}, year = {2004}, note = {Type: Journal Article} } D. Bartels, S. Kespohl, S. Albaum, T. Druke, A. Goesmann, J. Herold, O. Kaiser, A. Puhler, F. Pfeiffer, G. Raddatz, J. Stoye, Folker Meyer, and S. C. Schuster. BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics. 2004. [url] BibTeX @article{bartels_baccardi_2004, title = {{BACCardI} - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15514001}, journal = {Bioinformatics}, author = {Bartels, D. and Kespohl, S. and Albaum, S. and Druke, T. and Goesmann, A. and Herold, J. and Kaiser, O. and Puhler, A. and Pfeiffer, F. and Raddatz, G. and Stoye, J. and Meyer, Folker and Schuster, S. C.}, year = {2004}, note = {Type: Journal Article} } Alice C McHardy, Alexander Goesmann, Alfred Pühler, and Folker Meyer. Development of joint application strategies for two microbial gene finders. Bioinformatics. 2004. BibTeX @article{mchardy_development_2004-1, title = {Development of joint application strategies for two microbial gene finders}, volume = {20}, journal = {Bioinformatics}, author = {McHardy, Alice C and Goesmann, Alexander and Pühler, Alfred and Meyer, Folker}, year = {2004}, note = {Publisher: Oxford University Press} } Alice C McHardy, Alfred Pühler, Jörn Kalinowski, and Folker Meyer. Comparing expression level-dependent features in codon usage with protein abundance: an analysis of ‘predictive proteomics’. Proteomics. 2004. BibTeX @article{mchardy_comparing_2004-1, title = {Comparing expression level-dependent features in codon usage with protein abundance: an analysis of ‘predictive proteomics’}, volume = {4}, journal = {Proteomics}, author = {McHardy, Alice C and Pühler, Alfred and Kalinowski, Jörn and Meyer, Folker}, year = {2004}, note = {Publisher: WILEY-VCH Verlag Weinheim} } H. Kuster, N. Hohnjec, F. Krajinski, F. El Yahyaoui, K. Manthey, J. Gouzy, M. Dondrup, Folker Meyer, J. Kalinowski, L. Brechenmacher, D. van Tuinen, V. Gianinazzi-Pearson, A. Puhler, P. Gamas, and A. Becker. Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula. Journal of Biotechnology. 2004. [doi] BibTeX @article{kuster_construction_2004-2, title = {Construction and validation of {cDNA}-based {Mt6k}-{RIT} macro- and microarrays to explore root endosymbioses in the model legume {Medicago} truncatula}, volume = {108}, doi = {10.1016/j.jbiotec.2003.11.011}, journal = {Journal of Biotechnology}, author = {Kuster, H. and Hohnjec, N. and Krajinski, F. and El Yahyaoui, F. and Manthey, K. and Gouzy, J. and Dondrup, M. and Meyer, Folker and Kalinowski, J. and Brechenmacher, L. and van Tuinen, D. and Gianinazzi-Pearson, V. and Puhler, A. and Gamas, P. and Becker, A.}, year = {2004}, note = {Type: Journal Article} } 2003 A. Wilke, C. Ruckert, D. Bartels, M. Dondrup, A. Goesmann, A. T. Huser, S. Kespohl, B. Linke, M. Mahne, A. McHardy, A. Puhler, and Folker Meyer. Bioinformatics support for high-throughput proteomics. J Biotechnol. 2003. [url] BibTeX @article{wilke_bioinformatics_2003, title = {Bioinformatics support for high-throughput proteomics}, volume = {106}, url = {https://www.ncbi.nlm.nih.gov/pubmed/14651857}, journal = {J Biotechnol}, author = {Wilke, A. and Ruckert, C. and Bartels, D. and Dondrup, M. and Goesmann, A. and Huser, A. T. and Kespohl, S. and Linke, B. and Mahne, M. and McHardy, A. and Puhler, A. and Meyer, Folker}, year = {2003}, note = {Type: Journal Article} } F. J. Vorholter, T. Thias, Folker Meyer, T. Bekel, O. Kaiser, A. Puhler, and K. Niehaus. Comparison of two Xanthomonas campestris pathovar campestris genomes revealed differences in their gene composition. J Biotechnol. 2003. [url] BibTeX @article{vorholter_comparison_2003, title = {Comparison of two {Xanthomonas} campestris pathovar campestris genomes revealed differences in their gene composition}, volume = {106}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14651861}, journal = {J Biotechnol}, author = {Vorholter, F. J. and Thias, T. and Meyer, Folker and Bekel, T. and Kaiser, O. and Puhler, A. and Niehaus, K.}, year = {2003}, note = {Type: Journal Article} } A. Tauch, A. Schluter, N. Bischoff, A. Goesmann, Folker Meyer, and A. Puhler. The 79,370-bp conjugative plasmid pB4 consists of an IncP-1beta backbone loaded with a chromate resistance transposon, the strA-strB streptomycin resistance gene pair, the oxacillinase gene bla(NPS-1), and a tripartite antibiotic efflux system of the resistance-nodulation-division family. Mol Genet Genomics. 2003. [url] BibTeX @article{tauch_79370-bp_2003, title = {The 79,370-bp conjugative plasmid {pB4} consists of an {IncP}-1beta backbone loaded with a chromate resistance transposon, the {strA}-{strB} streptomycin resistance gene pair, the oxacillinase gene bla({NPS}-1), and a tripartite antibiotic efflux system of the resistance-nodulation-division family}, volume = {268}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12589432}, journal = {Mol Genet Genomics}, author = {Tauch, A. and Schluter, A. and Bischoff, N. and Goesmann, A. and Meyer, Folker and Puhler, A.}, year = {2003}, note = {Type: Journal Article} } S. Ruberg, Z. X. Tian, E. Krol, B. Linke, Folker Meyer, Y. P. Wang, A. Puhler, S. Weidner, and A. Becker. Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression. Journal of Biotechnology. 2003. [doi] BibTeX @article{ruberg_construction_2003, title = {Construction and validation of a {Sinorhizobium} meliloti whole genome {DNA} microarray: genome-wide profiling of osmoadaptive gene expression}, volume = {106}, doi = {10.1016/j.jbiotec.2003.08.005}, journal = {Journal of Biotechnology}, author = {Ruberg, S. and Tian, Z. X. and Krol, E. and Linke, B. and Meyer, Folker and Wang, Y. P. and Puhler, A. and Weidner, S. and Becker, A.}, year = {2003}, note = {Type: Journal Article} } O. Nyamsuren, F. Colditz, S. Rosendahl, M. Tamasloukht, T. Bekel, Folker Meyer, H. Kuester, P. Franken, and F. Krajinski. Transcriptional profiling of Medicago truncatula roots after infection with Aphanomyces euteiches (oomycota) identifies novel genes upregulated during this pathogenic interaction. Physiological and Molecular Plant Pathology. 2003. [doi] BibTeX @article{nyamsuren_transcriptional_2003, title = {Transcriptional profiling of {Medicago} truncatula roots after infection with {Aphanomyces} euteiches (oomycota) identifies novel genes upregulated during this pathogenic interaction}, volume = {63}, doi = {10.1016/j.pmpp.2003.09.001}, journal = {Physiological and Molecular Plant Pathology}, author = {Nyamsuren, O. and Colditz, F. and Rosendahl, S. and Tamasloukht, M. and Bekel, T. and Meyer, Folker and Kuester, H. and Franken, P. and Krajinski, F.}, year = {2003}, note = {Type: Journal Article} } Folker Meyer, A. Goesmann, A. C. McHardy, D. Bartels, T. Bekel, J. Clausen, J. Kalinowski, B. Linke, O. Rupp, R. Giegerich, and A. Puhler. GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Research. 2003. [doi] BibTeX @article{meyer_gendb_2003, title = {{GenDB} - an open source genome annotation system for prokaryote genomes}, volume = {31}, doi = {10.1093/nar/gkg312}, journal = {Nucleic Acids Research}, author = {Meyer, Folker and Goesmann, A. and McHardy, A. C. and Bartels, D. and Bekel, T. and Clausen, J. and Kalinowski, J. and Linke, B. and Rupp, O. and Giegerich, R. and Puhler, A.}, year = {2003}, note = {Type: Journal Article} } J. Kalinowski, B. Bathe, D. Bartels, N. Bischoff, M. Bott, A. Burkovski, N. Dusch, L. Eggeling, B. J. Eikmanns, L. Gaigalat, A. Goesmann, M. Hartmann, K. Huthmacher, R. Kramer, B. Linke, A. C. McHardy, Folker Meyer, B. Mockel, W. Pfefferle, A. Puhler, D. A. Rey, C. Ruckert, O. Rupp, H. Sahm, V. F. Wendisch, I. Wiegrabe, and A. Tauch. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J Biotechnol. 2003. [url] BibTeX @article{kalinowski_complete_2003, title = {The complete {Corynebacterium} glutamicum {ATCC} 13032 genome sequence and its impact on the production of {L}-aspartate-derived amino acids and vitamins}, volume = {104}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12948626}, journal = {J Biotechnol}, author = {Kalinowski, J. and Bathe, B. and Bartels, D. and Bischoff, N. and Bott, M. and Burkovski, A. and Dusch, N. and Eggeling, L. and Eikmanns, B. J. and Gaigalat, L. and Goesmann, A. and Hartmann, M. and Huthmacher, K. and Kramer, R. and Linke, B. and McHardy, A. C. and Meyer, Folker and Mockel, B. and Pfefferle, W. and Puhler, A. and Rey, D. A. and Ruckert, C. and Rupp, O. and Sahm, H. and Wendisch, V. F. and Wiegrabe, I. and Tauch, A.}, year = {2003}, note = {Type: Journal Article} } O. Kaiser, D. Bartels, T. Bekel, A. Goesmann, S. Kespohl, A. Puhler, and Folker Meyer. Whole genome shotgun sequencing guided by bioinformatics pipelines–an optimized approach for an established technique. J Biotechnol. 2003. [url] BibTeX @article{kaiser_whole_2003, title = {Whole genome shotgun sequencing guided by bioinformatics pipelines–an optimized approach for an established technique}, volume = {106}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14651855}, journal = {J Biotechnol}, author = {Kaiser, O. and Bartels, D. and Bekel, T. and Goesmann, A. and Kespohl, S. and Puhler, A. and Meyer, Folker}, year = {2003}, note = {Type: Journal Article} } M. Dondrup, A. Goesmann, D. Bartels, J. Kalinowski, L. Krause, B. Linke, O. Rupp, A. Sczyrba, A. Puhler, and Folker Meyer. EMMA: a platform for consistent storage and efficient analysis of microarray data. Journal of Biotechnology. 2003. [doi] BibTeX @article{dondrup_emma_2003, title = {{EMMA}: a platform for consistent storage and efficient analysis of microarray data}, volume = {106}, doi = {10.1016/j.jbiotec.2003.08.010}, journal = {Journal of Biotechnology}, author = {Dondrup, M. and Goesmann, A. and Bartels, D. and Kalinowski, J. and Krause, L. and Linke, B. and Rupp, O. and Sczyrba, A. and Puhler, A. and Meyer, Folker}, year = {2003}, note = {Type: Journal Article} } C. Baar, M. Eppinger, G. Raddatz, J. Simon, C. Lanz, O. Klimmek, R. Nandakumar, R. Gross, A. Rosinus, H. Keller, P. Jagtap, B. Linke, Folker Meyer, H. Lederer, and S. C. Schuster. Complete genome sequence and analysis of Wolinella succinogenes. Proceedings of the National Academy of Sciences of the United States of America. 2003. [doi] BibTeX @article{baar_complete_2003, title = {Complete genome sequence and analysis of {Wolinella} succinogenes}, volume = {100}, doi = {10.1073/pnas.1932838100}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, author = {Baar, C. and Eppinger, M. and Raddatz, G. and Simon, J. and Lanz, C. and Klimmek, O. and Nandakumar, R. and Gross, R. and Rosinus, A. and Keller, H. and Jagtap, P. and Linke, B. and Meyer, Folker and Lederer, H. and Schuster, S. C.}, year = {2003}, note = {Type: Journal Article} } Anne Wulf, Katja Manthey, Jasmin Doll, Andreas M Perlick, Burkhard Linke, Thomas Bekel, Folker Meyer, Philipp Franken, Helge Küster, and Franziska Krajinski. Transcriptional changes in response to arbuscular mycorrhiza development in the model plant Medicago truncatula. Molecular Plant-Microbe Interactions. 2003. BibTeX @article{wulf_transcriptional_2003-2, title = {Transcriptional changes in response to arbuscular mycorrhiza development in the model plant {Medicago} truncatula}, volume = {16}, journal = {Molecular Plant-Microbe Interactions}, author = {Wulf, Anne and Manthey, Katja and Doll, Jasmin and Perlick, Andreas M and Linke, Burkhard and Bekel, Thomas and Meyer, Folker and Franken, Philipp and Küster, Helge and Krajinski, Franziska}, year = {2003}, note = {Publisher: The American Phytopathological Society} } Andreas Tauch, Andreas Schlüter, N Bischoff, Alexander Goesmann, F Meyer, and Alfred Pühler. The 79,370-bp conjugative plasmid pB4 consists of an IncP-1β backbone loaded with a chromate resistance transposon, the strA-strB streptomycin resistance gene pair, the oxacillinase gene bla NPS-1, and a tripartite antibiotic efflux system of the resistance-nodulation-division family. Molecular Genetics and Genomics. 2003. BibTeX @article{tauch_79370-bp_2003-1, title = {The 79,370-bp conjugative plasmid {pB4} consists of an {IncP}-1β backbone loaded with a chromate resistance transposon, the {strA}-{strB} streptomycin resistance gene pair, the oxacillinase gene bla {NPS}-1, and a tripartite antibiotic efflux system of the resistance-nodulation-division family}, volume = {268}, journal = {Molecular Genetics and Genomics}, author = {Tauch, Andreas and Schlüter, Andreas and Bischoff, N and Goesmann, Alexander and Meyer, F and Pühler, Alfred}, year = {2003}, note = {Publisher: Springer-Verlag} } Alexander Goesmann, Burkhard Linke, Oliver Rupp, Lutz Krause, Daniela Bartels, Michael Dondrup, Alice C McHardy, Andreas Wilke, Alfred Pühler, and Folker Meyer. Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology. Journal of biotechnology. 2003. BibTeX @article{goesmann_building_2003-1, title = {Building a {BRIDGE} for the integration of heterogeneous data from functional genomics into a platform for systems biology}, volume = {106}, journal = {Journal of biotechnology}, author = {Goesmann, Alexander and Linke, Burkhard and Rupp, Oliver and Krause, Lutz and Bartels, Daniela and Dondrup, Michael and McHardy, Alice C and Wilke, Andreas and Pühler, Alfred and Meyer, Folker}, year = {2003}, note = {Publisher: Elsevier} } Olaf Kaiser, Daniela Bartels, Thomas Bekel, Alexander Goesmann, Sebastian Kespohl, Alfred Pühler, and Folker Meyer. Whole genome shotgun sequencing guided by bioinformatics pipelines—an optimized approach for an established technique. Journal of biotechnology. 2003. BibTeX @article{kaiser_whole_2003-1, title = {Whole genome shotgun sequencing guided by bioinformatics pipelines—an optimized approach for an established technique}, volume = {106}, journal = {Journal of biotechnology}, author = {Kaiser, Olaf and Bartels, Daniela and Bekel, Thomas and Goesmann, Alexander and Kespohl, Sebastian and Pühler, Alfred and Meyer, Folker}, year = {2003}, note = {Publisher: Elsevier} } M Dondrup, A Goesmann, D Bartels, J Kalinowski, L Krause, B Linke, O Rupp, A Sczyrba, A Pühler, and Folker Meyer. Archer, DA, see Punt, PJ (106) 23. Journal of Biotechnology. 2003. BibTeX @article{dondrup_archer_2003, title = {Archer, {DA}, see {Punt}, {PJ} (106) 23}, volume = {106}, journal = {Journal of Biotechnology}, author = {Dondrup, M and Goesmann, A and Bartels, D and Kalinowski, J and Krause, L and Linke, B and Rupp, O and Sczyrba, A and Pühler, A and Meyer, Folker}, year = {2003} } Jörn Kalinowski, Brigitte Bathe, Daniela Bartels, Nicole Bischoff, Michael Bott, Andreas Burkovski, Nicole Dusch, Lothar Eggeling, Bernhard J Eikmanns, Lars Gaigalat, and Folker Meyer. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of l-aspartate-derived amino acids and vitamins. Journal of Biotechnology. 2003. BibTeX @article{kalinowski_complete_2004, title = {The complete {Corynebacterium} glutamicum {ATCC} 13032 genome sequence and its impact on the production of l-aspartate-derived amino acids and vitamins}, volume = {104}, journal = {Journal of Biotechnology}, author = {Kalinowski, Jörn and Bathe, Brigitte and Bartels, Daniela and Bischoff, Nicole and Bott, Michael and Burkovski, Andreas and Dusch, Nicole and Eggeling, Lothar and Eikmanns, Bernhard J and Gaigalat, Lars and Meyer, Folker}, year = {2003} } 2002 A. Goesmann, M. Haubrock, Folker Meyer, J. Kalinowski, and R. Giegerich. PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics. 2002. [url] BibTeX @article{goesmann_pathfinder_2002, title = {{PathFinder}: reconstruction and dynamic visualization of metabolic pathways}, volume = {18}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11836220}, journal = {Bioinformatics}, author = {Goesmann, A. and Haubrock, M. and Meyer, Folker and Kalinowski, J. and Giegerich, R.}, year = {2002}, note = {Type: Journal Article} } 2001 Folker Meyer. GENDB: a second generation genome annotation system. 2001. BibTeX @article{meyer_gendb_2001, title = {{GENDB}: a second generation genome annotation system}, author = {Meyer, Folker}, year = {2001} } 1998 J. Stoye, D. Evers, and Folker Meyer. Rose: generating sequence families. Bioinformatics. 1998. [url] BibTeX @article{stoye_rose_1998, title = {Rose: generating sequence families}, volume = {14}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9545448}, journal = {Bioinformatics}, author = {Stoye, J. and Evers, D. and Meyer, Folker}, year = {1998}, note = {Type: Journal Article} } Jens Stoye, Dirk Evers, and Folker Meyer. Rose: generating sequence families.. Bioinformatics (Oxford, England). 1998. BibTeX @article{stoye_rose_1998-2, title = {Rose: generating sequence families.}, volume = {14}, journal = {Bioinformatics (Oxford, England)}, author = {Stoye, Jens and Evers, Dirk and Meyer, Folker}, year = {1998} } 1997 Jens Stoye, Dirk Evers, and Folker Meyer. Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions.. Ismb. 1997. BibTeX @inproceedings{stoye_generating_1997-1, title = {Generating {Benchmarks} for {Multiple} {Sequence} {Alignments} and {Phylogenic} {Reconstructions}.}, booktitle = {Ismb}, author = {Stoye, Jens and Evers, Dirk and Meyer, Folker}, year = {1997} } 1996 R. Giegerich, Folker Meyer, and C. Schleiermacher. GeneFisher–software support for the detection of postulated genes. Proc Int Conf Intell Syst Mol Biol. 1996. [url] BibTeX @article{giegerich_genefishersoftware_1996, title = {{GeneFisher}–software support for the detection of postulated genes}, volume = {4}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8877506}, journal = {Proc Int Conf Intell Syst Mol Biol}, author = {Giegerich, R. and Meyer, Folker and Schleiermacher, C.}, year = {1996}, note = {Type: Journal Article} } Robert Giegerich, Folker Meyer, and Chris Schleiermacher. GeneFisher-software support for the detection of postulated genes.. ISMB. 1996. BibTeX @inproceedings{giegerich_genefisher-software_1996, title = {{GeneFisher}-software support for the detection of postulated genes.}, volume = {4}, booktitle = {{ISMB}}, author = {Giegerich, Robert and Meyer, Folker and Schleiermacher, Chris}, year = {1996} } </div>
@article{handley_complete_2014, title = {The complete genome sequence for putative {H}(2)- and {S}-oxidizer {Candidatus} {Sulfuricurvum} sp., assembled de novo from an aquifer-derived metagenome}, volume = {16}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24628880}, doi = {10.1111/1462-2920.12453}, journal = {Environ Microbiol}, author = {Handley, K. M. and Bartels, D. and O'Loughlin, E. J. and Williams, K. H. and Trimble, W. L. and Skinner, K. and Gilbert, J. A. and Desai, N. and Glass, E. M. and Paczian, T. and Wilke, A. and Antonopoulos, D. and Kemner, K. M. and Meyer, Folker}, year = {2014}, note = {Type: Journal Article} }
@article{glass_mixs-be_2014, title = {{MIxS}-{BE}: a {MIxS} extension defining a minimum information standard for sequence data from the built environment}, volume = {8}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24152717}, doi = {10.1038/ismej.2013.176}, journal = {ISME J}, author = {Glass, E. M. and Dribinsky, Y. and Yilmaz, P. and Levin, H. and Van Pelt, R. and Wendel, D. and Wilke, A. and Eisen, J. A. and Huse, S. and Shipanova, A. and Sogin, M. and Stajich, J. and Knight, R. and Meyer, Folker and Schriml, L. M.}, year = {2014}, note = {Type: Journal Article} }
@article{field_genomic_2014, title = {Genomic standards consortium projects}, volume = {9}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25197446}, doi = {10.4056/sigs.5559680}, journal = {Stand Genomic Sci}, author = {Field, D. and Sterk, P. and Kottmann, R. and De Smet, J. W. and Amaral-Zettler, L. and Cochrane, G. and Cole, J. R. and Davies, N. and Dawyndt, P. and Garrity, G. M. and Gilbert, J. A. and Glockner, F. O. and Hirschman, L. and Klenk, H. P. and Knight, R. and Kyrpides, N. and Meyer, Folker and Karsch-Mizrachi, I. and Morrison, N. and Robbins, R. and San Gil, I. and Sansone, S. and Schriml, L. and Tatusova, T. and Ussery, D. and Yilmaz, P. and White, O. and Wooley, J. and Caporaso, G.}, year = {2014}, note = {Type: Journal Article} }
@article{bischof_metazen_2014, title = {Metazen - metadata capture for metagenomes}, volume = {9}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25780508}, doi = {10.1186/1944-3277-9-18}, journal = {Stand Genomic Sci}, author = {Bischof, J. and Harrison, T. and Paczian, T. and Glass, E. and Wilke, A. and Meyer, Folker}, year = {2014}, note = {Type: Journal Article} }
@incollection{thomas_123_2014, title = {123 of {Metagenomics}}, booktitle = {Encyclopedia of {Metagenomics}}, publisher = {Springer New York}, author = {Thomas, T. and Gilbert, J. and Meyer, Folker}, year = {2014} }
@article{owens_characterizing_2014, title = {Characterizing {Sequencing} {Samples} with k-mer {Spectra} for {Good} and {Evil}}, volume = {25}, journal = {Journal of biomolecular techniques: JBT}, author = {Owens, Sarah and Keegan, Kevin and Meyer, Folker and Trimble, William}, year = {2014}, note = {Publisher: The Association of Biomolecular Resource Facilities} }
@inproceedings{tang_workload_2014, title = {Workload characterization for {MG}-{RAST} metagenomic data analytics service in the cloud}, booktitle = {2014 {IEEE} {International} {Conference} on {Big} {Data} ({Big} {Data})}, publisher = {IEEE}, author = {Tang, Wei and Bischof, Jared and Desai, Narayan and Mahadik, Kanak and Gerlach, Wolfgang and Harrison, Travis and Wilke, Andreas and Meyer, Folker}, year = {2014} }
@inproceedings{tang_data-aware_2014, title = {Data-aware resource scheduling for multicloud workflows: {A} fine-grained simulation approach}, booktitle = {2014 {IEEE} 6th {International} {Conference} on {Cloud} {Computing} {Technology} and {Science}}, publisher = {IEEE}, author = {Tang, Wei and Jenkins, Jonathan and Meyer, Folker and Ross, Robert and Kettimuthu, Rajkumar and Winkler, Linda and Yang, Xi and Lehman, Thomas and Desai, Narayan}, year = {2014} }
@inproceedings{gerlach_skyport-container-based_2014, title = {Skyport-container-based execution environment management for multi-cloud scientific workflows}, booktitle = {2014 5th {International} {Workshop} on {Data}-{Intensive} {Computing} in the {Clouds}}, publisher = {IEEE}, author = {Gerlach, Wolfgang and Tang, Wei and Keegan, Kevin and Harrison, Travis and Wilke, Andreas and Bischof, Jared and D'Souza, Mark and Devoid, Scott and Murphy-Olson, Daniel and Desai, Narayan and Meyer, Folker}, year = {2014} }
@article{bischof_metazen_2014-1, title = {Metazen - {Metadata} {Capture} for {Metagenomes}}, volume = {9}, journal = {Standards in Genomic Science}, author = {Bischof, Jared and Harrison, Travis and Paczian, Tobias and Glass, Elizabeth and Wilke, Andreas and Meyer, Folker}, year = {2014} }
@article{handley_complete_2014-2, title = {The complete genome sequence for putative {H} 2-and {S}-oxidizer {C} andidatus {Sulfuricurvum} sp., assembled de novo from an aquifer-derived metagenome}, volume = {16}, journal = {Environmental microbiology}, author = {Handley, Kim M and Bartels, Daniela and O'Loughlin, Edward J and Williams, Kenneth H and Trimble, William L and Skinner, Kelly and Gilbert, Jack A and Desai, Narayan and Glass, Elizabeth M and Paczian, Tobias and {others}}, year = {2014} }
@article{davies_founding_2014-1, title = {The founding charter of the {Genomic} {Observatories} {Network}}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24606731}, doi = {10.1186/2047-217X-3-2}, journal = {Gigascience}, author = {Davies, N. and Field, D. and Amaral-Zettler, L. and Clark, M. S. and Deck, J. and Drummond, A. and Faith, D. P. and Geller, J. and Gilbert, J. and Glockner, F. O. and Hirsch, P. R. and Leong, J. A. and Meyer, C. and Obst, M. and Planes, S. and Scholin, C. and Vogler, A. P. and Gates, R. D. and Toonen, R. and Berteaux-Lecellier, V. and Barbier, M. and Barker, K. and Bertilsson, S. and Bicak, M. and Bietz, M. J. and Bobe, J. and Bodrossy, L. and Borja, A. and Coddington, J. and Fuhrman, J. and Gerdts, G. and Gillespie, R. and Goodwin, K. and Hanson, P. C. and Hero, J. M. and Hoekman, D. and Jansson, J. and Jeanthon, C. and Kao, R. and Klindworth, A. and Knight, R. and Kottmann, R. and Koo, M. S. and Kotoulas, G. and Lowe, A. J. and Marteinsson, V. T. and Meyer, Folker and Morrison, N. and Myrold, D. D. and Pafilis, E. and Parker, S. and Parnell, J. J. and Polymenakou, P. N. and Ratnasingham, S. and Roderick, G. K. and Rodriguez-Ezpeleta, N. and Schonrogge, K. and Simon, N. and Valette-Silver, N. J. and Springer, Y. P. and Stone, G. N. and Stones-Havas, S. and Sansone, S. A. and Thibault, K. M. and Wecker, P. and Wichels, A. and Wooley, J. C. and Yahara, T. and Zingone, A. and COS, G. Os}, year = {2014}, note = {Type: Journal Article} }
@article{kyrpides_genomic_2014-1, title = {Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains}, volume = {12}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25093819}, doi = {10.1371/journal.pbio.1001920}, journal = {PLoS Biol}, author = {Kyrpides, N. C. and Hugenholtz, P. and Eisen, J. A. and Woyke, T. and Goker, M. and Parker, C. T. and Amann, R. and Beck, B. J. and Chain, P. S. and Chun, J. and Colwell, R. R. and Danchin, A. and Dawyndt, P. and Dedeurwaerdere, T. and DeLong, E. F. and Detter, J. C. and De Vos, P. and Donohue, T. J. and Dong, X. Z. and Ehrlich, D. S. and Fraser, C. and Gibbs, R. and Gilbert, J. and Gilna, P. and Glockner, F. O. and Jansson, J. K. and Keasling, J. D. and Knight, R. and Labeda, D. and Lapidus, A. and Lee, J. S. and Li, W. J. and Ma, J. and Markowitz, V. and Moore, E. R. and Morrison, M. and Meyer, Folker and Nelson, K. E. and Ohkuma, M. and Ouzounis, C. A. and Pace, N. and Parkhill, J. and Qin, N. and Rossello-Mora, R. and Sikorski, J. and Smith, D. and Sogin, M. and Stevens, R. and Stingl, U. and Suzuki, K. and Taylor, D. and Tiedje, J. M. and Tindall, B. and Wagner, M. and Weinstock, G. and Weissenbach, J. and White, O. and Wang, J. and Zhang, L. and Zhou, Y. G. and Field, D. and Whitman, W. B. and Garrity, G. M. and Klenk, H. P.}, year = {2014}, note = {Type: Journal Article}, keywords = {DNA, Archaea/classification/genetics Bacteria/classification/genetics Databases, Archaeal/*genetics Genome, Bacterial/*genetics *Genomics Phylogeny *Sequence Analysis, Genetic Genome} }
@article{myrold_terragenome-soil_2014-1, title = {Terragenome-{The} {Soil} {Metagenome} {Network}}, author = {Myrold, David and Bailey, Mark and Jansson, Janet and Meyer, Folker and Tiedje, James and Triplett, Eric and Vogel, Timothy}, year = {2014} }
@inproceedings{aufdenkampe_community-driven_2014-1, title = {The community-driven {BiG} {CZ} software system for integration and analysis of bio- and geoscience data in the critical zone}, volume = {2014}, booktitle = {{AGU} {Fall} {Meeting} {Abstracts}}, author = {Aufdenkampe, A. K. and Mayorga, E. and Horsburgh, J. S. and Lehnert, K. A. and Zaslavsky, I. and Valentine, D. W., Jr. and Richard, S. M. and Cheetham, R. and Meyer, Folker and Henry, C. and Berg-Cross, G. and Packman, A. I. and Aronson, E. L.}, year = {2014}, keywords = {1904 Community standards, 1908 Cyberinfrastructure, 1972 Sensor web, 9805 Instruments useful in three or more fields} }
@incollection{meyer_metagenomics_2014-1, title = {{METAGENOMICS}: {A} {GUIDE} {FROM} {SAMPLING} {TO} {DATA} {ANALYSIS}}, booktitle = {The {Role} of {Bioinformatics} in {Agriculture}}, publisher = {Apple Academic Press}, author = {Meyer, Folker}, year = {2014} }
@article{RN30, author = {Rambow, F. and Bechadergue, A. and Saintigny, G. and Morizot, F. and Mahe, C. and Larue, L.}, title = {miR-330-5p targets tyrosinase and induces depigmentation}, journal = {J Invest Dermatol}, volume = {134}, number = {11}, pages = {2846-2849}, issn = {1523-1747 (Electronic) 0022-202X (Linking)}, doi = {10.1038/jid.2014.231}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24862846}, year = {2014}, type = {Journal Article} }
@article{RN11, author = {Domingues, M. J. and Rambow, F. and Job, B. and Papon, L. and Liu, W. and Larue, L. and Bonaventure, J.}, title = {beta-catenin inhibitor ICAT modulates the invasive motility of melanoma cells}, journal = {Cancer Res}, volume = {74}, number = {7}, pages = {1983-95}, issn = {1538-7445 (Electronic) 0008-5472 (Linking)}, doi = {10.1158/0008-5472.CAN-13-0920}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24514042}, year = {2014}, type = {Journal Article} }
@article{althoff_mir-137_2013, title = {{MiR}-137 functions as a tumor suppressor in neuroblastoma by downregulating {KDM1A}}, volume = {133}, copyright = {Copyright © 2013 UICC}, issn = {1097-0215}, url = {http://onlinelibrary.wiley.com/doi/10.1002/ijc.28091/abstract}, doi = {10.1002/ijc.28091}, language = {en}, number = {5}, urldate = {2013-09-19}, journal = {International Journal of Cancer}, author = {Althoff, Kristina and Beckers, Anneleen and Odersky, Andrea and Mestdagh, Pieter and Köster, Johannes and Bray, Isabella M. and Bryan, Kenneth and Vandesompele, Jo and Speleman, Frank and Stallings, Raymond L. and Schramm, Alexander and Eggert, Angelika and Sprüssel, Annika and Schulte, Johannes H.}, year = {2013}, keywords = {Epigenetics, LSD1, miR-137, neuroblastoma}, pages = {1064--1073}, file = {Althoff et al_2013_MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A.pdf:/vol/home/koester/Dropbox/xpapers/Althoff et al_2013_MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/53ZUJG3J/abstract.html:text/html} }
@article{schramm_next-generation_2013, title = {Next-generation {RNA} sequencing reveals differential expression of {MYCN} target genes and suggests the {mTOR} pathway as a promising therapy target in {MYCN}-amplified neuroblastoma}, volume = {132}, copyright = {Copyright © 2012 UICC}, issn = {1097-0215}, url = {http://onlinelibrary.wiley.com/doi/10.1002/ijc.27787/abstract}, doi = {10.1002/ijc.27787}, language = {en}, number = {3}, urldate = {2013-09-19}, journal = {International Journal of Cancer}, author = {Schramm, Alexander and Köster, Johannes and Marschall, Tobias and Martin, Marcel and Schwermer, Melanie and Fielitz, Kathrin and Büchel, Gabriele and Barann, Matthias and Esser, Daniela and Rosenstiel, Philip and Rahmann, Sven and Eggert, Angelika and Schulte, Johannes H.}, year = {2013}, keywords = {next-generation sequencing, neuroblastoma, mTOR pathway, MYCN}, pages = {E106--E115}, file = {Schramm et al_2013_Next-generation RNA sequencing reveals differential expression of MYCN target.pdf:/vol/home/koester/Dropbox/xpapers/Schramm et al_2013_Next-generation RNA sequencing reveals differential expression of MYCN target.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/AVDZP6HP/abstract\;jsessionid=4DCF5E43C6EE4F573A82C5543C1AE118.html:text/html} }
@article{RN301, author = {Magin, Simon. and Saha, J. and Wang, M. and Mladenova, V. and Coym, N. and Iliakis, G.}, title = {Lipofection and nucleofection of substrate plasmid can generate widely different readings of DNA end-joining efficiency in different cell lines}, journal = {DNA repair}, volume = {12}, number = {2}, pages = {148-60}, note = {Magin, Simon Saha, Janapriya Wang, Minli Mladenova, Veronika Coym, Nadine Iliakis, George Netherlands DNA Repair (Amst). 2013 Feb 1;12(2):148-60. doi: 10.1016/j.dnarep.2012.11.008. Epub 2013 Jan 1.}, issn = {1568-7856 (Electronic) 1568-7856 (Linking)}, doi = {10.1016/j.dnarep.2012.11.008}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23286905}, year = {2013}, type = {Journal Article} }
@article{RN318, author = {Mladenov, E. and Magin, Simon. and Soni, A. and Iliakis, G.}, title = {DNA double-strand break repair as determinant of cellular radiosensitivity to killing and target in radiation therapy}, journal = {Frontiers in oncology}, volume = {3}, pages = {113}, note = {Mladenov, Emil Magin, Simon Soni, Aashish Iliakis, George Switzerland Front Oncol. 2013 May 10;3:113. doi: 10.3389/fonc.2013.00113. Print 2013.}, issn = {2234-943X (Electronic) 2234-943X (Linking)}, doi = {10.3389/fonc.2013.00113}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23675572}, year = {2013}, type = {Journal Article} }
@article{Kraiselburd2013TheLP, title = {The LOV Protein of Xanthomonas citri subsp. citri Plays a Significant Role in the Counteraction of Plant Immune Responses during Citrus Canker}, author = {Kraiselburd, Ivana and Daurelio, Lucas Dami{\'a}n and Tondo, Mar{\'i}a Laura and Merelo, Paz and Cortadi, Adriana A. and Tal{\'o}n, Manuel and Tadeo, Francisco R and Orellano, Elena G}, journal = {PLoS ONE}, year = {2013}, volume = {8} }
@inproceedings{schmithausen2013association, title = {Association of antibiotic usage with MRSA and ESBL prevalence in pig farms}, author = {Schmithausen, Ricarda M. and Schulze-Geisthoevel, S and Stemmer, F and Bierbaum, G and Hoerauf, A and Exner, M and Bekeredjian-Ding, I and Petersen, B}, booktitle = {INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY}, volume = {303}, year = {2013}, organization = {ELSEVIER GMBH, URBAN \& FISCHER VERLAG OFFICE JENA, PO BOX 100537, 07705 JENA~…} }
@article{williams_rapid_2013, title = {Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes}, volume = {14}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23924250}, doi = {10.1186/1471-2164-14-537}, journal = {BMC Genomics}, author = {Williams, D. and Trimble, W. L. and Shilts, M. and Meyer, Folker and Ochman, H.}, year = {2013}, note = {Type: Journal Article} }
@article{claud_bacterial_2013, title = {Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants}, volume = {1}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24450928}, doi = {10.1186/2049-2618-1-20}, journal = {Microbiome}, author = {Claud, E. C. and Keegan, K. P. and Brulc, J. M. and Lu, L. and Bartels, D. and Glass, E. and Chang, E. B. and Meyer, Folker and Antonopoulos, D. A.}, year = {2013}, note = {Type: Journal Article} }
@article{vincent_analysis_2013, title = {Analysis of {Shotgun} {Metagenomes} with {MG}-{RAST}}, volume = {24}, journal = {Journal of Biomolecular Techniques: JBT}, author = {Vincent, James and Wilke, A and Bischof, J and Desai, N and D'Souza, M and Glass, E and Handley, K and Harrison, T and Howe, A and Keegan, K and Meyer, Folker}, year = {2013}, note = {Publisher: The Association of Biomolecular Resource Facilities} }
@article{wilke_mg-rast_2013, title = {{MG}-{RAST} technical report and manual for version 3.3. 6–{Rev} 1}, journal = {Lemont, IL: Argonne National Laboratory}, author = {Wilke, Andreas and Glass, E and Bischof, Jared and Braithwaite, Daniel and Souza, M and Gerlach, Wolfgang}, year = {2013} }
@incollection{wilke_metagenomics_2013, title = {A metagenomics portal for a democratized sequencing world}, volume = {531}, booktitle = {Methods in {Enzymology}}, publisher = {Academic Press}, author = {Wilke, Andreas and Glass, Elizabeth M and Bartels, Daniela and Bischof, Jared and Braithwaite, Daniel and D’Souza, Mark and Gerlach, Wolfgang and Harrison, Travis and Keegan, Kevin and Matthews, Hunter and Meyer, Folker}, year = {2013} }
@inproceedings{elizabeth_m_glass_mixs-be_2013, title = {{MIxS}-{BE}: a {MIxS} extension defining a minimum information standard for sequence data from the built environment}, booktitle = {{ISME}}, author = {Glass, Elizabeth M. and Dribinsky, Yekaterina and Yilamz, Pelin and Meyer, Folker and Schriml, Lynn M.}, year = {2013} }
@inproceedings{tang_scalable_2013, title = {A {Scalable} {Data} {Analysis} {Platform} for {Metagenomics}}, booktitle = {2013 {IEEE} {International} {Conference} on {Big} {Data}}, author = {Tang, Wei and Wilkening, Jared and Desai, Narayan and Gerlach, Wolfgang and Wilke, Andreas and Meyer, Folker}, year = {2013} }
@article{tang_building_2013, title = {Building {Scalable} {Data} {Management} and {Analysis} {Infrastructure} for {Metagenomics}}, author = {Tang, Wei and Wilkening, Jared and Bischof, Jared and Gerlach, Wolfgang and Wilke, Andreas and Desai, Narayan and Meyer, Folker}, year = {2013} }
@inproceedings{meyer30_big_2013, title = {{BIG} {DATA} {IN} {BIOLOGY}: {PITFALLS} {WHEN} {USING} {SHOTGUN} {METAGENOMICS} {TO} {DEFINE} {HYPOTHESES} {ABOUT} {MICROBIAL} {COMMUNITIES}}, booktitle = {The {Science} and {Applications} of {Microbial} {Genomics}: {Workshop} {Summary}}, publisher = {National Academies Press}, author = {Meyer30, Folker}, year = {2013} }
@article{young_multiphasic_2013-1, title = {Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis}, volume = {1}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24451366}, doi = {10.1186/2049-2618-1-9}, journal = {Microbiome}, author = {Young, V. B. and Raffals, L. H. and Huse, S. M. and Vital, M. and Dai, D. and Schloss, P. D. and Brulc, J. M. and Antonopoulos, D. A. and Arrieta, R. L. and Kwon, J. H. and Reddy, K. G. and Hubert, N. A. and Grim, S. L. and Vineis, J. H. and Dalal, S. and Morrison, H. G. and Eren, A. M. and Meyer, Folker and Schmidt, T. M. and Tiedje, J. M. and Chang, E. B. and Sogin, M. L.}, year = {2013}, note = {Type: Journal Article} }
@article{RN14, author = {Gallagher, S. J. and Rambow, F. and Kumasaka, M. and Champeval, D. and Bellacosa, A. and Delmas, V. and Larue, L.}, title = {Beta-catenin inhibits melanocyte migration but induces melanoma metastasis}, journal = {Oncogene}, volume = {32}, number = {17}, pages = {2230-8}, issn = {1476-5594 (Electronic) 0950-9232 (Linking)}, doi = {10.1038/onc.2012.229}, url = {https://www.ncbi.nlm.nih.gov/pubmed/22665063}, year = {2013}, type = {Journal Article} }
@article{koster_snakemakescalable_2012, title = {Snakemake—a scalable bioinformatics workflow engine}, volume = {28}, issn = {1367-4803}, url = {https://academic.oup.com/bioinformatics/article/28/19/2520/290322}, doi = {10.1093/bioinformatics/bts480}, language = {en}, number = {19}, urldate = {2019-05-03}, journal = {Bioinformatics}, author = {Köster, Johannes and Rahmann, Sven}, month = oct, year = {2012}, pages = {2520--2522}, file = {Full Text PDF:/home/johannes/Zotero/storage/88LHZAD5/Köster and Rahmann - 2012 - Snakemake—a scalable bioinformatics workflow engin.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/GCC3G4A6/290322.html:text/html} }
@inproceedings{koster_building_2012, address = {Dagstuhl, Germany}, series = {{OpenAccess} {Series} in {Informatics} ({OASIcs})}, title = {Building and {Documenting} {Workflows} with {Python}-{Based} {Snakemake}}, volume = {26}, copyright = {All rights reserved}, isbn = {978-3-939897-44-6}, url = {http://drops.dagstuhl.de/opus/volltexte/2012/3717}, doi = {http://dx.doi.org/10.4230/OASIcs.GCB.2012.49}, booktitle = {German {Conference} on {Bioinformatics} 2012}, publisher = {Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik}, author = {Köster, Johannes and Rahmann, Sven}, editor = {Böcker, Sebastian and Hufsky, Franziska and Scheubert, Kerstin and Schleicher, Jana and Schuster, Stefan}, year = {2012}, pages = {49--56}, annote = {Keywords: workflow engine, dependency graph, knapsack problem, Python, high-throughput sequencing, next-generation sequencing} }
@article{Kraiselburd2012ALP, title = {A LOV Protein Modulates the Physiological Attributes of Xanthomonas axonopodis pv. citri Relevant for Host Plant Colonization}, author = {Kraiselburd, Ivana and Alet, Anal{\'i}a I. and Tondo, Mar{\'i}a Laura and Petrocelli, Silvana and Daurelio, Lucas Dami{\'a}n and Monz{\'o}n, Jesica and Ruiz, Oscar Adolfo and Losi, Aba and Orellano, Elena G}, journal = {PLoS ONE}, year = {2012}, volume = {7} }
@article{schmithausen2012mrsa, title = {MRSA in Mensch, Tier und Lebensmitteln--Eine {\"U}bersicht}, author = {Schmithausen, Ricarda M. and Raab, V and Petersen, B}, journal = {Aktuelle Ern{\"a}hrungsmedizin}, volume = {37}, year = {2012} }
@article{wilke_m5nr_2012, title = {The {M5nr}: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools}, volume = {13}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22720753}, doi = {10.1186/1471-2105-13-141}, journal = {BMC Bioinformatics}, author = {Wilke, A. and Harrison, T. and Wilkening, J. and Field, D. and Glass, E. M. and Kyrpides, N. and Mavrommatis, K. and Meyer, Folker}, year = {2012}, note = {Type: Journal Article} }
@article{trimble_short-read_2012, title = {Short-read reading-frame predictors are not created equal: sequence error causes loss of signal}, volume = {13}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22839106}, doi = {10.1186/1471-2105-13-183}, journal = {BMC Bioinformatics}, author = {Trimble, W. L. and Keegan, K. P. and D'Souza, M. and Wilke, A. and Wilkening, J. and Gilbert, J. and Meyer, Folker}, year = {2012}, note = {Type: Journal Article} }
@article{thomas_metagenomics_2012, title = {Metagenomics - a guide from sampling to data analysis}, volume = {2}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22587947}, doi = {10.1186/2042-5783-2-3}, journal = {Microb Inform Exp}, author = {Thomas, T. and Gilbert, J. and Meyer, Folker}, year = {2012}, note = {Type: Journal Article} }
@article{mcdonald_biological_2012, title = {The {Biological} {Observation} {Matrix} ({BIOM}) format or: how {I} learned to stop worrying and love the ome-ome}, volume = {1}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23587224}, doi = {10.1186/2047-217X-1-7}, journal = {Gigascience}, author = {McDonald, D. and Clemente, J. C. and Kuczynski, J. and Rideout, J. R. and Stombaugh, J. and Wendel, D. and Wilke, A. and Huse, S. and Hufnagle, J. and Meyer, Folker and Knight, R. and Caporaso, J. G.}, year = {2012}, note = {Type: Journal Article} }
@article{knight_unlocking_2012, title = {Unlocking the potential of metagenomics through replicated experimental design}, volume = {30}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22678395}, doi = {10.1038/nbt.2235}, journal = {Nat Biotechnol}, author = {Knight, R. and Jansson, J. and Field, D. and Fierer, N. and Desai, N. and Fuhrman, J. A. and Hugenholtz, P. and van der Lelie, D. and Meyer, Folker and Stevens, R. and Bailey, M. J. and Gordon, J. I. and Kowalchuk, G. A. and Gilbert, J. A.}, year = {2012}, note = {Type: Journal Article} }
@article{keegan_platform-independent_2012, title = {A platform-independent method for detecting errors in metagenomic sequencing data: {DRISEE}}, volume = {8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22685393}, doi = {10.1371/journal.pcbi.1002541}, journal = {PLoS Comput Biol}, author = {Keegan, K. P. and Trimble, W. L. and Wilkening, J. and Wilke, A. and Harrison, T. and D'Souza, M. and Meyer, Folker}, year = {2012}, note = {Type: Journal Article} }
@article{gilbert_report_2012, title = {Report of the 13(th) {Genomic} {Standards} {Consortium} {Meeting}, {Shenzhen}, {China}, {March} 4-7, 2012}, volume = {6}, url = {https://www.ncbi.nlm.nih.gov/pubmed/22768370}, doi = {10.4056/sigs.2876184}, journal = {Stand Genomic Sci}, author = {Gilbert, J. A. and Bao, Y. and Wang, H. and Sansone, S. A. and Edmunds, S. C. and Morrison, N. and Meyer, Folker and Schriml, L. M. and Davies, N. and Sterk, P. and Wilkening, J. and Garrity, G. M. and Field, D. and Robbins, R. and Smith, D. P. and Mizrachi, I. and Moreau, C.}, year = {2012}, note = {Type: Journal Article} }
@article{desai_genomics_2012, title = {From genomics to metagenomics}, volume = {23}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22227326}, doi = {10.1016/j.copbio.2011.12.017}, journal = {Curr Opin Biotechnol}, author = {Desai, N. and Antonopoulos, D. and Gilbert, J. A. and Glass, E. M. and Meyer, Folker}, year = {2012}, note = {Type: Journal Article} }
@article{delmont_structure_2012, title = {Structure, fluctuation and magnitude of a natural grassland soil metagenome}, volume = {6}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22297556}, doi = {10.1038/ismej.2011.197}, journal = {ISME J}, author = {Delmont, T. O. and Prestat, E. and Keegan, K. P. and Faubladier, M. and Robe, P. and Clark, I. M. and Pelletier, E. and Hirsch, P. R. and Meyer, Folker and Gilbert, J. A. and Le Paslier, D. and Simonet, P. and Vogel, T. M.}, year = {2012}, note = {Type: Journal Article} }
@incollection{glass_analysis_2012, title = {Analysis of metagenomics data}, booktitle = {Bioinformatics for {High} {Throughput} {Sequencing}}, publisher = {Springer, New York, NY}, author = {Glass, Elizabeth M and Meyer, Folker}, year = {2012} }
@article{thomas_metagenomics-guide_2012, title = {Metagenomics-a guide from sampling to data analysis}, volume = {2}, journal = {Microbial informatics and experimentation}, author = {Thomas, Torsten and Gilbert, Jack and Meyer, Folker}, year = {2012}, note = {Publisher: BioMed Central} }
@article{gilbert_modeling_2012, title = {Modeling the {Earth} {Microbiome} – {Careful} planning can reduce sampling and measurement biases while building data sets describing microbes across multiple ecosystems}, journal = {ASM Microbe}, author = {Gilbert, J and Meyer, Folker}, year = {2012} }
@article{gilbert_conceptualizing_2012, title = {Conceptualizing a {Genomics} {Software} {Institute} ({GSI})}, volume = {6}, journal = {Standards in genomic sciences}, author = {Gilbert, Jack A and Catlett, Charlie and Desai, Narayan and Knight, Rob and White, Owen and Robbins, Robert and Sankaran, Rajesh and Sansone, Susanna-Assunta and Field, Dawn and Meyer, Folker}, year = {2012}, note = {Publisher: BioMed Central} }
@misc{phung_draft_2012, title = {Draft genome sequence of {Alcaligenes} faecalis subsp. faecalis {NCIB} 8687 ({CCUG} 2071)}, publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC}, author = {Phung, Le T and Trimble, William L and Meyer, Folker and Gilbert, Jack A and Silver, Simon}, year = {2012} }
@article{olivas_intestinal_2012, title = {Intestinal tissues induce an {SNP} mutation in {Pseudomonas} aeruginosa that enhances its virulence: possible role in anastomotic leak}, author = {Olivas, Andrea D and Shogan, Benjamin D and Valuckaite, Vesta and Zaborin, Alexander and Belogortseva, Natalya and Musch, Mark and Meyer, Folker and L. Trimble, William and An, Gary and Gilbert, Jack and Alverdy, John}, year = {2012}, note = {Publisher: Public Library of Science San Francisco, USA} }
@article{meyer_functional_2012, title = {Functional predictions from inference and observation in sequence-based inflammatory bowel disease research}, volume = {13}, journal = {Genome Biology}, author = {Meyer, F and Trimble, WL and Chang, EB and Handley, KM}, year = {2012} }
@misc{trimble_draft_2012, title = {Draft genome sequence of {Achromobacter} piechaudii strain {HLE}}, publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC}, author = {Trimble, William L and Phung, Le T and Meyer, Folker and Silver, Simon and Gilbert, Jack A}, year = {2012} }
@misc{trimble_draft_2012-1, title = {Draft genome sequence of {Agrobacterium} albertimagni strain {AOL15}}, publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC}, author = {Trimble, William L and Phung, Le T and Meyer, Folker and Gilbert, Jack A and Silver, Simon}, year = {2012} }
@article{gilbert_draft_2012, title = {Draft {Genome} {Sequence} of {Achromobacter}}, volume = {194}, journal = {J. Bacteriol}, author = {Gilbert, Jack A and Trimble, William L and Phung, Le T and Meyer, Folker and Silver, Simon}, year = {2012} }
@article{RN23, author = {Makhzami, S. and Rambow, F. and Delmas, V. and Larue, L.}, title = {Efficient gene expression profiling of laser-microdissected melanoma metastases}, journal = {Pigment Cell Melanoma Res}, volume = {25}, number = {6}, pages = {783-91}, issn = {1755-148X (Electronic) 1755-1471 (Linking)}, doi = {10.1111/pcmr.12013}, url = {https://www.ncbi.nlm.nih.gov/pubmed/22934821}, year = {2012}, type = {Journal Article} }
@article{RN6, author = {Colombo, S. and Champeval, D. and Rambow, F. and Larue, L.}, title = {Transcriptomic analysis of mouse embryonic skin cells reveals previously unreported genes expressed in melanoblasts}, journal = {J Invest Dermatol}, volume = {132}, number = {1}, pages = {170-8}, issn = {1523-1747 (Electronic) 0022-202X (Linking)}, doi = {10.1038/jid.2011.252}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21850021}, year = {2012}, type = {Journal Article} }
@article{RN5, author = {Berlin, I. and Luciani, F. and Gallagher, S. J. and Rambow, F. and Conde-Perez, A. and Colombo, S. and Champeval, D. and Delmas, V. and Larue, L.}, title = {General strategy to analyse coat colour phenotypes in mice}, journal = {Pigment Cell Melanoma Res}, volume = {25}, number = {1}, pages = {117-9}, issn = {1755-148X (Electronic) 1755-1471 (Linking)}, doi = {10.1111/j.1755-148X.2011.00912.x}, url = {https://www.ncbi.nlm.nih.gov/pubmed/22085368}, year = {2012}, type = {Journal Article} }
@techreport{koster_protein_2011, type = {{arXiv} e-print}, title = {Protein {Hypernetworks}: a {Logic} {Framework} for {Interaction} {Dependencies} and {Perturbation} {Effects} in {Protein} {Networks}}, copyright = {All rights reserved}, shorttitle = {Protein {Hypernetworks}}, url = {http://arxiv.org/abs/1106.2562}, number = {1106.2562}, urldate = {2013-10-08}, author = {Köster, Johannes and Zamir, Eli and Rahmann, Sven}, month = jun, year = {2011}, keywords = {Quantitative Biology - Molecular Networks}, annote = {Comment: Preprint, submitted to Bioinformatics; 7 pages, 5 figures, 4 pages supplement For further information, see http://www.rahmannlab.de/research/hypernetworks}, file = {arXiv.org Snapshot:/home/johannes/Zotero/storage/SNEFRU2G/1106.html:text/html;Köster et al_2011_Protein Hypernetworks.pdf:/vol/home/koester/Dropbox/xpapers/Köster et al_2011_Protein Hypernetworks.pdf:application/pdf} }
@article{kirschbaum2011optimization, title = {Optimization and validation of CEDIA drugs of abuse immunoassay tests in serum on Hitachi 912}, author = {Kirschbaum, Katrin M and Musshoff, Frank and Schmithausen, Ricarda and Stockhausen, Sarah and Madea, Burkhard}, journal = {Forensic science international}, volume = {212}, year = {2011}, publisher = {Elsevier} }
@phdthesis{schmithausen2011optinierung, title = {Optinierung laborinterner Cut-off-Werte fur die immunchemische Vortestung auf Amphetamine und Cannabinoide im forensischen Labor}, author = {Schmithausen, Ricarda Maria}, year = {2011}, school = {Rheinische Friedrich-Wilhelms-Universit{\"a}t in Bonn} }
@article{yilmaz_minimum_2011, title = {Minimum information about a marker gene sequence ({MIMARKS}) and minimum information about any (x) sequence ({MIxS}) specifications}, volume = {29}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21552244}, doi = {10.1038/nbt.1823}, journal = {Nat Biotechnol}, author = {Yilmaz, P. and Kottmann, R. and Field, D. and Knight, R. and Cole, J. R. and Amaral-Zettler, L. and Gilbert, J. A. and Karsch-Mizrachi, I. and Johnston, A. and Cochrane, G. and Vaughan, R. and Hunter, C. and Park, J. and Morrison, N. and Rocca-Serra, P. and Sterk, P. and Arumugam, M. and Bailey, M. and Baumgartner, L. and Birren, B. W. and Blaser, M. J. and Bonazzi, V. and Booth, T. and Bork, P. and Bushman, F. D. and Buttigieg, P. L. and Chain, P. S. and Charlson, E. and Costello, E. K. and Huot-Creasy, H. and Dawyndt, P. and DeSantis, T. and Fierer, N. and Fuhrman, J. A. and Gallery, R. E. and Gevers, D. and Gibbs, R. A. and San Gil, I. and Gonzalez, A. and Gordon, J. I. and Guralnick, R. and Hankeln, W. and Highlander, S. and Hugenholtz, P. and Jansson, J. and Kau, A. L. and Kelley, S. T. and Kennedy, J. and Knights, D. and Koren, O. and Kuczynski, J. and Kyrpides, N. and Larsen, R. and Lauber, C. L. and Legg, T. and Ley, R. E. and Lozupone, C. A. and Ludwig, W. and Lyons, D. and Maguire, E. and Methe, B. A. and Meyer, Folker and Muegge, B. and Nakielny, S. and Nelson, K. E. and Nemergut, D. and Neufeld, J. D. and Newbold, L. K. and Oliver, A. E. and Pace, N. R. and Palanisamy, G. and Peplies, J. and Petrosino, J. and Proctor, L. and Pruesse, E. and Quast, C. and Raes, J. and Ratnasingham, S. and Ravel, J. and Relman, D. A. and Assunta-Sansone, S. and Schloss, P. D. and Schriml, L. and Sinha, R. and Smith, M. I. and Sodergren, E. and Spo, A. and Stombaugh, J. and Tiedje, J. M. and Ward, D. V. and Weinstock, G. M. and Wendel, D. and White, O. and Whiteley, A. and Wilke, A. and Wortman, J. R. and Yatsunenko, T. and Glockner, F. O.}, year = {2011}, note = {Type: Journal Article} }
@article{wilke_experience_2011, title = {An experience report: porting the {MG}‐{RAST} rapid metagenomics analysis pipeline to the cloud.}, volume = {23}, journal = {Concurrency and Computation: Practice and Experience}, author = {Wilke, A. and Wilkening, J. and Glass, E. M. and Desai, N. and Meyer, Folker}, year = {2011}, note = {Type: Journal Article} }
@article{wilke_experience_2011-1, title = {An experience report: porting the {MG}-{RAST} rapid metagenomics analysis pipeline to the cloud}, volume = {23}, journal = {Concurrency and Computation: Practice and Experience}, author = {Wilke, A. and Wilkening, J. and Glass, E.M. and Desai, N. and Meyer, Folker}, year = {2011}, note = {Type: Journal Article} }
@article{mitra_functional_2011, title = {Functional analysis of metagenomes and metatranscriptomes using {SEED} and {KEGG}}, volume = {12}, journal = {BMC bioinformatics}, author = {Mitra, Suparna and Rupek, Paul and Richter, Daniel C and Urich, Tim and Gilbert, Jack A and Meyer, Folker and Wilke, Andreas and Huson, Daniel H}, year = {2011}, note = {Publisher: BioMed Central} }
@article{lemke_bmp_2011, title = {{BMP} signaling components in embryonic transcriptomes of the hover fly {Episyrphus} balteatus ({Syrphidae})}, volume = {12}, journal = {Bmc Genomics}, author = {Lemke, Steffen and Antonopoulos, Dionysios A and Meyer, Folker and Domanus, Marc H and Schmidt-Ott, Urs}, year = {2011}, note = {Publisher: BioMed Central} }
@article{henry_connecting_2011, title = {Connecting genotype to phenotype in the era of high-throughput sequencing}, volume = {1810}, journal = {Biochimica et Biophysica Acta (BBA)-General Subjects}, author = {Henry, Christopher S and Overbeek, Ross and Xia, Fangfang and Best, Aaron A and Glass, Elizabeth and Gilbert, Jack and Larsen, Peter and Edwards, Rob and Disz, Terry and Meyer, Folker and Stevens, Rick}, year = {2011}, note = {Publisher: Elsevier} }
@article{wilke_porting_2011, title = {Porting the {MG}-{RAST} metagenomic data analysis pipeline to the cloud}, volume = {23}, journal = {Concurrency and Computation: Practice \& Experience}, author = {Wilke, Andreas and Wilkening, Jared and Glass, Elizabeth M and Desai, Narayan L and Meyer, Folker}, year = {2011}, note = {Publisher: John Wiley and Sons Ltd.} }
@article{larsen_predicted_2011, title = {Predicted {Relative} {Metabolomic} {Turnover} ({PRMT}): determining metabolic turnover from a coastal marine metagenomic dataset}, volume = {1}, journal = {Microbial informatics and experimentation}, author = {Larsen, Peter E and Collart, Frank R and Field, Dawn and Meyer, Folker and Keegan, Kevin P and Henry, Christopher S and McGrath, John and Quinn, John and Gilbert, Jack A}, year = {2011}, note = {Publisher: BioMed Central} }
@incollection{antonopoulos_analyzing_2011, title = {Analyzing {Metagenomic} data: inferring microbial community function with {MG}-{RAST}}, booktitle = {Metagenomics and its applications in agriculture, biomedicine, and environmental studies publisher}, publisher = {Nova Science Publishers}, author = {Antonopoulos, D. A. and Glass, E. M. and Meyer, Folker}, year = {2011} }
@inproceedings{meyer_proposal_2011, title = {Proposal for {Open} {Discussion}-{Informatics} {Challenges} for {Next} {Generation} {Sequencing} {Metagenomics} {Experiments}.}, booktitle = {{BIOINFORMATICS}}, author = {Meyer, Folker and Kyrpides, Nikos}, year = {2011} }
@inproceedings{larsen_predicted_2011-1, title = {{PREDICTED} {RELATIVE} {METABOLOMIC} {TURNOVER}-{Predicting} {Changes} in the {Environmental} {Metabolome} from the {Metagenome}}, volume = {2}, booktitle = {International {Joint} {Conference} on {Biomedical} {Engineering} {Systems} and {Technologies}}, publisher = {SCITEPRESS}, author = {Larsen, Peter E and Collart, Frank and Meyer, Folker and Gilbert, Jack A}, year = {2011} }
@article{larsen_predicted_2011-2, title = {{PREDICTED} {RELATIVE} {METABOLOMIC} {TURNOVER}}, author = {Larsen, Peter E and Collart, Frank and Meyer, Folker and Gilbert, Jack A}, year = {2011} }
@article{meyer_proposal_2011-1, title = {{PROPOSAL} {FOR} {OPEN} {DISCUSSION}}, author = {Meyer, Folker and Kyrpides, Nikos}, year = {2011} }
@article{larsen_relative_2011, title = {Relative metabolomic flux: {Predicting} changes in the environmental metabolome from the metagenome}, volume = {1}, journal = {Microbial Informatics and Experimentation}, author = {Larsen, Peter E and Collart, Frank R and Field, Dawn and Meyer, Folker and Keegan, Kevin P and Henry, Christopher S and McGrath, John and Quinn, John and Gilbert, Jack A}, year = {2011}, note = {Publisher: BioMed Central Ltd.} }
@article{birmingham_meeting_2011-1, title = {Meeting report of the {RNA} {Ontology} {Consortium} {January} 8-9, 2011}, volume = {4}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21677862}, doi = {10.4056/sigs.1724282}, journal = {Stand Genomic Sci}, author = {Birmingham, A. and Clemente, J. C. and Desai, N. and Gilbert, J. and Gonzalez, A. and Kyrpides, N. and Meyer, Folker and Nawrocki, E. and Sterk, P. and Stombaugh, J. and Weinberg, Z. and Wendel, D. and Leontis, N. B. and Zirbel, C. and Knight, R. and Laederach, A.}, year = {2011}, note = {Type: Journal Article} }
@article{RN22, author = {Lindsay, C. R. and Lawn, S. and Campbell, A. D. and Faller, W. J. and Rambow, F. and Mort, R. L. and Timpson, P. and Li, A. and Cammareri, P. and Ridgway, R. A. and Morton, J. P. and Doyle, B. and Hegarty, S. and Rafferty, M. and Murphy, I. G. and McDermott, E. W. and Sheahan, K. and Pedone, K. and Finn, A. J. and Groben, P. A. and Thomas, N. E. and Hao, H. and Carson, C. and Norman, J. C. and Machesky, L. M. and Gallagher, W. M. and Jackson, I. J. and Van Kempen, L. and Beermann, F. and Der, C. and Larue, L. and Welch, H. C. and Ozanne, B. W. and Sansom, O. J.}, title = {P-Rex1 is required for efficient melanoblast migration and melanoma metastasis}, journal = {Nat Commun}, volume = {2}, pages = {555}, issn = {2041-1723 (Electronic) 2041-1723 (Linking)}, doi = {10.1038/ncomms1560}, url = {https://www.ncbi.nlm.nih.gov/pubmed/22109529}, year = {2011}, type = {Journal Article} }
@article{RN13, author = {Gallagher, S. J. and Luciani, F. and Berlin, I. and Rambow, F. and Gros, G. and Champeval, D. and Delmas, V. and Larue, L.}, title = {General strategy to analyse melanoma in mice}, journal = {Pigment Cell Melanoma Res}, volume = {24}, number = {5}, pages = {987-8}, issn = {1755-148X (Electronic) 1755-1471 (Linking)}, doi = {10.1111/j.1755-148X.2011.00907.x}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21955491}, year = {2011}, type = {Journal Article} }
@article{RN9, author = {Cortellino, S. and Xu, J. and Sannai, M. and Moore, R. and Caretti, E. and Cigliano, A. and Le Coz, M. and Devarajan, K. and Wessels, A. and Soprano, D. and Abramowitz, L. K. and Bartolomei, M. S. and Rambow, F. and Bassi, M. R. and Bruno, T. and Fanciulli, M. and Renner, C. and Klein-Szanto, A. J. and Matsumoto, Y. and Kobi, D. and Davidson, I. and Alberti, C. and Larue, L. and Bellacosa, A.}, title = {Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair}, journal = {Cell}, volume = {146}, number = {1}, pages = {67-79}, issn = {1097-4172 (Electronic) 0092-8674 (Linking)}, doi = {10.1016/j.cell.2011.06.020}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21722948}, year = {2011}, type = {Journal Article} }
@article{kyrpides_meeting_2010, title = {Meeting {Report} from the {Genomic} {Standards} {Consortium} ({GSC}) {Workshop} 8}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304696}, doi = {10.4056/sigs.1022942}, journal = {Stand Genomic Sci}, author = {Kyrpides, N. and Field, D. and Sterk, P. and Kottmann, R. and Glockner, F. O. and Hirschman, L. and Garrity, G. M. and Cochrane, G. and Wooley, J.}, year = {2010}, note = {Type: Journal Article} }
@article{glass_meeting_2010, title = {Meeting {Report} from the {Genomic} {Standards} {Consortium} ({GSC}) {Workshop} 10}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304723}, doi = {10.4056/sigs.1423520}, journal = {Stand Genomic Sci}, author = {Glass, E. and Meyer, Folker and Gilbert, J. A. and Field, D. and Hunter, S. and Kottmann, R. and Kyrpides, N. and Sansone, S. and Schriml, L. and Sterk, P. and White, O. and Wooley, J.}, year = {2010}, note = {Type: Journal Article} }
@article{gilbert_meeting_2010, title = {Meeting report: {GSC} {M5} roundtable at the 13th {International} {Society} for {Microbial} {Ecology} meeting in {Seattle}, {WA}, {USA} {August} 22-27, 2010}, volume = {3}, doi = {10.4056/sigs.1333437}, journal = {Stand Genomic Sci}, author = {Gilbert, J. A. and Meyer, Folker and Knight, R. and Field, D. and Kyrpides, N. and Yilmaz, P. and Wooley, J.}, year = {2010}, note = {Type: Journal Article} }
@article{young_role_2010, title = {The {Role} of the {Gut} {Microbiota} in {Ulcerative} {Colitis}}, author = {Young, Vincent B and Chang, Eugene B and Meyer, Folker and Sogin, Mitchell L and Schmidt, Thomas M and Tiedje, James}, year = {2010}, note = {Publisher: Nature Publishing Group} }
@article{glass_using_2010, title = {Using the metagenomics {RAST} server ({MG}-{RAST}) for analyzing shotgun metagenomes}, volume = {2010}, journal = {Cold Spring Harbor Protocols}, author = {Glass, Elizabeth M and Wilkening, Jared and Wilke, Andreas and Antonopoulos, Dionysios and Meyer, Folker}, year = {2010}, note = {Publisher: Cold Spring Harbor Laboratory Press} }
@article{lemke_maternal_2010, title = {Maternal activation of gap genes in the hover fly {Episyrphus}}, volume = {137}, journal = {Development}, author = {Lemke, Steffen and Busch, Stephanie E and Antonopoulos, Dionysios A and Meyer, Folker and Domanus, Marc H and Schmidt-Ott, Urs}, year = {2010}, note = {Publisher: Company of Biologists} }
@article{wang_laser_2010-1, title = {Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon}, volume = {88}, journal = {Applied microbiology and biotechnology}, author = {Wang, Yunwei and Antonopoulos, Dionysios A and Zhu, Xiaorong and Harrell, Laura and Hanan, Ira and Alverdy, John C and Meyer, Folker and Musch, Mark W and Young, Vincent B and Chang, Eugene B}, year = {2010}, note = {Publisher: Springer-Verlag} }
@article{pfister_metagenomic_2010, title = {Metagenomic profiling of a microbial assemblage associated with the {California} mussel: a node in networks of carbon and nitrogen cycling}, volume = {5}, journal = {PLoS One}, author = {Pfister, Catherine A and Meyer, Folker and Antonopoulos, Dionysios A}, year = {2010}, note = {Publisher: Public Library of Science} }
@article{gilbert_future_2010, title = {The {Future} of microbial metagenomics (or is ignorance bliss?)}, volume = {5}, journal = {The ISME Journal}, author = {Gilbert, Jack A and Meyer, Folker and Bailey, Mark J}, year = {2010}, note = {Publisher: Nature Publishing Group} }
@article{gilbert_meeting_2010-2, title = {Meeting report: {GSC} {M5} roundtable at the 13th {International} {Society} for {Microbial} {Ecology} meeting in {Seattle}, {WA}, {USA} {August} 22–27, 2010}, volume = {3}, journal = {Standards in genomic sciences}, author = {Gilbert, Jack A and Meyer, Folker and Knight, Rob and Field, Dawn and Kyrpides, Nikos and Yilmaz, Pelin and Wooley, John}, year = {2010}, note = {Publisher: BioMed Central} }
@article{obrien_meeting_2010, title = {Meeting {Report}: {The} 2nd {Annual} {Argonne} {Soils} {Workshop}, {Argonne} {National} {Laboratory}, {Chicago} {USA}, {October} 6-8, 2010}, author = {O’Brien, Sarah L and Glass, Elizabeth M and Brulc, Jennifer M and Gilbert, Jack A and Antonopoulos, Dionysios A and Meyer, Folker}, year = {2010} }
@article{gilbert_metagenomes_2010, title = {Metagenomes and metatranscriptomes from the {L4} long-term coastal monitoring station in the {Western} {English} {Channel}}, volume = {3}, journal = {Standards in genomic sciences}, author = {Gilbert, Jack A and Meyer, Folker and Schriml, Lynn and Joint, Ian R and Mühling, Martin and Field, Dawn}, year = {2010}, note = {Publisher: BioMed Central} }
@article{gilbert_metagenomics_2010, title = {Metagenomics: {A} foundling finds its feet}, volume = {3}, journal = {Standards in genomic sciences}, author = {Gilbert, Jack A and Meyer, Folker and Field, Dawn and Schriml, Lynn M and Garrity, George M}, year = {2010}, note = {Publisher: BioMed Central} }
@techreport{meyer_casting_2010, title = {Casting a {Wider} {Net}: {Distributed} {Resources} for {Metagenomics} (2010 {JGI}/{ANL} {HPC} {Workshop})}, institution = {DOE Joint Genome Institute (JGI), LBNL (Lawrence Berkeley National …}, author = {Meyer, Folker}, year = {2010} }
@article{yilmaz_minimum_2010-1, title = {The “minimum information about an environmental sequence”({MIENS}) specification}, url = {https://www.nature.com/articles/npre.2010.5252.1.pdf?proof=t}, journal = {Nature Precedings}, author = {Yilmaz, Pelin and Kottmann, Renzo and Field, Dawn and Knight, Rob and Cole, James and Amaral-Zettler, Linda and Gilbert, Jack and Karsch-Mizrachi, Ilene and Johnston, Anjanette and Cochrane, Guy and Meyer, Folker}, year = {2010} }
@article{gilbert_earth_2010-1, title = {The {Earth} {Microbiome} {Project}: {Meeting} report of the "1 {EMP} meeting on sample selection and acquisition" at {Argonne} {National} {Laboratory} {October} 6 2010}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304728}, doi = {10.4056/aigs.1443528}, journal = {Stand Genomic Sci}, author = {Gilbert, J. A. and Meyer, Folker and Jansson, J. and Gordon, J. and Pace, N. and Tiedje, J. and Ley, R. and Fierer, N. and Field, D. and Kyrpides, N. and Glockner, F. O. and Klenk, H. P. and Wommack, K. E. and Glass, E. and Docherty, K. and Gallery, R. and Stevens, R. and Knight, R.}, year = {2010}, note = {Type: Journal Article} }
@article{gilbert_meeting_2010-3, title = {Meeting report: the terabase metagenomics workshop and the vision of an {Earth} microbiome project}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304727}, doi = {10.4056/sigs.1433550}, journal = {Stand Genomic Sci}, author = {Gilbert, J. A. and Meyer, Folker and Antonopoulos, D. and Balaji, P. and Brown, C. T. and Brown, C. T. and Desai, N. and Eisen, J. A. and Evers, D. and Field, D. and Feng, W. and Huson, D. and Jansson, J. and Knight, R. and Knight, J. and Kolker, E. and Konstantindis, K. and Kostka, J. and Kyrpides, N. and Mackelprang, R. and McHardy, A. and Quince, C. and Raes, J. and Sczyrba, A. and Shade, A. and Stevens, R.}, year = {2010}, note = {Type: Journal Article} }
@article{field_meeting_2010-2, title = {Meeting {Report}: {BioSharing} at {ISMB} 2010}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304729}, doi = {10.4056/sigs/1403501}, journal = {Stand Genomic Sci}, author = {Field, D. and Sansone, S. and Delong, E. F. and Sterk, P. and Friedberg, I. and Gaudet, P. and Lewis, S. and Kottmann, R. and Hirschman, L. and Garrity, G. and Cochrane, G. and Wooley, J. and Meyer, Folker and Hunter, S. and White, O. and Bramlett, B. and Gregurick, S. and Lapp, H. and Orchard, S. and Rocca-Serra, P. and Ruttenberg, A. and Shah, N. and Taylor, C. and Thessen, A.}, year = {2010}, note = {Type: Journal Article} }
@article{hather_united_2010-1, title = {The {United} {States} of {America} and scientific research}, volume = {5}, url = {https://www.ncbi.nlm.nih.gov/pubmed/20808949}, doi = {10.1371/journal.pone.0012203}, journal = {PLoS One}, author = {Hather, G. J. and Haynes, W. and Higdon, R. and Kolker, N. and Stewart, E. A. and Arzberger, P. and Chain, P. and Field, D. and Franza, B. R. and Lin, B. and Meyer, Folker and Ozdemir, V. and Smith, C. V. and van Belle, G. and Wooley, J. and Kolker, E.}, year = {2010}, note = {Type: Journal Article} }
@article{field_meeting_2010-3, title = {Meeting {Report}: {Metagenomics}, {Metadata} and {MetaAnalysis} ({M3}) at {ISMB} 2010}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304724}, doi = {10.4056/sigs.1383476}, journal = {Stand Genomic Sci}, author = {Field, D. and Sansone, S. and Delong, E. F. and Sterk, P. and Friedberg, I. and Kottmann, R. and Hirschman, L. and Garrity, G. and Cochrane, G. and Wooley, J. and Meyer, Folker and Hunter, S. and White, O.}, year = {2010}, note = {Type: Journal Article} }
@article{hirschman_meeting_2010-1, title = {Meeting {Report}: "{Metagenomics}, {Metadata} and {Meta}-analysis" ({M3}) {Workshop} at the {Pacific} {Symposium} on {Biocomputing} 2010}, volume = {2}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304719}, doi = {10.4056/sigs.802738}, journal = {Stand Genomic Sci}, author = {Hirschman, L. and Sterk, P. and Field, D. and Wooley, J. and Cochrane, G. and Gilbert, J. and Kolker, E. and Kyrpides, N. and Meyer, Folker and Mizrachi, I. and Nakamura, Y. and Sansone, S. A. and Schriml, L. and Tatusova, T. and White, O. and Yilmaz, P.}, year = {2010}, note = {Type: Journal Article} }
@article{davidsen_meeting_2010-3, title = {Meeting {Report} from the {Genomic} {Standards} {Consortium} ({GSC}) {Workshop} 9}, volume = {3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/21304722}, doi = {10.4056/sigs.1353455}, journal = {Stand Genomic Sci}, author = {Davidsen, T. and Madupu, R. and Sterk, P. and Field, D. and Garrity, G. and Gilbert, J. and Glockner, F. O. and Hirschman, L. and Kolker, E. and Kottmann, R. and Kyrpides, N. and Meyer, Folker and Morrison, N. and Schriml, L. and Tatusova, T. and Wooley, J.}, year = {2010}, note = {Type: Journal Article} }
@article{RN32, author = {Rambow, F. and Larue, L.}, title = {The quest for the melanoma stem cell: still more questions than answers}, journal = {Pigment Cell Melanoma Res}, volume = {23}, number = {3}, pages = {307-9}, issn = {1755-148X (Electronic) 1755-1471 (Linking)}, doi = {10.1111/j.1755-148X.2010.00713.x}, url = {https://www.ncbi.nlm.nih.gov/pubmed/20444202}, year = {2010}, type = {Journal Article} }
@article{meyer_figfams_2009, title = {{FIGfams}: yet another set of protein families}, volume = {37}, doi = {10.1093/nar/gkp698}, journal = {Nucleic Acids Res}, author = {Meyer, Folker and Overbeek, R. and Rodriguez, A.}, year = {2009}, note = {Type: Journal Article} }
@article{bekel_sequence_2009, title = {The {Sequence} {Analysis} and {Management} {System} - {SAMS}-2.0: {Data} management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies}, volume = {140}, doi = {10.1016/j.jbiotec.2009.01.006}, journal = {Journal of Biotechnology}, author = {Bekel, T. and Henckel, K. and Kuster, H. and Meyer, Folker and Runte, V. M. and Neuweger, H. and Paarmann, D. and Rupp, O. and Zakrzewski, M. and Puehler, A. and Stoye, J. and Goesmann, A.}, year = {2009}, note = {Type: Journal Article} }
@inproceedings{wilkening_using_2009, title = {Using clouds for metagenomics: a case study}, booktitle = {2009 {IEEE} {International} {Conference} on {Cluster} {Computing} and {Workshops}}, publisher = {IEEE}, author = {Wilkening, Jared and Wilke, Andreas and Desai, Narayan and Meyer, Folker}, year = {2009} }
@article{wang_w1622_2009, title = {W1622 {Metagenomic} {Analysis} of {Intact} {Mucosa}-{Associated} {Microbial} {Communities} of the {Human} {Colon}}, volume = {5}, journal = {Gastroenterology}, author = {Wang, Yunwei and Antonopoulos, Dionysios and Zhu, Xiaorong and Lichtenstein, Lev and Drabik, Kenneth and Alverdy, John C and Meyer, Folker and Young, Vincent and Chang, Eugene B}, year = {2009} }
@techreport{glockner_flash_2009, title = {Flash {Updates} of {GSC} projects ({GSC8} {Meeting})}, institution = {DOE Joint Genome Institute (JGI), LBNL (Lawrence Berkeley National …}, author = {Glockner, Frank Oliver and Markowitz, Victor and Kyrpides, Nikos and Meyer, Folker and Amaral-Zettler, Linda and Cole, James}, year = {2009} }
@article{field_meeting_2009-5, title = {Meeting {Report}:“{Metagenomics}, {Metadata} and {Meta}-analysis”({M3}) {Special} {Interest} {Group} at {ISMB} 2009}, volume = {1}, journal = {Standards in genomic sciences}, author = {Field, Dawn and Friedberg, Iddo and Sterk, Peter and Kottmann, Renzo and Glöckner, Frank Oliver and Hirschman, Lynette and Garrity, George M and Cochrane, Guy and Wooley, John and Gilbert, Jack}, year = {2009}, note = {Publisher: BioMed Central} }
@article{angly_gaas_2009-2, title = {The {GAAS} metagenomic tool and its estimations of viral and microbial average genome size in four major biomes}, volume = {5}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20011103}, doi = {10.1371/journal.pcbi.1000593}, journal = {PLoS Comput Biol}, author = {Angly, F. E. and Willner, D. and Prieto-Davo, A. and Edwards, R. A. and Schmieder, R. and Vega-Thurber, R. and Antonopoulos, D. A. and Barott, K. and Cottrell, M. T. and Desnues, C. and Dinsdale, E. A. and Furlan, M. and Haynes, M. and Henn, M. R. and Hu, Y. and Kirchman, D. L. and McDole, T. and McPherson, J. D. and Meyer, Folker and Miller, R. M. and Mundt, E. and Naviaux, R. K. and Rodriguez-Mueller, B. and Stevens, R. and Wegley, L. and Zhang, L. and Zhu, B. and Rohwer, F.}, year = {2009}, note = {Type: Journal Article} }
@article{bekel_sequence_2009-2, title = {The {Sequence} {Analysis} and {Management} {System} – {SAMS}-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies}, volume = {140}, url = {https://www.ncbi.nlm.nih.gov/pubmed/19297685}, doi = {10.1016/j.jbiotec.2009.01.006}, journal = {J Biotechnol}, author = {Bekel, T. and Henckel, K. and Kuster, H. and Meyer, Folker and Mittard Runte, V. and Neuweger, H. and Paarmann, D. and Rupp, O. and Zakrzewski, M. and Puhler, A. and Stoye, J. and Goesmann, A.}, year = {2009}, note = {Type: Journal Article}, keywords = {Bacterial Genomics Information Management/*methods Information Storage and Retrieval/*methods Oligonucleotide Array Sequence Analysis Sequence Analysis, Cluster Analysis Computational Biology Databases, DNA/*methods *Software User-Computer Interface, Genetic Expressed Sequence Tags Gene Library *Genome} }
@article{sievert_genome_2008, title = {Genome of the epsilonproteobacterial chemolithoautotroph {Sulfurimonas} denitrificans}, volume = {74}, doi = {10.1128/aem.01844-07}, journal = {Applied and Environmental Microbiology}, author = {Sievert, S. M. and Scott, K. A. and Klotz, M. G. and Chain, P. S. G. and Hauser, L. J. and Hemp, J. and Hugler, M. and Land, M. and Lapidus, A. and Larimer, F. W. and Lucas, S. and Malfatti, S. A. and Meyer, Folker and Paulsen, I. T. and Ren, Q. and Simon, J. and Class, U. S. F. Genom}, year = {2008}, note = {Type: Journal Article} }
@article{meyer_metagenomics_2008, title = {The metagenomics {RAST} server - a public resource for the automatic phylogenetic and functional analysis of metagenomes}, volume = {9}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18803844}, doi = {10.1186/1471-2105-9-386}, journal = {BMC Bioinformatics}, author = {Meyer, Folker and Paarmann, D. and D'Souza, M. and Olson, R. and Glass, E. M. and Kubal, M. and Paczian, T. and Rodriguez, A. and Stevens, R. and Wilke, A. and Wilkening, J. and Edwards, R. A.}, year = {2008}, note = {Type: Journal Article} }
@article{garrity_toward_2008, title = {Toward a standards-compliant genomic and metagenomic publication record}, volume = {12}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18564916}, doi = {10.1089/omi.2008.A2B2}, journal = {Omics}, author = {Garrity, G. M. and Field, D. and Kyrpides, N. and Hirschman, L. and Sansone, S. A. and Angiuoli, S. and Cole, J. R. and Glockner, F. O. and Kolker, E. and Kowalchuk, G. and Moran, M. A. and Ussery, D. and White, O.}, year = {2008}, note = {Type: Journal Article} }
@article{field_minimum_2008, title = {The minimum information about a genome sequence ({MIGS}) specification}, volume = {26}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18464787}, doi = {10.1038/nbt1360}, journal = {Nat Biotechnol}, author = {Field, D. and Garrity, G. and Gray, T. and Morrison, N. and Selengut, J. and Sterk, P. and Tatusova, T. and Thomson, N. and Allen, M. J. and Angiuoli, S. V. and Ashburner, M. and Axelrod, N. and Baldauf, S. and Ballard, S. and Boore, J. and Cochrane, G. and Cole, J. and Dawyndt, P. and De Vos, P. and DePamphilis, C. and Edwards, R. and Faruque, N. and Feldman, R. and Gilbert, J. and Gilna, P. and Glockner, F. O. and Goldstein, P. and Guralnick, R. and Haft, D. and Hancock, D. and Hermjakob, H. and Hertz-Fowler, C. and Hugenholtz, P. and Joint, I. and Kagan, L. and Kane, M. and Kennedy, J. and Kowalchuk, G. and Kottmann, R. and Kolker, E. and Kravitz, S. and Kyrpides, N. and Leebens-Mack, J. and Lewis, S. E. and Li, K. and Lister, A. L. and Lord, P. and Maltsev, N. and Markowitz, V. and Martiny, J. and Methe, B. and Mizrachi, I. and Moxon, R. and Nelson, K. and Parkhill, J. and Proctor, L. and White, O. and Sansone, S. A. and Spiers, A. and Stevens, R. and Swift, P. and Taylor, C. and Tateno, Y. and Tett, A. and Turner, S. and Ussery, D. and Vaughan, B. and Ward, N. and Whetzel, T. and San Gil, I. and Wilson, G. and Wipat, A.}, year = {2008}, note = {Type: Journal Article} }
@article{aziz_rast_2008, title = {The {RAST} server: {Rapid} annotations using subsystems technology}, volume = {9}, doi = {10.1186/1471-2164-9-75}, journal = {BMC Genomics}, author = {Aziz, R. K. and Bartels, D. and Best, A. A. and DeJongh, M. and Disz, T. and Edwards, R. A. and Formsma, K. and Gerdes, S. and Glass, E. M. and Kubal, M. and Meyer, Folker and Olsen, G. J. and Olson, R. and Osterman, A. L. and Overbeek, R. A. and McNeil, L. K. and Paarmann, D. and Paczian, T. and Parrello, B. and Pusch, G. D. and Reich, C. and Stevens, R. and Vassieva, O. and Vonstein, V. and Wilke, A. and Zagnitko, O.}, year = {2008}, note = {Type: Journal Article} }
@article{aziz_rast_2008-1, title = {The {RAST} {Server}: {Rapid} {Annotations} using {Subsystems} {Technology}}, journal = {BMC Genomics}, author = {Aziz, R. K. and Bartels, D. and Best, A. A. and DeJongh, M. and Disz, T. and Edwards, R. A. and Formsma, K. and Gerdes, S. and Glass, E. M. and Kubal, M. and Meyer, Folker and Olsen, G. J. and Olson, R. and Osterman, A. L. and Overbeek, R. A. and McNeil, L. K. and Paarmann, D. and Paczian, T. and Parrello, B. and Pusch, G. D. and Reich, C. and Stevens, R. and Vassieva, O. and Vonstein, V. and Wilke, A. and Zagnitko, O.}, year = {2008}, note = {Type: Journal Article} }
@article{battle_hybrid_2008-1, title = {Hybrid pathogenicity island {PAGI}-5 contributes to the highly virulent phenotype of a {Pseudomonas} aeruginosa isolate in mammals}, volume = {190}, journal = {Journal of bacteriology}, author = {Battle, Scott E and Meyer, Folker and Rello, Jordi and Kung, Vanderlene L and Hauser, Alan R}, year = {2008}, note = {Publisher: American Society for Microbiology} }
@article{mela_comparative_2008-1, title = {Comparative genomics of the {pIPO2}/{pSB102} family of environmental plasmids: sequence, evolution, and ecology of {pTer331} isolated from {Collimonas} fungivorans {Ter331}}, volume = {66}, journal = {FEMS microbiology ecology}, author = {Mela, Francesca and Fritsche, Kathrin and Boersma, Hidde and Van Elsas, Jan D and Bartels, Daniela and Meyer, Folker and De Boer, Wietse and Van Veen, Johannes A and Leveau, Johan HJ}, year = {2008}, note = {Publisher: Blackwell Publishing Ltd Oxford, UK} }
@article{kottmann_standard_2008-1, title = {A standard {MIGS}/{MIMS} compliant {XML} {Schema}: toward the development of the {Genomic} {Contextual} {Data} {Markup} {Language} ({GCDML})}, volume = {12}, journal = {Omics a journal of integrative biology}, author = {Kottmann, Renzo and Gray, Tanya and Murphy, Sean and Kagan, Leonid and Kravitz, Saul and Lombardot, Thierry and Field, Dawn and Glöckner, Frank Oliver and Consortium, Genomic Standards}, year = {2008}, note = {Publisher: Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 …} }
@article{mela_collimonas_2008, title = {Collimonas fungivorans {Ter331}}, author = {Mela, Francesca and Fritsche, Kathrin and Boersma, Hidde and van Elsas, Jan D and Bartels, Daniela and Meyer, Folker and de Boer, Wietse and van Veen, Johannes A and Leveau, Johan HJ}, year = {2008} }
@article{gartemann_genome_2008-2, title = {The genome sequence of the tomato-pathogenic actinomycete {Clavibacter} michiganensis subsp. michiganensis {NCPPB382} reveals a large island involved in pathogenicity}, volume = {190}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18192381}, doi = {10.1128/JB.01595-07}, journal = {J Bacteriol}, author = {Gartemann, K. H. and Abt, B. and Bekel, T. and Burger, A. and Engemann, J. and Flugel, M. and Gaigalat, L. and Goesmann, A. and Grafen, I. and Kalinowski, J. and Kaup, O. and Kirchner, O. and Krause, L. and Linke, B. and McHardy, A. and Meyer, Folker and Pohle, S. and Ruckert, C. and Schneiker, S. and Zellermann, E. M. and Puhler, A. and Eichenlaub, R. and Kaiser, O. and Bartels, D.}, year = {2008}, note = {Type: Journal Article}, keywords = {Bacterial/genetics *Genome, Actinobacteria/*genetics/pathogenicity Base Composition/genetics DNA, Bacterial Genomic Islands/genetics Lycopersicon esculentum/*microbiology Models, Bacterial/chemistry/*genetics Electrophoresis, DNA Serine Endopeptidases/genetics, Gel, Genetic Molecular Sequence Data Operon/genetics Plasmids/genetics Sequence Analysis, Pulsed-Field Genes} }
@article{gross_missing_2008-2, title = {The missing link: {Bordetella} petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic {Bordetellae}}, volume = {9}, doi = {10.1186/1471-2164-9-449}, journal = {BMC Genomics}, author = {Gross, R. and Guzman, C. A. and Sebaihia, M. and dos Santos, Vapm and Pieper, D. H. and Koebnik, R. and Lechner, M. and Bartels, D. and Buhrmester, J. and Choudhuri, J. V. and Ebensen, T. and Gaigalat, L. and Herrmann, S. and Khachane, A. N. and Larisch, C. and Link, S. and Linke, B. and Meyer, Folker and Mormann, S. and Nakunst, D. and Rukert, C. and Schneiker-Bekel, S. and Schulze, K. and Vorholter, F. J. and Yevsa, T. and Engle, J. T. and Goldman, W. E. and Puhler, A. and Gobel, U. B. and Goesmann, A. and Blocker, H. and Kaiser, O. and Martinez-Arias, R.}, year = {2008}, note = {Type: Journal Article} }
@article{RN35, author = {Rambow, F. and Piton, G. and Bouet, S. and Leplat, J. J. and Baulande, S. and Marrau, A. and Stam, M. and Horak, V. and Vincent-Naulleau, S.}, title = {Gene expression signature for spontaneous cancer regression in melanoma pigs}, journal = {Neoplasia}, volume = {10}, number = {7}, pages = {714-26, 1 p following 726}, issn = {1476-5586 (Electronic) 1476-5586 (Linking)}, doi = {10.1593/neo.08344}, url = {https://www.ncbi.nlm.nih.gov/pubmed/18592010}, year = {2008}, type = {Journal Article} }
@article{RN33, author = {Rambow, F. and Malek, O. and Geffrotin, C. and Leplat, J. J. and Bouet, S. and Piton, G. and Hugot, K. and Bevilacqua, C. and Horak, V. and Vincent-Naulleau, S.}, title = {Identification of differentially expressed genes in spontaneously regressing melanoma using the MeLiM swine model}, journal = {Pigment Cell Melanoma Res}, volume = {21}, number = {2}, pages = {147-61}, issn = {1755-1471 (Print) 1755-1471 (Linking)}, doi = {10.1111/j.1755-148X.2008.00442.x}, url = {https://www.ncbi.nlm.nih.gov/pubmed/18426408}, year = {2008}, type = {Journal Article} }
@article{schneiker_complete_2007, title = {Complete genome sequence of the myxobacterium {Sorangium} cellulosum}, volume = {25}, doi = {10.1038/nbt1354}, journal = {Nat Biotechnol}, author = {Schneiker, S. and Perlova, O. and Kaiser, O. and Gerth, K. and Alici, A. and Altmeyer, M. O. and Bartels, D. and Bekel, T. and Beyer, S. and Bode, E. and Bode, H. B. and Bolten, C. J. and Choudhuri, J. V. and Doss, S. and Elnakady, Y. A. and Frank, B. and Gaigalat, L. and Goesmann, A. and Groeger, C. and Gross, F. and Jelsbak, L. and Kalinowski, J. and Kegler, C. and Knauber, T. and Konietzny, S. and Kopp, M. and Krause, L. and Krug, D. and Linke, B. and Mahmud, T. and Martinez-Arias, R. and McHardy, A. C. and Merai, M. and Meyer, Folker and Mormann, S. and Munoz-Dorado, J. and Perez, J. and Pradella, S. and Rachid, S. and Raddatz, G. and Rosenau, F. and Rueckert, C. and Sasse, F. and Scharfe, M. and Schuster, S. C. and Suen, G. and Treuner-Lange, A. and Velicer, G. J. and Vorholter, F. J. and Weissman, K. J. and Dwelch, R. and Wenzel, S. C. and Whitworth, D. E. and Wilhelm, S. and Wittmann, C. and Blocker, H. and Puhler, A. and Mueller, R.}, year = {2007}, note = {Type: Journal Article} }
@article{overbeek_annotation_2007, title = {Annotation of {Bacterial} and {Archaeal} {Genomes}: {Improving} {Accuracy} and {Consistency}}, journal = {Chemical Reviews}, author = {Overbeek, R. and Bartels, D. and Vonstein, V. and Meyer, Folker}, year = {2007}, note = {Type: Journal Article} }
@article{mcneil_national_2007, title = {The {National} {Microbial} {Pathogen} {Database} {Resource} ({NMPDR}): a genomics platform based on subsystem annotation}, volume = {35}, doi = {10.1093/nar/gkl947}, journal = {Nucleic Acids Research}, author = {McNeil, L. K. and Reich, C. and Aziz, R. K. and Bartels, D. and Cohoon, M. and Disz, T. and Edwards, R. A. and Gerdes, S. and Hwang, K. and Kubal, M. and Margaryan, G. R. and Meyer, Folker and Mihalo, W. and Olsen, G. J. and Olson, R. and Osterman, A. and Paarmann, D. and Paczian, T. and Parrello, B. and Pusch, G. D. and Rodionov, D. A. and Shi, X. H. and Vassieva, O. and Vonstein, V. and Zagnitko, O. and Xia, F. F. and Zinner, J. and Overbeek, R. and Stevens, R.}, year = {2007}, note = {Type: Journal Article} }
@article{krause_gismo_2007, title = {{GISMO} - gene identification using a support vector machine for {ORF} classification}, volume = {35}, doi = {10.1093/nar/gkl1083}, journal = {Nucleic Acids Research}, author = {Krause, L. and McHardy, A. C. and Nattkemper, T. W. and Puhler, A. and Stoye, J. and Meyer, Folker}, year = {2007}, note = {Type: Journal Article} }
@article{krause_gismogene_2007, title = {{GISMO}—gene identification using a support vector machine for {ORF} classification}, volume = {35}, journal = {Nucleic acids research}, author = {Krause, Lutz and McHardy, Alice C and Nattkemper, Tim W and Pühler, Alfred and Stoye, Jens and Meyer, Folker}, year = {2007}, note = {Publisher: Oxford University Press} }
@article{overbeek_annotation_2007-1, title = {Annotation of bacterial and archaeal genomes: improving accuracy and consistency}, volume = {107}, journal = {Chemical reviews}, author = {Overbeek, Ross and Bartels, Daniela and Vonstein, Veronika and Meyer, Folker}, year = {2007}, note = {Publisher: American Chemical Society} }
@article{kuster_development_2007-2, title = {Development of bioinformatic tools to support {EST}-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses}, volume = {68}, url = {https://www.ncbi.nlm.nih.gov/pubmed/17081576}, doi = {10.1016/j.phytochem.2006.09.026}, journal = {Phytochemistry}, author = {Kuster, H. and Becker, A. and Firnhaber, C. and Hohnjec, N. and Manthey, K. and Perlick, A. M. and Bekel, T. and Dondrup, M. and Henckel, K. and Goesmann, A. and Meyer, Folker and Wipf, D. and Requena, N. and Hildebrandt, U. and Hampp, R. and Nehls, U. and Krajinski, F. and Franken, P. and Puhler, A.}, year = {2007}, note = {Type: Journal Article}, keywords = {Computational Biology/*methods *Expressed Sequence Tags Mycorrhizae/*genetics Oligonucleotide Array Sequence Analysis/*methods Symbiosis/*genetics Transcription, Genetic/*genetics} }
@article{RN45, author = {Velten, F. W. and Rambow, F. and Metharom, P. and Goerdt, S.}, title = {Enhanced T-cell activation and T-cell-dependent IL-2 production by CD83+, CD25high, CD43high human monocyte-derived dendritic cells}, journal = {Mol Immunol}, volume = {44}, number = {7}, pages = {1544-50}, issn = {0161-5890 (Print) 0161-5890 (Linking)}, doi = {10.1016/j.molimm.2006.08.020}, url = {https://www.ncbi.nlm.nih.gov/pubmed/17023048}, year = {2007}, type = {Journal Article} }
@article{scott_genome_2006, title = {The genome of deep-sea vent chemolithoautotroph {Thiomicrospira} crunogena {XCL}-2}, volume = {4}, doi = {10.1371/journal.pbio.0040383}, journal = {Plos Biology}, author = {Scott, K. M. and Sievert, S. M. and Abril, F. N. and Ball, L. A. and Barrett, C. J. and Blake, R. A. and Boller, A. J. and Chain, P. S. G. and Clark, J. A. and Davis, C. R. and Detter, C. and Do, K. F. and Dobrinski, K. P. and Faza, B. I. and Fitzpatrick, K. A. and Freyermuth, S. K. and Harmer, T. L. and Hauser, L. J. and Hugler, M. and Kerfeld, C. A. and Klotz, M. G. and Kong, W. W. and Land, M. and Lapidus, A. and Larimer, F. W. and Longo, D. L. and Lucas, S. and Malfatti, S. A. and Massey, S. E. and Martin, D. D. and McCuddin, Z. and Meyer, Folker and Moore, J. L. and Ocampo, L. H. and Paul, J. H. and Paulsen, I. T. and Reep, D. K. and Ren, Q. H. and Ross, R. L. and Sato, P. Y. and Thomas, P. and Tinkham, L. E. and Zeruth, G. T.}, year = {2006}, note = {Type: Journal Article} }
@article{schneiker_genome_2006, title = {Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium {Alcanivorax} borkumensis}, volume = {24}, doi = {10.1038/nbt1232}, journal = {Nat Biotechnol}, author = {Schneiker, S. and dos Santos, Vapm and Bartels, D. and Bekel, T. and Brecht, M. and Buhrmester, J. and Chernikova, T. N. and Denaro, R. and Ferrer, M. and Gertler, C. and Goesmann, A. and Golyshina, O. V. and Kaminski, F. and Khachane, A. N. and Lang, S. and Linke, B. and McHardy, A. C. and Meyer, Folker and Nechitaylo, T. and Puhler, A. and Regenhardt, D. and Rupp, O. and Sabirova, J. S. and Selbitschka, W. and Yakimov, M. M. and Timmis, K. N. and Vorholter, F. J. and Weidner, S. and Kaiser, O. and Golyshin, P. N.}, year = {2006}, note = {Type: Journal Article} }
@article{pobigaylo_construction_2006, title = {Construction of a large signature-tagged mini-{Tn5} transposon library and its application to mutagenesis of {Sinorhizobium} meliloti}, volume = {72}, doi = {10.1128/aem.03072-05}, journal = {Applied and Environmental Microbiology}, author = {Pobigaylo, N. and Wetter, D. and Szymczak, S. and Schiller, U. and Kurtz, S. and Meyer, Folker and Nattkemper, T. W. and Becker, A.}, year = {2006}, note = {Type: Journal Article} }
@article{linke_reganor_2006, title = {{REGANOR}: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes}, volume = {5}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16922601}, journal = {Appl Bioinformatics}, author = {Linke, B. and McHardy, A. C. and Neuweger, H. and Krause, L. and Meyer, Folker}, year = {2006}, note = {Type: Journal Article} }
@article{krause_finding_2006, title = {Finding novel genes in bacterial communities isolated from the environment}, volume = {22}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16873483}, journal = {Bioinformatics}, author = {Krause, L. and Diaz, N. N. and Bartels, D. and Edwards, R. A. and Puhler, A. and Rohwer, F. and Meyer, Folker and Stoye, J.}, year = {2006}, note = {Type: Journal Article} }
@article{hain_whole-genome_2006, title = {Whole-genome sequence of {Listeria} welshimeri reveals common steps in genome reduction with {Listeria} innocua as compared to {Listeria} monocytogenes}, volume = {188}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16936040}, doi = {10.1128/JB.00758-06}, journal = {J Bacteriol}, author = {Hain, T. and Steinweg, C. and Kuenne, C. T. and Billion, A. and Ghai, R. and Chatterjee, S. S. and Domann, E. and Karst, U. and Goesmann, A. and Bekel, T. and Bartels, D. and Kaiser, O. and Meyer, Folker and Puhler, A. and Weisshaar, B. and Wehland, J. and Liang, C. and Dandekar, T. and Lampidis, R. and Kreft, J. and Goebel, W. and Chakraborty, T.}, year = {2006}, note = {Type: Journal Article} }
@article{bauer_whole_2006, title = {Whole genome analysis of the marine {Bacteroidetes} '{Gramella} forsetii' reveals adaptations to degradation of polymeric organic matter}, volume = {8}, doi = {10.1111/j.1462-2920.2006.01152.x}, journal = {Environ Microbiol}, author = {Bauer, M. and Kube, M. and Teeling, H. and Richter, M. and Lombardot, T. and Allers, E. and Wurdemann, C. A. and Quast, C. and Kuhl, H. and Knaust, F. and Woebken, D. and Bischof, K. and Mussmann, M. and Choudhuri, J. V. and Meyer, Folker and Reinhardt, R. and Amann, R. I. and Glockner, F. O.}, year = {2006}, note = {Type: Journal Article} }
@article{pobigaylo_construction_2006-1, title = {Construction of a large signature-tagged mini-{Tn} 5 transposon library and its application to mutagenesis of {Sinorhizobium} meliloti}, volume = {72}, journal = {Applied and environmental microbiology}, author = {Pobigaylo, Nataliya and Wetter, Danijel and Szymczak, Silke and Schiller, Ulf and Kurtz, Stefan and Meyer, Folker and Nattkemper, Tim W and Becker, Anke}, year = {2006}, note = {Publisher: American Society for Microbiology} }
@article{linke_reganor_2006-1, title = {Reganor}, volume = {5}, journal = {Applied bioinformatics}, author = {Linke, Burkhard and McHardy, Alice C and Neuweger, Heiko and Krause, Lutz and Meyer, Folker}, year = {2006}, note = {Publisher: Springer International Publishing} }
@article{meyer_genome_2006, title = {Genome sequencing vs. moore’s law: {Cyber} challenges for the next decade}, volume = {2}, journal = {CTWatch Quarterly}, author = {Meyer, Folker}, year = {2006} }
@article{tauch_complete_2005, title = {Complete genome sequence and analysis of the multiresistant nosocomial pathogen {Corynebacterium} jeikeium {K411}, a lipid-requiring bacterium of the human skin flora}, volume = {187}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15968079}, doi = {10.1128/JB.187.13.4671-4682.2005}, journal = {J Bacteriol}, author = {Tauch, A. and Kaiser, O. and Hain, T. and Goesmann, A. and Weisshaar, B. and Albersmeier, A. and Bekel, T. and Bischoff, N. and Brune, I. and Chakraborty, T. and Kalinowski, J. and Meyer, Folker and Rupp, O. and Schneiker, S. and Viehoever, P. and Puhler, A.}, year = {2005}, note = {Type: Journal Article} }
@article{overbeek_subsystems_2005, title = {The {Subsystems} {Approach} to {Genome} {Annotation} and its {Use} in the {Project} to {Annotate} 1000 {Genomes}}, volume = {33}, journal = {Nucleic Acids Res}, author = {Overbeek, R. and Begley, T. and Butler, R.M. and Choudhuri, J.V. and Diaz, N. and Chuang, H.-Y. and Cohoon, M. and de Crécy-Lagard, V. and Disz, T. and Edwards, R and Fonstein, M and Frank, E.D. and Gerdes, S. and Glass, E.M. and Goesmann, A. and Krause, L. and Linke, B. and McHardy, A.C. and Meyer, Folker and Hanson, A. and Iwata-Reuyl, D. and Jensen, R. and Jamshidi, N. and Kubal, M. and Larsen, N. and Neuweger, H. and Rückert, C. and Olsen, G. J. and Olson, R. and Osterman, A. and Portnoy, V. and Pusch, G.D. and Rodionov, D.A. and Steiner, J. and Stevens, R. and Thiele, I. and Vassieva, O. and Ye, Y. and Zagnitko, O. and Vonstein, V.}, year = {2005}, note = {Type: Journal Article} }
@article{goesmann_brigep_2005, title = {{BRIGEP} - the {BRIDGE}-based genome-transcriptome-proteome browser}, volume = {33}, doi = {10.1093/nar/gki400}, journal = {Nucleic Acids Research}, author = {Goesmann, A. and Linke, B. and Bartels, D. and Dondrup, M. and Krause, L. and Neuweger, H. and Oehm, S. and Paczian, T. and Wilke, A. and Meyer, Folker}, year = {2005}, note = {Type: Journal Article} }
@article{frenzel_combined_2005-1, title = {Combined transcriptome profiling reveals a novel family of arbuscular mycorrhizal-specific {Medicago} truncatula lectin genes}, volume = {18}, journal = {Molecular plant-microbe interactions}, author = {Frenzel, André and Manthey, Katja and Perlick, Andreas M and Meyer, Folker and Pühler, Alfred and Küster, Helge and Krajinski, Franziska}, year = {2005}, note = {Publisher: Am Phytopath Society} }
@article{bartels_baccarditool_2005, title = {{BACCardI}—a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison}, volume = {21}, journal = {Bioinformatics}, author = {Bartels, Daniela and Kespohl, Sebastian and Albaum, Stefan and Drüke, Tanja and Goesmann, Alexander and Herold, Julia and Kaiser, Olaf and Pühler, Alfred and Pfeiffer, Friedhelm and Raddatz, Günter and Meyer, Folker}, year = {2005}, note = {Publisher: Oxford University Press} }
@article{goesmann_brigepbridge-based_2005, title = {{BRIGEP}—the {BRIDGE}-based genome–transcriptome–proteome browser}, volume = {33}, journal = {Nucleic acids research}, author = {Goesmann, Alexander and Linke, Burkhard and Bartels, Daniela and Dondrup, Michael and Krause, Lutz and Neuweger, Heiko and Oehm, Sebastian and Paczian, Tobias and Wilke, Andreas and Meyer, Folker}, year = {2005}, note = {Publisher: Oxford University Press} }
@article{overbeek_subsystems_2006, title = {The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes}, volume = {33}, doi = {10.1093/nar/gki866}, journal = {Nucleic Acids Res}, author = {Overbeek, R. and Begley, T. and Butler, R. M. and Choudhuri, J. V. and Chuang, H. Y. and Cohoon, M. and de Crecy-Lagard, V. and Diaz, N. and Disz, T. and Edwards, R. and Fonstein, M. and Frank, E. D. and Gerdes, S. and Glass, E. M. and Goesmann, A. and Hanson, A. and Iwata-Reuyl, D. and Jensen, R. and Jamshidi, N. and Krause, L. and Kubal, M. and Larsen, N. and Linke, B. and McHardy, A. C. and Meyer, Folker and Neuweger, H. and Olsen, G. and Olson, R. and Osterman, A. and Portnoy, V. and Pusch, G. D. and Rodionov, D. A. and Ruckert, C. and Steiner, J. and Stevens, R. and Thiele, I. and Vassieva, O. and Ye, Y. and Zagnitko, O. and Vonstein, V.}, year = {2005}, note = {Type: Journal Article}, keywords = {Acyl Coenzyme A/metabolism Coenzyme A/biosynthesis Computational Biology *Genome, Archaeal *Genome, Bacterial Genomics/*methods Internet Leucine/metabolism Ribosomal Proteins/classification *Software Terminology as Topic Vocabulary, Controlled} }
@article{thieme_insights_2005-2, title = {Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium {Xanthomonas} campestris pv. vesicatoria revealed by the complete genome sequence}, volume = {187}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16237009}, doi = {10.1128/JB.187.21.7254-7266.2005}, journal = {J Bacteriol}, author = {Thieme, F. and Koebnik, R. and Bekel, T. and Berger, C. and Boch, J. and Buttner, D. and Caldana, C. and Gaigalat, L. and Goesmann, A. and Kay, S. and Kirchner, O. and Lanz, C. and Linke, B. and McHardy, A. C. and Meyer, Folker and Mittenhuber, G. and Nies, D. H. and Niesbach-Klosgen, U. and Patschkowski, T. and Ruckert, C. and Rupp, O. and Schneiker, S. and Schuster, S. C. and Vorholter, F. J. and Weber, E. and Puhler, A. and Bonas, U. and Bartels, D. and Kaiser, O.}, year = {2005}, note = {Type: Journal Article}, keywords = {Adhesins, Bacterial Legionella pneumophila/genetics Molecular Sequence Data Plasmids/genetics Polysaccharides, Bacterial/*chemistry/*genetics Gene Order *Genome, Bacterial/genetics Base Composition Chromosomes, Bacterial/genetics Coxiella burnetii/genetics DNA, Bacterial/genetics Protein Transport/genetics *Sequence Analysis, DNA Synteny Virulence/genetics Virulence Factors/genetics Xanthomonas campestris/*genetics/physiology} }
@article{rendulic_predator_2004, title = {A predator unmasked: life cycle of {Bdellovibrio} bacteriovorus from a genomic perspective}, volume = {303}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14752164}, journal = {Science}, author = {Rendulic, S. and Jagtap, P. and Rosinus, A. and Eppinger, M. and Baar, C. and Lanz, C. and Keller, H. and Lambert, C. and Evans, K. J. and Goesmann, A. and Meyer, Folker and Sockett, R. E. and Schuster, S. C.}, year = {2004}, note = {Type: Journal Article} }
@article{bartels_baccardi_2004, title = {{BACCardI} - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15514001}, journal = {Bioinformatics}, author = {Bartels, D. and Kespohl, S. and Albaum, S. and Druke, T. and Goesmann, A. and Herold, J. and Kaiser, O. and Puhler, A. and Pfeiffer, F. and Raddatz, G. and Stoye, J. and Meyer, Folker and Schuster, S. C.}, year = {2004}, note = {Type: Journal Article} }
@article{mchardy_development_2004-1, title = {Development of joint application strategies for two microbial gene finders}, volume = {20}, journal = {Bioinformatics}, author = {McHardy, Alice C and Goesmann, Alexander and Pühler, Alfred and Meyer, Folker}, year = {2004}, note = {Publisher: Oxford University Press} }
@article{mchardy_comparing_2004-1, title = {Comparing expression level-dependent features in codon usage with protein abundance: an analysis of ‘predictive proteomics’}, volume = {4}, journal = {Proteomics}, author = {McHardy, Alice C and Pühler, Alfred and Kalinowski, Jörn and Meyer, Folker}, year = {2004}, note = {Publisher: WILEY-VCH Verlag Weinheim} }
@article{kuster_construction_2004-2, title = {Construction and validation of {cDNA}-based {Mt6k}-{RIT} macro- and microarrays to explore root endosymbioses in the model legume {Medicago} truncatula}, volume = {108}, doi = {10.1016/j.jbiotec.2003.11.011}, journal = {Journal of Biotechnology}, author = {Kuster, H. and Hohnjec, N. and Krajinski, F. and El Yahyaoui, F. and Manthey, K. and Gouzy, J. and Dondrup, M. and Meyer, Folker and Kalinowski, J. and Brechenmacher, L. and van Tuinen, D. and Gianinazzi-Pearson, V. and Puhler, A. and Gamas, P. and Becker, A.}, year = {2004}, note = {Type: Journal Article} }
@article{wilke_bioinformatics_2003, title = {Bioinformatics support for high-throughput proteomics}, volume = {106}, url = {https://www.ncbi.nlm.nih.gov/pubmed/14651857}, journal = {J Biotechnol}, author = {Wilke, A. and Ruckert, C. and Bartels, D. and Dondrup, M. and Goesmann, A. and Huser, A. T. and Kespohl, S. and Linke, B. and Mahne, M. and McHardy, A. and Puhler, A. and Meyer, Folker}, year = {2003}, note = {Type: Journal Article} }
@article{vorholter_comparison_2003, title = {Comparison of two {Xanthomonas} campestris pathovar campestris genomes revealed differences in their gene composition}, volume = {106}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14651861}, journal = {J Biotechnol}, author = {Vorholter, F. J. and Thias, T. and Meyer, Folker and Bekel, T. and Kaiser, O. and Puhler, A. and Niehaus, K.}, year = {2003}, note = {Type: Journal Article} }
@article{tauch_79370-bp_2003, title = {The 79,370-bp conjugative plasmid {pB4} consists of an {IncP}-1beta backbone loaded with a chromate resistance transposon, the {strA}-{strB} streptomycin resistance gene pair, the oxacillinase gene bla({NPS}-1), and a tripartite antibiotic efflux system of the resistance-nodulation-division family}, volume = {268}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12589432}, journal = {Mol Genet Genomics}, author = {Tauch, A. and Schluter, A. and Bischoff, N. and Goesmann, A. and Meyer, Folker and Puhler, A.}, year = {2003}, note = {Type: Journal Article} }
@article{ruberg_construction_2003, title = {Construction and validation of a {Sinorhizobium} meliloti whole genome {DNA} microarray: genome-wide profiling of osmoadaptive gene expression}, volume = {106}, doi = {10.1016/j.jbiotec.2003.08.005}, journal = {Journal of Biotechnology}, author = {Ruberg, S. and Tian, Z. X. and Krol, E. and Linke, B. and Meyer, Folker and Wang, Y. P. and Puhler, A. and Weidner, S. and Becker, A.}, year = {2003}, note = {Type: Journal Article} }
@article{nyamsuren_transcriptional_2003, title = {Transcriptional profiling of {Medicago} truncatula roots after infection with {Aphanomyces} euteiches (oomycota) identifies novel genes upregulated during this pathogenic interaction}, volume = {63}, doi = {10.1016/j.pmpp.2003.09.001}, journal = {Physiological and Molecular Plant Pathology}, author = {Nyamsuren, O. and Colditz, F. and Rosendahl, S. and Tamasloukht, M. and Bekel, T. and Meyer, Folker and Kuester, H. and Franken, P. and Krajinski, F.}, year = {2003}, note = {Type: Journal Article} }
@article{meyer_gendb_2003, title = {{GenDB} - an open source genome annotation system for prokaryote genomes}, volume = {31}, doi = {10.1093/nar/gkg312}, journal = {Nucleic Acids Research}, author = {Meyer, Folker and Goesmann, A. and McHardy, A. C. and Bartels, D. and Bekel, T. and Clausen, J. and Kalinowski, J. and Linke, B. and Rupp, O. and Giegerich, R. and Puhler, A.}, year = {2003}, note = {Type: Journal Article} }
@article{kalinowski_complete_2003, title = {The complete {Corynebacterium} glutamicum {ATCC} 13032 genome sequence and its impact on the production of {L}-aspartate-derived amino acids and vitamins}, volume = {104}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12948626}, journal = {J Biotechnol}, author = {Kalinowski, J. and Bathe, B. and Bartels, D. and Bischoff, N. and Bott, M. and Burkovski, A. and Dusch, N. and Eggeling, L. and Eikmanns, B. J. and Gaigalat, L. and Goesmann, A. and Hartmann, M. and Huthmacher, K. and Kramer, R. and Linke, B. and McHardy, A. C. and Meyer, Folker and Mockel, B. and Pfefferle, W. and Puhler, A. and Rey, D. A. and Ruckert, C. and Rupp, O. and Sahm, H. and Wendisch, V. F. and Wiegrabe, I. and Tauch, A.}, year = {2003}, note = {Type: Journal Article} }
@article{kaiser_whole_2003, title = {Whole genome shotgun sequencing guided by bioinformatics pipelines–an optimized approach for an established technique}, volume = {106}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14651855}, journal = {J Biotechnol}, author = {Kaiser, O. and Bartels, D. and Bekel, T. and Goesmann, A. and Kespohl, S. and Puhler, A. and Meyer, Folker}, year = {2003}, note = {Type: Journal Article} }
@article{dondrup_emma_2003, title = {{EMMA}: a platform for consistent storage and efficient analysis of microarray data}, volume = {106}, doi = {10.1016/j.jbiotec.2003.08.010}, journal = {Journal of Biotechnology}, author = {Dondrup, M. and Goesmann, A. and Bartels, D. and Kalinowski, J. and Krause, L. and Linke, B. and Rupp, O. and Sczyrba, A. and Puhler, A. and Meyer, Folker}, year = {2003}, note = {Type: Journal Article} }
@article{baar_complete_2003, title = {Complete genome sequence and analysis of {Wolinella} succinogenes}, volume = {100}, doi = {10.1073/pnas.1932838100}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, author = {Baar, C. and Eppinger, M. and Raddatz, G. and Simon, J. and Lanz, C. and Klimmek, O. and Nandakumar, R. and Gross, R. and Rosinus, A. and Keller, H. and Jagtap, P. and Linke, B. and Meyer, Folker and Lederer, H. and Schuster, S. C.}, year = {2003}, note = {Type: Journal Article} }
@article{wulf_transcriptional_2003-2, title = {Transcriptional changes in response to arbuscular mycorrhiza development in the model plant {Medicago} truncatula}, volume = {16}, journal = {Molecular Plant-Microbe Interactions}, author = {Wulf, Anne and Manthey, Katja and Doll, Jasmin and Perlick, Andreas M and Linke, Burkhard and Bekel, Thomas and Meyer, Folker and Franken, Philipp and Küster, Helge and Krajinski, Franziska}, year = {2003}, note = {Publisher: The American Phytopathological Society} }
@article{tauch_79370-bp_2003-1, title = {The 79,370-bp conjugative plasmid {pB4} consists of an {IncP}-1β backbone loaded with a chromate resistance transposon, the {strA}-{strB} streptomycin resistance gene pair, the oxacillinase gene bla {NPS}-1, and a tripartite antibiotic efflux system of the resistance-nodulation-division family}, volume = {268}, journal = {Molecular Genetics and Genomics}, author = {Tauch, Andreas and Schlüter, Andreas and Bischoff, N and Goesmann, Alexander and Meyer, F and Pühler, Alfred}, year = {2003}, note = {Publisher: Springer-Verlag} }
@article{goesmann_building_2003-1, title = {Building a {BRIDGE} for the integration of heterogeneous data from functional genomics into a platform for systems biology}, volume = {106}, journal = {Journal of biotechnology}, author = {Goesmann, Alexander and Linke, Burkhard and Rupp, Oliver and Krause, Lutz and Bartels, Daniela and Dondrup, Michael and McHardy, Alice C and Wilke, Andreas and Pühler, Alfred and Meyer, Folker}, year = {2003}, note = {Publisher: Elsevier} }
@article{kaiser_whole_2003-1, title = {Whole genome shotgun sequencing guided by bioinformatics pipelines—an optimized approach for an established technique}, volume = {106}, journal = {Journal of biotechnology}, author = {Kaiser, Olaf and Bartels, Daniela and Bekel, Thomas and Goesmann, Alexander and Kespohl, Sebastian and Pühler, Alfred and Meyer, Folker}, year = {2003}, note = {Publisher: Elsevier} }
@article{dondrup_archer_2003, title = {Archer, {DA}, see {Punt}, {PJ} (106) 23}, volume = {106}, journal = {Journal of Biotechnology}, author = {Dondrup, M and Goesmann, A and Bartels, D and Kalinowski, J and Krause, L and Linke, B and Rupp, O and Sczyrba, A and Pühler, A and Meyer, Folker}, year = {2003} }
@article{kalinowski_complete_2004, title = {The complete {Corynebacterium} glutamicum {ATCC} 13032 genome sequence and its impact on the production of l-aspartate-derived amino acids and vitamins}, volume = {104}, journal = {Journal of Biotechnology}, author = {Kalinowski, Jörn and Bathe, Brigitte and Bartels, Daniela and Bischoff, Nicole and Bott, Michael and Burkovski, Andreas and Dusch, Nicole and Eggeling, Lothar and Eikmanns, Bernhard J and Gaigalat, Lars and Meyer, Folker}, year = {2003} }
@article{goesmann_pathfinder_2002, title = {{PathFinder}: reconstruction and dynamic visualization of metabolic pathways}, volume = {18}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11836220}, journal = {Bioinformatics}, author = {Goesmann, A. and Haubrock, M. and Meyer, Folker and Kalinowski, J. and Giegerich, R.}, year = {2002}, note = {Type: Journal Article} }
@article{meyer_gendb_2001, title = {{GENDB}: a second generation genome annotation system}, author = {Meyer, Folker}, year = {2001} }
@article{stoye_rose_1998, title = {Rose: generating sequence families}, volume = {14}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9545448}, journal = {Bioinformatics}, author = {Stoye, J. and Evers, D. and Meyer, Folker}, year = {1998}, note = {Type: Journal Article} }
@article{stoye_rose_1998-2, title = {Rose: generating sequence families.}, volume = {14}, journal = {Bioinformatics (Oxford, England)}, author = {Stoye, Jens and Evers, Dirk and Meyer, Folker}, year = {1998} }
@inproceedings{stoye_generating_1997-1, title = {Generating {Benchmarks} for {Multiple} {Sequence} {Alignments} and {Phylogenic} {Reconstructions}.}, booktitle = {Ismb}, author = {Stoye, Jens and Evers, Dirk and Meyer, Folker}, year = {1997} }
@article{giegerich_genefishersoftware_1996, title = {{GeneFisher}–software support for the detection of postulated genes}, volume = {4}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8877506}, journal = {Proc Int Conf Intell Syst Mol Biol}, author = {Giegerich, R. and Meyer, Folker and Schleiermacher, C.}, year = {1996}, note = {Type: Journal Article} }
@inproceedings{giegerich_genefisher-software_1996, title = {{GeneFisher}-software support for the detection of postulated genes.}, volume = {4}, booktitle = {{ISMB}}, author = {Giegerich, Robert and Meyer, Folker and Schleiermacher, Chris}, year = {1996} }
