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@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} }
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@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} }
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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} }
@article{Pozniak2022.08.11.502598, author = {Pozniak, Joanna and Pedri, Dennis and Landeloos, Ewout and Herck, Yannick Van and Antoranz, Asier and Karras, Panagiotis and Nowosad, Ada and Makhzami, Samira and Bervoets, Greet and Dewaele, Michael and Vanwynsberghe, Lukas and Cinque, Sonia and Kint, Sam and Vandereyken, Katy and Voet, Thierry and Vernaillen, Frank and Annaert, Wim and Lambrechts, Diether and Boecxstaens, Veerle and van den Oord, Joost and Bosisio, Francesca and Leucci, Eleonora and Rambow, Florian and Bechter, Oliver and Marine, Jean-Christophe}, title = {A TCF4/BRD4-dependent regulatory network confers cross-resistance to targeted and immune checkpoint therapy in melanoma}, elocation-id = {2022.08.11.502598}, year = {2022}, doi = {10.1101/2022.08.11.502598}, publisher = {Cold Spring Harbor Laboratory}, url = {https://www.biorxiv.org/content/early/2022/08/13/2022.08.11.502598}, eprint = {https://www.biorxiv.org/content/early/2022/08/13/2022.08.11.502598.full.pdf}, journal = {bioRxiv} }
@article{RN48, author = {Verginadis, II and Avgousti, H. and Monslow, J. and Skoufos, G. and Chinga, F. and Kim, K. and Leli, N. M. and Karagounis, I. V. and Bell, B. I. and Velalopoulou, A. and Salinas, C. S. and Wu, V. S. and Li, Y. and Ye, J. and Scott, D. A. and Osterman, A. L. and Sengupta, A. and Weljie, A. and Huang, M. and Zhang, D. and Fan, Y. and Radaelli, E. and Tobias, J. W. and Rambow, F. and Karras, P. and Marine, J. C. and Xu, X. and Hatzigeorgiou, A. G. and Ryeom, S. and Diehl, J. A. and Fuchs, S. Y. and Pure, E. and Koumenis, C.}, title = {A stromal Integrated Stress Response activates perivascular cancer-associated fibroblasts to drive angiogenesis and tumour progression}, journal = {Nat Cell Biol}, volume = {24}, number = {6}, pages = {940-953}, issn = {1476-4679 (Electronic) 1465-7392 (Linking)}, doi = {10.1038/s41556-022-00918-8}, url = {https://www.ncbi.nlm.nih.gov/pubmed/35654839}, year = {2022}, type = {Journal Article} }
@article{RN55, author = {Pedri, D. and Karras, P. and Landeloos, E. and Marine, J. C. and Rambow, F.}, title = {Epithelial-to-mesenchymal-like transition events in melanoma}, journal = {FEBS J}, volume = {289}, number = {5}, pages = {1352-1368}, issn = {1742-4658 (Electronic) 1742-464X (Linking)}, doi = {10.1111/febs.16021}, url = {https://www.ncbi.nlm.nih.gov/pubmed/33999497}, year = {2022}, type = {Journal Article} }
@article{cormier_go_2021, title = {Go {Get} {Data} ({GGD}) is a framework that facilitates reproducible access to genomic data}, volume = {12}, copyright = {2021 The Author(s)}, issn = {2041-1723}, url = {https://www.nature.com/articles/s41467-021-22381-z}, doi = {10.1038/s41467-021-22381-z}, language = {en}, number = {1}, urldate = {2021-06-30}, journal = {Nature Communications}, author = {Cormier, Michael J. and Belyeu, Jonathan R. and Pedersen, Brent S. and Brown, Joseph and Köster, Johannes and Quinlan, Aaron R.}, month = apr, year = {2021}, note = {Bandiera\_abtest: a Cc\_license\_type: cc\_by Cg\_type: Nature Research Journals Number: 1 Primary\_atype: Research Publisher: Nature Publishing Group Subject\_term: Data acquisition;Data integration;Data publication and archiving;Genomics Subject\_term\_id: data-acquisition;data-integration;data-publication-and-archiving;genomics}, pages = {2151}, file = {Full Text PDF:/home/johannes/Zotero/storage/H8AV5FN8/Cormier et al. - 2021 - Go Get Data (GGD) is a framework that facilitates .pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/EWQIQ5FE/s41467-021-22381-z.html:text/html} }
@article{molder_sustainable_2021, title = {Sustainable data analysis with {Snakemake}}, volume = {10}, issn = {2046-1402}, url = {https://f1000research.com/articles/10-33/v1}, doi = {10.12688/f1000research.29032.1}, language = {en}, urldate = {2021-03-01}, journal = {F1000Research}, author = {Mölder, Felix and Jablonski, Kim Philipp and Letcher, Brice and Hall, Michael B. and Tomkins-Tinch, Christopher H. and Sochat, Vanessa and Forster, Jan and Lee, Soohyun and Twardziok, Sven O. and Kanitz, Alexander and Wilm, Andreas and Holtgrewe, Manuel and Rahmann, Sven and Nahnsen, Sven and Köster, Johannes}, month = jan, year = {2021}, pages = {33}, file = {Full Text:/home/johannes/Zotero/storage/89YMUV3F/Mölder et al. - 2021 - Sustainable data analysis with Snakemake.pdf:application/pdf;Sustainable data analysis with Snakemake | F1000Research:/home/johannes/Zotero/storage/W55Y2PPD/v1.html:text/html} }
@article{vriesComparingThreeMachine2021, title = {Comparing Three Machine Learning Approaches to Design a Risk Assessment Tool for Future Fractures: Predicting a Subsequent Major Osteoporotic Fracture in Fracture Patients with Osteopenia and Osteoporosis}, author = {de Vries, Bram C. S. and Hegeman, Johannes H. and Nijmeijer, Wieke and Geerdink, Jeroen and Seifert, Christin and {Groothuis-Oudshoorn}, Karin G. M.}, year = {2021}, month = jan, journal = {Osteoporosis International}, issn = {1433-2965}, doi = {10.1007/s00198-020-05735-z} }
@article{libbiGeneratingSyntheticTraining2021, title = {Generating {{Synthetic Training Data}} for {{Supervised De-Identification}} of {{Electronic Health Records}}}, author = {Libbi, Claudia Alessandra and Trienes, Jan and Trieschnigg, Dolf and Seifert, Christin}, year = {2021}, journal = {Future Internet}, volume = {13}, number = {5}, issn = {1999-5903}, doi = {10.3390/fi13050136} }
@incollection{liuRewritingFictionalTexts2021, title = {Rewriting {{Fictional Texts Using Pivot Paraphrase Generation}} and {{Character Modification}}}, booktitle = {Text, {{Speech}}, and {{Dialogue}}}, author = {Liu, Dou and Zhu, Tingting and Schl{\"o}tterer, J{\"o}rg and Seifert, Christin and Wang, Shenghui}, year = {2021}, pages = {73--85}, publisher = {{Springer International Publishing}}, doi = {10.1007/978-3-030-83527-9_6} }
@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} }
@inproceedings{nautaNeuralPrototypeTrees2021, title = {Neural {{Prototype Trees}} for {{Interpretable Fine-grained Image Recognition}}}, booktitle = {{{IEEE}}/{{CVF Conference}} on {{Computer Vision}} and {{Pattern Recognition}} ({{CVPR}})}, author = {Nauta, Meike and van Bree, Ron and Seifert, Christin}, year = {2021}, pages = {14933--14943} }
@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} }
@article{pathakSTQSInterpretableMultimodal2021, title = {{{STQS}}: {{Interpretable}} Multi-Modal {{Spatial-Temporal-seQuential}} Model for Automatic {{Sleep}} Scoring}, author = {Pathak, Shreyasi and Lu, Changqing and Nagaraj, Sunil Belur and van Putten, Michel and Seifert, Christin}, year = {2021}, journal = {Artificial Intelligence in Medicine}, volume = {114}, pages = {102038}, issn = {0933-3657}, doi = {10.1016/j.artmed.2021.102038}, keywords = {Deep learning,EEG,EMG signals,EOG,Explainable AI,Post-hoc interpretability,Sleep scoring,Sleep stage annotation}, file = {/Users/andrea/Zotero/storage/ILEJPEMP/Pathak et al. - 2021 - STQS Interpretable multi-modal Spatial-Temporal-s.pdf} }
@inproceedings{schmidtTrustworthySecureReliable2021, title = {Towards a Trustworthy, Secure and Reliable Enclave for Machine Learning in a Hospital Setting: The {{Essen Medical Computing Platform}} ({{EMCP}})}, booktitle = {Proc. {{International Conference}} on {{Cognitive Machine Intelligence}}}, author = {Schmidt, Hendrik and Schl{\"o}tterer, J{\"o}rg and Bargull, Marcell and Nasca, Enrico and Aydelott, Ryan and Seifert, Christin and Meyer, Folker}, year = {2021}, publisher = {{IEEE}} }
@inproceedings{zerhoudiQueryChangeContextual2021, title = {Query {{Change}} as a {{Contextual Markov Model}} for {{Simulating User Search Behaviour}}}, booktitle = {Proceedings of the 12th {{Forum}} for {{Information Retrieval Evaluation}}}, author = {Zerhoudi, Saber and Granitzer, Michael and Schl{\"o}tterer, J{\"o}rg and Seifert, Christin}, year = {2021}, series = {{{FIRE}} '21}, publisher = {{Association for Computing Machinery}}, doi = {10.1145/3503162.3503165} }
@article{RN1742, author = {Magin, S. and Meher, P. K. and Iliakis, G.}, title = {Nucleoside Analogs Radiosensitize G0 Cells by Activating DNA End Resection and Alternative End-Joining}, journal = {Radiat Res}, volume = {195}, number = {5}, pages = {412-426}, note = {Magin, Simon Meher, Prabodha Kumar Iliakis, George eng Research Support, Non-U.S. Gov't 2021/03/24 Radiat Res. 2021 May 1;195(5):412-426. doi: 10.1667/RADE-20-00195.1.}, keywords = {Animals Cell Line Cell Proliferation/drug effects/genetics/radiation effects DNA Breaks, Double-Stranded/drug effects/radiation effects DNA End-Joining Repair/*drug effects/radiation effects Dose-Response Relationship, Radiation Humans Mice Nucleosides/*analogs & derivatives/*pharmacology Radiation-Sensitizing Agents/*chemistry/*pharmacology Resting Phase, Cell Cycle/drug effects/*genetics/radiation effects Tumor Suppressor p53-Binding Protein 1/metabolism}, issn = {1938-5404 (Electronic) 0033-7587 (Linking)}, doi = {10.1667/RADE-20-00195.1}, url = {https://www.ncbi.nlm.nih.gov/pubmed/33755161}, year = {2021}, type = {Journal Article} }
@article{schreiber2021clinically, title = {Clinically relevant antibiotic-resistant bacteria in aquatic environments--An optimized culture-based approach}, author = {Schreiber, Christiane and Zacharias, Nicole and Essert, Sarah M and Wasser, Felix and M{\"u}ller, Heike and Sib, Esther and Precht, Tabea and Parcina, Marijo and Bierbaum, Gabriele and Schmithausen, Ricarda M and others}, journal = {Science of The Total Environment}, volume = {750}, year = {2021}, publisher = {Elsevier} }
@article{savin2021clinically, title = {Clinically relevant Escherichia coli isolates from process waters and wastewater of poultry and pig slaughterhouses in Germany}, author = {Savin, Mykhailo and Bierbaum, Gabriele and Kreyenschmidt, Judith and Schmithausen, Ricarda Maria and Sib, Esther and Schmoger, Silvia and K{\"a}sbohrer, Annemarie and Hammerl, Jens Andre}, journal = {Microorganisms}, volume = {9}, year = {2021}, publisher = {MDPI} }
@article{richter2021detectable, title = {Detectable SARS-CoV-2 RNAemia in critically Ill patients, but not in mild and asymptomatic infections}, author = {Richter, Enrico and Al Arashi, Doaa and Schulte, Bianca and Bode, Christian and Marx, Benjamin and Aldabbagh, Souhaib and Schl{\"u}ter, Celina and K{\"u}mmerer, Beate Mareike and Oldenburg, Johannes and Funk, Markus B and others}, journal = {Transfusion Medicine and Hemotherapy}, volume = {48}, year = {2021}, publisher = {Karger Publishers} }
@article{ludwig2021lamp, title = {LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding}, author = {Ludwig, Kerstin U and Schmithausen, Ricarda M and Li, David and Jacobs, Max L and Hollstein, Ronja and Blumenstock, Katja and Liebing, Jana and S{\l}abicki, Miko{\l}aj and Ben-Shmuel, Amir and Israeli, Ofir and others}, journal = {Nature Biotechnology}, volume = {39}, year = {2021}, publisher = {Nature Publishing Group} }
@article{exner2021reply, title = {Reply to the letter to the editor by R. Papke}, 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 = {16}, year = {2021}, publisher = {German Medical Science} }
@article{savin2021antibiotic, title = {Antibiotic-resistant bacteria, antibiotic resistance genes, and antibiotic residues in wastewater from a poultry slaughterhouse after conventional and advanced treatments}, author = {Savin, Mykhailo and Alexander, Johannes and Bierbaum, Gabriele and Hammerl, Jens Andre and Hembach, Norman and Schwartz, Thomas and Schmithausen, Ricarda Maria and Sib, Esther and Voigt, Alexander and Kreyenschmidt, Judith}, journal = {Scientific Reports}, volume = {11}, year = {2021}, publisher = {Nature Publishing Group} }
@article{wessendorf2021analysis, title = {Analysis of the Dynamics, Outcome, and Prerequisites of the first German SARS-CoV-2 Superspreading Event}, 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 = {medRxiv}, year = {2021}, publisher = {Cold Spring Harbor Laboratory Press} }
@inproceedings{schmidt_towards_2021, title = {Towards a {Trustworthy}, {Secure} and {Reliable} {Enclave} for {Machine} {Learning} in a {Hospital} {Setting}: {The} {Essen} {Medical} {Computing} {Platform} ({EMCP})}, doi = {10.1109/CogMI52975.2021.00023}, booktitle = {Third {IEEE} {International} {Conference} on {Cognitive} {Machine} {Intelligence}, {CogMI} 2021, {Atlanta}, {GA}, {USA}, {December} 13-15, 2021}, publisher = {IEEE}, author = {Schmidt, Hendrik F. R. and Schlötterer, Jörg and Bargull, Marcel and Nasca, Enrico and Aydelott, Ryan and Seifert, Christin and Meyer, Folker}, year = {2021} }
@article{DBLP:journals/corr/abs-2112-00661, title = {{{MOMO}} - {{Deep Learning-driven}} Classification of External {{DICOM}} Studies for {{PACS}} Archivation}, author = {Jonske, Frederic and Dederichs, Maximilian and Kim, Moon-Sung and Egger, Jan and Umutlu, Lale and Forsting, Michael and Nensa, Felix and Kleesiek, Jens}, year = {2021}, journal = {CoRR}, volume = {abs/2112.00661}, eprint = {2112.00661}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2112.00661}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2112-00661.bib}, timestamp = {Tue, 07 Dec 2021 00:00:00 +0100} }
@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} }
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@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} }
@article{DBLP:journals/corr/abs-2111-11269, title = {Automated Cross-Sectional View Selection in {{CT}} Angiography of Aortic Dissections with Uncertainty Awareness and Retrospective Clinical Annotations}, author = {Pepe, Antonio and Egger, Jan and Codari, Marina and Willemink, Martin J. and Gsaxner, Christina and Li, Jianning and Roth, Peter M. and Mistelbauer, Gabriel and Schmalstieg, Dieter and Fleischmann, Dominik}, year = {2021}, journal = {CoRR}, volume = {abs/2111.11269}, eprint = {2111.11269}, eprinttype = {arxiv}, url = {https://arxiv.org/abs/2111.11269}, archiveprefix = {arXiv}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/corr/abs-2111-11269.bib}, timestamp = {Fri, 26 Nov 2021 00:00:00 +0100} }
@article{DBLP:journals/mia/LiCPGWCZTKDSSE21, title = {Automatic Skull Defect Restoration and Cranial Implant Generation for Cranioplasty}, author = {Li, Jianning and {von Campe}, Gord and Pepe, Antonio and Gsaxner, Christina and Wang, Enpeng and Chen, Xiaojun and Zefferer, Ulrike and T{\"o}dtling, Martin and Krall, Marcell and Deutschmann, Hannes and Sch{\"a}fer, Ute and Schmalstieg, Dieter and Egger, Jan}, year = {2021}, journal = {Medical Image Anal.}, volume = {73}, pages = {102171}, doi = {10.1016/j.media.2021.102171}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/mia/LiCPGWCZTKDSSE21.bib}, timestamp = {Sat, 09 Apr 2022 01:00:00 +0200} }
@article{DBLP:journals/peerj-cs/EggerPGJLK21, title = {Deep Learning - a First Meta-Survey of Selected Reviews across Scientific Disciplines, Their Commonalities, Challenges and Research Impact}, author = {Egger, Jan and Pepe, Antonio and Gsaxner, Christina and Jin, Yuan and Li, Jianning and Kern, Roman}, year = {2021}, journal = {PeerJ Computer Science}, volume = {7}, pages = {e773}, doi = {10.7717/peerj-cs.773}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/peerj-cs/EggerPGJLK21.bib}, timestamp = {Wed, 16 Mar 2022 00:00:00 +0100} }
@article{DBLP:journals/tmi/LiPSELZCDRS0MNF21, title = {{{AutoImplant}} 2020-{{First MICCAI}} Challenge on Automatic Cranial Implant Design}, author = {Li, Jianning and Pimentel, Pedro and Szengel, Angelika and Ehlke, Moritz and Lamecker, Hans and Zachow, Stefan and Cerquin, Laura Jovani Estacio and Doenitz, Christian and Ramm, Heiko and Shi, Haochen and Chen, Xiaojun and Matzkin, Franco and Newcombe, Virginia F. J. and Ferrante, Enzo and Jin, Yuan and Ellis, David G. and Aizenberg, Michele R. and Kodym, Oldrich and Spanel, Michal and Herout, Adam and Mainprize, James G. and Fishman, Zachary and Hardisty, Michael R. and Bayat, Amirhossein and Shit, Suprosanna and Wang, Bomin and Liu, Zhi and Eder, Matthias and Pepe, Antonio and Gsaxner, Christina and Alves, Victor and Zefferer, Ulrike and {von Campe}, Gord and Pistracher, Karin and Sch{\"a}fer, Ute and Schmalstieg, Dieter and Menze, Bjoern H. and Glocker, Ben and Egger, Jan}, year = {2021}, journal = {IEEE Trans. Medical Imaging}, volume = {40}, number = {9}, pages = {2329--2342}, doi = {10.1109/TMI.2021.3077047}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/tmi/LiPSELZCDRS0MNF21.bib}, timestamp = {Sat, 09 Apr 2022 01:00:00 +0200} }
@article{RN52, author = {Talon, I. and Janiszewski, A. and Theeuwes, B. and Lefevre, T. and Song, J. and Bervoets, G. and Vanheer, L. and De Geest, N. and Poovathingal, S. and Allsop, R. and Marine, J. C. and Rambow, F. and Voet, T. and Pasque, V.}, title = {Enhanced chromatin accessibility contributes to X chromosome dosage compensation in mammals}, journal = {Genome Biol}, volume = {22}, number = {1}, pages = {302}, issn = {1474-760X (Electronic) 1474-7596 (Linking)}, doi = {10.1186/s13059-021-02518-5}, url = {https://www.ncbi.nlm.nih.gov/pubmed/34724962}, year = {2021}, type = {Journal Article} }
@article{RN51, author = {Rapino, F. and Delaunay, S. and Rambow, F. and Zhou, Z. and Tharun, L. and De Tullio, P. and Sin, O. and Shostak, K. and Schmitz, S. and Piepers, J. and Ghesquiere, B. and Karim, L. and Charloteaux, B. and Jamart, D. and Florin, A. and Lambert, C. and Rorive, A. and Jerusalem, G. and Leucci, E. and Dewaele, M. and Vooijs, M. and Leidel, S. A. and Georges, M. and Voz, M. and Peers, B. and Buttner, R. and Marine, J. C. and Chariot, A. and Close, P.}, title = {Author Correction: Codon-specific translation reprogramming promotes resistance to targeted therapy}, journal = {Nature}, volume = {599}, number = {7886}, pages = {E14}, issn = {1476-4687 (Electronic) 0028-0836 (Linking)}, doi = {10.1038/s41586-021-04074-1}, url = {https://www.ncbi.nlm.nih.gov/pubmed/34764478}, year = {2021}, type = {Journal Article} }
@article{RN50, author = {Najem, A. and Wouters, J. and Krayem, M. and Rambow, F. and Sabbah, M. and Sales, F. and Awada, A. and Aerts, S. and Journe, F. and Marine, J. C. and Ghanem, G. E.}, title = {Tyrosine-Dependent Phenotype Switching Occurs Early in Many Primary Melanoma Cultures Limiting Their Translational Value}, journal = {Front Oncol}, volume = {11}, pages = {780654}, issn = {2234-943X (Print) 2234-943X (Linking)}, doi = {10.3389/fonc.2021.780654}, url = {https://www.ncbi.nlm.nih.gov/pubmed/34869032}, year = {2021}, type = {Journal Article} }
@article{RN24, author = {Marin-Bejar, O. and Rogiers, A. and Dewaele, M. and Femel, J. and Karras, P. and Pozniak, J. and Bervoets, G. and Van Raemdonck, N. and Pedri, D. and Swings, T. and Demeulemeester, J. and Borght, S. V. and Lehnert, S. and Bosisio, F. and van den Oord, J. J. and Bempt, I. V. and Lambrechts, D. and Voet, T. and Bechter, O. and Rizos, H. and Levesque, M. P. and Leucci, E. and Lund, A. W. and Rambow, F. and Marine, J. C.}, title = {Evolutionary predictability of genetic versus nongenetic resistance to anticancer drugs in melanoma}, journal = {Cancer Cell}, volume = {39}, number = {8}, pages = {1135-1149 e8}, issn = {1878-3686 (Electronic) 1535-6108 (Linking)}, doi = {10.1016/j.ccell.2021.05.015}, url = {https://www.ncbi.nlm.nih.gov/pubmed/34143978}, year = {2021}, type = {Journal Article} }
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@article{RN16, author = {Gautron, A. and Bachelot, L. and Aubry, M. and Leclerc, D. and Quemener, A. M. and Corre, S. and Rambow, F. and Paris, A. and Tardif, N. and Leclair, H. M. and Marin-Bejar, O. and Coulouarn, C. and Marine, J. C. and Galibert, M. D. and Gilot, D.}, title = {CRISPR screens identify tumor-promoting genes conferring melanoma cell plasticity and resistance}, journal = {EMBO Mol Med}, volume = {13}, number = {5}, pages = {e13466}, issn = {1757-4684 (Electronic) 1757-4676 (Linking)}, doi = {10.15252/emmm.202013466}, url = {https://www.ncbi.nlm.nih.gov/pubmed/33724679}, year = {2021}, type = {Journal Article} }
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@article{keulenScalableInterdisciplinaryData2020, title = {Scalable {{Interdisciplinary Data Science Teaching}} at the {{University}} of {{Twente}}}, author = {van Keulen, Maurice and Seifert, Christin and Poel, Mannes and {Groothuis-Oudshoorn}, Karin}, year = {2020}, month = dec, journal = {Berlin Journal of Data Science}, volume = {1}, issn = {978-3-00-064614-0}, langid = {english} }
@article{wiesweg_machine_2020, title = {Machine learning reveals a {PD}-{L1}–independent prediction of response to immunotherapy of non-small cell lung cancer by gene expression context}, volume = {140}, issn = {0959-8049}, url = {https://www.sciencedirect.com/science/article/pii/S0959804920305219}, doi = {10.1016/j.ejca.2020.09.015}, language = {en}, urldate = {2021-06-30}, journal = {European Journal of Cancer}, author = {Wiesweg, Marcel and Mairinger, Fabian and Reis, Henning and Goetz, Moritz and Kollmeier, Jens and Misch, Daniel and Stephan-Falkenau, Susann and Mairinger, Thomas and Walter, Robert F. H. and Hager, Thomas and Metzenmacher, Martin and Eberhardt, Wilfried E. E. and Zaun, Gregor and Köster, Johannes and Stuschke, Martin and Aigner, Clemens and Darwiche, Kaid and Schmid, Kurt W. and Rahmann, Sven and Schuler, Martin}, month = nov, year = {2020}, keywords = {Immunotherapy, Lung cancer, Machine learning, PD-L1, Predictive factors}, pages = {76--85}, file = {ScienceDirect Snapshot:/home/johannes/Zotero/storage/LSUG97NM/S0959804920305219.html:text/html} }
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@article{koster_varlociraptor_2020, title = {Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery}, volume = {21}, issn = {1474-760X}, shorttitle = {Varlociraptor}, url = {https://doi.org/10.1186/s13059-020-01993-6}, doi = {10.1186/s13059-020-01993-6}, number = {1}, urldate = {2020-04-28}, journal = {Genome Biology}, author = {Köster, Johannes and Dijkstra, Louis J. and Marschall, Tobias and Schönhuth, Alexander}, month = apr, year = {2020}, pages = {98}, file = {Snapshot:/home/johannes/Zotero/storage/C96TEUVF/s13059-020-01993-6.html:text/html} }
@inproceedings{legoyRcATTRetrievingATT2020, title = {{{rcATT}}: Retrieving {{ATT}}\&{{CK}} Tactics and Techniques in Cyber Threat Reports}, booktitle = {{{FIRST Cyber Threat Intelligence Symposium}}}, author = {Legoy, Valentine and Caselli, Marco and Peter, Andreas and Seifert, Christin}, year = {2020}, month = mar, address = {{Zurich}} }
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@article{marazzaAutomaticProcessComparison2020, title = {Automatic {{Process Comparison}} for {{Subpopulations}}: {{Application}} in {{Cancer Care}}}, author = {Marazza, Francesca and Bukhsh, Faiza Allah and Geerdink, Jeroen and Vijlbrief, Onno and Pathak, Shreyasi and van Keulen, Maurice and Seifert, Christin}, year = {2020}, journal = {Int. J. Environ. Res. Public Health}, volume = {17}, number = {16}, doi = {10.3390/ijerph1716570} }
@inproceedings{marinEffectivenessNeuralLanguage2020, title = {Effectiveness of Neural Language Models for Word Prediction of Textual Mammography Reports}, booktitle = {Proc. {{IEEE International Conference}} on {{Systems}}, {{Man}}, and {{Cybernetics}}}, author = {Marin, Mihai David and Mocanu, Elena and Seifert, Christin}, year = {2020}, series = {{{IEEE SMC}}} }
@inproceedings{nautaInteractiveExplanationsInternal2020, title = {Interactive {{Explanations}} of {{Internal Representations}} of {{Neural Network Layers}}: {{An Exploratory Study}} on {{Outcome Prediction}} of {{Comatose Patients}}}, booktitle = {International {{Workshop}} on {{Knowledge Discovery}} in {{Healthcare Data}}}, author = {Nauta, Meike and van Putten, Michel J. A. M. and {Tjepkema-Cloostermans}, Marleen C. and Bos, Jeroen Peter and van Keulen, Maurice and Seifert, Christin}, year = {2020}, series = {{{KDH}}}, volume = {2675} }
@inproceedings{nguyenHybridTextClassification2020, title = {A {{Hybrid Text Classification}} and {{Language Generation Model}} for {{Automated Summarization}} of {{Dutch Breast Cancer Radiology Reports}}}, booktitle = {Proceedings {{International Conference}} on {{Cognitive Machine Intelligence}}}, author = {Nguyen, Elisa and Theodorakopoulos, Daphne and Pathak, Shreyasik and Geerdink, Jeroen and Vijlbrief, Onno and van Keulen, Maurice and Seifert, Christin}, year = {2020}, series = {{{CogMI}}}, publisher = {{IEEE}} }
@inproceedings{ruisHumanintheloopLanguageagnosticExtraction2020, title = {Human-in-the-Loop {{Language-agnostic Extraction}} of {{Medication Data}} from {{Highly Unstructured Electronic Health Records}}}, booktitle = {Proc. {{International Conference}} on {{Data Mining Workshops}}}, author = {Ruis, Frank and Pathak, Shreyasi and Geerdink, Jeroen and Hegeman, Johannes H. and Seifert, Christin and van Keulen, Maurice}, year = {2020}, publisher = {{IEEE}} }
@article{schlottererQueryCrumbsSearchHistory2020, title = {{{QueryCrumbs Search History Visualization}} - {{Usability}}, {{Transparency}} and {{Long-term Usage}}}, author = {Schl{\"o}tterer, J{\"o}rg and Seifert, Christin and Granitzer, Michael}, year = {2020}, journal = {Journal of Computer Languages}, volume = {57}, issn = {2590-1184}, doi = {10.1016/j.cola.2020.100941} }
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@article{RN1741, author = {Magin, S. and Georgoulis, A. and Papadimitriou, K. and Iliakis, G. and Vorgias, C. E.}, title = {Complete Genome Sequence of the Deep-Sea Bacterium Moritella marina MP-1 (ATCC 15381)}, journal = {Microbiol Resour Announc}, volume = {9}, number = {4}, note = {Magin, Simon Georgoulis, Anastasios Papadimitriou, Konstantinos Iliakis, George Vorgias, Constantinos E eng 2020/01/25 Microbiol Resour Announc. 2020 Jan 23;9(4). pii: 9/4/e01321-19. doi: 10.1128/MRA.01321-19.}, issn = {2576-098X (Electronic) 2576-098X (Linking)}, doi = {10.1128/MRA.01321-19}, url = {https://www.ncbi.nlm.nih.gov/pubmed/31974151}, year = {2020}, type = {Journal Article} }
@article{Moyano2020BacteriophytochromesFP, title = {Bacteriophytochromes from Pseudomonas syringae pv. tomato DC3000 modulate the early stages of plant colonization during bacterial speck disease}, author = {Moyano, Laura and Carrau, Anal{\'i}a and Petrocelli, Silvana and Kraiselburd, Ivana and G{\"a}rtner, Wolfgang and Orellano, Elena G}, journal = {European Journal of Plant Pathology}, year = {2020}, volume = {156}, pages = {695 - 712} }
@article{dohla2020assessment, title = {Assessment of the prevalence of antibiotic-resistant bacteria and the concentration of antibiotics in EU bathing waters in western Germany}, author = {D{\"o}hla, Manuel and Sib, Esther and Dericks, Barbara and Grobe, Susanne and Behringer, Katja and Frechen, Monika and Simon, Katharina and F{\"a}rber, Harald and Lenz, Franziska and Parcina, Marijo and others}, journal = {Exposure and Health}, volume = {12}, year = {2020}, publisher = {Springer Netherlands} }
@article{voigt2020association, title = {Association between antibiotic residues, antibiotic resistant bacteria and antibiotic resistance genes in anthropogenic wastewater--An evaluation of clinical influences}, author = {Voigt, AM and Zacharias, N and Timm, C and Wasser, F and Sib, E and Skutlarek, D and Parcina, M and Schmithausen, RM and Schwartz, T and Hembach, N and others}, journal = {Chemosphere}, volume = {241}, year = {2020}, publisher = {Pergamon} }
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@article{exner2020questionnaire, title = {Questionnaire based evaluation of the motivation of surgically treated patients to participate in preventative hygiene measures}, author = {Exner, Daniel Philipp and Stoffels, Meike Elisabeth and Exner, Martin and Engelhart, Steffen and Kalff, J{\"o}rg Christoph and Schmithausen, Ricarda Maria}, journal = {GMS Hygiene and Infection Control}, volume = {15}, year = {2020}, publisher = {German Medical Science} }
@article{dohla2020rapid, title = {Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity}, author = {D{\"o}hla, M and Boesecke, C and Schulte, B and Diegmann, C and Sib, E and Richter, E and Eschbach-Bludau, M and Aldabbagh, S and Marx, B and Eis-H{\"u}binger, A-M and others}, journal = {Public health}, volume = {182}, year = {2020}, publisher = {WB Saunders} }
@article{streeck2020infection, title = {Infection fatality rate of SARS-CoV-2 infection in a German community with a super-spreading event}, 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 = {medrxiv}, year = {2020}, publisher = {Cold Spring Harbor Laboratory Press} }
@article{schmithausen2020characteristic, title = {Characteristic temporary loss of taste and olfactory senses in SARS-CoV-2-positive-individuals with mild symptoms}, author = {Schmithausen, Ricarda M and D{\"o}hla, Manuel and Sch{\"o}$\beta$ler, Heidrun and Diegmann, Christin and Schulte, Bianca and Richter, Enrico and Eis-H{\"u}binger, Anna-Maria and Streeck, Hendrik}, journal = {Pathogens and Immunity}, volume = {5}, year = {2020}, publisher = {Faculty at Case Western Reserve University School of Medicine} }
@article{schmid2020lamp, title = {LAMP-Seq: population-scale COVID-19 diagnostics using combinatorial barcoding}, author = {Schmid-Burgk, Jonathan L and Schmithausen, Ricarda M and Li, David and Hollstein, Ronja and Ben-Shmuel, Amir and Israeli, Ofir and Weiss, Shay and Paran, Nir and Wilbring, Gero and Liebing, Jana and others}, journal = {biorxiv}, year = {2020}, publisher = {Cold Spring Harbor Laboratory} }
@article{sib2020bacteria, title = {Bacteria isolated from hospital, municipal and slaughterhouse wastewaters show characteristic, different resistance profiles}, author = {Sib, Esther and Lenz-Plet, Franziska and Barabasch, Vanessa and Klanke, Ursula and Savin, Mykhailo and Hembach, Norman and Schallenberg, Anna and Kehl, Katja and Albert, Cathrin and Gajdiss, Mike and others}, journal = {Science of The Total Environment}, volume = {746}, year = {2020}, publisher = {Elsevier} }
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@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} }
@article{DBLP:journals/mia/PepeLRGCHE20, title = {Detection, Segmentation, Simulation and Visualization of Aortic Dissections: {{A}} Review}, author = {Pepe, Antonio and Li, Jianning and {Rolf-Pissarczyk}, Malte and Gsaxner, Christina and Chen, Xiaojun and Holzapfel, Gerhard A. and Egger, Jan}, year = {2020}, journal = {Medical Image Anal.}, volume = {65}, pages = {101773}, doi = {10.1016/j.media.2020.101773}, bibsource = {dblp computer science bibliography, https://dblp.org}, biburl = {https://dblp.org/rec/journals/mia/PepeLRGCHE20.bib}, timestamp = {Tue, 11 Jan 2022 00:00:00 +0100} }
@article{RN47, author = {Wouters, J. and Kalender-Atak, Z. and Minnoye, L. and Spanier, K. I. and De Waegeneer, M. and Bravo Gonzalez-Blas, C. and Mauduit, D. and Davie, K. and Hulselmans, G. and Najem, A. and Dewaele, M. and Pedri, D. and Rambow, F. and Makhzami, S. and Christiaens, V. and Ceyssens, F. and Ghanem, G. and Marine, J. C. and Poovathingal, S. and Aerts, S.}, title = {Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma}, journal = {Nat Cell Biol}, volume = {22}, number = {8}, pages = {986-998}, issn = {1476-4679 (Electronic) 1465-7392 (Linking)}, doi = {10.1038/s41556-020-0547-3}, url = {https://www.ncbi.nlm.nih.gov/pubmed/32753671}, year = {2020}, type = {Journal Article} }
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@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{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} }
@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} }
@article{RN1740, author = {Soni, A. and Murmann-Konda, T. and Magin, S. and Iliakis, G.}, title = {A method for the cell-cycle-specific analysis of radiation-induced chromosome aberrations and breaks}, journal = {Mutat Res}, volume = {815}, pages = {10-19}, note = {Soni, Aashish Murmann-Konda, Tamara Magin, Simon Iliakis, George eng Research Support, Non-U.S. Gov't Netherlands 2019/04/19 Mutat Res. 2019 May;815:10-19. doi: 10.1016/j.mrfmmm.2019.04.001. Epub 2019 Apr 6.}, keywords = {Animals CHO Cells Cell Line Cell Line, Tumor Chromosome Aberrations/*radiation effects Chromosome Breakage/drug effects Chromosomes/*genetics/radiation effects Cricetulus DNA Repair/genetics/radiation effects G2 Phase/genetics/radiation effects HCT116 Cells Humans Kinetics Metaphase/*genetics/*radiation effects Radiation, Ionizing S Phase/genetics/radiation effects *Cell cycle *Chromosomal aberrations *DNA double strand breaks repair *EdU-ClickIT(R) *G(2) radiosensitivity assay}, issn = {1873-135X (Electronic) 0027-5107 (Linking)}, doi = {10.1016/j.mrfmmm.2019.04.001}, url = {https://www.ncbi.nlm.nih.gov/pubmed/30999232}, year = {2019}, type = {Journal Article} }
@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} }
@article{sib2019antibiotic, title = {Antibiotic resistant bacteria and resistance genes in biofilms in clinical wastewater networks}, author = {Sib, E and Voigt, AM and Wilbring, G and Schreiber, C and Faerber, HA and Skutlarek, D and Parcina, M and Mahn, R and Wolf, D and Brossart, P and others}, journal = {International journal of hygiene and environmental health}, volume = {222}, year = {2019}, publisher = {Urban \& Fischer} }
@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} }
@article{schmithausen2019washing, title = {The washing machine as a reservoir for transmission of extended-spectrum-beta-lactamase (CTX-M-15)-producing Klebsiella oxytoca ST201 to newborns}, author = {Schmithausen, Ricarda M and Sib, Esther and Exner, Martin and Hack, Sylvia and R{\"o}sing, Claudia and Ciorba, Patrick and Bierbaum, Gabriele and Savin, Mykhailo and Bloomfield, Sally F and Kaase, Martin and others}, journal = {Applied and Environmental Microbiology}, volume = {85}, year = {2019}, publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC} }
@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} }
@article{chaterji_federation_2019, title = {Federation in genomics pipelines: techniques and challenges}, volume = {20}, journal = {Briefings in bioinformatics}, author = {Chaterji, Somali and Koo, Jinkyu and Li, Ninghui and Meyer, Folker and Grama, Ananth and Bagchi, Saurabh}, year = {2019}, note = {Publisher: Oxford University Press} }
@article{meyer_mg-rast_2019, title = {{MG}-{RAST} version 4—lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis}, volume = {20}, journal = {Briefings in bioinformatics}, author = {Meyer, Folker and Bagchi, Saurabh and Chaterji, Somali and Gerlach, Wolfgang and Grama, Ananth and Harrison, Travis and Paczian, Tobias and Trimble, William L and Wilke, Andreas}, year = {2019}, note = {Publisher: Oxford University Press} }
@inproceedings{mahgoub_sophia_2019, title = {\$\{\${SOPHIA}\$\}\$: {Online} {Reconfiguration} of {Clustered} \$\{\${NoSQL}\$\}\$ {Databases} for \$\{\${Time}-{Varying}\$\}\$ {Workloads}}, booktitle = {2019 {USENIX} {Annual} {Technical} {Conference} ({USENIX} {ATC} 19)}, author = {Mahgoub, Ashraf and Wood, Paul and Medoff, Alexander and Mitra, Subrata and Meyer, Folker and Chaterji, Somali and Bagchi, Saurabh}, year = {2019} }
@article{paczian_mg-rast_2019, title = {The {MG}-{RAST} {API} explorer: an on-ramp for {RESTful} query composition}, volume = {20}, journal = {BMC bioinformatics}, author = {Paczian, Tobias and Trimble, William L and Gerlach, Wolfgang and Harrison, Travis and Wilke, Andreas and Meyer, Folker}, year = {2019}, note = {Publisher: BioMed Central} }
@inproceedings{mahgoub_sophia_2019-1, title = {SOPHIA: {Online} {Reconfiguration} of {Clustered} \$\{\${NoSQL}\$\}\$ {Databases} for \$\{\${Time}-{Varying}\$\}\$ {Workloads}}, booktitle = {2019 {USENIX} {Annual} {Technical} {Conference} ({USENIX} {ATC} 19)}, author = {Mahgoub, Ashraf and Wood, Paul and Medoff, Alexander and Mitra, Subrata and Meyer, Folker and Chaterji, Somali and Bagchi, Saurabh}, year = {2019} }
@article{RN39, author = {Rogiers, A. and Thomas, D. and Vander Borght, S. and van den Oord, J. J. and Bechter, O. and Dewaele, M. and Rambow, F. and Marine, J. C. and Wolter, P.}, title = {Dabrafenib plus trametinib in BRAF K601E-mutant melanoma}, journal = {Br J Dermatol}, volume = {180}, number = {2}, pages = {421-422}, issn = {1365-2133 (Electronic) 0007-0963 (Linking)}, doi = {10.1111/bjd.17250}, url = {https://www.ncbi.nlm.nih.gov/pubmed/30248172}, year = {2019}, type = {Journal Article} }
@article{RN34, author = {Rambow, F. and Marine, J. C. and Goding, C. R.}, title = {Melanoma plasticity and phenotypic diversity: therapeutic barriers and opportunities}, journal = {Genes Dev}, volume = {33}, number = {19-20}, pages = {1295-1318}, issn = {1549-5477 (Electronic) 0890-9369 (Linking)}, doi = {10.1101/gad.329771.119}, url = {https://www.ncbi.nlm.nih.gov/pubmed/31575676}, year = {2019}, type = {Journal Article} }
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@article{RN1, author = {Adriaens, C. and Rambow, F. and Bervoets, G. and Silla, T. and Mito, M. and Chiba, T. and Asahara, H. and Hirose, T. and Nakagawa, S. and Jensen, T. H. and Marine, J. C.}, title = {The long noncoding RNA NEAT1_1 is seemingly dispensable for normal tissue homeostasis and cancer cell growth}, journal = {RNA}, volume = {25}, number = {12}, pages = {1681-1695}, issn = {1469-9001 (Electronic) 1355-8382 (Linking)}, doi = {10.1261/rna.071456.119}, url = {https://www.ncbi.nlm.nih.gov/pubmed/31551298}, year = {2019}, type = {Journal Article} }
@article{gruning_bioconda:_2018, title = {Bioconda: sustainable and comprehensive software distribution for the life sciences}, volume = {15}, copyright = {2018 The Author(s)}, issn = {1548-7105}, shorttitle = {Bioconda}, url = {https://www.nature.com/articles/s41592-018-0046-7}, doi = {10.1038/s41592-018-0046-7}, language = {en}, number = {7}, urldate = {2019-08-20}, journal = {Nature Methods}, author = {Grüning, Björn and Dale, Ryan and Sjödin, Andreas and Chapman, Brad A. and Rowe, Jillian and Tomkins-Tinch, Christopher H. and Valieris, Renan and Köster, Johannes}, month = jul, year = {2018}, pages = {475--476}, file = {Full Text PDF:/home/johannes/Zotero/storage/XI4PBRWR/Grüning et al. - 2018 - Bioconda sustainable and comprehensive software d.pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/6SJ8FQIP/s41592-018-0046-7.html:text/html} }
@article{gruning_practical_2018, title = {Practical {Computational} {Reproducibility} in the {Life} {Sciences}}, volume = {6}, issn = {2405-4712}, url = {http://www.sciencedirect.com/science/article/pii/S2405471218301406}, doi = {10.1016/j.cels.2018.03.014}, number = {6}, urldate = {2019-07-02}, journal = {Cell Systems}, author = {Grüning, Björn and Chilton, John and Köster, Johannes and Dale, Ryan and Soranzo, Nicola and van den Beek, Marius and Goecks, Jeremy and Backofen, Rolf and Nekrutenko, Anton and Taylor, James}, month = jun, year = {2018}, keywords = {reproducibility}, pages = {631--635}, file = {ScienceDirect Full Text PDF:/home/johannes/Zotero/storage/9Y84JDMM/Grüning et al. - 2018 - Practical Computational Reproducibility in the Lif.pdf:application/pdf;ScienceDirect Snapshot:/home/johannes/Zotero/storage/3Z8DHFA6/S2405471218301406.html:text/html} }
@article{schulte_cancer_2018, title = {Cancer evolution, mutations, and clonal selection in relapse neuroblastoma}, copyright = {All rights reserved}, issn = {0302-766X, 1432-0878}, url = {https://link.springer.com/article/10.1007/s00441-018-2810-5}, doi = {10.1007/s00441-018-2810-5}, language = {en}, urldate = {2018-02-27}, journal = {Cell and Tissue Research}, author = {Schulte, Marc and Köster, Johannes and Rahmann, Sven and Schramm, Alexander}, month = feb, year = {2018}, pages = {1--6}, file = {Full Text PDF:/home/johannes/Zotero/storage/6PQR45YK/Schulte et al. - 2018 - Cancer evolution, mutations, and clonal selection .pdf:application/pdf;Snapshot:/home/johannes/Zotero/storage/YQXFX25L/s00441-018-2810-5.html:text/html} }
@article{stocker_modeling_2018, title = {Modeling and simulating networks of interdependent protein interactions}, volume = {10}, issn = {1757-9708}, doi = {10.1039/c8ib00012c}, language = {eng}, number = {5}, journal = {Integrative Biology: Quantitative Biosciences from Nano to Macro}, author = {Stöcker, Bianca K. and Köster, Johannes and Zamir, Eli and Rahmann, Sven}, year = {2018}, pmid = {29676773}, keywords = {Algorithms, Computational Biology, Humans, Software, Computer Simulation, Proteins, Cell Adhesion Molecules, Databases, Protein, Integrins, Models, Biological, Protein Interaction Maps, Systems Biology}, pages = {290--305} }
@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} }
@article{westphal2018umwelt, title = {Die Umwelt als Reservoir f{\"u}r Antibiotikaresistenzen}, 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}, publisher = {Springer Berlin Heidelberg} }
@article{schmithausen2018washing, title = {The washing machine as a reservoir for transmission of ESBL-producing Klebsiella oxytoca in newborns}, author = {Schmithausen, Ricarda Maria and Exner, Martin and R{\"o}sing, Claudia and Savin, Michael and Hack, Sylvia and Bloomfield, SF and Kaase, Martin and Gebel, J{\"u}rgen and Engelhart, Steffen and Exner, Daniel}, journal = {bioRxiv}, year = {2018}, publisher = {Cold Spring Harbor Laboratory} }
@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} }
@article{muller2018dissemination, title = {Dissemination of multi-resistant Gram-negative bacteria into German wastewater and surface waters}, author = {Müller, Heike and Sib, Esther and Gajdiss, Mike and Klanke, Ursula and Lenz-Plet, Franziska and Barabasch, Vanessa and Albert, Cathrin and Schallenberg, Anna and Timm, Christian and Zacharias, Nicole and M., Schmithausen Ricarda and Engelhart, S. and Exner, M. and Parcina, M. and Schreiber, C. and Bierbaum, G.}, journal = {FEMS microbiology ecology}, volume = {94}, year = {2018}, publisher = {Oxford University Press} }
@article{el2018correction, title = {Correction: 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 = {13}, year = {2018}, publisher = {Public Library of Science San Francisco, CA USA} }
@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{Kraiselburd2017BacterialPP, title = {Bacterial Photosensory Proteins and Their Role in Plant–pathogen Interactions}, author = {Kraiselburd, Ivana and Moyano, Laura and Carrau, Anal{\'i}a and Tano, Josefina and Orellano, Elena G}, journal = {Photochemistry and Photobiology}, year = {2017}, volume = {93} }
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@article{ten_hoopen_metagenomic_2017, title = {The metagenomic data life-cycle: standards and best practices}, volume = {6}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28637310}, doi = {10.1093/gigascience/gix047}, journal = {Gigascience}, author = {Ten Hoopen, P. and Finn, R. D. and Bongo, L. A. and Corre, E. and Fosso, B. and Meyer, Folker and Mitchell, A. and Pelletier, E. and Pesole, G. and Santamaria, M. and Willassen, N. P. and Cochrane, G.}, year = {2017}, note = {Type: Journal Article} }
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@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} }
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@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} }
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@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} }
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@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} }
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@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} }
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@article{koster_massively_2014, title = {Massively parallel read mapping on {GPUs} with the q -group index and {PEANUT}}, volume = {2}, copyright = {All rights reserved}, issn = {2167-8359}, url = {https://peerj.com/articles/606/}, doi = {10.7717/peerj.606}, language = {en}, urldate = {2014-10-02}, journal = {PeerJ}, author = {Köster, Johannes and Rahmann, Sven}, month = sep, year = {2014}, pages = {e606}, file = {Massively parallel read mapping on GPUs with the q-group index and PEANUT [PeerJ]:/home/johannes/Zotero/storage/KWZGXATG/606.html:text/html} }
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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} }
