| The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) R Overbeek, R Olson, GD Pusch, GJ Olsen, JJ Davis, T Disz, RA Edwards, ... Nucleic acids research 42 (D1), D206-D214, 2014 | 4379 | 2014 |
| RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes T Brettin, JJ Davis, T Disz, RA Edwards, S Gerdes, GJ Olsen, R Olson, ... Scientific reports 5 (1), 1-6, 2015 | 2315 | 2015 |
| Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center AR Wattam, JJ Davis, R Assaf, S Boisvert, T Brettin, C Bun, N Conrad, ... Nucleic acids research 45 (D1), D535-D542, 2017 | 1482 | 2017 |
| KBase: the United States department of energy systems biology knowledgebase AP Arkin, RW Cottingham, CS Henry, NL Harris, RL Stevens, S Maslov, ... Nature biotechnology 36 (7), 566-569, 2018 | 1030 | 2018 |
| The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities JJ Davis, AR Wattam, RK Aziz, T Brettin, R Butler, RM Butler, P Chlenski, ... Nucleic acids research 48 (D1), D606-D612, 2020 | 825 | 2020 |
| Assemblathon 1: a competitive assessment of de novo short read assembly methods D Earl, K Bradnam, JS John, A Darling, D Lin, J Fass, HOK Yu, V Buffalo, ... Genome research 21 (12), 2224-2241, 2011 | 632 | 2011 |
| Recovering complete and draft population genomes from metagenome datasets N Sangwan, F Xia, JA Gilbert Microbiome 4, 1-11, 2016 | 270 | 2016 |
| Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR RD Olson, R Assaf, T Brettin, N Conrad, C Cucinell, JJ Davis, ... Nucleic acids research 51 (D1), D678-D689, 2023 | 269 | 2023 |
| SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models RK Aziz, S Devoid, T Disz, RA Edwards, CS Henry, GJ Olsen, R Olson, ... PloS one 7 (10), e48053, 2012 | 223 | 2012 |
| Antimicrobial resistance prediction in PATRIC and RAST JJ Davis, S Boisvert, T Brettin, RW Kenyon, C Mao, R Olson, R Overbeek, ... Scientific reports 6 (1), 27930, 2016 | 217 | 2016 |
| Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae M Nguyen, T Brettin, SW Long, JM Musser, RJ Olsen, R Olson, M Shukla, ... Scientific reports 8 (1), 421, 2018 | 166 | 2018 |
| Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance … SW Long, RJ Olsen, TN Eagar, SB Beres, P Zhao, JJ Davis, T Brettin, ... MBio 8 (3), 10.1128/mbio. 00489-17, 2017 | 152 | 2017 |
| Converting tabular data into images for deep learning with convolutional neural networks Y Zhu, T Brettin, F Xia, A Partin, M Shukla, H Yoo, YA Evrard, ... Scientific reports 11 (1), 11325, 2021 | 124 | 2021 |
| Predicting tumor cell line response to drug pairs with deep learning F Xia, M Shukla, T Brettin, C Garcia-Cardona, J Cohn, JE Allen, S Maslov, ... BMC bioinformatics 19, 71-79, 2018 | 121 | 2018 |
| The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation LK McNeil, C Reich, RK Aziz, D Bartels, M Cohoon, T Disz, RA Edwards, ... Nucleic acids research 35 (suppl_1), D347-D353, 2007 | 121 | 2007 |
| Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model K Tanaka, CS Henry, JF Zinner, E Jolivet, MP Cohoon, F Xia, V Bidnenko, ... Nucleic acids research 41 (1), 687-699, 2013 | 109 | 2013 |
| PATRIC as a unique resource for studying antimicrobial resistance DA Antonopoulos, R Assaf, RK Aziz, T Brettin, C Bun, N Conrad, JJ Davis, ... Briefings in bioinformatics 20 (4), 1094-1102, 2019 | 105 | 2019 |
| Assembly, annotation, and comparative genomics in PATRIC, the all bacterial bioinformatics resource center AR Wattam, T Brettin, JJ Davis, S Gerdes, R Kenyon, D Machi, C Mao, ... Comparative genomics: Methods and protocols, 79-101, 2018 | 91 | 2018 |
| CANDLE/Supervisor: A workflow framework for machine learning applied to cancer research JM Wozniak, R Jain, P Balaprakash, J Ozik, NT Collier, J Bauer, F Xia, ... BMC bioinformatics 19, 59-69, 2018 | 87 | 2018 |
| The DOE systems biology knowledgebase (KBase) AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ... BioRxiv, 096354, 2016 | 77 | 2016 |
Rick StevensProfessor of Computer Science, University of Chicagoכתובת אימייל מאומתת בדומיין ci.uchicago.edu
