| 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 | 4751 | 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, 2015 | 2676 | 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 | 1648 | 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 | 1306 | 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 | 951 | 2020 |
| 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 | 602 | 2023 |
| Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidal Salmonella M Nguyen, SW Long, PF McDermott, RJ Olsen, R Olson, RL Stevens, ... BioRxiv, 380782, 2018 | 278* | 2018 |
| 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 | 245 | 2016 |
| Signals of significantly increased vaccine breakthrough, decreased hospitalization rates, and less severe disease in patients with coronavirus disease 2019 caused by the … PA Christensen, RJ Olsen, SW Long, R Snehal, JJ Davis, MO Saavedra, ... The American journal of pathology 192 (4), 642-652, 2022 | 243 | 2022 |
| Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer SV Kuchipudi, M Surendran-Nair, RM Ruden, M Yon, RH Nissly, ... Proceedings of the National Academy of Sciences 119 (6), e2121644119, 2022 | 230 | 2022 |
| PATtyFams: protein families for the microbial genomes in the PATRIC database JJ Davis, S Gerdes, GJ Olsen, R Olson, GD Pusch, M Shukla, V Vonstein, ... Frontiers in microbiology 7, 118, 2016 | 211 | 2016 |
| Whole-genome sequencing of human clinical Klebsiella pneumoniae isolates reveals misidentification and misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and … SW Long, SE Linson, M Ojeda Saavedra, C Cantu, JJ Davis, T Brettin, ... Msphere 2 (4), 10.1128/mspheredirect. 00290-17, 2017 | 203 | 2017 |
| 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 | 187 | 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 | 164 | 2017 |
| Molecular architecture of early dissemination and massive second wave of the SARS-CoV-2 virus in a major metropolitan area SW Long, RJ Olsen, PA Christensen, DW Bernard, JJ Davis, M Shukla, ... MBio 11 (6), 10.1128/mbio. 02707-20, 2020 | 137 | 2020 |
| 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 | 117 | 2019 |
| Delta variants of SARS-CoV-2 cause significantly increased vaccine breakthrough COVID-19 cases in Houston, Texas PA Christensen, RJ Olsen, SW Long, S Subedi, JJ Davis, P Hodjat, ... The American journal of pathology 192 (2), 320-331, 2022 | 112 | 2022 |
| 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 | 99 | 2018 |
| GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics M Zvyagin, A Brace, K Hippe, Y Deng, B Zhang, CO Bohorquez, A Clyde, ... The International Journal of High Performance Computing Applications 37 (6 …, 2023 | 94 | 2023 |
| The DOE systems biology knowledgebase (KBase) AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ... BioRxiv, 096354, 2016 | 79 | 2016 |
