| 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 | 4547 | 2014 |
| 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 | 4098* | 2020 |
| 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 | 2484 | 2015 |
| 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 | 1161 | 2018 |
| 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 | 410 | 2023 |
| Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life JJ Gillespie, K Williams, M Shukla, EE Snyder, EK Nordberg, SM Ceraul, ... PloS one 3 (4), e2018, 2008 | 238 | 2008 |
| 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 | 228 | 2016 |
| Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine JI Watkinson, AA Sioson, C Vasquez-Robinet, M Shukla, D Kumar, M Ellis, ... Plant Physiology 133 (4), 1702-1716, 2003 | 203 | 2003 |
| A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle JJ Gillespie, V Joardar, KP Williams, T Driscoll, JB Hostetler, E Nordberg, ... Journal of bacteriology 194 (2), 376-394, 2012 | 190 | 2012 |
| 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 | 188 | 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 | 177 | 2018 |
| 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 | 161 | 2021 |
| Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin JZ Ruscio, D Kumar, M Shukla, MG Prisant, TM Murali, AV Onufriev Proceedings of the National Academy of Sciences 105 (27), 9204-9209, 2008 | 157 | 2008 |
| Analysis of Ten Brucella Genomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle AR Wattam, KP Williams, EE Snyder, NF Almeida Jr, M Shukla, ... Journal of bacteriology 191 (11), 3569-3579, 2009 | 156 | 2009 |
| 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 | 144* | 2020 |
| Defining the risk of SARS-CoV-2 variants on immune protection MM DeGrace, E Ghedin, MB Frieman, F Krammer, A Grifoni, A Alisoltani, ... Nature 605 (7911), 640-652, 2022 | 142 | 2022 |
| Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence AR Wattam, JT Foster, SP Mane, SM Beckstrom-Sternberg, ... Journal of bacteriology 196 (5), 920-930, 2014 | 136 | 2014 |
| 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 | 130 | 2018 |
| 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 | 109 | 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 | 94 | 2018 |
