| 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, 2013 | 2021 | 2013 |
| 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, 2016 | 1325* | 2016 |
| 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, 8365, 2015 | 531 | 2015 |
| 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 | 165 | 2003 |
| 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 | 148 | 2008 |
| 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 | 138 | 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, M Shukla, ... Journal of bacteriology 191 (11), 3569-3579, 2009 | 112 | 2009 |
| 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 | 97 | 2012 |
| 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), 2018 | 78 | 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, 27930, 2016 | 67 | 2016 |
| VANILREP1 polynucleotides and VANILREP1 polypeptides DM Duckworth, PD Hayes, HJ Meadows, JB Davis US Patent 6,239,267, 2001 | 63 | 2001 |
| 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 | 61 | 2014 |
| Host-interactive genes in Amerindian Helicobacter pylori diverge from their Old World homologs and mediate inflammatory responses SP Mane, MG Dominguez-Bello, MJ Blaser, BW Sobral, R Hontecillas, ... Journal of bacteriology 192 (12), 3078-3092, 2010 | 60 | 2010 |
| An Evaluation of Information Visualization in Attention-Limited Environments. JP Somervell, DS McCrickard, C North, M Shukla VisSym, 211-216, 2002 | 56 | 2002 |
| Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway AR Wattam, TJ Inzana, KP Williams, SP Mane, M Shukla, NF Almeida, ... MBio 3 (5), e00246-12, 2012 | 35 | 2012 |
| 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, 2017 | 34 | 2017 |
| The DOE systems biology knowledgebase (KBase) AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ... BioRxiv, 096354, 2016 | 34 | 2016 |
| Database resources for the tuberculosis community JM Lew, C Mao, M Shukla, A Warren, R Will, D Kuznetsov, I Xenarios, ... Tuberculosis 93 (1), 12-17, 2013 | 30 | 2013 |
| 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 | 26 | 2018 |
| Curation, integration and visualization of bacterial virulence factors in PATRIC C Mao, D Abraham, AR Wattam, MJC Wilson, M Shukla, HS Yoo, ... Bioinformatics 31 (2), 252-258, 2014 | 26 | 2014 |
