Seuraa
James Davis
James Davis
Computational Biologist, Argonne National Laboratory
Vahvistettu sähköpostiosoite verkkotunnuksessa anl.gov
Nimike
Viittaukset
Viittaukset
Vuosi
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
43472014
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
22872015
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
14652017
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
10092018
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
8192020
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
2492023
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
229*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
2162016
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
2122022
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
1852022
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
1642018
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
1642017
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
1632016
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
1502017
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
1232020
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
1032019
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
982022
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
912018
The DOE systems biology knowledgebase (KBase)
AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ...
BioRxiv, 096354, 2016
762016
Daptomycin resistance in clinical MRSA strains is associated with a high biological fitness cost
M Roch, P Gagetti, J Davis, P Ceriana, L Errecalde, A Corso, AE Rosato
Frontiers in microbiology 8, 309849, 2017
682017
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Artikkelit 1–20