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James Davis
James Davis
Computational Biologist, Argonne National Laboratory
Verifierad e-postadress på anl.gov
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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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Artiklar 1–20