James Davis
James Davis
Computational Biologist, Argonne National Laboratory
כתובת אימייל מאומתת בדומיין anl.gov
כותרת
צוטט על ידי
צוטט על ידי
שנה
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
29612014
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
11402015
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
9142017
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
3602018
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), 1-12, 2016
1312016
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
1192020
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, ...
Journal of Clinical Microbiology, JCM. 01260-18, 2018
100*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), e00489-17, 2017
932017
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), 1-11, 2018
772018
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), e00290-17, 2017
762017
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
602016
The DOE systems biology knowledgebase (KBase)
AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ...
BioRxiv, 096354, 2016
552016
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
522019
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, 79-101, 2018
482018
Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome
KA Karberg, GJ Olsen, JJ Davis
Proceedings of the National Academy of Sciences 108 (50), 20154-20159, 2011
422011
Modal codon usage: assessing the typical codon usage of a genome
JJ Davis, GJ Olsen
Molecular biology and evolution 27 (4), 800-810, 2010
402010
Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes
JJ Davis, F Xia, RA Overbeek, GJ Olsen
International journal of systematic and evolutionary microbiology 63 (Pt 7 …, 2013
392013
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), e02707-20, 2020
382020
Characterizing the native codon usages of a genome: an axis projection approach
JJ Davis, GJ Olsen
Molecular biology and evolution 28 (1), 211-221, 2011
372011
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, 2303, 2017
362017
המערכת אינה יכולה לבצע את הפעולה כעת. נסה שוב מאוחר יותר.
מאמרים 1–20