JamesJosephDavisMD

PubMed

• HASH(0x25300d0)
  Nguyen, M.,Long, S. W.,McDermott, P. F.,Olsen, R. J.,Olson, R.,Stevens, R. L.,Tyson, G. H.,Zhao, S.,Davis, J. J.> ;J. Clin. Microbiol.. 2018 Oct 19
• KBase: The United States Department of Energy Systems Biology Knowledgebase.
  Arkin, A. P.,Cottingham, R. W.,Henry, C. S.,Harris, N. L.,Stevens, R. L.,Maslov, S.,Dehal, P.,Ware, D.,Perez, F.,Canon, S.,Sneddon, M. W.,Henderson, M. L.,Riehl, W. J....> ;Nat. Biotechnol.. 2018 Jul 07
• Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae.
  Nguyen, M.,Brettin, T.,Long, S. W.,Musser, J. M.,Olsen, R. J.,Olson, R.,Shukla, M.,Stevens, R. L.,Xia, F.,Yoo, H.,Davis, J. J.> ;Sci Rep. 2018 Jan 13
• Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.
  Wattam, A. R.,Brettin, T.,Davis, J. J.,Gerdes, S.,Kenyon, R.,Machi, D.,Mao, C.,Olson, R.,Overbeek, R.,Pusch, G. D.,Shukla, M. P.,Stevens, R.,Vonstein, V.,Warren, A.,Xi...> ;Methods Mol. Biol.. 2017 Dec 27
• Journal Club: Developing a user-friendly report for electronically assisted surveillance of catheter-associated urinary tract infections.
  Estinville, M. F.,Hessels, A.,Davis, J.> ;Am J Infect Control. 2017 Aug 05
• Antimicrobial Resistance Prediction in PATRIC and RAST.
  Davis JJ, Boisvert S, Brettin T, Kenyon RW, Mao C, Olson R, Overbeek R, Santerre J, Shukla M, Wattam AR, Will R, Xia F, Stevens R> ;Sci Rep. 2016-06-14
• Humans perceive flicker artifacts at 500 Hz.
  Davis J, Hsieh Y, Lee H> ;Sci Rep. 2015-02-03
• The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).
  Overbeek, R.,Olson, R.,Pusch, G. D.,Olsen, G. J.,Davis, J. J.,Disz, T.,Edwards, R. A.,Gerdes, S.,Parrello, B.,Shukla, M.,Vonstein, V.,Wattam, A. R.,Xia, F.,Stevens, R.> ;Nucleic Acids Res.. 2013 Dec 03
• The Genomes of the Erysipelotrichia Clarify the Firmicute Origin of the Mollicutes.
  Davis, J. J.,Xia, F.,Overbeek, R. A.,Olsen, G. J.> ;Int. J. Syst. Evol. Microbiol.. 2013 Jul
• Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome.
  Karberg, K.A., Olsen, G.J., Davis, J.J.> ;Proc Natl Acad Sci U S A. 2011 Dec 13
• Characterizing the native codon usages of a genome: an axis projection approach.
  Davis, J.J., Olsen, G.J.> ;Mol Biol Evol. 2011 Jan
• Modal codon usage: assessing the typical codon usage of a genome.
  Davis, J.J., Olsen, G.J.> ;Mol Biol Evol. 2010 Apr
• Isolation of predation-deficient mutants of Bdellovibrio bacteriovorus by using transposon mutagenesis.
  Tudor, J.J., Davis, J.J., Panichella, M., Zwolak, A.> ;Appl Environ Microbiol. 2008 Sep
• PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database.
  Davis, J. J.,Gerdes, S.,Olsen, G. J.,Olson, R.,Pusch, G. D.,Shukla, M.,Vonstein, V.,Wattam, A. R.,Yoo, H.> ;Front Microbiol. 2016 Feb 24
• RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.
  Brettin, T.,Davis, J. J.,Disz, T.,Edwards, R. A.,Gerdes, S.,Olsen, G. J.,Olson, R.,Overbeek, R.,Parrello, B.,Pusch, G. D.,Shukla, M.,Thomason, J. A.,Stevens, R.,Vonste...> ;Sci Rep. 2015 Feb 11
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