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Reverse-engineering transcription control networks.
Gardner TS, Faith JJ. Gardner TS, et al. Among authors: faith jj. Phys Life Rev. 2005 Mar;2(1):65-88. doi: 10.1016/j.plrev.2005.01.001. Phys Life Rev. 2005. PMID: 20416858
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata.
Faith JJ, Driscoll ME, Fusaro VA, Cosgrove EJ, Hayete B, Juhn FS, Schneider SJ, Gardner TS. Faith JJ, et al. Nucleic Acids Res. 2008 Jan;36(Database issue):D866-70. doi: 10.1093/nar/gkm815. Epub 2007 Oct 11. Nucleic Acids Res. 2008. PMID: 17932051 Free PMC article.
Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.
Faith JJ, Olson AJ, Gardner TS, Sachidanandam R. Faith JJ, et al. BMC Bioinformatics. 2007 Sep 18;8:344. doi: 10.1186/1471-2105-8-344. BMC Bioinformatics. 2007. PMID: 17877794 Free PMC article.
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.
Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Faith JJ, et al. PLoS Biol. 2007 Jan;5(1):e8. doi: 10.1371/journal.pbio.0050008. PLoS Biol. 2007. PMID: 17214507 Free PMC article.
EGenBio: a data management system for evolutionary genomics and biodiversity.
Nahum LA, Reynolds MT, Wang ZO, Faith JJ, Jonna R, Jiang ZJ, Meyer TJ, Pollock DD. Nahum LA, et al. Among authors: faith jj. BMC Bioinformatics. 2006 Sep 6;7 Suppl 2(Suppl 2):S7. doi: 10.1186/1471-2105-7-S2-S7. BMC Bioinformatics. 2006. PMID: 17118150 Free PMC article.
Evolution of base-substitution gradients in primate mitochondrial genomes.
Raina SZ, Faith JJ, Disotell TR, Seligmann H, Stewart CB, Pollock DD. Raina SZ, et al. Among authors: faith jj. Genome Res. 2005 May;15(5):665-73. doi: 10.1101/gr.3128605. Genome Res. 2005. PMID: 15867428 Free PMC article.
Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes.
Faith JJ, Pollock DD. Faith JJ, et al. Genetics. 2003 Oct;165(2):735-45. Genetics. 2003. PMID: 14573484 Free PMC article.
A functional genomics predictive network model identifies regulators of inflammatory bowel disease.
Peters LA, Perrigoue J, Mortha A, Iuga A, Song WM, Neiman EM, Llewellyn SR, Di Narzo A, Kidd BA, Telesco SE, Zhao Y, Stojmirovic A, Sendecki J, Shameer K, Miotto R, Losic B, Shah H, Lee E, Wang M, Faith JJ, Kasarskis A, Brodmerkel C, Curran M, Das A, Friedman JR, Fukui Y, Humphrey MB, Iritani BM, Sibinga N, Tarrant TK, Argmann C, Hao K, Roussos P, Zhu J, Zhang B, Dobrin R, Mayer LF, Schadt EE. Peters LA, et al. Among authors: faith jj. Nat Genet. 2017 Oct;49(10):1437-1449. doi: 10.1038/ng.3947. Epub 2017 Sep 11. Nat Genet. 2017. PMID: 28892060 Free PMC article.
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts.
Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R. Lozupone C, et al. Among authors: faith jj. Genome Res. 2012 Oct;22(10):1974-84. doi: 10.1101/gr.138198.112. Epub 2012 Jun 4. Genome Res. 2012. PMID: 22665442 Free PMC article.
Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORĪ³t+ Regulatory T Cells and Exacerbate Colitis in Mice.
Britton GJ, Contijoch EJ, Mogno I, Vennaro OH, Llewellyn SR, Ng R, Li Z, Mortha A, Merad M, Das A, Gevers D, McGovern DPB, Singh N, Braun J, Jacobs JP, Clemente JC, Grinspan A, Sands BE, Colombel JF, Dubinsky MC, Faith JJ. Britton GJ, et al. Among authors: faith jj. Immunity. 2019 Jan 15;50(1):212-224.e4. doi: 10.1016/j.immuni.2018.12.015. Immunity. 2019. PMID: 30650377 Free PMC article.
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