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Items: 29

1.

Diet Modifies Colonic Microbiota and CD4+ T Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-cell Expression of Interleukin 23.

Chen L, He Z, Iuga AC, Martins Filho SN, Faith JJ, Clemente JC, Deshpande M, Jayaprakash A, Colombel JF, Lafaille JJ, Sachidanandam R, Furtado GC, Lira SA.

Gastroenterology. 2018 Jun 14. pii: S0016-5085(18)34654-7. doi: 10.1053/j.gastro.2018.06.034. [Epub ahead of print]

PMID:
29909020
2.

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.

Beaulaurier J, Zhu S, Deikus G, Mogno I, Zhang XS, Davis-Richardson A, Canepa R, Triplett EW, Faith JJ, Sebra R, Schadt EE, Fang G.

Nat Biotechnol. 2018 Jan;36(1):61-69. doi: 10.1038/nbt.4037. Epub 2017 Dec 11.

3.

Interactions Between Diet and the Intestinal Microbiota Alter Intestinal Permeability and Colitis Severity in Mice.

Llewellyn SR, Britton GJ, Contijoch EJ, Vennaro OH, Mortha A, Colombel JF, Grinspan A, Clemente JC, Merad M, Faith JJ.

Gastroenterology. 2018 Mar;154(4):1037-1046.e2. doi: 10.1053/j.gastro.2017.11.030. Epub 2017 Nov 23.

PMID:
29174952
4.

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.

Nat Genet. 2017 Oct;49(10):1437-1449. doi: 10.1038/ng.3947. Epub 2017 Sep 11.

PMID:
28892060
5.

Neutrophil ageing is regulated by the microbiome.

Zhang D, Chen G, Manwani D, Mortha A, Xu C, Faith JJ, Burk RD, Kunisaki Y, Jang JE, Scheiermann C, Merad M, Frenette PS.

Nature. 2015 Sep 24;525(7570):528-32. doi: 10.1038/nature15367. Epub 2015 Sep 16.

6.

Metabolic labeling puts the microbiome under the microscope.

Britton GJ, Faith JJ.

Nat Med. 2015 Sep;21(9):977-8. doi: 10.1038/nm.3941. No abstract available.

PMID:
26340118
7.

Bridging the knowledge gap: from microbiome composition to function.

Faith JJ.

Mol Syst Biol. 2015 Mar;11(3):793. doi: 10.15252/msb.20156045.

8.

Identifying strains that contribute to complex diseases through the study of microbial inheritance.

Faith JJ, Colombel JF, Gordon JI.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):633-40. doi: 10.1073/pnas.1418781112. Epub 2015 Jan 9.

9.

Mining the human gut microbiota for effector strains that shape the immune system.

Ahern PP, Faith JJ, Gordon JI.

Immunity. 2014 Jun 19;40(6):815-23. doi: 10.1016/j.immuni.2014.05.012.

10.

Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice.

Faith JJ, Ahern PP, Ridaura VK, Cheng J, Gordon JI.

Sci Transl Med. 2014 Jan 22;6(220):220ra11. doi: 10.1126/scitranslmed.3008051.

11.

Gut microbiota from twins discordant for obesity modulate metabolism in mice.

Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI.

Science. 2013 Sep 6;341(6150):1241214. doi: 10.1126/science.1241214.

12.

The long-term stability of the human gut microbiota.

Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, Gordon JI.

Science. 2013 Jul 5;341(6141):1237439. doi: 10.1126/science.1237439.

13.

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.

Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG.

Nat Methods. 2013 Jan;10(1):57-9. doi: 10.1038/nmeth.2276. Epub 2012 Dec 2.

14.

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.

Genome Res. 2012 Oct;22(10):1974-84. doi: 10.1101/gr.138198.112. Epub 2012 Jun 4.

15.

The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins.

McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL, Henrissat B, Oozeer R, Cools-Portier S, Gobert G, Chervaux C, Knights D, Lozupone CA, Knight R, Duncan AE, Bain JR, Muehlbauer MJ, Newgard CB, Heath AC, Gordon JI.

Sci Transl Med. 2011 Oct 26;3(106):106ra106. doi: 10.1126/scitranslmed.3002701.

16.

Predicting a human gut microbiota's response to diet in gnotobiotic mice.

Faith JJ, McNulty NP, Rey FE, Gordon JI.

Science. 2011 Jul 1;333(6038):101-4. doi: 10.1126/science.1206025. Epub 2011 May 19.

17.

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice.

Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, Dantas G, Gordon JI.

Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6252-7. doi: 10.1073/pnas.1102938108. Epub 2011 Mar 21.

18.

Creating and characterizing communities of human gut microbes in gnotobiotic mice.

Faith JJ, Rey FE, O'Donnell D, Karlsson M, McNulty NP, Kallstrom G, Goodman AL, Gordon JI.

ISME J. 2010 Sep;4(9):1094-8. doi: 10.1038/ismej.2010.110. Epub 2010 Jul 22. Review. No abstract available.

19.

Dissecting the in vivo metabolic potential of two human gut acetogens.

Rey FE, Faith JJ, Bain J, Muehlbauer MJ, Stevens RD, Newgard CB, Gordon JI.

J Biol Chem. 2010 Jul 16;285(29):22082-90. doi: 10.1074/jbc.M110.117713. Epub 2010 May 5.

20.

Reverse-engineering transcription control networks.

Gardner TS, Faith JJ.

Phys Life Rev. 2005 Mar;2(1):65-88. doi: 10.1016/j.plrev.2005.01.001.

PMID:
20416858
21.

The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.

Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI.

Sci Transl Med. 2009 Nov 11;1(6):6ra14. doi: 10.1126/scitranslmed.3000322.

22.

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.

Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI.

Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7503-8. doi: 10.1073/pnas.1002355107. Epub 2010 Apr 2.

23.

Response of gastric epithelial progenitors to Helicobacter pylori Isolates obtained from Swedish patients with chronic atrophic gastritis.

Giannakis M, Bäckhed HK, Chen SL, Faith JJ, Wu M, Guruge JL, Engstrand L, Gordon JI.

J Biol Chem. 2009 Oct 30;284(44):30383-94. doi: 10.1074/jbc.M109.052738. Epub 2009 Sep 1.

24.

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.

Nucleic Acids Res. 2008 Jan;36(Database issue):D866-70. Epub 2007 Oct 11.

25.

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

Faith JJ, Olson AJ, Gardner TS, Sachidanandam R.

BMC Bioinformatics. 2007 Sep 18;8:344.

26.

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.

PLoS Biol. 2007 Jan;5(1):e8.

27.

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.

BMC Bioinformatics. 2006 Sep 6;7 Suppl 2:S7.

28.

Evolution of base-substitution gradients in primate mitochondrial genomes.

Raina SZ, Faith JJ, Disotell TR, Seligmann H, Stewart CB, Pollock DD.

Genome Res. 2005 May;15(5):665-73.

29.

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