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Items: 1 to 20 of 271

1.

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease.

Greenblum S, Turnbaugh PJ, Borenstein E.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):594-9. doi: 10.1073/pnas.1116053109. Epub 2011 Dec 19.

2.

A core gut microbiome in obese and lean twins.

Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI.

Nature. 2009 Jan 22;457(7228):480-4. doi: 10.1038/nature07540. Epub 2008 Nov 30.

3.

The chemical interactome space between the human host and the genetically defined gut metabotypes.

Jacobsen UP, Nielsen HB, Hildebrand F, Raes J, Sicheritz-Ponten T, Kouskoumvekaki I, Panagiotou G.

ISME J. 2013 Apr;7(4):730-42. doi: 10.1038/ismej.2012.141. Epub 2012 Nov 22.

4.

Metagenomic analysis of the pygmy loris fecal microbiome reveals unique functional capacity related to metabolism of aromatic compounds.

Xu B, Xu W, Yang F, Li J, Yang Y, Tang X, Mu Y, Zhou J, Huang Z.

PLoS One. 2013;8(2):e56565. doi: 10.1371/journal.pone.0056565. Epub 2013 Feb 15.

5.
6.

Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome.

Jones BV, Sun F, Marchesi JR.

BMC Genomics. 2010 Jan 19;11:46. doi: 10.1186/1471-2164-11-46.

7.

Healthy human gut phageome.

Manrique P, Bolduc B, Walk ST, van der Oost J, de Vos WM, Young MJ.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10400-5. doi: 10.1073/pnas.1601060113. Epub 2016 Aug 29.

8.

Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities.

Yildirim S, Yeoman CJ, Sipos M, Torralba M, Wilson BA, Goldberg TL, Stumpf RM, Leigh SR, White BA, Nelson KE.

PLoS One. 2010 Nov 12;5(11):e13963. doi: 10.1371/journal.pone.0013963.

9.

Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules.

Levy R, Borenstein E.

Gut Microbes. 2014 Mar-Apr;5(2):265-70. doi: 10.4161/gmic.28261. Epub 2014 Feb 20.

10.

A metagenomic insight into our gut's microbiome.

Lepage P, Leclerc MC, Joossens M, Mondot S, Blottière HM, Raes J, Ehrlich D, Doré J.

Gut. 2013 Jan;62(1):146-58. doi: 10.1136/gutjnl-2011-301805. Epub 2012 Apr 23. Review.

PMID:
22525886
11.

mmnet: An R Package for Metagenomics Systems Biology Analysis.

Cao Y, Zheng X, Li F, Bo X.

Biomed Res Int. 2015;2015:167249. doi: 10.1155/2015/167249. Epub 2015 Sep 3.

12.

Computational systems biology and in silico modeling of the human microbiome.

Borenstein E.

Brief Bioinform. 2012 Nov;13(6):769-80. doi: 10.1093/bib/bbs022. Epub 2012 May 15. Review.

PMID:
22589385
13.

A geographically-diverse collection of 418 human gut microbiome pathway genome databases.

Hahn AS, Altman T, Konwar KM, Hanson NW, Kim D, Relman DA, Dill DL, Hallam SJ.

Sci Data. 2017 Apr 11;4:170035. doi: 10.1038/sdata.2017.35.

14.

The human gut microbiome: implications for future health care.

Kinross JM, von Roon AC, Holmes E, Darzi A, Nicholson JK.

Curr Gastroenterol Rep. 2008 Aug;10(4):396-403. Review.

PMID:
18627653
15.

Extensive strain-level copy-number variation across human gut microbiome species.

Greenblum S, Carr R, Borenstein E.

Cell. 2015 Feb 12;160(4):583-94. doi: 10.1016/j.cell.2014.12.038. Epub 2015 Jan 29.

16.

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant.

Morowitz MJ, Denef VJ, Costello EK, Thomas BC, Poroyko V, Relman DA, Banfield JF.

Proc Natl Acad Sci U S A. 2011 Jan 18;108(3):1128-33. doi: 10.1073/pnas.1010992108. Epub 2010 Dec 29. Erratum in: Proc Natl Acad Sci U S A. 2011 Mar 15;108(11):4512.

17.

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.

Pasolli E, Truong DT, Malik F, Waldron L, Segata N.

PLoS Comput Biol. 2016 Jul 11;12(7):e1004977. doi: 10.1371/journal.pcbi.1004977. eCollection 2016 Jul.

18.

Adapting functional genomic tools to metagenomic analyses: investigating the role of gut bacteria in relation to obesity.

Liu Y, Zhang C, Zhao L, Nardini C.

Brief Funct Genomics. 2010 Dec;9(5-6):355-61. doi: 10.1093/bfgp/elq011. Epub 2010 May 6.

19.

Host responses to the human microbiome.

Bäckhed F.

Nutr Rev. 2012 Aug;70 Suppl 1:S14-7. doi: 10.1111/j.1753-4887.2012.00496.x. Review.

PMID:
22861802
20.

Metagenomics: key to human gut microbiota.

Maccaferri S, Biagi E, Brigidi P.

Dig Dis. 2011;29(6):525-30. doi: 10.1159/000332966. Epub 2011 Dec 12. Review.

PMID:
22179207

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