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Items: 1 to 20 of 103

1.

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults.

Kolmeder CA, Salojärvi J, Ritari J, de Been M, Raes J, Falony G, Vieira-Silva S, Kekkonen RA, Corthals GL, Palva A, Salonen A, de Vos WM.

PLoS One. 2016 Apr 12;11(4):e0153294. doi: 10.1371/journal.pone.0153294. eCollection 2016.

2.

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.

Cornejo-Castillo FM, Cabello AM, Salazar G, Sánchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R, Acinas SG.

Nat Commun. 2016 Mar 22;7:11071. doi: 10.1038/ncomms11071.

3.

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.

Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R.

ISME J. 2016 Feb 23. doi: 10.1038/ismej.2015.235. [Epub ahead of print]

PMID:
26905627
4.

Plankton networks driving carbon export in the oligotrophic ocean.

Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum JR, Coelho LP, Espinoza JC, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S; Tara Oceans Consortium Coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G.

Nature. 2016 Apr 28;532(7600):465-70. doi: 10.1038/nature16942. Epub 2016 Feb 10.

PMID:
26863193
5.

Meta-omics in inflammatory bowel disease research: applications, challenges, and guidelines.

Valles-Colomer M, Darzi Y, Vieira-Silva S, Falony G, Raes J, Joossens M.

J Crohns Colitis. 2016 Jan 22. pii: jjw024. [Epub ahead of print] Review.

PMID:
26802086
6.

Microbiome-based companion diagnostics: no longer science fiction?

Raes J.

Gut. 2016 Jan 22. pii: gutjnl-2015-311015. doi: 10.1136/gutjnl-2015-311015. [Epub ahead of print] No abstract available.

7.

Characteristics of a Dysphonic Population Referred for Voice Assessment and/or Voice Therapy.

De Bodt M, Van den Steen L, Mertens F, Raes J, Van Bel L, Heylen L, Pattyn J, Gordts F, van de Heyning P.

Folia Phoniatr Logop. 2015;67(4):178-86. doi: 10.1159/000369339. Epub 2016 Jan 15.

PMID:
26766133
8.

Computational approaches to predict bacteriophage-host relationships.

Edwards RA, McNair K, Faust K, Raes J, Dutilh BE.

FEMS Microbiol Rev. 2016 Mar;40(2):258-72. doi: 10.1093/femsre/fuv048. Epub 2015 Dec 9. Review.

PMID:
26657537
9.

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Igor Costea P, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J; MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O.

Nature. 2015 Dec 10;528(7581):262-6. doi: 10.1038/nature15766. Epub 2015 Dec 2.

PMID:
26633628
10.

Towards biome-specific analysis of meta-omics data.

Darzi Y, Falony G, Vieira-Silva S, Raes J.

ISME J. 2016 May;10(5):1025-8. doi: 10.1038/ismej.2015.188. Epub 2015 Dec 1. No abstract available.

PMID:
26623543
11.

Cross-biome comparison of microbial association networks.

Faust K, Lima-Mendez G, Lerat JS, Sathirapongsasuti JF, Knight R, Huttenhower C, Lenaerts T, Raes J.

Front Microbiol. 2015 Oct 27;6:1200. doi: 10.3389/fmicb.2015.01200. eCollection 2015.

12.

Donor Species Richness Determines Faecal Microbiota Transplantation Success in Inflammatory Bowel Disease.

Vermeire S, Joossens M, Verbeke K, Wang J, Machiels K, Sabino J, Ferrante M, Van Assche G, Rutgeerts P, Raes J.

J Crohns Colitis. 2016 Apr;10(4):387-94. doi: 10.1093/ecco-jcc/jjv203. Epub 2015 Oct 29.

PMID:
26519463
13.

Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design.

Laukens D, Brinkman BM, Raes J, De Vos M, Vandenabeele P.

FEMS Microbiol Rev. 2016 Jan;40(1):117-32. doi: 10.1093/femsre/fuv036. Epub 2015 Aug 30. Review.

14.

Microbiology Meets Big Data: The Case of Gut Microbiota-Derived Trimethylamine.

Falony G, Vieira-Silva S, Raes J.

Annu Rev Microbiol. 2015;69:305-21. doi: 10.1146/annurev-micro-091014-104422. Epub 2015 Aug 13.

PMID:
26274026
15.

Towards microbial fermentation metabolites as markers for health benefits of prebiotics.

Verbeke KA, Boobis AR, Chiodini A, Edwards CA, Franck A, Kleerebezem M, Nauta A, Raes J, van Tol EA, Tuohy KM.

Nutr Res Rev. 2015 Jun;28(1):42-66. doi: 10.1017/S0954422415000037. Review.

16.

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates.

Vandeputte D, Falony G, Vieira-Silva S, Tito RY, Joossens M, Raes J.

Gut. 2016 Jan;65(1):57-62. doi: 10.1136/gutjnl-2015-309618. Epub 2015 Jun 11.

17.

Metagenomics meets time series analysis: unraveling microbial community dynamics.

Faust K, Lahti L, Gonze D, de Vos WM, Raes J.

Curr Opin Microbiol. 2015 Jun;25:56-66. doi: 10.1016/j.mib.2015.04.004. Epub 2015 May 22. Review.

18.

Ocean plankton. Determinants of community structure in the global plankton interactome.

Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans coordinators, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J.

Science. 2015 May 22;348(6237):1262073. doi: 10.1126/science.1262073.

PMID:
25999517
19.

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean.

de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horák A, Jaillon O, Lima-Mendez G, Lukeš J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans Coordinators, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E.

Science. 2015 May 22;348(6237):1261605. doi: 10.1126/science.1261605.

PMID:
25999516
20.

Ocean plankton. Structure and function of the global ocean microbiome.

Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans coordinators, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P.

Science. 2015 May 22;348(6237):1261359. doi: 10.1126/science.1261359.

PMID:
25999513
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