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Items: 1 to 20 of 108

1.

Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD.

Sabino J, Vieira-Silva S, Machiels K, Joossens M, Falony G, Ballet V, Ferrante M, Van Assche G, Van der Merwe S, Vermeire S, Raes J.

Gut. 2016 May 20. pii: gutjnl-2015-311004. doi: 10.1136/gutjnl-2015-311004. [Epub ahead of print]

2.

A web application for sample size and power calculation in case-control microbiome studies.

Mattiello F, Verbist B, Faust K, Raes J, Shannon WD, Bijnens L, Thas O.

Bioinformatics. 2016 Feb 19. pii: btw099. [Epub ahead of print]

PMID:
27153704
3.

IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data.

Mysara M, Leys N, Raes J, Monsieurs P.

BMC Bioinformatics. 2016 Apr 29;17(1):192. doi: 10.1186/s12859-016-1061-2.

4.

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA; LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J.

Science. 2016 Apr 29;352(6285):565-9. doi: 10.1126/science.aad3369. Epub 2016 Apr 28.

PMID:
27126040
5.

Population-level analysis of gut microbiome variation.

Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J.

Science. 2016 Apr 29;352(6285):560-4. doi: 10.1126/science.aad3503. Epub 2016 Apr 28.

PMID:
27126039
6.

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.

7.

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.

8.

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
9.

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
10.

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
11.

Microbiome-based companion diagnostics: no longer science fiction?

Raes J.

Gut. 2016 Jun;65(6):896-7. doi: 10.1136/gutjnl-2015-311015. Epub 2016 Jan 22. No abstract available.

12.

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
13.

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
14.

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
15.

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
16.

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.

17.

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
18.

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.

19.

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
20.

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.

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