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Items: 20

1.

Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota.

Tito RY, Chaffron S, Caenepeel C, Lima-Mendez G, Wang J, Vieira-Silva S, Falony G, Hildebrand F, Darzi Y, Rymenans L, Verspecht C, Bork P, Vermeire S, Joossens M, Raes J.

Gut. 2018 Aug 31. pii: gutjnl-2018-316106. doi: 10.1136/gutjnl-2018-316106. [Epub ahead of print]

2.

Mechanically induced development and maturation of human intestinal organoids in vivo.

Poling HM, Wu D, Brown N, Baker M, Hausfeld TA, Huynh N, Chaffron S, Dunn JCY, Hogan SP, Wells JM, Helmrath MA, Mahe MM.

Nat Biomed Eng. 2018 Jun;2(6):429-442. doi: 10.1038/s41551-018-0243-9. Epub 2018 Jun 4.

3.

Modelling plankton ecosystems in the meta-omics era. Are we ready?

Stec KF, Caputi L, Buttigieg PL, D'Alelio D, Ibarbalz FM, Sullivan MB, Chaffron S, Bowler C, Ribera d'Alcalà M, Iudicone D.

Mar Genomics. 2017 Apr;32:1-17. doi: 10.1016/j.margen.2017.02.006. Epub 2017 Mar 7. Review.

PMID:
28283424
4.

Species-function relationships shape ecological properties of the human gut microbiome.

Vieira-Silva S, Falony G, Darzi Y, Lima-Mendez G, Garcia Yunta R, Okuda S, Vandeputte D, Valles-Colomer M, Hildebrand F, Chaffron S, Raes J.

Nat Microbiol. 2016 Jun 13;1(8):16088. doi: 10.1038/nmicrobiol.2016.88.

PMID:
27573110
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.

6.

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 J, Coelho LP, Espinoza JCI, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S; Tara Oceans 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):465-470. doi: 10.1038/nature16942. Epub 2016 Feb 10.

7.

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes.

Takeuchi Y, Chaffron S, Salcher MM, Shimizu-Inatsugi R, Kobayashi MJ, Diway B, von Mering C, Pernthaler J, Shimizu KK.

Syst Appl Microbiol. 2015 Jul;38(5):330-9. doi: 10.1016/j.syapm.2015.05.006. Epub 2015 Jun 16.

8.

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.

9.

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.

10.

Ocean plankton. Patterns and ecological drivers of ocean viral communities.

Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Bork P, Bowler C, Sunagawa S, Wincker P, Karsenti E, Sullivan MB.

Science. 2015 May 22;348(6237):1261498. doi: 10.1126/science.1261498. Erratum in: Science. 2016 Aug 12;353(6300). pii: aah6502. doi: 10.1126/science.aah6502.

11.

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.

12.

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice.

Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, von Mering C, Vorholt JA.

ISME J. 2012 Jul;6(7):1378-90. doi: 10.1038/ismej.2011.192. Epub 2011 Dec 22.

13.

The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea.

Endt K, Stecher B, Chaffron S, Slack E, Tchitchek N, Benecke A, Van Maele L, Sirard JC, Mueller AJ, Heikenwalder M, Macpherson AJ, Strugnell R, von Mering C, Hardt WD.

PLoS Pathog. 2010 Sep 9;6(9):e1001097. doi: 10.1371/journal.ppat.1001097.

14.

A global network of coexisting microbes from environmental and whole-genome sequence data.

Chaffron S, Rehrauer H, Pernthaler J, von Mering C.

Genome Res. 2010 Jul;20(7):947-59. doi: 10.1101/gr.104521.109. Epub 2010 May 10.

15.

Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria.

Stecher B, Chaffron S, Käppeli R, Hapfelmeier S, Freedrich S, Weber TC, Kirundi J, Suar M, McCoy KD, von Mering C, Macpherson AJ, Hardt WD.

PLoS Pathog. 2010 Jan;6(1):e1000711. doi: 10.1371/journal.ppat.1000711. Epub 2010 Jan 8.

16.

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria.

Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA.

Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16428-33. doi: 10.1073/pnas.0905240106. Epub 2009 Sep 4.

17.

STRING 8--a global view on proteins and their functional interactions in 630 organisms.

Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C.

Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6. doi: 10.1093/nar/gkn760. Epub 2008 Oct 21.

18.

Termites in the woodwork.

Chaffron S, von Mering C.

Genome Biol. 2007;8(11):229. Review.

19.

Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota.

Stecher B, Robbiani R, Walker AW, Westendorf AM, Barthel M, Kremer M, Chaffron S, Macpherson AJ, Buer J, Parkhill J, Dougan G, von Mering C, Hardt WD.

PLoS Biol. 2007 Oct;5(10):2177-89.

20.

STRING 7--recent developments in the integration and prediction of protein interactions.

von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P.

Nucleic Acids Res. 2007 Jan;35(Database issue):D358-62. Epub 2006 Nov 10.

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