M
Marc Jan Bonder
Researcher at European Bioinformatics Institute
Publications - 117
Citations - 15800
Marc Jan Bonder is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: DNA methylation & Expression quantitative trait loci. The author has an hindex of 46, co-authored 108 publications receiving 10517 citations. Previous affiliations of Marc Jan Bonder include Netherlands Cancer Institute & German Cancer Research Center.
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Journal ArticleDOI
Population-level analysis of gut microbiome variation
Gwen Falony,Marie Joossens,Marie Joossens,Sara Vieira-Silva,Jun Wang,Youssef Darzi,Youssef Darzi,Karoline Faust,Karoline Faust,Alexander Kurilshikov,Marc Jan Bonder,Mireia Valles-Colomer,Doris Vandeputte,Doris Vandeputte,Raul Y. Tito,Raul Y. Tito,Samuel Chaffron,Samuel Chaffron,Leen Rymenans,Leen Rymenans,Chloë Verspecht,Lise De Sutter,Lise De Sutter,Gipsi Lima-Mendez,Kevin D'hoe,Kevin D'hoe,Karl Jonckheere,Karl Jonckheere,Daniel Homola,Daniel Homola,Roberto Garcia,Roberto Garcia,Ettje F. Tigchelaar,Linda Eeckhaudt,Linda Eeckhaudt,Jingyuan Fu,Liesbet Henckaerts,Alexandra Zhernakova,Cisca Wijmenga,Jeroen Raes,Jeroen Raes +40 more
TL;DR: Stool consistency showed the largest effect size, whereas medication explained largest total variance and interacted with other covariate-microbiota associations, and proposed disease marker genera associated to host covariates were found associated to microbiota compositional variation with a 92% replication rate.
Journal ArticleDOI
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.
Alexandra Zhernakova,Alexander Kurilshikov,Marc Jan Bonder,Ettje F. Tigchelaar,Melanie Schirmer,Tommi Vatanen,Zlatan Mujagic,Arnau Vich Vila,Gwen Falony,Sara Vieira-Silva,Sara Vieira-Silva,Jun Wang,Jun Wang,Floris Imhann,Eelke Brandsma,Soesma A Jankipersadsing,Marie Joossens,María Carmen Cenit,Patrick Deelen,Morris A. Swertz,Rinse K. Weersma,Edith J. M. Feskens,Mihai G. Netea,Dirk Gevers,Daisy Jonkers,Lude Franke,Yurii S. Aulchenko,Curtis Huttenhower,Curtis Huttenhower,Jeroen Raes,Jeroen Raes,Jeroen Raes,Marten H. Hofker,Ramnik J. Xavier,Cisca Wijmenga,Jingyuan Fu +35 more
TL;DR: Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors, and an important step toward a better understanding of environment-diet-microbe-host interactions.
Journal ArticleDOI
Proton pump inhibitors affect the gut microbiome
Floris Imhann,Marc Jan Bonder,Arnau Vich Vila,Jingyuan Fu,Zlatan Mujagic,Lisa Vork,Ettje F. Tigchelaar,Soesma A Jankipersadsing,María Carmen Cenit,Hermie J. M. Harmsen,Gerard Dijkstra,Lude Franke,Ramnik J. Xavier,Daisy Jonkers,Cisca Wijmenga,Rinse K. Weersma,Alexandra Zhernakova +16 more
TL;DR: The differences between PPI users and non-users observed in this study are consistently associated with changes towards a less healthy gut microbiome, in line with known changes that predispose to C. difficile infections.
Journal ArticleDOI
Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
Melanie Schirmer,Melanie Schirmer,Sanne P. Smeekens,Hera Vlamakis,Martin Jaeger,Marije Oosting,Eric A. Franzosa,Eric A. Franzosa,Rob ter Horst,Trees Jansen,Liesbeth Jacobs,Marc Jan Bonder,Alexander Kurilshikov,Alexander Kurilshikov,Jingyuan Fu,Jingyuan Fu,Leo A. B. Joosten,Alexandra Zhernakova,Curtis Huttenhower,Curtis Huttenhower,Cisca Wijmenga,Mihai G. Netea,Ramnik J. Xavier +22 more
TL;DR: Validation of two predicted host-microbial interactions reveal that TNFα and IFNγ production are associated with specific microbial metabolic pathways: palmitoleic acid metabolism andtryptophan degradation to tryptophol.
Journal ArticleDOI
Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity
Simone Wahl,Alexander W. Drong,Benjamin Lehne,Marie Loh,Marie Loh,Marie Loh,William R. Scott,William R. Scott,Sonja Kunze,Pei-Chien Tsai,Janina S. Ried,Weihua Zhang,Weihua Zhang,Youwen Yang,Sili Tan,Giovanni Fiorito,Lude Franke,Simonetta Guarrera,Silva Kasela,Jennifer Kriebel,Rebecca C Richmond,Marco Adamo,Uzma Afzal,Uzma Afzal,Mika Ala-Korpela,Mika Ala-Korpela,Mika Ala-Korpela,Benedetta Albetti,Ole Ammerpohl,Jane F. Apperley,Marian Beekman,Pier Alberto Bertazzi,S. Lucas Black,Christine Blancher,Marc Jan Bonder,Mario Brosch,Maren Carstensen-Kirberg,Anton J. M. de Craen,Simon de Lusignan,Abbas Dehghan,Mohamed Elkalaawy,Krista Fischer,Oscar H. Franco,Tom R. Gaunt,Jochen Hampe,Majid Hashemi,Aaron Isaacs,Andrew Jenkinson,Sujeet Jha,Norihiro Kato,Vittorio Krogh,Michael Laffan,Christa Meisinger,Thomas Meitinger,Zuan Yu Mok,Valeria Motta,Hong Kiat Ng,Zacharoula Nikolakopoulou,Georgios Nteliopoulos,Salvatore Panico,Natalia Pervjakova,Holger Prokisch,Wolfgang Rathmann,Michael Roden,Federica Rota,Michelle Ann Rozario,Johanna K. Sandling,Johanna K. Sandling,Clemens Schafmayer,Katharina Schramm,Reiner Siebert,Reiner Siebert,P. Eline Slagboom,Pasi Soininen,Pasi Soininen,Lisette Stolk,Konstantin Strauch,E-Shyong Tai,Letizia Tarantini,Barbara Thorand,Ettje F. Tigchelaar,Rosario Tumino,André G. Uitterlinden,Cornelia M. van Duijn,Joyce B. J. van Meurs,Paolo Vineis,Ananda R. Wickremasinghe,Cisca Wijmenga,Tsun-Po Yang,Wei Yuan,Wei Yuan,Alexandra Zhernakova,Rachel L. Batterham,George Davey Smith,Panos Deloukas,Panos Deloukas,Panos Deloukas,Bastiaan T. Heijmans,Christian Herder,Albert Hofman,Cecilia M. Lindgren,Cecilia M. Lindgren,Lili Milani,Pim van der Harst,Annette Peters,Thomas Illig,Caroline L Relton,Melanie Waldenberger,Marjo-Riitta Järvelin,Valentina Bollati,Richie Soong,Tim D. Spector,James Scott,Mark I. McCarthy,Mark I. McCarthy,Mark I. McCarthy,Paul Elliott,Paul Elliott,Jordana T. Bell,Giuseppe Matullo,Christian Gieger,Jaspal S. Kooner,Harald Grallert,John C. Chambers +123 more
TL;DR: In this article, the authors used epigenome-wide association to show that body mass index (BMI), a key measure of adiposity, is associated with widespread changes in DNA methylation.