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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Large-scale association analyses identify host factors influencing human gut microbiome composition
Alexander Kurilshikov,Carolina Medina-Gomez,Rodrigo Bacigalupe,Djawad Radjabzadeh,Jun Wang,Ayse Demirkan,Ayse Demirkan,Caroline I. Le Roy,Juan Antonio Raygoza Garay,Juan Antonio Raygoza Garay,Casey T. Finnicum,Xingrong Liu,Daria V. Zhernakova,Daria V. Zhernakova,Marc Jan Bonder,Tue H. Hansen,Fabian Frost,Malte C. Rühlemann,Williams Turpin,Williams Turpin,Jee-Young Moon,Han-Na Kim,Kreete Lüll,Elad Barkan,Shiraz A. Shah,Myriam Fornage,Joanna Szopinska-Tokov,Zachary D. Wallen,Dmitrii Borisevich,Lars Agréus,Anna Andreasson,Corinna Bang,Larbi Bedrani,Jordana T. Bell,Hans Bisgaard,Michael Boehnke,Dorret I. Boomsma,Robert D. Burk,Annique Claringbould,Kenneth Croitoru,Kenneth Croitoru,Gareth E. Davies,Cornelia M. van Duijn,Cornelia M. van Duijn,Liesbeth Duijts,Gwen Falony,Jingyuan Fu,Adriaan van der Graaf,Torben Hansen,Georg Homuth,David A. Hughes,Richard G. IJzerman,Matthew A. Jackson,Matthew A. Jackson,Vincent W. V. Jaddoe,Marie Joossens,Torben Jørgensen,Daniel Keszthelyi,Rob Knight,Markku Laakso,Matthias Laudes,Lenore J. Launer,Wolfgang Lieb,Aldons J. Lusis,Ad A.M. Masclee,Henriette A. Moll,Zlatan Mujagic,Qi Qibin,Daphna Rothschild,Hocheol Shin,Søren J. Sørensen,Claire J. Steves,Jonathan Thorsen,Nicholas J. Timpson,Raul Y. Tito,Sara Vieira-Silva,Uwe Völker,Henry Völzke,Urmo Võsa,Kaitlin H Wade,Susanna Walter,Kyoko Watanabe,Stefan Weiss,Frank Ulrich Weiss,Omer Weissbrod,Harm-Jan Westra,Gonneke Willemsen,Haydeh Payami,Daisy Jonkers,Alejandro Arias Vasquez,Eco J. C. de Geus,Katie A. Meyer,Jakob Stokholm,Eran Segal,Elin Org,Cisca Wijmenga,Hyung Lae Kim,Robert C. Kaplan,Tim D. Spector,André G. Uitterlinden,Fernando Rivadeneira,Andre Franke,Markus M. Lerch,Lude Franke,Serena Sanna,Serena Sanna,Mauro D'Amato,Oluf Pedersen,Andrew D. Paterson,Robert Kraaij,Jeroen Raes,Alexandra Zhernakova +111 more
TL;DR: A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome has causal effects in ulcerative colitis and rheumatoid arthritis.
Journal Article
Proton pump inhibitors affect the gut microbiome
Floris Imhann,Marc Jan Bonder,A 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: In this paper, the influence of Proton pump inhibitors (PPIs) on the gut microbiome was investigated and the differences between PPI users and non-users observed in this study are consistently associated with changes towards a less healthy gut microbiome.
Journal ArticleDOI
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
Anna S E Cuomo,Daniel D Seaton,Davis J. McCarthy,Davis J. McCarthy,Iker Martinez,Marc Jan Bonder,Marc Jan Bonder,Jose Garcia-Bernardo,Shradha Amatya,Pedro Madrigal,Abigail Isaacson,Florian Buettner,Andrew J Knights,Kedar Nath Natarajan,Kedar Nath Natarajan,Ludovic Vallier,Ludovic Vallier,John C. Marioni,John C. Marioni,John C. Marioni,Mariya Chhatriwala,Oliver Stegle,Oliver Stegle +22 more
TL;DR: Induced pluripotent stem cells from 125 donors are exploited to track gene expression changes and expression quantitative trait loci at single cell resolution during in vitro endoderm differentiation to identify molecular markers that are predictive of differentiation efficiency of individual lines.
Journal ArticleDOI
The influence of a short-term gluten-free diet on the human gut microbiome
Marc Jan Bonder,Ettje F. Tigchelaar,Xianghang Cai,Gosia Trynka,María Carmen Cenit,Barbara Hrdličková,Huanzi Zhong,Tommi Vatanen,Tommi Vatanen,Dirk Gevers,Cisca Wijmenga,Yang Wang,Alexandra Zhernakova +12 more
TL;DR: A GFD changes the gut microbiome composition and alters the activity of microbial pathways and observes strong relations between the predicted activity of pathways and biomarker measurements.
Genome-wide analysis identifies 12 loci influencing human reproductive behavior
Nicola Barban,Rick Jansen,Ronald de Vlaming,Ahmad Vaez,Jornt J. Mandemakers,Felix C. Tropf,Xia Shen,James F. Wilson,Daniel I. Chasman,Illa M. Nolte,Vinicius Tragante,Sander W. van der Laan,John R. B. Perry,Augustine Kong,Tarunveer S. Ahluwalia,Eva Albrecht,Laura M. Yerges-Armstrong,Gil Atzmon,Kirsi Auro,Kristin L. Ayers,Andrew Bakshi,Danny Ben-Avraham,Klaus Berger,Aviv Bergman,Lars Bertram,Lawrence F. Bielak,Gyda Bjornsdottir,Marc Jan Bonder,Linda Broer,Minh Bui,Caterina Barbieri,Alana Cavadino,Jorge E. Chavarro,Constance Turman,Maria Pina Concas,Heather J. Cordell,Gail Davies,Peter Eibich,Nicholas Eriksson,Tõnu Esko,Joel Eriksson,Fahimeh Falahi,Janine F. Felix,Mark Alan Fontana,Lude Franke,Ilaria Gandin,Audrey J. Gaskins,Christian Gieger,Erica P. Gunderson,Xiuqing Guo,Caroline Hayward,Chunyan He,Edith Hofer,Hongyan Huang,Peter K. Joshi,Stavroula Kanoni,Robert Karlsson,Stefan Kiechl,Annette Kifley,Alexander Kluttig,Peter Kraft,Vasiliki Lagou,Cécile Lecoeur,Jari Lahti,Ruifang Li-Gao,Penelope A. Lind,Tian Liu,Enes Makalic,Crysovalanto Mamasoula,Lindsay K. Matteson,Hamdi Mbarek,Patrick F. McArdle,George McMahon,S. Fleur W. Meddens,Evelin Mihailov,Michael B. Miller,Stacey A. Missmer,Claire Monnereau,Peter J. van der Most,Ronny Myhre,Mike A. Nalls,Teresa Nutile,Ioanna P. Kalafati,Eleonora Porcu,Inga Prokopenko,Kumar B. Rajan,Janet W. Rich-Edwards,Cornelius A. Rietveld,Antonietta Robino,Lynda M. Rose,Rico Rueedi,Kathleen-A Ryan,Yasaman Saba,Daniel F. Schmidt,Jennifer A. Smith,Lisette Stolk,Elizabeth A. Streeten,Anke Toenjes,Gudmar Thorleifsson,Sheila Ulivi,Juho Wedenoja,Juergen Wellmann,Peter Willeit,Jie Yao,Loic Yengo,Jing Hua Zhao,Wei Zhao,Dania V. Zhernakova,Najaf Amin,Howard Andrews,Beverley Balkau,Nir Barzilai,Sven Bergmann,Ginevra Biino,Hans Bisgaard,Klaus Bønnelykke,Dorret I. Boomsma,Julie E. Buring,Harry Campbell,Stefania Cappellani,Marina Ciullo,Simon R. Cox,Francesco Cucca,Daniela Toniolo,George Davey-Smith,Ian J. Deary,George Dedoussis,Panos Deloukas,Cornelia M. van Duijn,Eco J. C. de Geus,Johan G. Eriksson,Denis A. Evans,Jessica D. Faul,Cinzia Sala,Philippe Froguel,Paolo Gasparini,Giorgia Girotto,Hans-Joergen Grabe,Karin Halina Greiser,Patrick J. F. Groenen,Hugoline G. de Haan,Johannes Haerting,Tamara B. Harris,Andrew C. Heath,Kauko Heikkilä,Albert Hofman,Georg Homuth,Elizabeth G. Holliday,John L. Hopper,Elina Hyppönen,Bo Jacobsson,Vincent W. V. Jaddoe,Magnus Johannesson,Mika Kähönen,Eero Kajantie,Sharon L.R. Kardia,Bernard Keavney,Ivana Kolcic,P Koponen,Peter Kovacs,Florian Kronenberg,Zoltán Kutalik,Martina La Bianca,Genevieve Lachance,William G. Iacono,Sandra Lai,Terho Lehtimäki,David C. Liewald,Cecilia M. Lindgren,Yongmei Liu,Robert Luben,Michael Lucht,Riitta Luoto,Per Magnus,Patrik K. E. Magnusson,Nicholas G. Martin,Matt McGue,Ruth McQuillan,Sarah E. Medland,Christa Meisinger,Dan Mellström,Andres Metspalu,Michela Traglia,Lili Milani,Paul Mitchell,Grant W. Montgomery,Dennis O. Mook-Kanamori,Renée de Mutsert,Ellen A. Nohr,Claes Ohlsson,Porn Olsen,Ken K. Ong,Lavinia Paternoster,Alison Pattie,Brenda W.J.H. Penninx,Markus Perola,Patricia A. Peyser,Mario Pirastu,Ozren Polasek,Chris Power,Jaakko Kaprio,Leslie J. Raffel,Katri Räikkönen,Olli T. Raitakari,Paul M. Ridker,Susan M. Ring,Kathryn Roll,Igor Rudan,Daniela Ruggiero,Dan Rujescu,Veikko Salomaa,David Schlessinger,Helena Schmidt,Reinhold Schmidt,Nicole Schupf,Johannes W. A. Smit,Rossella Sorice,Tim D. Spector,John M. Starr,Doris Stöckl,Konstantin Strauch,Michael Stumvoll,Morris A. Swertz,Unnur Thorsteinsdottir,Roy Thurik,Nicholas J. Timpson,Joyce Y. Tung,André G. Uitterlinden,Simona Vaccargiu,J. Viikari,Veronique Vitart,Henry Voelzke,Peter Vollenweider,Dragana Vuckovic,Johannes Waage,Gert G. Wagner,Jie Jin Wang,Nicholas J. Wareham,David R. Weir,Gonneke Willemsen,Johann Willeit,Alan F. Wright,Krina T. Zondervan,Kari Stefansson,Robert F. Krueger,James J. Lee,Daniel J. Benjamin,David Cesarini,Philipp Koellinger,Marcel den Hoed,Harold Snieder,Melinda Mills +251 more