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
Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Peter Ebert,Peter A. Audano,Qihui Zhu,Bernardo Rodriguez-Martin,David Porubsky,Marc Jan Bonder,Marc Jan Bonder,Arvis Sulovari,Jana Ebler,Weichen Zhou,Rebecca Serra Mari,Feyza Yilmaz,Xuefang Zhao,Xuefang Zhao,PingHsun Hsieh,Joyce V. Lee,Sushant Kumar,Jiadong Lin,Tobias Rausch,Yu Chen,Jingwen Ren,Martin Santamarina,Wolfram Höps,Hufsah Ashraf,Nelson T. Chuang,Xiaofei Yang,Katherine M. Munson,Alexandra P. Lewis,Susan Fairley,Luke J. Tallon,Wayne E. Clarke,Anna O. Basile,Marta Byrska-Bishop,André Corvelo,Uday S. Evani,Tsung Yu Lu,Mark Chaisson,Junjie Chen,Chong Li,Harrison Brand,Harrison Brand,Aaron M. Wenger,Maryam Ghareghani,Maryam Ghareghani,Maryam Ghareghani,William T. Harvey,Benjamin Raeder,Patrick Hasenfeld,Allison A. Regier,Haley J. Abel,Ira M. Hall,Paul Flicek,Oliver Stegle,Oliver Stegle,Mark Gerstein,Jose M. C. Tubio,Zepeng Mu,Yang I. Li,Xinghua Shi,Alex Hastie,Kai Ye,Kai Ye,Zechen Chong,Ashley D. Sanders,Michael C. Zody,Michael E. Talkowski,Michael E. Talkowski,Ryan E. Mills,Scott E. Devine,Charles Lee,Charles Lee,Jan O. Korbel,Tobias Marschall,Evan E. Eichler +73 more
TL;DR: In this article, the authors present 64 assembled haplotypes from 32 diverse human genomes, which integrate all forms of genetic variation, even across complex loci, and identify 107,590 structural variants (SVs), of which 68% were not discovered with short-read sequencing.
Journal ArticleDOI
Large-scale association analyses identify host factors influencing human gut microbiome composition
Alexander Kurilshikov,Carolina Medina-Gomez,Rodrigo Bacigalupe,Djawad Radjabzadeh,Jun Wang,Jun Wang,Ayse Demirkan,Ayse Demirkan,Caroline I. Le Roy,Juan Antonio Raygoza Garay,Casey T. Finnicum,Xingrong Liu,Daria V. Zhernakova,Marc Jan Bonder,Tue H. Hansen,Fabian Frost,Malte C. Rühlemann,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,Gareth E. Davies,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 +109 more
TL;DR: In this article, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts) and found high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples.
Journal ArticleDOI
Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation
Norihiro Kato,Marie Loh,Marie Loh,Marie Loh,Fumihiko Takeuchi,Niek Verweij,Xu Wang,Weihua Zhang,Tanika NKelly,Danish Saleheen,Danish Saleheen,Benjamin Lehne,Irene Mateo Leach,Alexander W. Drong,James Abbott,Simone Wahl,Sian Tsung Tan,William R. Scott,Gianluca Campanella,Marc Chadeau-Hyam,Uzma Afzal,Tarunveer S. Ahluwalia,Tarunveer S. Ahluwalia,Marc Jan Bonder,Peng Chen,Abbas Dehghan,Todd L. Edwards,Tõnu Esko,Min Jin Go,Sarah E. Harris,Jaana Hartiala,Silva Kasela,Anuradhani Kasturiratne,Chiea Chuen Khor,Marcus E. Kleber,Huaixing Li,Zuan Yu Mok,Masahiro Nakatochi,Nur Sabrina Sapari,Richa Saxena,Alexandre F.R. Stewart,Lisette Stolk,Yasuharu Tabara,Ai Ling Teh,Ying Wu,Jer-Yuarn Wu,Yi Zhang,Imke Aits,Alexessander Couto Alves,Shikta Das,Rajkumar Dorajoo,Jemma CHopewell,Yun Kyoung Kim,Robert WKoivula,Jian'an Luan,Leo-Pekka Lyytikäinen,Quang NNguyen,Mark A. Pereira,Iris Postmus,Olli TRaitakari,Molly Scannell Bryan,Robert A. Scott,Rossella Sorice,Vinicius Tragante,Michela Traglia,Jon White,Ken Yamamoto,Yonghong Zhang,Linda S. Adair,Alauddin Ahmed,Koichi Akiyama,Rasheed Asif,Tin Aung,Inês Barroso,Andrew Bjonnes,Timothy R. Braun,Hui Cai,Li Ching Chang,Chien Hsiun Chen,Ching-Yu Cheng,Yap Seng Chong,Yap Seng Chong,Rory Collins,Regina Courtney,Gail Davies,Graciela E. Delgado,Loi D. Do,Pieter A. Doevendans,Ron T. Gansevoort,Yu-Tang Gao,Tanja B. Grammer,Niels Grarup,Jagvir Grewal,Dongfeng Gu,Gurpreet SWander,Anna-Liisa Hartikainen,Stanley L. Hazen,Jing He,Chew-Kiat Heng,E. James Ames Hixso,Albert Hofman,Chris Hsu,Wei Huang,Lise Lotte N. Husemoen,Joo Yeon Hwang,Sahoko Ichihara,Michiya Igase,Masato Isono,Johanne Marie Justesen,Tomohiro Katsuya,Muhammad GKibriya,Young Jin Kim,Miyako Kishimoto,Woon-Puay Koh,Katsuhiko Kohara,Meena Kumari,Kenneth Kwek,Nanette R. Lee,Jeannette Lee,Jiemin Liao,Jiemin Liao,Wolfgang Lieb,David C. Liewald,Tatsuaki Matsubara,Yumi Matsushita,Thomas Meitinger,Evelin Mihailov,Lili Milani,Rebecca Mills,Nina Mononen,Martina Müller-Nurasyid,Toru Nabika,Eitaro Nakashima,Hong Kiat Ng,Kjell Nikus,Teresa Nutile,Takayoshi Ohkubo,Keizo Ohnaka,Sarah Parish,Lavinia Paternoster,Hao Peng,Annette Peters,Son TPham,M.J. Pinidiyapathirage,Mahfuzar Rahman,Hiromi Rakugi,Olov Rolandsson,Michelle Ann Rozario,Daniela Ruggiero,Cinzia Sala,Ralhan Sarju,Kazuro Shimokawa,Harold Snieder,Thomas Sparsø,Wilko Spiering,John M. Starr,David J. Stott,Daniel OStram,Takao Sugiyama,Silke Szymczak,W.H. Wilson Tang,Lin Tong,Stella Trompet,Väinö Turjanmaa,Hirotsugu Ueshima,André G. Uitterlinden,Satoshi Umemura,Marja Vääräsmäki,Rob M. van Dam,Wiek H. van Gilst,Dirk J. van Veldhuisen,Jorma Viikari,Melanie Waldenberger,Yiqin Wang,Aili Wang,Rory P. Wilson,Tien Yin Wong,Tien Yin Wong,Yong-Bing Xiang,Shuhei Yamaguchi,Xingwang Ye,Robin Young,Terri L. Young,Jian-Min Yuan,Xueya Zhou,Folkert W. Asselbergs,Folkert W. Asselbergs,Marina Ciullo,Robert Clarke,Panos Deloukas,Panos Deloukas,Andre Franke,W. Frank Paul,Steve Franks,Yechiel Friedlander,Myron D. Gross,Zhirong Guo,Torben Hansen,Marjo-Riitta Järvelin,Marjo-Riitta Järvelin,Torben Jørgensen,J. Wouter Jukema,Mika Kähönen,Hiroshi Kajio,Mika Kivimäki,Jong-Young Lee,Terho Lehtimäki,Allan Linneberg,Tetsuro Miki,Oluf Pedersen,Nilesh J. Samani,Thorkild I. A. Sørensen,Thorkild I. A. Sørensen,Ryoichi Takayanagi,Daniela Toniolo,Habibul Ahsan,Hooman Allayee,Yuan-Tsong Chen,John Danesh,John Danesh,Ian J. Deary,Oscar H. Franco,Lude Franke,Bastiaan THeijman,Joanna D. Holbrook,Aaron Isaacs,Bong Jo Kim,Xu Lin,Jianjun Liu,Winfried März,Andres Metspalu,Karen L. Mohlke,K. Sangher,Dharambir Harambir,Xiao-Ou Shu,Joyce B. J. van Meurs,Eranga N. Vithana,Ananda R. Wickremasinghe,Cisca Wijmenga,Bruce H W Wolffenbuttel,Mitsuhiro Yokota,Wei Zheng,Dingliang Zhu,Paolo Vineis,Soterios A. Kyrtopoulos,Jos C. S. Kleinjans,Mark I. McCarthy,Richie Soong,Christian Gieger,James Scott,Yik Ying Teo,Jiang He,Paul Elliott,E. Shyong Tai,Pim van der Harst,Jaspal S. Kooner,John C. Chambers +256 more
TL;DR: The trans-ancestry genome-wide association and replication study of blood pressure phenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry finds genetic variants at 12 new loci to be associated with blood pressure, providing new evidence for the role of DNA methylation in blood pressure regulation.
Journal ArticleDOI
Genome-wide analysis identifies 12 loci influencing human reproductive behavior
Nicola Barban,Rick Jansen,Ronald de Vlaming,Ahmad Vaez,Ahmad Vaez,Jornt J. Mandemakers,Felix C. Tropf,Xia Shen,Xia Shen,James F. Wilson,Daniel I. Chasman,Ilja M. Nolte,Vinicius Tragante,Sander W. van der Laan,John R. B. Perry,Augustine Kong,Augustine Kong,Tarunveer S. Ahluwalia,Tarunveer S. Ahluwalia,Eva Albrecht,Laura M. Yerges-Armstrong,Gil Atzmon,Gil Atzmon,Kirsi Auro,Kirsi Auro,Kristin L. Ayers,Andrew Bakshi,Danny Ben-Avraham,Klaus Berger,Aviv Bergman,Lars Bertram,Lars Bertram,Lawrence F. Bielak,Gyda Bjornsdottir,Marc Jan Bonder,Linda Broer,Minh Bui,Caterina Barbieri,Alana Cavadino,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,Vasiliki Lagou,Cecile 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,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,Inga Prokopenko,Kumar B. Rajan,Janet W. Rich-Edwards,Cornelius A. Rietveld,Antonietta Robino,Lynda M. Rose,Rico Rueedi,Rico Rueedi,Kathleen A. Ryan,Yasaman Saba,Daniel F. Schmidt,Jennifer A. Smith,Lisette Stolk,Elizabeth A. Streeten,Anke Tönjes,Gudmar Thorleifsson,Sheila Ulivi,Juho Wedenoja,Juergen Wellmann,Peter Willeit,Jie Yao,Loic Yengo,Jing Hua Zhao,Wei Zhao,Daria V. Zhernakova,Najaf Amin,Howard Andrews,Beverley Balkau,Nir Barzilai,Sven Bergmann,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,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 J. Grabe,Karin Halina Greiser,Patrick J. F. Groenen,Hugoline G. de Haan,Johannes Haerting,Tamara B. Harris,Andrew C. Heath,Kauko Heikkilä,Albert Hofman,Albert Hofman,Georg Homuth,Elizabeth G. Holliday,John L. Hopper,Elina Hyppönen,Elina Hyppönen,Bo Jacobsson,Bo Jacobsson,Vincent W. V. Jaddoe,Magnus Johannesson,Astanand Jugessur,Mika Kähönen,Eero Kajantie,Eero Kajantie,Eero Kajantie,Sharon L.R. Kardia,Bernard Keavney,Bernard Keavney,Ivana Kolcic,P Koponen,Peter Kovacs,Florian Kronenberg,Zoltán Kutalik,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,Matt McGue,Ruth McQuillan,Sarah E. Medland,Christa Meisinger,Dan Mellström,Andres Metspalu,Andres Metspalu,Michela Traglia,Lili Milani,Paul Mitchell,Grant W. Montgomery,Grant W. Montgomery,Dennis O. Mook-Kanamori,Dennis O. Mook-Kanamori,Renée de Mutsert,Ellen A. Nohr,Claes Ohlsson,Jørn Olsen,Ken K. Ong,Lavinia Paternoster,Alison Pattie,Brenda W.J.H. Penninx,Markus Perola,Markus Perola,Markus Perola,Patricia A. Peyser,Mario Pirastu,Ozren Polasek,Chris Power,Jaakko Kaprio,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,Unnur Thorsteinsdottir,Roy Thurik,Nicholas J. Timpson,Joyce Y. Tung,André G. Uitterlinden,Simona Vaccargiu,J. Viikari,Veronique Vitart,Henry Völzke,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,Kari Stefansson,Robert F. Krueger,James J. Lee,Daniel J. Benjamin,Daniel J. Benjamin,David Cesarini,Philipp Koellinger,Philipp Koellinger,Marcel den Hoed,Harold Snieder,Melinda Mills +284 more
TL;DR: In this article, the authors reported a large genome-wide association study of both sexes including 251,151 individuals for AB and 343,072 individuals for NEB and identified 12 independent loci that are significantly associated with AB and NEB.
Journal ArticleDOI
Controlling bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution.
Maarten van Iterson,Erik W. van Zwet,Bastiaan T. Heijmans,Peter A C 't Hoen,Joyce B. J. van Meurs,Rick Jansen,Lude Franke,Dorret I. Boomsma,René Pool,Jenny van Dongen,Jouke J. Hottenga,Marleen J. van Greevenbroek,Coen D.A. Stehouwer,Carla J.H. van der Kallen,Casper G. Schalkwijk,Cisca Wijmenga,Sasha Zhernakova,Ettje F. Tigchelaar,P. Eline Slagboom,Marian Beekman,Joris Deelen,Diana van Heemst,Jan H. Veldink,Leonard H. van den Berg,Cornelia M. van Duijn,Bert A. Hofman,Aaron Isaacs,André G. Uitterlinden,P. Mila Jhamai,Michael M. P. J. Verbiest,H. Eka D. Suchiman,Marijn Verkerk,Ruud van der Breggen,Jeroen van Rooij,Nico Lakenberg,Hailiang Mei,Michiel van Galen,Jan Bot,Dasha V. Zhernakova,Peter Van ‘t Hof,Patrick Deelen,Irene Nooren,Matthijs Moed,Martijn Vermaat,René Luijk,Marc Jan Bonder,Freerk van Dijk,Wibowo Arindrarto,Szymon M. Kielbasa,Morris A. Swertz,Peter Bram 't Hoen +50 more
TL;DR: A Bayesian method to control bias and inflation in EWAS and TWAS based on estimation of the empirical null distribution is proposed and it is demonstrated that the method maximizes power while properly controlling the false positive rate.