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
Comparing clustering and pre-processing in taxonomy analysis
TL;DR: This work assessed combinations of data pre-processing steps and clustering algorithms on cluster accuracy for oral microbial sequence data and could not identify a single best clustering algorithm.
Journal ArticleDOI
Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative
Jun Wang,Jun Wang,Alexander Kurilshikov,Djawad Radjabzadeh,Williams Turpin,Williams Turpin,Kenneth Croitoru,Marc Jan Bonder,Marc Jan Bonder,Matthew A. Jackson,Carolina Medina-Gomez,Fabian Frost,Georg Homuth,Malte C. Rühlemann,David A. Hughes,Han na Kim,Tim D. Spector,Jordana T. Bell,Claire J. Steves,N J Timpson,Andre Franke,Cisca Wijmenga,Katie A. Meyer,Tim Kacprowski,Lude Franke,Andrew D. Paterson,Jeroen Raes,Robert Kraaij,Alexandra Zhernakova +28 more
TL;DR: The MiBioGen consortium initiative, which has assembled 18 population-level cohorts and some 19,000 participants, is presented, which is the largest consortium to date devoted to microbiota-GWAS and can reduce the potential artifacts introduced by technical differences in generating microbiota data.
Journal ArticleDOI
Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels
Patrick Deelen,Daria V. Zhernakova,Mark de Haan,Marijke R. van der Sijde,Marc Jan Bonder,Juha Karjalainen,K. Joeri van der Velde,Kristin M. Abbott,Jingyuan Fu,Cisca Wijmenga,Richard J. Sinke,Morris A. Swertz,Lude Franke +12 more
TL;DR: By deriving and imputing genotypes from RNA-seq data, it is possible to identify both eQTLs and ASE effects, and it is expected this approach will become especially relevant for studying the effects of tissue-specific and rare pathogenic genetic variants to aid clinical interpretation of exome and genome sequencing.
Journal ArticleDOI
Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome
Daria V. Zhernakova,Daria V. Zhernakova,Trang H. Le,Alexander Kurilshikov,Biljana Atanasovska,Marc Jan Bonder,Serena Sanna,Annique Claringbould,Urmo Võsa,Patrick Deelen,Lude Franke,Rudolf A. de Boer,Folkert Kuipers,Mihai G. Netea,Mihai G. Netea,Marten H. Hofker,Cisca Wijmenga,Cisca Wijmenga,Alexandra Zhernakova,Jingyuan Fu +19 more
TL;DR: In this article, a system-genome-wide and metagenomewide association study was conducted on plasma concentrations of 92 cardiovascular-disease-related proteins in the population cohort LifeLines-DEEP.
Journal ArticleDOI
An epigenome-wide association study meta-analysis of educational attainment
R. Karlsson Linner,R. Karlsson Linner,Riccardo E. Marioni,Cornelius A. Rietveld,Andrew J Simpkin,Neil M Davies,Kyoko Watanabe,Nicola J. Armstrong,Kirsi Auro,Kirsi Auro,Clemens Baumbach,Marc Jan Bonder,Jadwiga Buchwald,Giovanni Fiorito,Khadeeja Ismail,Stella Iurato,Anni Joensuu,Anni Joensuu,Pauliina Karell,Silva Kasela,Jari Lahti,Allan F. McRae,Pooja R. Mandaviya,Ilkka Seppälä,Yunzhang Wang,Laura Baglietto,Elisabeth B. Binder,Elisabeth B. Binder,Sarah E. Harris,Allison M. Hodge,Allison M. Hodge,Steve Horvath,Mikko Hurme,Magnus Johannesson,Antti Latvala,Karen A. Mather,S. E. Medland,A. Metspalu,Lili Milani,Roger L. Milne,Roger L. Milne,Alison Pattie,Nancy L. Pedersen,Annette Peters,Silvia Polidoro,Katri Räikkönen,Gianluca Severi,Gianluca Severi,John M. Starr,Lisette Stolk,M. Waldenberger,Johan G. Eriksson,Johan G. Eriksson,Tõnu Esko,Tõnu Esko,Lude Franke,C Gieger,G.G. Giles,G.G. Giles,Sara Hägg,Pekka Jousilahti,Jaakko Kaprio,Mika Kähönen,Terho Lehtimäki,Nicholas G. Martin,J B C van Meurs,Miina Ollikainen,Markus Perola,Markus Perola,Danielle Posthuma,Olli T. Raitakari,Olli T. Raitakari,Perminder S. Sachdev,Erdogan Taskesen,Erdogan Taskesen,A.G. Uitterlinden,A.G. Uitterlinden,Paolo Vineis,Cisca Wijmenga,Margaret J. Wright,Caroline L Relton,G Davey Smith,Ian J. Deary,Philipp Koellinger,Philipp Koellinger,Daniel J. Benjamin +85 more
TL;DR: In this paper, the associations between epigenetic modifications and educational attainment (EA), a biologically distal environmental factor that is arguably among the most important life-shaping experiences for individuals, were investigated.