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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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,Jose Garcia-Bernardo,Shradha Amatya,Pedro Madrigal,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: This work exploits human iPS cell lines from 125 donors, a pooled experimental design, and single-cell RNA-sequencing to study population variation of endoderm differentiation and identifies molecular markers that are predictive of differentiation efficiency.
Posted ContentDOI
A linear mixed model approach to study multivariate gene-environment interactions
Rachel Moore,Francesco Paolo Casale,Marc Jan Bonder,Danilo Horta,Lude Franke,Inês Barroso,Oliver Stegle,Oliver Stegle +7 more
TL;DR: The structured linear mixed model (StructLMM) is proposed, a computationally efficient method to test for and characterize loci that interact with multiple environments and can be used to study interactions with hundreds of environmental variables.
Journal ArticleDOI
Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats.
David Jakubosky,Erin N. Smith,Matteo D’Antonio,Marc Jan Bonder,William W. Greenwald,Agnieszka D'Antonio-Chronowska,Hiroko Matsui,Oliver Stegle,Oliver Stegle,Stephen B. Montgomery,Christopher DeBoever,Kelly A. Frazer +11 more
TL;DR: A comprehensive SV and STR callset from whole-genome sequencing of 477 individuals from iPSCORE and HipSci is reported using five algorithms to create one of the most complete and well characterized maps of SVs and STRs to date.
Journal ArticleDOI
Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS
Paul J. Hop,Ramona A. J. Zwamborn,Eilis Hannon,Gemma Shireby,Marta F. Nabais,Emma Walker,Wouter van Rheenen,Joke J.F.A. van Vugt,Annelot M. Dekker,Henk-Jan Westeneng,Gijs H.P. Tazelaar,Kristel R. van Eijk,Matthieu Moisse,Denis Baird,Ahmad Al Khleifat,Alfredo Iacoangeli,Nicola Ticozzi,Antonia Ratti,Jonathan Cooper-Knock,Karen E. Morrison,Pamela J. Shaw,A. Nazli Basak,Andrea Calvo,Cristina Moglia,Antonio Canosa,Maura Brunetti,Maurizio Grassano,Marc Gotkine,Yossef Lerner,Michal Zabari,Patrick Vourc'h,Philippe Corcia,Philippe Couratier,Jesus S. Mora Pardina,Teresa Salas,Patrick A. Dion,Jay P. Ross,Robert D. Henderson,Susan Mathers,Pamela A. McCombe,Merrilee Needham,Garth A. Nicholson,Dominic B. Rowe,Roger Pamphlett,Karen A. Mather,Perminder S. Sachdev,Sarah Furlong,Fleur C. Garton,Anjali K. Henders,Tian Lin,Shyuan T. Ngo,Frederik J. Steyn,Leanne Wallace,Kelly L. Williams,Miguel Mitne Neto,Ruben J. Cauchi,Ian A. Blair,Matthew C. Kiernan,Vivian E. Drory,Mònica Povedano,Mamede de Carvalho,Susana Pinto,Markus Weber,Guy A. Rouleau,Vincenzo Silani,John Landers,Christopher Shaw,Peter Andersen,Allan F. McRae,Michael A. van Es,R. Jeroen Pasterkamp,Naomi R. Wray,Russell L. McLaughlin,Orla Hardiman,Kevin P. Kenna,Ellen A. Tsai,Heiko Runz,Leonard H. van den Berg,Philip Van Damme,Jonathan Mill,Bastiaan T. Heijmans,Peter A C 't Hoen,J. Van Meurs,Rick Jansen,Lude Franke,Dorret I. Boomsma,René Pool,Jenny van Dongen,Joukje J Hottenga,Marleen M.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,Cornelia M. van Duijn,Bert 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,Maarten van Iterson,Michiel van Galen,Jan Bot,D. V. Zhernakova,Peter Van ‘t Hof,P.M. Van Deelen,Irene M.A. Nooren,Matthijs Moed,Martijn Vermaat,René Luijk,Marc Jan Bonder,Freerk van Dijk,Wibowo Arindrarto,Szymon M. Kielbasa,Morris A. Swertz,Erik W. van Zwet,Ammar Al-Chalabi,Gilbert Bensimon,Adriano Chiò,George Davey Smith +132 more
TL;DR: Analysis of DNA methylation patterns implicates metabolism, inflammation, and cholesterol pathways in ALS disease and survival, which will help the identification of disease-relevant mechanisms that could be targeted to block or delay ALS progression.
Posted ContentDOI
Population-scale proteome variation in human induced pluripotent stem cells
Bogdan Mirauta,Daniel D Seaton,Dalila Bensaddek,Alejandro Brenes,Marc Jan Bonder,Helena Kilpinen,Oliver Stegle,Oliver Stegle,Angus I. Lamond +8 more
TL;DR: This work characterise the major genetic determinants affecting proteome and transcriptome variation across iPSC lines and identify key regulatory mechanisms affecting variation in protein abundance, and discovered that pQTLs show increased enrichment in disease-linked GWAS variants, compared with RNA-based eQTLS.