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.
Papers
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Structural variant classes and short tandem repeats differentially impact gene expression and complex traits
David Jakubosky,Matteo D’Antonio,Marc Jan Bonder,Craig Smail,Margaret K.R. Donovan,William W. Greenwald,Agnieszka D'Antonio-Chronowska,Hiroko Matsui,Oliver Stegle,Oliver Stegle,Erin N. Smith,Stephen B. Montgomery,Christopher DeBoever,Kelly A. Frazer,Kelly A. Frazer +14 more
TL;DR: This study identified a set of high-impact SVs/STRs associated with the expression of three or more eGenes via chromatin loops and showed they are highly enriched for being associated with GWAS traits.
Peer ReviewDOI
Author response: The single-cell eQTLGen consortium
Monique G. P. van der Wijst,DH de Vries,Hilde E. Groot,Gosia Trynka,CC Hon,Marc Jan Bonder,Oliver Stegle,Martijn C. Nawijn,Youssef Idaghdour,P. van der Harst,Chun Jimmie Ye,Joseph E. Powell,Fabian J. Theis,Ahmed Mahfouz,Ahmed Mahfouz,Matthias Heinig,Lude Franke +16 more
Posted ContentDOI
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: In this paper, a set of 719 deep whole genome sequencing (WGS) samples from 477 distinct individuals were used to discover and genotype a wide spectrum of structural variants and short tandem repeat (STR) variants using five algorithms.
Posted ContentDOI
Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease
Matteo D’Antonio,Joaquin Reyna,David Jakubosky,Margaret K.R. Donovan,Marc Jan Bonder,Hiroko Matsui,Oliver Stegle,Naoki Nariai,Agnieszka D'Antonio-Chronowska,Kelly A. Frazer +9 more
TL;DR: This study provides insights into the genetic architecture of the MHC region and pinpoints disease associations that are due to differential expression of HLA genes and non-HLA genes.
Journal ArticleDOI
pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls
TL;DR: In this article , pycoMeth , a toolbox to store, manage and analyze DNA methylation calls from long-read sequencing data obtained using the Oxford Nanopore Technologies sequencing platform, is presented.