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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Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
Julie Jerber,Daniel D Seaton,Anna S E Cuomo,Natsuhiko Kumasaka,James Haldane,Juliette Steer,Minal Patel,Daniel Pearce,Malin Andersson,Marc Jan Bonder,Ed Mountjoy,Maya Ghoussaini,Madeline A. Lancaster,John C. Marioni,John C. Marioni,John C. Marioni,Florian T. Merkle,Oliver Stegle,Daniel J. Gaffney +18 more
TL;DR: This study uses an efficient pooling strategy to differentiate 215 iPS cell lines towards a midbrain neural fate, and profiles over 1 million cells sampled across three differentiation timepoints using single cell RNA sequencing.
Journal Article
Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity (vol 167, pg 1125, 2016)
Melanie Schirmer,Sanne P. Smeekens,Hera Vlamakis,Martin Jaeger,Marije Oosting,Eric A. Franzosa,Rob ter Horst,Trees Jansen,Liesbeth Jacobs,Marc Jan Bonder,Alexander Kurilshikov,Jingyuan Fu,Leo A. B. Joosten,Alexandra Zhernakova,Curtis Huttenhower,Cisca Wijmenga,Mihai G. Netea,Ramnik J. Xavier +17 more
Journal ArticleDOI
Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1.
Daniel E. Martin-Herranz,Erfan Aref-Eshghi,Erfan Aref-Eshghi,Marc Jan Bonder,Thomas M. Stubbs,Sanaa Choufani,Rosanna Weksberg,Oliver Stegle,Oliver Stegle,Bekim Sadikovic,Bekim Sadikovic,Wolf Reik,Wolf Reik,Wolf Reik,Janet M. Thornton +14 more
TL;DR: It is demonstrated that loss-of-function mutations in the H3K36 histone methyltransferase NSD1, which cause Sotos syndrome, substantially accelerate epigenetic aging and the Horvath clock sites are characterized by a higher Shannon methylation entropy when compared with the rest of the genome.
Journal ArticleDOI
Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity
Stephanie M. Linker,Lara Urban,Stephen J. Clark,Mariya Chhatriwala,Shradha Amatya,Davis J. McCarthy,Ingo Ebersberger,Ludovic Vallier,Ludovic Vallier,Wolf Reik,Wolf Reik,Wolf Reik,Oliver Stegle,Oliver Stegle,Marc Jan Bonder +14 more
TL;DR: This study applies parallel DNA methylation and transcriptome sequencing to differentiating human induced pluripotent stem cells to characterize splicing variation (exon skipping) and its determinants and reveals a previously underappreciated link betweenDNA methylation variation and splicing.
Journal ArticleDOI
The emerging landscape of dynamic DNA methylation in early childhood.
Cheng-Jian Xu,Marc Jan Bonder,Cilla Söderhäll,Mariona Bustamante,Nour Baïz,Ulrike Gehring,Soesma A Jankipersadsing,Pieter van der Vlies,Cleo C. van Diemen,Bianca van Rijkom,Jocelyne Just,Inger Kull,Juha Kere,Juha Kere,Josep M. Antó,Jean Bousquet,Alexandra Zhernakova,Cisca Wijmenga,Isabella Annesi-Maesano,Jordi Sunyer,Erik Melén,Yang Li,Dirkje S. Postma,Gerard H. Koppelman +23 more
TL;DR: This study provides new insights into the dynamic epigenetic landscape of the first 8 years of life by identifying 14,150 consistent age-differential methylation sites (a-DMSs) at epigenome-wide significance of p < 1.14 × 10−7.