Breast cancer subtype specific classifiers of response to neoadjuvant chemotherapy do not outperform classifiers trained on all subtypes.

by Jorma J de Ronde, Marc Jan Bonder, Esther H Lips, Sjoerd Rodenhuis, Lodewyk F A Wessels
Published 2014-01-01

Optimizing expression quantitative trait locus mapping workflows for single-cell studies

by Anna S. E. Cuomo, Giordano Alvari, Christina B. Azodi, single-cell eQTLGen consortium, Davis J. McCarthy, Marc Jan Bonder
Published 2021-06-01

Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells

by Irene Hernando-Herraez, Brendan Evano, Thomas Stubbs, Pierre-Henri Commere, Marc Jan Bonder, Stephen Clark, Simon Andrews, Shahragim Tajbakhsh, Wolf Reik
Published 2019-09-01

Multi-tissue DNA methylation age predictor in mouse

by Thomas M. Stubbs, Marc Jan Bonder, Anne-Katrien Stark, Felix Krueger, BI Ageing Clock Team, Ferdinand von Meyenn, Oliver Stegle, Wolf Reik
Published 2017-04-01

Population-scale proteome variation in human induced pluripotent stem cells

by Bogdan Andrei Mirauta, Daniel D Seaton, Dalila Bensaddek, Alejandro Brenes, Marc Jan Bonder, Helena Kilpinen, HipSci Consortium, Oliver Stegle, Angus I Lamond
Published 2020-08-01

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease

by Matteo D'Antonio, Joaquin Reyna, David Jakubosky, Margaret KR Donovan, Marc-Jan Bonder, Hiroko Matsui, Oliver Stegle, Naoki Nariai, Agnieszka D'Antonio-Chronowska, Kelly A Frazer
Published 2019-11-01

Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1

by Daniel E. Martin-Herranz, Erfan Aref-Eshghi, Marc Jan Bonder, Thomas M. Stubbs, Sanaa Choufani, Rosanna Weksberg, Oliver Stegle, Bekim Sadikovic, Wolf Reik, Janet M. Thornton
Published 2019-08-01

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations

by Matthew A. Jackson, Marc Jan Bonder, Zhana Kuncheva, Jonas Zierer, Jingyuan Fu, Alexander Kurilshikov, Cisca Wijmenga, Alexandra Zhernakova, Jordana T. Bell, Tim D. Spector, Claire J. Steves
Published 2018-02-01

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

by Stephanie M. Linker, Lara Urban, Stephen J. Clark, Mariya Chhatriwala, Shradha Amatya, Davis J. McCarthy, Ingo Ebersberger, Ludovic Vallier, Wolf Reik, Oliver Stegle, Marc Jan Bonder
Published 2019-02-01

Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats

by David Jakubosky, Erin N. Smith, Matteo D’Antonio, Marc Jan Bonder, William W. Young Greenwald, Agnieszka D’Antonio-Chronowska, Hiroko Matsui, i2QTL Consortium, Oliver Stegle, Stephen B. Montgomery, Christopher DeBoever, Kelly A. Frazer
Published 2020-06-01

Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

by Anna S. E. Cuomo, Daniel D. Seaton, Davis J. McCarthy, Iker Martinez, Marc Jan Bonder, Jose Garcia-Bernardo, Shradha Amatya, Pedro Madrigal, Abigail Isaacson, Florian Buettner, Andrew Knights, Kedar Nath Natarajan, HipSci Consortium, Ludovic Vallier, John C. Marioni, Mariya Chhatriwala, Oliver Stegle
Published 2020-03-01

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

by Anna S. E. Cuomo, Daniel D. Seaton, Davis J. McCarthy, Iker Martinez, Marc Jan Bonder, Jose Garcia-Bernardo, Shradha Amatya, Pedro Madrigal, Abigail Isaacson, Florian Buettner, Andrew Knights, Kedar Nath Natarajan, HipSci Consortium, Ludovic Vallier, John C. Marioni, Mariya Chhatriwala, Oliver Stegle
Published 2020-02-01

Properties of structural variants and short tandem repeats associated with gene expression and complex traits

by David Jakubosky, Matteo D’Antonio, Marc Jan Bonder, Craig Smail, Margaret K. R. Donovan, William W. Young Greenwald, Hiroko Matsui, i2QTL Consortium, Agnieszka D’Antonio-Chronowska, Oliver Stegle, Erin N. Smith, Stephen B. Montgomery, Christopher DeBoever, Kelly A. Frazer
Published 2020-06-01

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative

by Jun Wang, Alexander Kurilshikov, Djawad Radjabzadeh, Williams Turpin, Kenneth Croitoru, Marc Jan Bonder, Matthew A. Jackson, Carolina Medina-Gomez, Fabian Frost, Georg Homuth, Malte Rühlemann, David Hughes, Han-na Kim, MiBioGen Consortium Initiative, Tim D. Spector, Jordana T. Bell, Claire J. Steves, Nicolas Timpson, Andre Franke, Cisca Wijmenga, Katie Meyer, Tim Kacprowski, Lude Franke, Andrew D. Paterson, Jeroen Raes, Robert Kraaij, Alexandra Zhernakova
Published 2018-06-01

Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA.

by Rudolf S N Fehrmann, Ritsert C Jansen, Jan H Veldink, Harm-Jan Westra, Danny Arends, Marc Jan Bonder, Jingyuan Fu, Patrick Deelen, Harry J M Groen, Asia Smolonska, Rinse K Weersma, Robert M W Hofstra, Wim A Buurman, Sander Rensen, Marcel G M Wolfs, Mathieu Platteel, Alexandra Zhernakova, Clara C Elbers, Eleanora M Festen, Gosia Trynka, Marten H Hofker, Christiaan G J Saris, Roel A Ophoff, Leonard H van den Berg, David A van Heel, Cisca Wijmenga, Gerard J Te Meerman, Lude Franke
Published 2011-08-01

Genetically defined elevated homocysteine levels do not result in widespread changes of DNA methylation in leukocytes.

by Pooja R Mandaviya, Roby Joehanes, Dylan Aïssi, Brigitte Kühnel, Riccardo E Marioni, Vinh Truong, Lisette Stolk, Marian Beekman, Marc Jan Bonder, Lude Franke, Christian Gieger, Tianxiao Huan, M Arfan Ikram, Sonja Kunze, Liming Liang, Jan Lindemans, Chunyu Liu, Allan F McRae, Michael M Mendelson, Martina Müller-Nurasyid, Annette Peters, P Eline Slagboom, John M Starr, David-Alexandre Trégouët, André G Uitterlinden, Marleen M J van Greevenbroek, Diana van Heemst, Maarten van Iterson, Philip S Wells, Chen Yao, Ian J Deary, France Gagnon, Bastiaan T Heijmans, Daniel Levy, Pierre-Emmanuel Morange, Melanie Waldenberger, Sandra G Heil, Joyce B J van Meurs, CHARGE Consortium Epigenetics group and BIOS Consortium
Published 2017-01-01