Jeroen de Ridder
Jeroen de Ridder
Associate professor University Medical Center Utrecht
Verified email at - Homepage
Cited by
Cited by
Eleven grand challenges in single-cell data science
D Lähnemann, J Köster, E Szczurek, DJ McCarthy, SC Hicks, ...
Genome biology 21 (1), 1-35, 2020
From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy
FJ Rang, WP Kloosterman, J de Ridder
Genome biology 19 (1), 90, 2018
The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma
PA Pérez-Mancera, AG Rust, L Van Der Weyden, G Kristiansen, A Li, ...
Nature 486 (7402), 266-270, 2012
Chromatin position effects assayed by thousands of reporters integrated in parallel
W Akhtar, J de Jong, AV Pindyurin, L Pagie, W Meuleman, J de Ridder, ...
Cell 154 (4), 914-927, 2013
Mapping and phasing of structural variation in patient genomes using nanopore sequencing
M Cretu Stancu, MJ Van Roosmalen, I Renkens, MM Nieboer, ...
Nature communications 8 (1), 1326, 2017
Computational pan-genomics: status, promises and challenges
Briefings in bioinformatics 19 (1), 118-135, 2018
Large-scale mutagenesis in p19ARF-and p53-deficient mice identifies cancer genes and their collaborative networks
AG Uren, J Kool, K Matentzoglu, J de Ridder, J Mattison, M van Uitert, ...
Cell 133 (4), 727-741, 2008
Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis
HN March, AG Rust, NA Wright, J ten Hoeve, J de Ridder, M Eldridge, ...
Nature genetics 43 (12), 1202-1209, 2011
Enhancer hubs and loop collisions identified from single-allele topologies
A Allahyar, C Vermeulen, BAM Bouwman, PHL Krijger, MJAM Verstegen, ...
Nature genetics 50 (8), 1151-1160, 2018
Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens
J De Ridder, A Uren, J Kool, M Reinders, L Wessels
PLoS computational biology 2 (12), e166, 2006
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
W Jiao, G Atwal, P Polak, R Karlic, E Cuppen, A Danyi, J De Ridder, ...
Nature communications 11 (1), 728, 2020
Chromatin landscapes of retroviral and transposon integration profiles
J de Jong, W Akhtar, J Badhai, AG Rust, R Rad, J Hilkens, A Berns, ...
PLoS genetics 10 (4), e1004250, 2014
Pattern recognition in bioinformatics
D de Ridder, J de Ridder, MJT Reinders
Briefings in bioinformatics 14 (5), 633-647, 2013
PAX5 is a tumor suppressor in mouse mutagenesis models of acute lymphoblastic leukemia
J Dang, L Wei, J De Ridder, X Su, AG Rust, KG Roberts, D Payne-Turner, ...
Blood, The Journal of the American Society of Hematology 125 (23), 3609-3617, 2015
Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data
C Klijn, H Holstege, J de Ridder, X Liu, M Reinders, J Jonkers, L Wessels
Nucleic acids research 36 (2), e13-e13, 2008
Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors
MA Rijlaarsdam, DMJ Tax, AJM Gillis, LCJ Dorssers, DC Koestler, ...
PLoS One 10 (4), e0122146, 2015
Hi-C chromatin interaction networks predict co-expression in the mouse cortex
S Babaei, A Mahfouz, M Hulsman, BPF Lelieveldt, J de Ridder, ...
PLoS computational biology 11 (5), e1004221, 2015
Novel Candidate Cancer Genes Identified by a Large-Scale Cross-Species Comparative Oncogenomics ApproachHuman/Mouse Cross-Species Cancer Gene Analysis
J Mattison, J Kool, AG Uren, J De Ridder, L Wessels, J Jonkers, ...
Cancer research 70 (3), 883-895, 2010
FERAL: network-based classifier with application to breast cancer outcome prediction
A Allahyar, J De Ridder
Bioinformatics 31 (12), i311-i319, 2015
Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion
S Babaei, M Hulsman, M Reinders, J Ridder
BMC bioinformatics 14, 1-12, 2013
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