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Author Details

Jeroen de Ridder
Center for Molecular Medicine, University Medical Center Utrecht
2006
66
23
PMIDPaper TitleJournal TitlePublished Year
36300617Echtvar: compressed variant representation for rapid annotation and filtering of SNPs and indels.Nucleic Acids Res2023
37286583Author Correction: Accurate detection of circulating tumor DNA using nanopore consensus sequencing.NPJ Genom Med2023
37041647Comprehensive benchmark and architectural analysis of deep learning models for nanopore sequencing basecalling.Genome Biol2023
37106015The genome-wide mutational consequences of DNA hypomethylation.Sci Rep2023
37236033WEE1 inhibitor adavosertib in combination with carboplatin in advanced TP53 mutated ovarian cancer: A biomarker-enriched phase II study.Gynecol Oncol2023
37031196Predicting response to enzalutamide and abiraterone in metastatic prostate cancer using whole-omics machine learning.Nat Commun2023
36732451Multi-country metabolic signature discovery for chicken health classification.Metabolomics2023
36481665Author Correction: A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.Nat Commun2022
35758773PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics.Bioinformatics2022
36778661Integration of multiple lineage measurements from the same cell reconstructs parallel tumor evolution.Cell Genom2022
34257393Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning.Sci Rep2021
33831168Allele-specific expression of GATA2 due to epigenetic dysregulation in CEBPA double-mutant AML.Blood2021
34887408Accurate detection of circulating tumor DNA using nanopore consensus sequencing.NPJ Genom Med2021
35054395Cancer Type Classification in Liquid Biopsies Based on Sparse Mutational Profiles Enabled through Data Augmentation and Integration.Life (Basel)2021
32913136Gene Networks Constructed Through Simulated Treatment Learning can Predict Proteasome Inhibitor Benefit in Multiple Myeloma.Clin Cancer Res2020
32033589Eleven grand challenges in single-cell data science.Genome Biol2020
31934500sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data.PeerJ2020
31932773Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies.Nat Protoc2020
32024849A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.Nat Commun2020
32047268Alternate approach to stroke phenotyping identifies a genetic risk locus for small vessel stroke.Eur J Hum Genet2020
33381833svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning.Bioinformatics2020
33381829RAINFOREST: a random forest approach to predict treatment benefit in data from (failed) clinical drug trials.Bioinformatics2020
32915321MetaboShiny: interactive analysis and metabolite annotation of mass spectrometry-based metabolomics data.Metabolomics2020
30726216A data-driven interactome of synergistic genes improves network-based cancer outcome prediction.PLoS Comput Biol2019
30218636A lentiviral vector-based insertional mutagenesis screen identifies mechanisms of resistance to MAPK inhibitors in melanoma.Pigment Cell Melanoma Res2019
31362950Three-dimensional analysis of single molecule FISH in human colon organoids.Biol Open2019
30470773Author Correction: Pan-cancer subtyping in a 2D-map shows substructures that are driven by specific combinations of molecular characteristics.Sci Rep2018
30054467Predicting treatment benefit in multiple myeloma through simulation of alternative treatment effects.Nat Commun2018
29988121Enhancer hubs and loop collisions identified from single-allele topologies.Nat Genet2018
30005597From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.Genome Biol2018
30496231TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors.PLoS One2018
30319454A Single Complex <i>Agpat2</i> Allele in a Patient With Partial Lipodystrophy.Front Physiol2018
29109544Mapping and phasing of structural variation in patient genomes using nanopore sequencing.Nat Commun2017
27109935Pan-cancer subtyping in a 2D-map shows substructures that are driven by specific combinations of molecular characteristics.Sci Rep2016
27587653ECCB 2016: The 15th European Conference on Computational Biology.Bioinformatics2016
27097319Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics.PLoS One2016
257218993D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes.Nat Commun2015
26442173Applications of DNA integrating elements: Facing the bias bully.Mob Genet Elements2015
26072498FERAL: network-based classifier with application to breast cancer outcome prediction.Bioinformatics2015
25859847Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors.PLoS One2015
25855603PAX5 is a tumor suppressor in mouse mutagenesis models of acute lymphoblastic leukemia.Blood2015
25965262Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex.PLoS Comput Biol2015
25734246Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia.BMC Bioinformatics2015
24706889Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis.Proc Natl Acad Sci U S A2014
24992198Soft skills: an important asset acquired from organizing regional student group activities.PLoS Comput Biol2014
24931989Scale-space measures for graph topology link protein network architecture to function.Bioinformatics2014
24586197Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis.PLoS Genet2014
24721906Chromatin landscapes of retroviral and transposon integration profiles.PLoS Genet2014
23343428Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion.BMC Bioinformatics2013
24148783The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models.Genome Biol2013
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Collaborators

Lodewyk F A Wessels
University Medical Centre Mannheim, University of Heidelberg
Co-authored papers 14
David J Adams
Wellcome Sanger Institute
Co-authored papers 10
Jos Jonkers
Oncode Institute, Netherlands Cancer Institute
Co-authored papers 5
Alexandra Danyi
Center for Molecular Medicine, University Medical Center Utrecht
Co-authored papers 4
Edwin Cuppen
Hartwig Medical Foundation
Co-authored papers 4
Martijn P Lolkema
Erasmus MC Cancer Institute
Co-authored papers 3
Neeltje Steeghs
Netherlands Cancer Institute-Antoni Van Leeuwenhoek
Co-authored papers 3
Derek L Stemple
Co-authored papers 2
Tim Hubbard
Co-authored papers 2
Paz Polak
McGill University
Co-authored papers 2
Phillip A Futreal
The University of Texas MD Anderson Cancer Center
Co-authored papers 2
Gurnit Atwal
Ontario Institute for Cancer Research Toronto
Co-authored papers 2
Quaid Morris
Sloan Kettering Institute
Co-authored papers 2
David A Largaespada
University of Minnesota
Co-authored papers 2
Boudewijn P F Lelieveldt
Leiden University Medical Center
Co-authored papers 2
Tobias Marschall
Center for Digital Medicine, Heinrich Heine University Dusseldorf
Co-authored papers 2
Gad Getz
Broad Institute of the Massachusetts Institute of Technology and Harvard
Co-authored papers 2
Adam Butler
Wellcome Sanger Institute
Co-authored papers 2
Jane Rogers
The Wellcome Trust Sanger Institute
Co-authored papers 2
Rosa Karlic
University of Zagreb
Co-authored papers 2
Serena Nik-Zainal
Early Cancer Institute, University of Cambridge
Co-authored papers 1
Braxton D Mitchell
Co-authored papers 1
Ultan McDermott
Wellcome Sanger Institute
Co-authored papers 1
David Jones
Wellcome Sanger Institute
Co-authored papers 1
Jinghui Zhang
Changhai Hospital, Second Military Medical University
Co-authored papers 1
Colin C Pritchard
University of Washington, USA Brotman Baty Institute for Precision Medicine
Co-authored papers 1
Peter Van Loo
The Francis Crick Institute
Co-authored papers 1
Ronald de Wit
Erasmus MC Cancer Institute
Co-authored papers 1
Szymon M Kieſbasa
Co-authored papers 1
Manasa Ramakrishna
Co-authored papers 1
Release 1.2