Jeroen de Ridder

24 papers Journal 19Unranked 4
YearRankTypeTitle / Venue / Authors
2022 J jnl
PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics.
Bioinform.
Joanna von Berg, Michelle ten Dam, Sander W. Van der Laan, Jeroen de Ridder
2020 J jnl
RAINFOREST: a random forest approach to predict treatment benefit in data from (failed) clinical drug trials.
Bioinform.
Joske Ubels, Tilman Schäfers, Cornelis Punt, Henk-Jan Guchelaar, Jeroen de Ridder
2020 J jnl
svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning.
Bioinform.
Marleentje Martha Nieboer, Jeroen de Ridder
2019 J jnl
12 Grand Challenges in Single-Cell Data Science.
PeerJ Prepr.
David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Niko Beerenwinkel, Kieran R. Campbell, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth
2019 J jnl
A data-driven interactome of synergistic genes improves network-based cancer outcome prediction.
PLoS Comput. Biol.
Amin Allahyar, Joske Ubels, Jeroen de Ridder
2018 — conf
A Portable and Scalable Workflow for Detecting Structural Variants in Whole-Genome Sequencing Data.
eScience
Arnold Kuzniar, Jason Maassen, Stefan Verhoeven, Luca Santuari, Carl Shneider, Wigard Kloosterman, Jeroen de Ridder
2016 J jnl
ECCB 2016: The 15th European Conference on Computational Biology.
Bioinform.
Jaap Heringa, Marcel J. T. Reinders, Sanne Abeln, Jeroen de Ridder
2015 J jnl
FERAL: network-based classifier with application to breast cancer outcome prediction.
Bioinform.
Amin Allahyar, Jeroen de Ridder
2015 J jnl
Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex.
PLoS Comput. Biol.
Sepideh Babaei, Ahmed Mahfouz, Marc Hulsman, Boudewijn P. F. Lelieveldt, Jeroen de Ridder, Marcel J. T. Reinders
2015 J jnl
Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia.
BMC Bioinform.
Erdogan Taskesen, Sepideh Babaei, Marcel J. T. Reinders, Jeroen de Ridder
2014 J jnl
Scale-space measures for graph topology link protein network architecture to function.
Bioinform.
Marc Hulsman, Christos Dimitrakopoulos, Jeroen de Ridder
2014 J jnl
Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities.
PLoS Comput. Biol.
Jeroen de Ridder, Pieter Meysman, Olugbenga Oluseun Oluwagbemi, Thomas Abeel
2013 J jnl
Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion.
BMC Bioinform.
Sepideh Babaei, Marc Hulsman, Marcel J. T. Reinders, Jeroen de Ridder
2013 J jnl
Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator.
PLoS Comput. Biol.
Jeroen de Ridder, Thomas Abeel, Magali Michaut, Venkata P. Satagopam, Nils Gehlenborg
2013 — conf
Mutational Genomics for Cancer Pathway Discovery.
PRIB
Jeroen de Ridder, Jaap Kool, Anthony Uren, Jan Bot, Johann de Jong, Alistair G. Rust, Anton Berns, Maarten van Lohuizen, David J. Adams, Lodewyk F. A. Wessels, Marcel J. T. Reinders
2013 J jnl
Pattern recognition in bioinformatics.
Briefings Bioinform.
Dick de Ridder, Jeroen de Ridder, Marcel J. T. Reinders
2013 J jnl
The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.
PLoS Comput. Biol.
Jeroen de Ridder, Yana Bromberg, Magali Michaut, Venkata P. Satagopam, Manuel Corpas, Geoff MacIntyre, Theodore Alexandrov
2011 — —
Computational approaches for dissecting cancer pathways from insertional mutagenesis data.
Jeroen de Ridder
2011 — conf
Integrating Protein Family Sequence Similarities with Gene Expression to Find Signature Gene Networks in Breast Cancer Metastasis.
PRIB
Sepideh Babaei, Erik van den Akker, Jeroen de Ridder, Marcel J. T. Reinders
2010 J jnl
HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data.
BMC Bioinform.
Erdogan Taskesen, Renee Beekman, Jeroen de Ridder, Bas J. Wouters, Justine K. Peeters, Ivo P. Touw, Marcel J. T. Reinders, Ruud Delwel
2010 J jnl
Inferring combinatorial association logic networks in multimodal genome-wide screens.
Bioinform.
Jeroen de Ridder, Alice Gerrits, Jan Bot, Gerald de Haan, Marcel J. T. Reinders, Lodewyk F. A. Wessels
2009 J jnl
Highlights from the 5
BMC Bioinform.
Thomas Abeel, Jeroen de Ridder, Lucia Peixoto
2007 — conf
Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes.
ISMB/ECCB (Supplement of Bioinformatics)
Jeroen de Ridder, Jaap Kool, Anthony Uren, Jan Bot, Lodewyk F. A. Wessels, Marcel J. T. Reinders
2006 J jnl
Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens.
PLoS Comput. Biol.
Jeroen de Ridder, Anthony Uren, Jaap Kool, Marcel J. T. Reinders, Lodewyk F. A. Wessels