List of works - Jeroen de Ridder

3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes.

scientific article published on 27 February 2015

A data-driven interactome of synergistic genes improves network-based cancer outcome prediction

article

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

scientific article published on 05 February 2020

Accurate detection of circulating tumor DNA using nanopore consensus sequencing

scientific article published on 09 December 2021

Alternate approach to stroke phenotyping identifies a genetic risk locus for small vessel stroke

scientific article published on 11 February 2020

Applications of DNA integrating elements: Facing the bias bully

scientific article

Chromatin landscapes of retroviral and transposon integration profiles

scientific article

Chromatin position effects assayed by thousands of reporters integrated in parallel

scientific article

Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion.

scientific article

Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens

scientific article

Enhancer hubs and loop collisions identified from single-allele topologies

scientific article published on 09 July 2018

FERAL: network-based classifier with application to breast cancer outcome prediction

scientific article published on June 2015

From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy

scientific article published on 13 July 2018

Gene networks constructed through simulated treatment learning can predict proteasome inhibitor benefit in Multiple Myeloma

scientific article published on 10 September 2020

Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors

scientific article published on 10 April 2015

HAT: hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data

scientific article

Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex.

scientific article published on 12 May 2015

Highlights from the 5th International Society for Computational Biology Student Council Symposium at the 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology

scientific article

Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis

scientific article

Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis

scientific article published on 6 November 2011

Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia

scientific article published on 23 February 2015

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks

scientific article published on May 2008

Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies

scientific article published on 13 January 2020

PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics

scientific article published in 2022

Predicting treatment benefit in multiple myeloma through simulation of alternative treatment effects

scientific article published in Nature Communications

Soft skills: an important asset acquired from organizing regional student group activities

scientific article

TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors

scientific article published in PLoS ONE

The young PI buzz: learning from the organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.

scientific article published on 7 November 2013

sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data

scientific article published on 06 January 2020

List of works by Jeroen de Ridder

3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes.

A data-driven interactome of synergistic genes improves network-based cancer outcome prediction

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Accurate detection of circulating tumor DNA using nanopore consensus sequencing

Alternate approach to stroke phenotyping identifies a genetic risk locus for small vessel stroke

Applications of DNA integrating elements: Facing the bias bully

Chromatin landscapes of retroviral and transposon integration profiles

Chromatin position effects assayed by thousands of reporters integrated in parallel

Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion.

Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens

Enhancer hubs and loop collisions identified from single-allele topologies

FERAL: network-based classifier with application to breast cancer outcome prediction

From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy

Gene networks constructed through simulated treatment learning can predict proteasome inhibitor benefit in Multiple Myeloma

Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors

HAT: hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data

Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex.

Highlights from the 5th International Society for Computational Biology Student Council Symposium at the 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology

Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis

Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis

Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks

Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies

PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics

Predicting treatment benefit in multiple myeloma through simulation of alternative treatment effects

Soft skills: an important asset acquired from organizing regional student group activities

TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors

The young PI buzz: learning from the organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.

sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data