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dr. ir. J. (Jeroen) de Ridder

Associate Professor

  • Group De Ridder, section Genetics

Research Output (41)

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

Jiao Wei, Atwal Gurnit, Polak Paz, Karlic Rosa, Cuppen Edwin, Danyi Alexandra, de Ridder Jeroen, van Herpen Carla, Lolkema Martijn P, Steeghs Neeltje, Getz Gad, Morris Quaid, Stein Lincoln D, 5 feb 2020, In: Nature Communications. 11 12 p.

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

Vermeulen Carlo, Allahyar Amin, Bouwman Britta A.M., Krijger Peter H.L., Verstegen Marjon J.A.M., Geeven Geert, Valdes-Quezada Christian, Renkens Ivo, Straver Roy, Kloosterman Wigard P., de Ridder Jeroen, de Laat Wouter 1 feb 2020, In: Nature Protocols. 15 , p. 364-397 34 p.

Three-dimensional analysis of single molecule FISH in human colon organoids

Omerzu Manja, Fenderico Nicola, De Barbanson Buys, Sprangers Joep, De Ridder Jeroen, Maurice Madelon M. 9 aug 2019, In: Biology Open. 8

Enhancer hubs and loop collisions identified from single-allele topologies

Allahyar Amin, Vermeulen Carlo, Bouwman Britta A.M., Krijger Peter H.L., Verstegen Marjon J.A.M., Geeven Geert, van Kranenburg Melissa, Pieterse Mark, Straver Roy, Haarhuis Judith H.I., Jalink Kees, Teunissen Hans, Renkens Ivo J., Kloosterman Wigard P., Rowland Benjamin D., de Wit Elzo, de Ridder Jeroen, de Laat Wouter 1 aug 2018, In: Nature Genetics. 50 , p. 1151-1160 10 p.

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

Cretu Stancu Mircea, van Roosmalen Markus J, Renkens Ivo, Nieboer Marleen M, Middelkamp Sjors, de Ligt Joep, Pregno Giulia, Giachino Daniela, Mandrile Giorgia, Espejo Valle-Inclan Jose, Korzelius Jerome, de Bruijn Ewart, Cuppen Edwin, Talkowski Michael E., Marschall Tobias, de Ridder Jeroen, Kloosterman Wigard P 6 nov 2017, In: Nature Communications [E]. 8

ECCB 2016:The 15th European Conference on Computational Biology

Heringa Jaap, Reinders Marcel J T, Abeln Sanne, De Ridder Jeroen 1 sep 2016, In: Bioinformatics. 32 , p. i389-i392

Pan-cancer subtyping in a 2D-map shows substructures that are driven by specific combinations of molecular characteristics

Taskesen Erdogan, Huisman Sjoerd M.H., Mahfouz Ahmed, Krijthe Jesse H., De Ridder Jeroen, Van De Stolpe Anja, Van Den Akker Erik, Verheagh Wim, Reinders Marcel J T 25 apr 2016, In: Scientific Reports. 6

Gamma-Retrovirus integration marks cell type-specific cancer genes:A novel profiling tool in cancer genomics

Gilroy Kathryn L., Terry Anne, Naseer Asif, De Ridder Jeroen, Allahyar Amin, Wang Weiwei, Carpenter Eric, Mason Andrew G., Wong Gane K.S., Cameron Ewan R., Kilbey Anna, Neil James C. 1 apr 2016, In: PLoS ONE [E]. 11

Erratum:Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors (PLoSONE (2015) 10:4 (e0122146) 10.1371/journal.pone.0122146)

Rijlaarsdam Martin A., Tax D.M.J., Gillis Ad J.M., Dorssers Lambert C.J., Koestler Devin C., De Ridder J. 14 jul 2015, In: PLoS ONE [E]. 10

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

Allahyar Amin, De Ridder Jeroen 15 jun 2015, In: Bioinformatics. 31 , p. i311-i319 9 p.