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dr. ir. J. (Jeroen) de Ridder

Associate Professor

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Research Output (44)

MetaboShiny:interactive analysis and metabolite annotation of mass spectrometry-based metabolomics data

Wolthuis Joanna C, Magnusdottir Stefania, Pras-Raves Mia, Moshiri Maryam, Jans Judith J M, Burgering Boudewijn, van Mil Saskia, de Ridder Jeroen 11 sep 2020, In: Metabolomics. 16 , p. 99

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

von Berg Joanna, van der Laan Sander W, McArdle Patrick F, Malik Rainer, Kittner Steven J, Mitchell Braxton D, Worrall Bradford B, de Ridder Jeroen, Pulit Sara L 11 feb 2020, In: European Journal of Human Genetics. 28 , p. 963-972 10 p.

Eleven grand challenges in single-cell data science

Lähnemann David, Köster Johannes, Szczurek Ewa, McCarthy Davis J, Hicks Stephanie C, Robinson Mark D, Vallejos Catalina A, Campbell Kieran R, Beerenwinkel Niko, Mahfouz Ahmed, Pinello Luca, Skums Pavel, Stamatakis Alexandros, Attolini Camille Stephan-Otto, Aparicio Samuel, Baaijens Jasmijn, Balvert Marleen, Barbanson Buys de, Cappuccio Antonio, Corleone Giacomo, Dutilh Bas E, Florescu Maria, Guryev Victor, Holmer Rens, Jahn Katharina, Lobo Thamar Jessurun, Keizer Emma M, Khatri Indu, Kielbasa Szymon M, Korbel Jan O, Kozlov Alexey M, Kuo Tzu-Hao, Lelieveldt Boudewijn P F, Mandoiu Ion I, Marioni John C, Marschall Tobias, Mölder Felix, Niknejad Amir, Raczkowski Lukasz, Reinders Marcel, Ridder Jeroen de, Saliba Antoine-Emmanuel, Somarakis Antonios, Stegle Oliver, Theis Fabian J, Yang Huan, Zelikovsky Alex, McHardy Alice C, Raphael Benjamin J, Shah Sohrab P, 7 feb 2020, In: Genome Biology. 21 , p. 1-35

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

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