Jeroen de Ridder

Full Professor

Strategic program(s):

Contact

jridder4@umcutrecht.nl

Pure profile

Research groups

Bioinformatics in molecular medicine

Research aim

We are a bioinformatics lab that creates and applies innovative data science methods to advance our understanding of disease biology and molecular medicine with a focus on cancer research.

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Recent publications

All publications

Regulatory grammar in human promoters uncovered by MPRA-based deep learning Lucía Barbadilla-Martínez, Noud Klaassen, Vinícius H. Franceschini-Santos, Jérémie Breda, Hatice Yücel, Miguel Hernández-Quiles, Tijs van Lieshout, Carlos G. Urzua Traslaviña, Minh Chau Luong Boi, Maryam Akbarzadeh, Celia Hermana-Garcia-Agullo, Sebastian Gregoricchio, Marcel de Haas, Roy Straver, Sarah Derks, Wilbert Zwart, Emile Voest, Lude Franke, Michiel Vermeulen, Jeroen de Ridder, Bas van Steensel
Nature, 2026, vol. 651, p.1107-1116

A computational framework to dissect imputation strategies for single-cell histone modification data Marta Moreno-González, Jeroen de Ridder, Jop Kind, Robin H van der Weide
NAR genomics and bioinformatics, 2025, vol. 7

Bacterial cell-free DNA profiling reveals the co-elevation of multiple bacteria in newborn foals with suspected sepsis Li Ting Chen, Emmy Wesdorp, Myrthe Jager, Esther W. Siegers, Mathijs J.P. Theelen, Nicolle Besselink, Carlo Vermeulen, Aldert L. Zomer, Els M. Broens, Jaap A. Wagenaar, Jeroen de Ridder
iScience, 2025, vol. 28

Correction to Christoph Geisenberger, Jeroen van den Berg, Vincent van Batenburg, Buys de Barbanson, Anna Lyubimova, Joe Verity-Legg, Xiufei Chen, Yibin Liu, Chun Xiao Song, Jeroen de Ridder, Alexander van Oudenaarden
Nature Methods, 2025, vol. 22, p.2686

Brain tumor classification from FFPE samples using nanopore methylation sequencing Galina Feinberg-Gorenshtein, Assaf Grunwald, Carlo Vermeulen, Nurit Gal Mark, Elena Shinderman-Maman, Adva Levy-Barda, Keren Shichrur, Michal Hameiri-Grossman, Orli Michaeli, Shira Amar, Suzanna Fichman, Abraham Natan, Tali Siegal, Shlomit Yust-Katz, Hanna Weiss, Osnat Konen, Amir Kershenovich, Andrew A. Kanner, Jeroen De Ridder, Helen Toledano, Shai Izraeli, Yehudit Birger, Yuval Ebenstein
NAR Cancer, 2025, vol. 7

Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance Christoph Geisenberger, Jeroen van den Berg, Vincent van Batenburg, Buys de Barbanson, Anna Lyubimova, Joe Verity-Legg, Xiufei Chen, Yibin Liu, Chun Xiao Song, Jeroen de Ridder, Alexander van Oudenaarden
Nature Methods, 2025, vol. 22, p.2042-2051