This study introduces a topological data analysis framework to analyze malignant-immune cell interactions in the tumor microenvironment using high-resolution imaging data.

npj Systems Biology and Applications · Jun 13, 2026Peer-reviewedBioinformatics

Site-dependent Treg cell transcriptional reprograming in a metastatic colorectal cancer model holds prognostic significance

Sonia Aristín Revilla, André Verheem, Cynthia Lisanne Frederiks, Yongsoo Kim, Theofilos Chalkiadakis, Bastiaan J. Viergever, Balázs Győrffy, Enric Mocholí, Onno Kranenburg, Stefan Preković, Paul James Coffer

The paper identifies location-specific transcriptional differences in tumor-infiltrating Treg cells across CRC metastases and links these to poor patient prognosis.

Cancer Letters · Jun 11, 2026Peer-reviewedImmunology

TET CpG sequence context specific DNA demeth-ylation shapes progression of IDH-mutant gliomas

Youri Hoogstrate, Santoesha A. Ghisai, Levi van Hijfte, Rania Head, Iris J. de Heer, Marta Padovan, Maurice de Wit, Wies Vallentgoed, Angelo Dipasquale, Maarten M.J. Wijnenga, Bas Weenink, Rosa Luning, Sybren L. N. Maas, Adé la Brzobohatá, Michael Weller, , Pim J. French

The paper identifies DNA methylation changes during IDH-mutant glioma progression, links them to TET enzyme activity, and develops a methylation-based grading system that outperforms WHO grading.

Cell Reports Medicine · Mar 1, 2026Peer-reviewedCancer Biology

Bulk RNA sequencing deconvolution of pancreatic ductal adenocarcinoma identifies cancer-associated fibroblast subsets associated with survival and tumor microenvironment composition

Nicole Dam, Mischa F.B. Steketee, Gaby J. Strijk, Willem de Koning, Lukas J.A.C. Hawinkels, Vera Kemp, Casper H.J. van Eijck, Yongsoo Kim, Casper W.F. van Eijck, Bram W. van Os

The paper uses bulk RNAseq deconvolution to identify CAF subtypes in early onset PDAC and links their abundance to survival and tumor microenvironment composition.

Cancer Treatment and Research Communications · Jan 1, 2026Peer-reviewedCancer Biology

Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output

Stacey E. P. Joosten, Sebastian Gregoricchio, Suzan Stelloo, Elif Yapıcı, Chia-Chi Flora Huang, Kerim Yavuz, Maria Donaldson Collier, Tunç Morova, Umut Berkay Altıntaş, Yongsoo Kim, Sander Canisius, Cathy Beatrice Moelans, P. J. van Diest, Gözde Korkmaz, Nathan A. Lack, , Wilbert T. Zwart

The paper identifies breast cancer risk SNPs that overlap with estrogen receptor binding sites, showing their role in altering estrogen signaling through chromatin interactions.

Genome Research · May 6, 2024Peer-reviewedGenomics

Multi-scale spatial modeling of immune cell distributions enables survival prediction in primary central nervous system lymphoma

Margaretha G.M. Roemer, Tim van de Brug, Erik Bosch, Daniella R. A. I. Berry, Nathalie J. Hijmering, Phylicia Stathi, Karin Weijers, Jeanette K. Doorduijn, Jacoline E. C. Bromberg, Mark A. van de Wiel, Bauke Ylstra, Daphne de Jong, Yongsoo Kim

The paper develops a computational framework to analyze spatial interactions in tumor microenvironments and shows that spatial context predicts survival in primary central nervous system lymphoma.

iScience · Jul 10, 2023Peer-reviewedSystems Biology

Identifying biomarkers of anti-cancer drug synergy using multi-task learning

Nanne Aben, Julian R. de Ruiter, Evert Bosdriesz, Yongsoo Kim, Gergana Bounova, Daniël J. Vis, Lodewyk F.A. Wessels, Magali Michaut

The paper uses multi-task learning to identify biomarkers of anti-cancer drug synergy using low-sample-size drug combination data from 85 cell lines and 167 drug combinations.

bioRxiv · Aug 23, 2018 · PreprintBioinformatics