This study examines how HP1α depletion and TGFβ activation affect 3D genome organization in human mammary epithelial cells, revealing opposing effects on chromatin compartments and gene expression.

bioRxiv · Feb 13, 2026 · PreprintGenomics

The 3D nuclear position and compartmentalization of genes prime their response to mechano-confinement

Saleh Oshagi, Oda Hovet, Andrea Halaburková, Cinzia Progida, Jonas Paulsen

The paper investigates how 3D nuclear positioning and compartmentalization of genes influence transcriptional responses to mechanical confinement using Hi-C and transcriptome analyses.

bioRxiv · Nov 6, 2025 · PreprintGenomics

Loss of multi-level 3D genome organization during breast cancer progression

Roberto Rossini, Mohammadsaleh Oshaghi, Maxim Nekrasov, Aurélie Bellanger, Renae Domaschenz, Yasmin Dijkwel, Mohamed Abdelhalim, Rahul Agrawal, Marit Ledsaak, Philippe Collas, Ragnhild Eskeland, David John Tremethick, Jonas Paulsen

This study investigates how 3D genome organization changes during breast cancer progression using Hi-C and epigenomic data, revealing structural alterations linked to oncogenic gene activation.

Genome Research · Oct 9, 2025Peer-reviewedGenomics

Translocations can drive expression changes of multiple genes in regulons covering entire chromosome arms

Anna Oncins, Roser Zaurín, Houyem Toukabri, Kimberly Quililan, José R Hernández Mora, Magdalena A. Karpińska, Erik Wernersson, Alastair Smith, Agostina Bianchi, Leone Albinati, Luca Cozzuto, Andrea Rivero, Chloe Gulliver, Jessica Velten, Johanna Denkena, , Renée Beekman

This study shows translocations can drive widespread gene expression changes across entire chromosome arms in MCL by altering chromatin organization and regulatory loops.

Nucleic Acids Research · Aug 11, 2025Peer-reviewedCancer Biology

StripePy: fast and robust characterization of architectural stripes

Andrea Raffo, Roberto Rossini, Jonas Paulsen

StripePy is a tool for detecting architectural stripes in Hi-C data, outperforming existing methods on benchmark datasets.

Bioinformatics · Jun 1, 2025Peer-reviewedBioinformatics

hictk: blazing fast toolkit to work with .hic and .cool files

Roberto Rossini, Jonas Paulsen

hictk is a toolkit for efficiently processing .hic and .cool files, outperforming existing tools and supporting both formats natively.

Bioinformatics · Jun 21, 2024Peer-reviewedBioinformatics

MoDLE: High-performance stochastic modeling of DNA loop extrusion interactions

Roberto Rossini, Vipin Kumar, Anthony Mathelier, Torbjørn Rognes, Jonas Paulsen

MoDLE is a computational tool that rapidly simulates DNA loop extrusion contact patterns, matching existing methods and Micro-C data with high accuracy.

Genome biology · Nov 30, 2022Peer-reviewedBioinformatics

Eight principal chromatin states functionally segregate the fly genome into developmental and housekeeping roles

Caroline Delandre, John P. D. McMullen, Jonas Paulsen, Philippe Collas, Owen J. Marshall

The paper identifies eight chromatin states in Drosophila that segregate the genome into developmental and housekeeping roles through chromatin protein and histone mark associations.

bioRxiv · Oct 30, 2022 · PreprintGenomics

TAD cliques predict key features of chromatin organization

Tharvesh M. Liyakat Ali, Annaël Brunet, Philippe Collas, Jonas Paulsen

The paper identifies TAD cliques as repressive chromatin domains with distinct structural and functional features across cell types.

BMC Genomics · Jul 3, 2021Peer-reviewedGenomics