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See all posts28/02/2025 - Outcomes
ChromDesign Publications
Here we proudly share our complete list of publications as of 28/02/2025—a collection that embodies our unique transdisciplinary approach. By seamlessly merging the expertise of chromatin biologists and design innovators, our network has driven forward research in chromatin architecture and epigenetics, while also exploring new ways to communicate complex science to society. Each of the 22 publications reflects a carefully balanced effort to advance both fundamental discovery and the practical integration of design principles, ensuring that our insights are as accessible as they are groundbreaking. We invite you to explore these contributions and join us in celebrating the strides made in the dynamic field of chromatin organization and design.
| Authors | Title | Year | Source title | DOI |
| Jusuf J. M.; Grosse-Holz, S.; Gabriele M.; Mach P.; Flyamer I. M.; Zechner C.; Giorgetti L.; Mirny L. A.; Hansen A. S. | Genome-wide absolute quantification of chromatin looping | 2025 | BioRxiv | 10.1101/2025.01.13.632736 |
| Hauth A, Panten J, Kneuss E, Picard C, Servant N, Rall I, Pérez-Rico YA, Clerquin L, Servaas N, Villacorta L, Jung F, Luong C, Chang HY, Zaugg JB, Stegle O, Odom DT, Loda A, Heard E. | Escape from X inactivation is directly modulated by levels of Xist non-coding RNA | 2024 | BioRxiv | 10.1101/2024.02.22.581559 |
| Karagyozova T, Almouzni G. | Replicating chromatin in the nucleus: A histone variant perspective | 2024 | Current Opinion Cell Biology | 10.1016/j.ceb.2024.102397 |
| Karagyozova T.; Gatto A.; Forest A.; Quivy J.P.; Marti-Renom M.; Mirny L.; Almouzni G. | HIRA defines early replication initiation zones independently of their genome compartment | 2024 | BioRxiv | 10.1101/2024.08.29.610220 |
| Kourosh Hayatigolkhatmi, Chiara Soriani, Emanuel Soda, Elena Ceccacci, Oualid El Menna, Sebastiano Peri, Ivan Negrelli, Giacomo Bertolini, Gian Martino Franchi, Roberta Carbone, Saverio Minucci, Simona Rodighiero | Automated workflow for the cell cycle analysis of (non-)adherent cells using a machine learning approach | 2024 | eLife | 10.7554/eLife.94689 |
| Kourosh Hayatigolkhatmi, Riccardo Valzelli, Oualid El Menna, Saverio Minucci | Epigenetic alterations in AML: Deregulated functions leading to new therapeutic options | 2024 | International Review of Cell and Molecular Biology | 10.1016/bs.ircmb.2024.06.003 |
| Paldi F.; Szalay M. F.; Di Stefano M.; Jost D.; Reboul H.; Cavalli G. | Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome folding | 2024 | BioRxiv | 10.1101/2024.11.21.624660 |
| Szalay M.-F.; Majchrzycka B.; Jerković I.; Cavalli G.; Ibrahim D.M. | Evolution and function of chromatin domains across the tree of life | 2024 | Nature Structural and Molecular Biology | 10.1038/s41594-024-01427-y |
| Jerkovic I.; Di Stefano M.; Reboul H.; Szalay M. F.; Normanno D.; Papadopoulos G.; Bantignies F.; Cavalli G. | A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation | 2024 | BioRxiv | 10.1101/2024.05.23.595561 |
| Bofeng Liu, Yuanlin He, Xiaotong Wu, Zili Lin, Jing Ma, Yuexin Qiu, Yunlong Xiang, Feng Kong, Fangnong Lai, Mrinmoy Pal, Peizhe Wang, Jia Ming, Bingjie Zhang, Qiujun Wang, Jingyi Wu, Weikun Xia, Weimin Shen, Jie Na, Maria-Elena Torres-Padilla, Jing Li & Wei Xie | Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulators | 2024 | Nature Cell Biology | 10.1038/s41556-024-01422-x |
| Arfe S.; Karagyozova T.; Forest A.; Hmidan H.; Meshorer E.; Quivy J.P.; Almouzni G. | H3.3 deposition counteracts the replication-dependent enrichment of H3.1 at chromocenters in embryonic stem cells | 2024 | BioRxiv | 10.1101/2024.07.04.601905 |
| Livia Condemi, Ivano Mocavini, Sergi Aranda & Luciano Di Croce | Polycomb function in early mouse development | 2024 | Cell Death & Differentiation | 10.1038/s41418-024-01340-3 |
| Tsunetoshi Nakatani, Tamas Schauer, Luis Altamirano-Pacheco, Kyle N. Klein, Andreas Ettinger, Mrinmoy Pal, David M. Gilbert & Maria-Elena Torres-Padilla | Emergence of replication timing during early mammalian development | 2023 | Nature | 10.1038/s41586-023-06872-1 |
| Mrinmoy Pal,; Luis Altamirano-Pacheco; Tamas Schauer; Maria-Elena Torres-Padilla | Reorganization of lamina-associated domains in early mouse embryos is regulated by RNA polymerase II activity | 2023 | Genes and Development | 10.1101/gad.350799.123 |
| Mach P.; Giorgetti L. | Integrative approaches to study enhancer–promoter communication | 2023 | Current Opinion in Genetics and Development | 10.1016/j.gde.2023.102052 |
| Hauth A.; Galupa R.; Servant N.; Villacorta L.; Hauschulz K.; van Bemmel J.G.; Loda A.; Heard E. | Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C | 2022 | Journal of Visualized Experiments | 10.3791/64166 |
| Aditya Sankar, Faizaan Mohammad, Arun Kumar Sundaramurthy, Hua Wang, Mads Lerdrup, Tulin Tatar & Kristian Helin | Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals | 2022 | Nature Genetics | 10.1038/s41588-022-01091-2 |
| Mas G.; Santoro F.; Blanco E.; Figueroa G.P.G.; Dily F.L.; Frigè G.; Vidal E.; Mugianesi F.; Ballaré C.; Gutierrez A.; Sparavier A.; Marti-Renom M.A.; Minucci S.; Di Croce L. | In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of Klf4 in suppressing early leukemic transformation | 2022 | Genes and Development | 10.1101/gad.349115.121 |
| Zuin J.; Roth G.; Zhan Y.; Cramard J.; Redolfi J.; Piskadlo E.; Mach P.; Kryzhanovska M.; Tihanyi G.; Kohler H.; Eder M.; Leemans C.; van Steensel B.; Meister P.; Smallwood S.; Giorgetti L. | Nonlinear control of transcription through enhancer–promoter interactions | 2022 | Nature | 10.1038/s41586-022-04570-y |
| Mach P.; Kos P.I.; Zhan Y.; Cramard J.; Gaudin S.; Tünnermann J.; Marchi E.; Eglinger J.; Zuin J.; Kryzhanovska M.; Smallwood S.; Gelman L.; Roth G.; Nora E.P.; Tiana G.; Giorgetti L. | Cohesin and CTCF control the dynamics of chromosome folding | 2022 | Nature Genetics | 10.1038/s41588-022-01232-7 |
| Molins-Pitarch, C. | Toolkit: Lab to Street. Tangible Science Framework – T-Sci | 2021 | Zenodo | 10.5281/zenodo.7642844 |
| Mrinmoy Pal; Jop Kind; Maria-Elena Torres-Padilla | DamID to map genome-protein interactions in preimplantation mouse embryos | 2021 | Methods in Molecular Biology | 10.1007/978-1-0716-0958-3_18 |
