PUBLICATIONS

Epromoters are new players in the regulatory landscape with potential pleiotropic roles

Juliette Malfait, Jing Wan, Salvatore Spicuglia

BioEssays – Published: 28 May 2023 https://doi.org/10.1002/bies.202300012

3D-GNOME 3.0: a three-dimensional genome modelling engine for analysing changes of promoter-enhancer contacts in the human genome

Michal Wlasnowolski, Michal Kadlof, Kaustav Sengupta, Dariusz Plewczynski

Nucleic Acids Research – Published: 5 July 2023 https://doi.org/10.1093/nar/gkad354

Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression

Artemy Zhigulev, Zandra Norberg, Julie Cordier, Rapolas Spalinskas, Hassan Bassereh, Niclas Björn, Sailendra Pradhananga, Henrik Gréen, Pelin Sahlén

Life Science Alliance – Published: 16 January 2024 DOI: 10.26508/lsa.202302244

The role of rare enhancer variants in bicuspid aortic valve pathology

A. Zhigulev, K. Lång, S. Pradhananga, H. Björck, P. Eriksson, P. Sahlén

Atherosclerosis – Published: August 2022 https://doi.org/10.1016/j.atherosclerosis.2022.06.194

Targeted Chromosome Conformation Capture (HiCap)

Artemy Zhigulev & Pelin Sahlén

Spatial Genome Organization: Methods and Protocols – Published: 23 July 2022 https://doi.org/10.1007/978-1-0716-2497-5_5

Chronic inflammation decreases HSC fitness by activating the druggable Jak/Stat3 signaling pathway

Srdjan Grusanovic, Petr Danek, Maria Kuzmina, Miroslava K Adamcova, Monika Burocziova, Romana Mikyskova, Karolina Vanickova, Sladjana Kosanovic, Jana Pokorna, Milan Reinis, Tomas Brdicka, and Meritxell Alberich?Jorda

EMBO Reports – Published: 7 November 2022 https://doi.org/10.15252/embr.202254729

Chronic inflammation promotes cancer progression as a second hit

Monika Burocziova, Srdjan Grusanovic, Karolina Vanickova, Sladjana Kosanovic, Meritxell Alberich-Jorda

Experimental Hematology – Published: September 12, 2023 https://doi.org/10.1016/j.exphem.2023.09.002

Hematopoietic stem cells undergo a lymphoid to myeloid switch in early stages of emergency granulopoiesis

Karolina Vanickova, Mirko Milosevic, Irina Ribeiro Bas, Monika Burocziova, Asumi Yokota, Petr Danek, Srdjan Grusanovic, Mateusz Chili?ski, Dariusz Plewczynski, Jakub Rohlena, Hideyo Hirai, Katerina Rohlenova, and Meritxell Alberich?Jorda

Pancreatic microexons regulate islet function and glucose homeostasis

Jonàs Juan-Mateu, Simon Bajew, Marta Miret-Cuesta, Luis P. Íñiguez, Amaya Lopez-Pascual, Sophie Bonnal, Goutham Atla, Sílvia Bonàs-Guarch, Jorge Ferrer, Juan Valcárcel & Manuel Irimia

Nature Metabolism – Published: 09 February 2023 https://doi.org/10.1038/s42255-022-00734-2

Regulatory de novo mutations underlying intellectual disability

Matias G De Vas, Fanny Boulet, Shweta S Joshi, Myles G Garstang, Tahir N Khan, Goutham Atla, David Parry, David Moore, Inês Cebola, Shuchen Zhang, Wei Cui, Anne K Lampe, Wayne W Lam; Genomics England Research Consortium; Jorge Ferrer, Madapura M Pradeepa, Santosh S Atanur

Life Sci Alliance – Published: 28 February 2023 DOI: 10.26508/lsa.202201843

Matters arising: Insufficient evidence that pancreatic ? cells are derived from adult ductal Neurog3-expressing progenitors

Judith Magenheim, Miguel Angel Maestro, Nadav Sharon, Pedro L Herrera, L Charles Murtaugh, Janel Kopp, Maike Sander, Guoqiang Gu, Douglas A Melton, Jorge Ferrer, Yuval Dor

Cell Stem Cell – Published: 06 April 2023  DOI: 10.1016/j.stem.2023.03.003

Concurrent Activation of Kras and Canonical Wnt Signaling Induces Premalignant Lesions That Progress to Extrahepatic Biliary Cancer in Mice

Munemasa Nagao, Akihisa Fukuda, Mayuki Omatsu, Mio Namikawa, Makoto Sono, Yuichi Fukunaga, Tomonori Masuda, Osamu Araki, Takaaki Yoshikawa, Satoshi Ogawa, Kenji Masuo, Norihiro Goto, Yukiko Hiramatsu, Yu Muta, Motoyuki Tsuda, Takahisa Maruno, Yuki Nakanishi, Makoto Mark Taketo, Jorge Ferrer, Tatsuaki Tsuruyama, Yasuni Nakanuma, Kojiro Taura, Shinji Uemoto, Hiroshi Seno

Cancer Res – Published: 3 May 2022  DOI: 10.1158/0008-5472.CAN-21-2176

Targeted Chromosome Conformation Capture (HiCap)

Artemy Zhigulev & Pelin Sahlén

Spatial Genome Organization: Methods and Protocols – Published: 23 July 2022 https://doi.org/10.1007/978-1-0716-2497-5_5

The role of rare enhancer variants in bicuspid aortic valve pathology

A. Zhigulev, K. Lång, S. Pradhananga, H. Björck, P. Eriksson, P. Sahlén

Atherosclerosis – Published: August 2022 https://doi.org/10.1016/j.atherosclerosis.2022.06.194

A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation

Gerard Llimos, Vincent Gardeux, Ute Koch, Judith F. Kribelbauer, Antonina Hafner, Daniel Alpern, Joern Pezoldt, Maria Litovchenko, Julie Russeil, Riccardo Dainese, Riccardo Moia, Abdurraouf Mokhtar Mahmoud, Davide Rossi, Gianluca Gaidano, Christoph Plass, Pavlo Lutsik, Clarissa Gerhauser, Sebastian M. Waszak, Alistair Boettiger, Freddy Radtke & Bart Deplancke

Nature Communications – Published: 19 April 2022 https://doi.org/10.1038/s41467-022-29625-6

Chromatin modules and their implication in genomic organization and gene regulation

Guido van Mierlo, Olga Pushkarev, Judith F. Kribelbauer, Bart Deplancke

Trends in Genetics – Published: February 2023 https://doi.org/10.1016/j.tig.2022.11.003

Context transcription factors establish cooperative environments and mediate enhancer communication

Judith F. Kribelbauer, Olga Pushkarev, Vincent Gardeux, Julie Russeil, Guido van Mierlo, Bart Deplancke

BioRxiv – Published: May 05, 2023 https://doi.org/10.1101/2023.05.05.539543

Non-coding variants impact cis-regulatory coordination in a cell type-specific manner

Olga Pushkarev, Guido van Mierlo, Judith F. Kribelbauer, Wouter Saelens, Vincent Gardeux, Bart Deplancke

bioRxiv – Published: October 11, 2023 https://doi.org/10.1101/2023.10.11.561870

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

Wouter Saelens, Olga Pushkarev, Bart Deplancke

bioRxiv – Published: July 25, 2023 https://doi.org/10.1101/2023.07.21.549899

GRaNIE and GRaNPA: inference and evaluation of enhancer?mediated gene regulatory networks

Aryan Kamal, Christian Arnold, Annique Claringbould, Rim Moussa, Nila H Servaas, Maksim Kholmatov, Neha Daga, Daria Nogina, Sophia Mueller?Dott, Armando Reyes?Palomares, Giovanni Palla, Olga Sigalova, Daria Bunina, Caroline Pabst, and Judith B Zaugg

Molecular Systems Biology – Published: 19 April 2023 https://doi.org/10.15252/msb.202311627

CDK7/12/13 inhibition targets an oscillating leukemia stem cell network and synergizes with venetoclax in acute myeloid leukemia

Lixiazi He, Christian Arnold, Judith Thoma, Christian Rohde, Maksim Kholmatov, Swati Garg, Cheng?Chih Hsiao, Linda Viol, Kaiqing Zhang, Rui Sun, Christina Schmidt, Maike Janssen, Tara MacRae, Karin Huber, Christian Thiede, Josée Hébert, Guy Sauvageau, Julia Spratte, Herbert Fluhr, Gabriela Aust, Carsten Müller?Tidow, Christof Niehrs, Gislene Pereira, Jörg Hamann, Motomu Tanaka, Judith B Zaugg and Caroline Pabst

EMBO Mol Med – Published: 7 March 2022 https://doi.org/10.15252/emmm.202114990

Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription

Marta Russo, Viviana Piccolo, Danilo Polizzese, Elena Prosperini, Carolina Borriero, Sara Polletti, Fabio Bedin, Mattia Marenda, Davide Michieletto, Gaurav Madappa Mandana, Simona Rodighiero, Alessandro Cuomo and Gioacchino Natoli

Genes and Development – Published: November 29, 2023 http://www.genesdev.org/cgi/doi/10.1101/gad.351057.123

Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide

Marta Russo, Francesco Gualdrini, Veronica Vallelonga, Elena Prosperini, Roberta Noberini, Silvia Pedretti, Carolina Borriero, Pierluigi Di Chiaro, Sara Polletti, Gabriele Imperato, Mattia Marenda, Chiara Ghirardi, Fabio Bedin, Alessandro Cuomo, Simona Rodighiero, Tiziana Bonaldi, Nico Mitro, Serena Ghisletti, Gioacchino Natoli

Molecular Cell – Published: 18 January 2024 https://doi.org/10.1016/j.molcel.2023.12.033

Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression

Artemy Zhigulev, Zandra Norberg, Julie Cordier, Rapolas Spalinskas, Hassan Bassereh, Niclas Björn, Sailendra Pradhananga, Henrik Gréen, Pelin Sahlén

Life Science Alliance – Published: 16 January 2024 DOI: 10.26508/lsa.202302244

A tool to predict the pathological effects of human structural variants

Víctor Sánchez-Gaya, Alvaro Rada-Iglesias

Nucleic Acids Research – Published: 22 May 2023 https://doi.org/10.1093/nar/gkad225

Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

Niels J. Rinzema, Konstantinos Sofiadis, Sjoerd J. D. Tjalsma, Marjon J. A. M. Verstegen, Yuva Oz, Christian Valdes-Quezada, Anna-Karina Felder, Teodora Filipovska, Stefan van der Elst, Zaria de Andrade dos Ramos, Ruiqi Han, Peter H. L. Krijger & Wouter de Laat

Nature Structural & Molecular Biology – Published: 16 June 2022 https://doi.org/10.1038/s41594-022-00787-7

ccLoopER: Deep Prediction of CTCF and cohesin Mediated Chromatin looping Using DNA Transformer Model

Anup Kumar Halder, Abhishek Agarwal, Sevastianos Korsak, Karolina Jodkowska & Dariusz Plewczynski

PReMI 2023: Pattern Recognition and Machine Intelligence – Published: 04 December 2023  https://doi.org/10.1007/978-3-031-45170-6_91

Consensus-Based Identification and Comparative Analysis of Structural Variants and Their Influence on 3D Genome Structure Using Long- and Short-Read Sequencing Technologies in Polish Families

Mateusz Chili?ski, Sachin Gadakh, Kaustav Sengupta, Karolina Jodkowska, Natalia Zawrotna, Jan Gawor, Michal Pietal & Dariusz Plewczynski

Proceedings of International Conference on Frontiers in Computing and Systems – Published: 28 June 2022 https://doi.org/10.1007/978-981-19-0105-8_5

ConsensuSV—from the whole-genome sequencing data to the complete variant list

Mateusz Chili?ski, Dariusz Plewczynski

Bioinformatics- Published: 15 December 2022 https://doi.org/10.1093/bioinformatics/btac709

cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling

Michal Wlasnowolski, Pawel Grabowski, Damian Roszczyk, Krzysztof Kaczmarski, Dariusz Plewczynski

Bioinformatics – Published: 10 October 2023 https://doi.org/10.1093/bioinformatics/btad588

Current challenges in understanding the role of enhancers in disease

Judith Barbara Zaugg, Pelin Sahlén, Robin Andersson, Meritxell Alberich-Jorda, Wouter de Laat, Bart Deplancke, Jorge Ferrer, Susanne Mandrup, Gioacchino Natoli, Dariusz Plewczynski, Alvaro Rada-Iglesias & Salvatore Spicuglia

Nature Structural & Molecular Biology – Published: 08 December 2022  https://doi.org/10.1038/s41594-022-00896-3

Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions

Mateusz Chili?ski, Jakub Lipi?ski, Abhishek Agarwal, Yijun Ruan & Dariusz Plewczynski

Scientific Report – Published: 20 July 2023 https://doi.org/10.1038/s41598-023-38865-5

Enhancer-associated H3K4 methylation safeguards in vitro germline competence

Tore Bleckwehl, Giuliano Crispatzu, Kaitlin Schaaf, Patricia Respuela, Michaela Bartusel, Laura Benson, Stephen J. Clark, Kristel M. Dorighi, Antonio Barral, Magdalena Laugsch, Wilfred F. J. van IJcken, Miguel Manzanares, Joanna Wysocka, Wolf Reik & Álvaro Rada-Iglesias

Nature Communications – Published: 01 October 2021 https://doi.org/10.5281/zenodo.5507612

Enhancer-gene specificity in development and disease

Tomás Pachano, Endika Haro, Alvaro Rada-Iglesias

Development – Published: 10 June 2022 https://doi.org/10.1242/dev.186536

Understanding enhancer function to understand human disease

Salvatore Spicuglia, Alvaro Rada-Iglesias

BioEssays – Published: 29 August 2023 https://doi.org/10.1002/bies.202300149

Epromoters function as a hub to recruit key transcription factors required for the inflammatory response

David Santiago-Algarra, Charbel Souaid, Himanshu Singh, Lan T. M. Dao, Saadat Hussain, Alejandra Medina-Rivera, Lucia Ramirez-Navarro, Jaime A. Castro-Mondragon, Nori Sadouni, Guillaume Charbonnier & Salvatore Spicuglia

Nature Communications – Published: 18 November 2021 https://doi.org/10.5281/zenodo.5507612

From DNA human sequence to the chromatin higher order organisation and its biological meaning: Using biomolecular interaction networks to understand the influence of structural variation on spatial genome organisation and its functional effect

Mateusz Chili?ski, Kaustav Sengupta, Dariusz Plewczynski

Seminars in Cell & Developmental Biology – Published: January 2022 https://doi.org/10.1016/j.semcdb.2021.08.007

Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows

Teresa Szczepi?ska, Ayatullah Faruk Mollah, and Dariusz Plewczynski

International Journal of Molecular Sciences – Published: 27 October 2021 https://doi.org/10.3390/ijms222111591

Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression

Erica S.M. Vos, Christian Valdes-Quezada, Yike Huang, Esther C.H. Uijttewaal, Peter H.L. Krijger, Wouter de Laat

Molecular Cell – Published: 30 June 2021 https://doi.org/10.1016/j.molcel.2021.06.008

Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells

Jesper G. S. Madsen, Maria S. Madsen, Alexander Rauch, Sofie Traynor, Elvira L. Van Hauwaert, Anders K. Haakonsson, Biola M. Javierre, Mette Hyldahl, Peter Fraser & Susanne Mandrup

Nature Genetics – Published: 05 October 2020 https://doi.org/10.1038/s41588-020-0709-z