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

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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

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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

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The role of rare enhancer variants in bicuspid aortic valve pathology

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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

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Targeted Chromosome Conformation Capture (HiCap)

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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

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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

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

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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

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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

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The role of rare enhancer variants in bicuspid aortic valve pathology

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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

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Interplay between regulatory elements and chromatin topology in cellular lineage determination

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Vallari Shukla, Anna Cetnarowska, Mette Hyldahl, Susanne Mandrup

Trends in Genetcs – Published: 10, October 2022 https://doi.org/10.1016/j.tig.2022.05.011

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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

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Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy

Zofia Parteka-Tojek, Jacqueline Jufen Zhu, Byoungkoo Lee, Karolina Jodkowska, Ping Wang, Jesse Aaron, Teng-Leong Chew, Krzysztof Banecki, Dariusz Plewczynski & Yijun Ruan

Scientific Reports- Published: 20 December 2022 https://doi.org/10.1038/s41598-022-12568-9

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MultiNet: A Diffusion-Based Approach to Assign Directionality in Protein Interactions Using a Consensus of Eight Protein Interaction Datasets

Kaustav Sengupta, Anna Gambin, Subhadip Basu & 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_2

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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

 

 

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Multi-scale phase separation by explosive percolation with single-chromatin loop resolution

Kaustav Sengupta, Micha? Denkiewicz, Mateusz Chili?ski, Teresa Szczepi?ska, Ayatullah Faruk Mollah, Sevastianos Korsak, Raissa D’Souza, Yijun Ruan, Dariusz Plewczynski

Computational and Structural Biotechnology Journal – Published: 2022 https://doi.org/10.1016/j.csbj.2022.06.063

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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

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Protocol to study sufficiency of cis-regulatory elements in mouse embryonic stem cells using a CRISPR-mediated knockin approach

Tomas Pachano, Alvaro Rada-Iglesias

STAR Protocols – Published: 16 September 2022 https://doi.org/10.1016/j.xpro.2022.101492

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

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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

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Current challenges in understanding the role of enhancers in disease

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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

 

 

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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

 

 

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Nicotinic Acetylcholine Receptors Expressed by Striatal Interneurons Inhibit Striatal Activity and Control Striatal-Dependent Behaviors

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Alice Abbondanza, Irina Ribeiro Bas, Martin Modrak, Martin Capek, Jessica Minich, Alexandra Tyshkevich, Shahed Naser, Revan Rangotis, Pavel Houdek, Alena Sumova, Sylvie Dumas, Veronique Bernard and Helena Janickova.

Journal of Neuroscience : 30 March 2022, https://doi.org/10.1523/JNEUROSCI.1627-21.2022

 

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Marie CurieThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 860002. The information contained in this website reflects only the authors’ view. REA and EC are not responsible for any use that may be made of this information.