Understanding enhancer function to understand human disease

Salvatore Spicuglia, Alvaro Rada-Iglesias

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

 

 

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

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Juliette Malfait, Jing Wan, Salvatore Spicuglia

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

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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

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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

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

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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

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

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Wouter Saelens, Olga Pushkarev, Bart Deplancke

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

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

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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

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Context transcription factors establish cooperative environments and mediate enhancer communication

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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

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Chromatin modules and their implication in genomic organization and gene regulation

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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

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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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Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression

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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

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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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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

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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

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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

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

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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

The EMBO Journal – Published: 17 October 2023 https://doi.org/10.15252/embj.2023113527
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Chronic inflammation promotes cancer progression as a second hit

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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

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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)

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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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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

/by

Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression

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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

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Integration of the Microbiome, Metabolome and Transcriptomics Data Identified Novel Metabolic Pathway Regulation in Colorectal Cancer

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Vartika Bisht ,Katrina Nash ,Yuanwei Xu ,Prasoon Agarwal ,Sofie Bosch ,Georgios V. Gkoutos and Animesh Acharjee.

International Journal of molecular science, Received: 29 April 2021 / Revised: 25 May 2021 / Accepted: 26 May 2021 / Published: 28 May 2021, https://doi.org/10.3390/ijms22115763

 

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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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PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies

Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Pawel Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska & Dariusz Plewczynski

BMC Bioinformatics – Published: 17 February 2021 https://doi.org/10.1186/s12859-021-03984-1

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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

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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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Prediction of chromatin looping using deep hybrid learning (DHL)

Mateusz Chili?ski, Anup Kumar Halder, Dariusz Plewczynski

Quantitative Biology – Published: 01 June 2023 https://doi.org/10.15302/J-QB-022-0315

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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

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

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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

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The dynamic role of cohesin in maintaining human genome architecture

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Abhishek Agarwal, Sevastianos Korsak, Ashutosh Choudhury, Dariusz Plewczynski

BioEssays: Pattern Recognition and Machine Intelligence – Published: 21 August 2023 https://doi.org/10.1002/bies.202200240

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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

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The Identification of Chromatin Contact Domains (CCD) in Human Genomes from ChIA-PET Data Using Graph Methods

Rafa? Chabasi?ski, Kaustav Sengupta & Dariusz Plewczynski

Algorithms for Intelligent Systems- Published: 22 November 2023 https://doi.org/10.1007/978-981-99-1509-5_23

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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.