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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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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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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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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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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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

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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

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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.