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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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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Transcription factors: Bridge between cell signaling and gene regulation

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Paula Weidemüller, Maksim Kholmatov, Evangelia Petsalaki, Judith B. Zaugg

Proteomics – Published: 27 July 2021 https://doi.org/10.1002/pmic.202000034

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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

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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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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

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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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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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Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness

Tomas Pachano, Víctor Sánchez-Gaya, Thais Ealo, Maria Mariner-Faulí, Tore Bleckwehl, Helena G. Asenjo, Patricia Respuela, Sara Cruz-Molina, María Muñoz-San Martín, Endika Haro, Wilfred F. J. van IJcken, David Landeira & Alvaro Rada-Iglesias

Nature Genetics – Published: 28 June 2021 https://doi.org/10.1038/s41588-021-00888-x

 

 

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The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo

Giuliano Crispatzu, Rizwan Rehimi, Tomas Pachano, Tore Bleckwehl, Sara Cruz-Molina, Cally Xiao, Esther Mahabir, Hisham Bazzi & Alvaro Rada-Iglesias

Nature Communications – Published: 16 July 2021 https://doi.org/10.1038/s41467-021-24641-4

 

 

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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

 

 

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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

 

 

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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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NFnetFu: A novel workflow for microbiome data fusion

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VartikaBisht, Animesh Acharjee and Georgios V.Gkoutos

Computers in Biology and Medicine : Published: 8 June 2021, https://doi.org/10.1016/j.compbiomed.2021.104556 

 

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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.