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Functions and evolutionary impact of transcriptomic novelties in the vertebrate brain

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Publications

Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism

Author(s): Neelroop N. Parikshak, Vivek Swarup, T. Grant Belgard, Manuel Irimia, Gokul Ramaswami, Michael J. Gandal, Christopher Hartl, Virpi Leppa, Luis de la Torre Ubieta, Jerry Huang, Jennifer K. Lowe, Benjamin J. Blencowe, Steve Horvath, Daniel H. Geschwind
Published in: Nature, Issue 540/7633, 2016, Page(s) 423-427, ISSN 0028-0836
DOI: 10.1038/nature20612

Nodal–Activin pathway is a conserved neural induction signal in chordates

Author(s): Yann Le Petillon, Guillaume Luxardi, Pierluigi Scerbo, Marie Cibois, Anthony Leon, Lucie Subirana, Manuel Irimia, Laurent Kodjabachian, Hector Escriva, Stephanie Bertrand
Published in: Nature Ecology & Evolution, Issue 1/8, 2017, Page(s) 1192-1200, ISSN 2397-334X
DOI: 10.1038/s41559-017-0226-3

Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders

Author(s): Mathieu Quesnel-Vallières, Zahra Dargaei, Manuel Irimia, Thomas Gonatopoulos-Pournatzis, Joanna Y. Ip, Mingkun Wu, Timothy Sterne-Weiler, Shinichi Nakagawa, Melanie A. Woodin, Benjamin J. Blencowe, Sabine P. Cordes
Published in: Molecular Cell, Issue 64/6, 2016, Page(s) 1023-1034, ISSN 1097-2765
DOI: 10.1016/j.molcel.2016.11.033

Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes

Author(s): Demian Burguera, Yamile Marquez, Claudia Racioppi, Jon Permanyer, Antonio Torres-Méndez, Rosaria Esposito, Beatriz Albuixech-Crespo, Lucía Fanlo, Ylenia D’Agostino, Andre Gohr, Enrique Navas-Perez, Ana Riesgo, Claudia Cuomo, Giovanna Benvenuto, Lionel A. Christiaen, Elisa Martí, Salvatore D’Aniello, Antonietta Spagnuolo, Filomena Ristoratore, Maria Ina Arnone, Jordi Garcia-Fernàndez, Manue
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
DOI: 10.1038/s41467-017-01961-y

Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain

Author(s): Beatriz Albuixech-Crespo, Laura López-Blanch, Demian Burguera, Ignacio Maeso, Luisa Sánchez-Arrones, Juan Antonio Moreno-Bravo, Ildiko Somorjai, Juan Pascual-Anaya, Eduardo Puelles, Paola Bovolenta, Jordi Garcia-Fernàndez, Luis Puelles, Manuel Irimia, José Luis Ferran
Published in: PLOS Biology, Issue 15/4, 2017, Page(s) e2001573, ISSN 1545-7885
DOI: 10.1371/journal.pbio.2001573

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

Author(s): Javier Tapial, Kevin C.H. Ha, Timothy Sterne-Weiler, André Gohr, Ulrich Braunschweig, Antonio Hermoso-Pulido, Mathieu Quesnel-Vallières, Jon Permanyer, Reza Sodaei, Yamile Marquez, Luca Cozzuto, Xinchen Wang, Melisa Gómez-Velázquez, Teresa Rayon, Miguel Manzanares, Julia Ponomarenko, Benjamin J. Blencowe, Manuel Irimia
Published in: Genome Research, Issue 27/10, 2017, Page(s) 1759-1768, ISSN 1088-9051
DOI: 10.1101/gr.220962.117

Amphioxus functional genomics and the origins of vertebrate gene regulation

Author(s): Ferdinand Marlétaz, Panos N. Firbas, Ignacio Maeso, Juan J. Tena, Ozren Bogdanovic, Malcolm Perry, Christopher D. R. Wyatt, Elisa de la Calle-Mustienes, Stephanie Bertrand, Demian Burguera, Rafael D. Acemel, Simon J. van Heeringen, Silvia Naranjo, Carlos Herrera-Ubeda, Ksenia Skvortsova, Sandra Jimenez-Gancedo, Daniel Aldea, Yamile Marquez, Lorena Buono, Iryna Kozmikova, Jon Permanyer, Alexandra
Published in: Nature, Issue 564/7734, 2018, Page(s) 64-70, ISSN 0028-0836
DOI: 10.1038/s41586-018-0734-6

RES complex is associated with intron definition and required for zebrafish early embryogenesis

Author(s): Juan Pablo Fernandez, Miguel Angel Moreno-Mateos, Andre Gohr, Liyun Miao, Shun Hang Chan, Manuel Irimia, Antonio J. Giraldez
Published in: PLOS Genetics, Issue 14/7, 2018, Page(s) e1007473, ISSN 1553-7404
DOI: 10.1371/journal.pgen.1007473

A novel L1CAM isoform with angiogenic activity generated by NOVA2-mediated alternative splicing

Author(s): Francesca Angiolini, Elisa Belloni, Marco Giordano, Matteo Campioni, Federico Forneris, Maria Paola Paronetto, Michela Lupia, Chiara Brandas, Davide Pradella, Anna Di Matteo, Costanza Giampietro, Giovanna Jodice, Chiara Luise, Giovanni Bertalot, Stefano Freddi, Matteo Malinverno, Manuel Irimia, Jon D Moulton, James Summerton, Antonella Chiapparino, Carmen Ghilardi, Raffaella Giavazzi, Daniel Nyqvi
Published in: eLife, Issue 8, 2019, ISSN 2050-084X
DOI: 10.7554/elife.44305

A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons

Author(s): Antonio Torres-Méndez, Sophie Bonnal, Yamile Marquez, Jonathan Roth, Marta Iglesias, Jon Permanyer, Isabel Almudí, Dave O’Hanlon, Tanit Guitart, Matthias Soller, Anne-Claude Gingras, Fátima Gebauer, Fabian Rentzsch, Benjamin J. Blencowe, Juan Valcárcel, Manuel Irimia
Published in: Nature Ecology & Evolution, Issue 3/4, 2019, Page(s) 691-701, ISSN 2397-334X
DOI: 10.1038/s41559-019-0813-6

Autism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing

Author(s): Alberto Parras, Héctor Anta, María Santos-Galindo, Vivek Swarup, Ainara Elorza, José L. Nieto-González, Sara Picó, Ivó H. Hernández, Juan I. Díaz-Hernández, Eulàlia Belloc, Annie Rodolosse, Neelroop N. Parikshak, Olga Peñagarikano, Rafael Fernández-Chacón, Manuel Irimia, Pilar Navarro, Daniel H. Geschwind, Raúl Méndez, José J. Lucas
Published in: Nature, Issue 560/7719, 2018, Page(s) 441-446, ISSN 0028-0836
DOI: 10.1038/s41586-018-0423-5

Srrm234, but not canonical SR and hnRNP proteins drive inclusion of Dscam exon 9 variable exons

Author(s): Pinar Ustaoglu, Irmgard U Haussmann, Hongzhi Liao, Antonio Torres-Mendez, Roland Arnold, Manuel Irimia, Matthias Soller
Published in: RNA, 2019, Page(s) rna.071316.119, ISSN 1355-8382
DOI: 10.1261/rna.071316.119

Matt : Unix tools for alternative splicing analysis

Author(s): André Gohr, Manuel Irimia
Published in: Bioinformatics, Issue 35/1, 2018, Page(s) 130-132, ISSN 1367-4803
DOI: 10.1093/bioinformatics/bty606

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing

Author(s): Lorea Blazquez, Warren Emmett, Rupert Faraway, Jose Mario Bello Pineda, Simon Bajew, Andre Gohr, Nejc Haberman, Christopher R. Sibley, Robert K. Bradley, Manuel Irimia, Jernej Ule
Published in: Molecular Cell, Issue 72/3, 2018, Page(s) 496-509.e9, ISSN 1097-2765
DOI: 10.1016/j.molcel.2018.09.033