Browsing by Author "Irimia Martínez, Manuel"

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  • Wyatt, Christopher Douglas Robert, 1988-; Pernaute, Barbara; Gohr, André; Miret-Cuesta, Marta; Goyeneche, Lucia; Rovira, Quirze; Salzer, Marion C.; Boke, Elvan; Bogdanovic, Ozren; Bonnal, Sophie; Irimia Martínez, Manuel (American Association for the Advancement of Science (AAAS), 2022)
    Transition from maternal to embryonic transcriptional control is crucial for embryogenesis. However, alternative splicing regulation during this process remains understudied. Using transcriptomic data from human, mouse, ...
  • Angiolini, Francesca; Irimia Martínez, Manuel; Chigna, Claudia (eLife, 2019)
    The biological players involved in angiogenesis are only partially defined. Here, we report that endothelial cells (ECs) express a novel isoform of the cell-surface adhesion molecule L1CAM, termed L1-ΔTM. The splicing ...
  • Torres Méndez, Antonio; Bonnal, Sophie; Marquez, Yamile; Roth, Jonathan; Iglesias, Marta; Permanyer, Jon; Almudi, Isabel; O'Hanlon, Dave; Guitart, Tanit; Soller, Matthias; Gingras, Anne-Claude; Gebauer, Fátima; Rentzsch, Fabian; Blencowe, Benjamin J.; Valcárcel, J. (Juan); Irimia Martínez, Manuel (Nature Research, 2019)
    The mechanisms by which entire programmes of gene regulation emerged during evolution are poorly understood. Neuronal microexons represent the most conserved class of alternative splicing in vertebrates, and are critical ...
  • García-Moreno, Fernando; Anderton, Edward; Jankowska, Marta; Begbie, Jo; Encinas, Juan Manuel; Irimia Martínez, Manuel; Molnár, Zoltán (Elsevier, 2018)
    Several neuronal populations orchestrate neocortical development during mammalian embryogenesis. These include the glutamatergic subplate-, Cajal-Retzius-, and ventral pallium-derived populations, which coordinate cortical ...
  • García-Castro, Helena; Kenny, Nathan J.; Iglesias, Marta; Álvarez Campos, Patricia; Mason, Vincent; Elek, Anamaria; Schönauer, Anna; Sleight, Victoria A.; Neiro, Jakke; Aboobaker, Aziz; Permanyer, Jon; Irimia Martínez, Manuel; Sebé-Pedrós, Arnau; Solana, Jordi (BioMed Central, 2021)
    Single-cell sequencing technologies are revolutionizing biology, but they are limited by the need to dissociate live samples. Here, we present ACME (ACetic-MEthanol), a dissociation approach for single-cell transcriptomics ...
  • Giampietro, Costanza; Wyatt, Christopher Douglas Robert, 1988-; Irimia Martínez, Manuel; Ghigna, Claudia (Nature Publishing Group, 2015)
    Vascular lumen formation is a fundamental step during angiogenesis; yet, the molecular mechanisms underlying this process are poorly understood. Recent studies have shown that neural and vascular systems share common ...
  • Martín, Guiomar; Márquez, Yamile; Mantica, Federica; Duque, Paula; Irimia Martínez, Manuel (BioMed Central, 2021)
    Background: Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, ...
  • Marlétaz, Ferdinand; Wyatt, Christopher Douglas Robert, 1988-; Burguera, Demián; Marquez, Yamile; Irimia Martínez, Manuel (Nature Research, 2018)
    Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus ...
  • Gueroussov, Serge; Gonatopoulos-Pournatzis, Thomas; Irimia Martínez, Manuel; Raj, Bushra; Lin, Zhen-Yuan; Gingras, Anne-Claude; Blencowe, Benjamin J. (American Association for the Advancement of Science (AAAS), 2015)
    Alternative splicing (AS) generates extensive transcriptomic and proteomic complexity. However, the functions of species- and lineage-specific splice variants are largely unknown. Here we show that mammalian-specific ...
  • Tapial Rodríguez, Javier, 1990-; Ha, Kevin C. H.; Sterne-Weiler, Thimothy; Gohr, André; Braunschweig, Ulrich; Hermoso Pulido, Antonio; Quesnel-Vallières, Mathieu; Permanyer, Jon; Sodaei, Reza, 1988-; Marquez, Yamile; Cozzuto, Luca; Wang, Xinchen; Gómez-Velázquez, Melisa; Rayon, Teresa; Manzanares, Miguel; Ponomarenko, Julia; Blencowe, Benjamin J.; Irimia Martínez, Manuel (Cold Spring Harbor Laboratory Press (CSHL Press), 2017)
    Alternative splicing (AS) generates remarkable regulatory and proteomic complexity in metazoans. However, the functions of most AS events are not known, and programs of regulated splicing remain to be identified. To address ...
  • Touceda-Suárez, María; Kita, Elizabeth M.; Acemel, Rafael D.; Firbas, Panos N.; Magri, Marta S.; Naranjo, Silvia; Tena, Juan J.; Gómez Skarmeta, José Luis; Maeso, Ignacio; Irimia Martínez, Manuel (Oxford University Press (OUP), 2020)
    We investigated how the two rounds of whole-genome duplication that occurred at the base of the vertebrate lineage have impacted ancient microsyntenic associations involving developmental regulators (known as genomic ...
  • Nielsen, Anne F.; Bindereif, Albrecht; Bozzoni, Irene; Hanan, Mor; Hansen, Thomas B.; Irimia Martínez, Manuel; Kadener, Sebastian; Kristensen, Lasse S.; Legnini, Ivano; Morlando, Mariangela; Jarlstad Olesen, Morten T.; Pasterkamp, Ronald Jeroen; Preibisch, Stephan; Rajewsky, Nicolaus; Suenkel, Christin; Kjems, Jørgen (Nature Research, 2022)
    Circular RNAs (circRNAs) are formed in all domains of life and via different mechanisms. There has been an explosion in the number of circRNA papers in recent years; however, as a relatively young field, circRNA biology ...
  • de Mendoza, Alex; Suga, Hiroshi; Permanyer, Jon; Irimia Martínez, Manuel; Ruiz Trillo, Iñaki (eLife, 2015)
    Cell-type specification through differential genome regulation is a hallmark of complex multicellularity. However, it remains unclear how this process evolved during the transition from unicellular to multicellular organisms. ...
  • de Mendoza, Alex; Suga, Hiroshi; Permanyer, Jon; Irimia Martínez, Manuel; Ruíz Trillo, Iñaki (eLife, 2015)
    Cell-type specification through differential genome regulation is a hallmark of complex multicellularity. However, it remains unclear how this process evolved during the transition from unicellular to multicellular organisms. ...
  • Irimia Martínez, Manuel; Vellutini, Bruno C.; Marlétaz, Ferdinand; Cetrangolo, Viviana; Cvetesic, Nevena; Thiel, Daniel; Henriet, Simon; Grau Bové, Xavier; Carrillo-Baltodano, Allan M.; Gu, Wenjia; Kerbl, Alexandra; Marquez, Yamile; Bekkouche, Nicolas; Chourrout, Daniel; Gómez Skarmeta, José Luis; Lenhard, Boris; Worsaae, Katrine; Hejnol, Andreas (Nature Research, 2020)
    The causes and consequences of genome reduction in animals are unclear because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact ...
  • Solana, Jordi; Irimia Martínez, Manuel; Ayoub, Salah; Rodriguez Orejuela, Marta; Zywitza, Vera; Jens, Marvin; Tapial Rodríguez, Javier, 1990-; Ray, Debashish; Morris, Quaid; Hughes, Timothy R.; Blencowe, Benjamin J.; Rajewsky, Nicolaus (eLife, 2016)
    In contrast to transcriptional regulation, the function of alternative splicing (AS) in stem cells is poorly understood. In mammals, MBNL proteins negatively regulate an exon program specific of embryonic stem cells; ...
  • Hoijman, Esteban; Häkkinen, Hanna-Maria; Tolosa-Ramon, Queralt; Jiménez-Delgado, Senda; Wyatt, Christopher Douglas Robert, 1988-; Miret-Cuesta, Marta; Irimia Martínez, Manuel; Callan-Jones, Andrew; Wieser, Stefan; Ruprecht, Verena (Nature Research, 2021)
    Errors in early embryogenesis are a cause of sporadic cell death and developmental failure1,2. Phagocytic activity has a central role in scavenging apoptotic cells in differentiated tissues3-6. However, how apoptotic cells ...
  • Wucher, Valentin; Sodaei, Reza, 1988-; Amador, Raziel; Irimia Martínez, Manuel; Guigó Serra, Roderic (Public Library of Science (PLoS), 2023)
    Circadian and circannual cycles trigger physiological changes whose reflection on human transcriptomes remains largely uncharted. We used the time and season of death of 932 individuals from GTEx to jointly investigate ...
  • López Blanch, Laura (2021-05-14)
    Neural microexons are the most conserved type of alternative splicing, suggesting a strong functional relevance. Consistently, mutation of their master regulators leads to dramatic neurodevelopmental alterations and ...
  • Espeso Gil, Sergio, 1985-; Holik, Aliaksei Z.; Bonnin, Sarah; Jhanwar, Shalu, 1986-; Chandrasekaran, Sandhya; Pique Regi, Roger; Albaigès-Ràfols, Júlia; Maher, Michael; Permanyer, Jon; Irimia Martínez, Manuel; Friedländer, Marc R.; Pons Espinal, Meritxell, 1986-; Akbarian, Schahram; Dierssen, Mara; Maass, Philipp G.; Hor, Charlotte N.; Ossowski, Stephan (Frontiers, 2021)
    In early development, the environment triggers mnemonic epigenomic programs resulting in memory and learning experiences to confer cognitive phenotypes into adulthood. To uncover how environmental stimulation impacts the ...

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