Browsing by Author "Marquez, Yamile"

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  • A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis
    Zhang, Runxuan; Marquez, Yamile; Brown, John W. S. (BioMed Central, 2022)
    Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies ...
  • A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons
    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 ...
  • Amphioxus functional genomics and the origins of vertebrate gene regulation
    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 ...
  • An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms
    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 ...
  • AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana
    Zhang, Runxuan; Calixto, Cristiane P. G.; Tzioutziou, Nikoleta A.; James, Allan B.; Simpson, Craig G.; Guo, Wenbin; Marquez, Yamile; Kalyna, Maria; Patro, Rob; Eyras Jiménez, Eduardo; Barta, Andrea; Nimmo, Hugh G.; Brown, John W. S. (Wiley, 2015)
    RNA-sequencing (RNA-seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of transcript variants generated by alternative splicing (AS) remains a challenge. We have developed ...
  • Conservative route to genome compaction in a miniature annelid
    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 ...
  • Evolution of tissue-specific expression of ancestral genes across vertebrates and insects
    Mantica, Federica; Iñiguez, Luis P.; Marquez, Yamile; Permanyer, Jon; Torres Méndez, Antonio; Cruz, Josefa; Franch-Marro, Xavier; Burguera, Demián; Martin, David; Irimia Martínez, Manuel (Nature Research, 2024)
    Regulation of gene expression is arguably the main mechanism underlying the phenotypic diversity of tissues within and between species. Here we assembled an extensive transcriptomic dataset covering 8 tissues across 20 ...

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