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Browsing by Author "Capella Gutiérrez, Salvador Jesús, 1985-"

Browsing by Author "Capella Gutiérrez, Salvador Jesús, 1985-"

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  • A phylogenomics approach for selecting robust sets of phylogenetic markers
    Capella Gutiérrez, Salvador Jesús, 1985-; Kauff, Frank; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2014)
    Reconstructing the evolutionary relationships of species is a major goal in biology. Despite the increasing number of completely sequenced genomes, a large number of phylogenetic projects rely on targeted sequencing and ...
  • Analysis of multiple protein sequence alignments and phylogenetic trees in the context of phylogenomics studies
    Capella Gutiérrez, Salvador Jesús, 1985- (Universitat Pompeu Fabra, 2012-11-16)
    Phylogenomics is a biological discipline which can be understood as the intersection of the fields of genomics and evolution. Its main focuses are the analyses of genomes through the evolutionary lens and the understanding ...
  • Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization.
    Mariotti, Marco, 1984-; Santesmasses Ruiz, Didac, 1978-; Capella Gutiérrez, Salvador Jesús, 1985-; Mateo, Andrea; Arnan Ros, Carme; Johnson, Rory; D’Aniello, Salvatore; Yim, Sun Hee; Gladyshev, Vadim N.; Serras Rigalt, Florenci; Corominas Guiu, Montserrat; Gabaldón Estevan, Juan Antonio, 1973-; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press, 2015)
    Selenoproteins are proteins that incorporate selenocysteine (Sec), a nonstandard amino acid encoded by UGA, normally a stop codon. Sec synthesis requires the enzyme Selenophosphate synthetase (SPS or SelD), conserved in ...
  • Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
    Abascal, Federico; Corvelo, André; Cruz, Fernando; Villanueva Cañas, José Luis, 1984-; Vlasova, Anna; Marcet Houben, Marina; Prieto Barja, Pablo, 1986-; Quilez Oliete, Javier; Frias, Leonor; Ribeca, Paolo; Capella Gutiérrez, Salvador Jesús, 1985-; Câmara Ferreira, Francisco; Lowy Gallego, Ernesto; Cozzuto, Luca; Erb, Ionas; Rodríguez Ales, José Luis; Ruiz Orera, Jorge, 1988-; Reverter, Ferran; Derdak, Sophia; Blanc, Julie; Gut, Marta; Lorente-Galdós, Belén, 1981-; Gut, Ivo Glynne; Guigó Serra, Roderic; Gabaldón Estevan, Juan Antonio, 1973-; Godoy, José A. (BioMed Central, 2016)
    Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective ...
  • The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede strigamia maritima
    Chipman, Ariel D; Capella Gutiérrez, Salvador Jesús, 1985-; Gabaldón Estevan, Juan Antonio, 1973-; Guigó Serra, Roderic; Mariotti, Marco, 1984-; Richards, Stephan (Public Library of Science (PLoS), 2014)
    Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda ...
  • Gearing up to handle the mosaic nature of life in the quest for orthologs
    Forslund, Kristoffer; Pereira, Cecile; Capella Gutiérrez, Salvador Jesús, 1985-; Sousa da Silva, Alan; Altenhoff, Adrian M.; Huerta Cepas, Jaime; Muffato, Matthieu; Patricio, Mateus; Vandepoele, Klaas; Ebersberger, Ingo; Blake, Judith; Fernández Breis, Jesualdo Tomás; Quest for Orthologs consortium; Boeckmann, Brigitte; Gabaldón Estevan, Juan Antonio, 1973-; Sonnhammer, Erik; Dessimoz, Christophe; Lewis, Suzanna E. (Oxford University Press, 2018)
    The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We ...
  • Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes
    Vlasova, Anna; Capella Gutiérrez, Salvador Jesús, 1985-; Erb, Ionas; Cámara, Francisco; Prieto Barja, Pablo, 1986-; Kedra, Darek; González Navarrete, Irene, 1983-; Cozzuto, Luca; Gómez Garrido, Jèssica; Aguilar Morón, María Asunción; Andreu Somavilla, Núria; Zehnsdorf, Maik; Alioto, Tyler; Notredame, Cedric; Gabaldón Estevan, Juan Antonio, 1973-; Guigó Serra, Roderic (BioMed Central, 2016)
    Background: Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million ...
  • Genomic history of the origin and domestication of common bean unveils its closest sister species
    Rendón-Anaya, Martha; Montero-Vargas, Josaphat M.; Saburido-Álvarez, Soledad; Vlasova, Anna; Capella Gutiérrez, Salvador Jesús, 1985-; Ordaz-Ortiz, José Juan; Aguilar, O. Mario; Vianello-Brondani, Rosana P.; Santalla, Marta; Delaye, Luis; Gabaldón Estevan, Juan Antonio, 1973-; Gepts, Paul; Winkler, Robert; Guigó Serra, Roderic; Delgado-Salinas, Alfonso; Herrera-Estrella, Alfredo (BioMed Central, 2017)
    Background: Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding ...
  • High-throughput proteomics reveals the unicellular roots of animal phosphosignaling and cell differentiation
    Sebé-Pedrós, Arnau; Peña Paz, Marcia I.; Capella Gutiérrez, Salvador Jesús, 1985-; Antó Subirats, Meritxell; Gabaldón Estevan, Juan Antonio, 1973-; Ruiz Trillo, Iñaki; Sabidó Aguadé, Eduard, 1981- (Elsevier, 2016)
    Cell-specific regulation of protein levels and activity is essential for the distribution of functions among multiple cell types in animals. The finding that many genes involved in these regulatory processes have a premetazoan ...
  • LimTox: A web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes
    Cañada, Andrés; Capella Gutiérrez, Salvador Jesús, 1985-; Rabal, Obdulia; Oyarzábal, Julen; Valencia, Alfonso; Krallinger, Martin (Oxford University Press, 2017)
    A considerable effort has been devoted to retrieve systematically information for genes and proteins as well as relationships between them. Despite the importance of chemical compounds and drugs as a central bio-entity in ...
  • PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
    Huerta Cepas, Jaime; Capella Gutiérrez, Salvador Jesús, 1985-; Pryszcz, Leszek Piotr, 1985-; Marcet Houben, Marina; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2014)
    Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and ...
  • Standardized benchmarking in the quest for orthologs
    Altenhoff, Adrian M.; Capella Gutiérrez, Salvador Jesús, 1985-; Pryszcz, Leszek Piotr, 1985-; Gabaldón Estevan, Juan Antonio, 1973-; Quest for Orthologs consortium; Dessimoz, Christophe (Nature Publishing Group, 2016)
    Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for ...
  • Ten steps to get started in Genome Assembly and Annotation
    Dominguez Del Angel, Victoria; Hjerde, Erik; Sterck, Lieven; Capella Gutiérrez, Salvador Jesús, 1985-; Notredame, Cedric; Vinnere Pettersson, Olga; Amselem, Joëlle; Bouri, Laurent; Bocs, Stephanie; Klopp, Christophe; Gibrat, Jean-François; Vlasova, Anna; Leskosek, Brane L.; Soler, Lucile; Binzer-Panchai, Mahesh; Lantz, Henrik (F1000Research, 2018)
    As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, ...
  • The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)
    Dohm, Juliane C.; Minoche, André E.; Holtgräwe, Daniela; Capella Gutiérrez, Salvador Jesús, 1985-; Zakrzewski, Falk; Tafer, Hakim; Rupp, Oliver; Sörensen, Thomas Rosleff; Stracke, Ralf; Reinhardt, Richard; Goesmann, Alexander; Kraft, Thomas; Schulz, Britta; Stadler, Peter F.; Schmidt, Thomas; Gabaldón Estevan, Juan Antonio, 1973-; Lehrach, Hans; Weisshaar, Bernd; Himmelbauer, Heinz (Nature Publishing Group, 2014)
    Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to ...
  • The landscape of expression and alternative splicing variation across human traits
    García Pérez, Raquel, 1989-; Ramirez, Jose Miguel; Ripoll Cladellas, Aida; Chazarra-Gil, Ruben; Oliveros, Winona; Soldatkina, Oleksandra; Bosio, Mattia; Rognon, Paul Joris; Capella Gutiérrez, Salvador Jesús, 1985-; Calvo, Miquel (Calvo Llorca); Reverter, Ferran; Guigó Serra, Roderic; Aguet, François; Ferreira, Pedro G.; Ardlie, Kristin G.; Melé Messeguer, Marta, 1982- (Elsevier, 2022)
    Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as ...
  • Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation
    Zhao, Pengshan; Capella Gutiérrez, Salvador Jesús, 1985-; Shi, Yong; Zhao, Xin; Chen, Guoxiong; Gabaldón Estevan, Juan Antonio, 1973-; Ma, Xiao-Fei (BioMed Central, 2014)
    Background. Sand rice (Agriophyllum squarrosum) is an annual desert plant adapted to mobile sand dunes in arid and semi-arid regions of Central Asia. The sand rice seeds have excellent nutrition value and have been ...