Browsing by Author "Huerta Cepas, Jaime"

Sort by: Order: Results:

  • Glover, Natasha; Dessimoz, Christophe; Ebersberger, Ingo; Forslund, Sofia K.; Gabaldón Estevan, Juan Antonio, 1973-; Huerta Cepas, Jaime; Martin, Maria-Jesus; Muffato, Matthieu; Patricio, Mateus; Pereira, Cecile; Sousa da Silva, Alan; Wang, Yan-Dong; Sonnhammer, Erik; Thomas, Paul D. (Oxford University Press, 2019)
    Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play ...
  • Baa-Puyoulet, Patrice; Parisot, Nicolas; Febvay, Gérard; Huerta Cepas, Jaime; Vellozo, Augusto F.; Gabaldón Estevan, Juan Antonio, 1973-; Calevro, Federica; Charles, Hubert; Colella, Stefano (Oxford University Press, 2016)
    Arthropods interact with humans at different levels with highly beneficial roles (e.g. as pollinators), as well as with a negative impact for example as vectors of human or animal diseases, or as agricultural pests. Several ...
  • Jiménez Guri, Eva; Huerta Cepas, Jaime; Cozzuto, Luca; Wotton, Karl R.; Kang, Hui; Himmelbauer, Heinz; Roma, Guglielmo; Gabaldón Estevan, Juan Antonio, 1973-; Jaeger, Johannes, 1973- (BioMed Central, 2013)
    BACKGROUND: Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. ...
  • Powell, Sean; Forslund, Kristoffer; Szklarczyk, Damian; Trachana, Kalliopi; Roth, Alexander; Huerta Cepas, Jaime; Gabaldón Estevan, Juan Antonio, 1973-; Rattei, Thomas; Creevey, Chris; Kuhn, Michael; Jensen, Lars J.; Mering, Christian von; Bork, Peer (Oxford University Press, 2014)
    With the increasing availability of various 'omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available ...
  • Huerta Cepas, Jaime; Serra, François; Bork, Peer (Oxford University Press, 2016)
    The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, ...
  • 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 ...
  • Pryszcz, Leszek Piotr, 1985-; Huerta Cepas, Jaime; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2011)
    Reliable prediction of orthology is central to comparative genomics. Approaches based on phylogenetic analyses closely resemble the original definition of orthology and paralogy and are known to be highly accurate. However, ...
  • 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 ...
  • Boeckmann, Brigitte; Marcet Houben, Marina; Rees, Jonathan A.; Forslund, Kristoffer; Huerta Cepas, Jaime; Muffato, Matthieu; Yilmaz, Pelin; Xenarios, Ioannis; Bork, Peer; Lewis, Suzanna E.; Gabaldón Estevan, Juan Antonio, 1973-; Quest for Orthologs Species Tree Working Group (Oxford University Press, 2015)
    Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between ...