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Browsing by Author "Gabaldón Estevan, Juan Antonio, 1973-"

Browsing by Author "Gabaldón Estevan, Juan Antonio, 1973-"

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  • Comparative genomics to unravel virulence mechanisms in fungal human pathogens
    Pryszcz, Leszek Piotr, 1985- (Universitat Pompeu Fabra, 2014-11-28)
    Las Candidas forman uno de los grupos con mayor n´umero de hongos pat´ogenos en humanos. La relaci ´on que tienen desde un punto de vista filogen´etico demuestra que la capacidad de infectar humanos ha surgido varias veces ...
  • Comparative transcriptomics of early dipteran development
    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. ...
  • Comparative transcriptomics of host-pathogen interactions and hybridization in Candida pathogens
    Hovhannisyan, Hrant, 1992- (Universitat Pompeu Fabra, 2020-12-15)
    Candida pathogenic yeasts represent a global healthcare problem. They comprise phylogenetically diverse species, including newly emerged pathogens. How human-Candida interactions vary across species, and what processes ...
  • Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina)
    Morales, Lucia; Noel, Benjamin; Porcel, Betina; Marcet Houben, Marina; Hullo, Marie-Françoise; Sacerdot, Christine; Tekaia, Fredj; Leh-Louis, Véronique; Despons, Laurence; Khanna, Varun; Aury, Jean-Marc; Barbe, Valérie; Coloux, Arnaud; Labadie, Karine; Pelletier, Eric; Souciet, Jean-Luc; Boekhout, Teun; Gabaldón Estevan, Juan Antonio, 1973-; Wincker, Patrick; Dujon, Bernard (Oxford University Press, 2013)
    The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present ...
  • The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.
    Kunze, Gotthard; Gabaldón Estevan, Juan Antonio, 1973-; Marcet Houben, Marina; Neuvéglise, Cécile (BioMed Central, 2014)
    Background: The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use ...
  • Contrasting genomic diversity in two closely related postharvest pathogens: penicillium digitatum and penicillium expansum
    Julca, Irene; Droby, Samir; Sela, Noa; Marcet Houben, Marina; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2015)
    Penicillium digitatum and Penicillium expansum are two closely related fungal plant pathogens causing green and blue mold in harvested fruit, respectively. The two species differ in their host specificity, being P. digitatum ...
  • Contrasting patterns of evolutionary diversification in the olfactory repertoires of reptile and bird genomes
    Vandewege, Michael W.; Mangum, Sarah F.; Gabaldón Estevan, Juan Antonio, 1973-; Castoe, Todd A.; Ray, David A.; Hoffmann, Federico G. (Oxford University Press, 2016)
    Olfactory receptors (ORs) are membrane proteins that mediate the detection of odorants in the environment, and are the largest vertebrate gene family. Comparative studies of mammalian genomes indicate that OR repertoires ...
  • CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies
    Hovhannisyan, Hrant, 1992-; Hafez, Ahmed; Llorens, Carlos, 1968-; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2020)
    MOTIVATION: Numerous sequencing studies, including transcriptomics of host-pathogen systems, sequencing of hybrid genomes, xenografts, mixed species systems, metagenomics and meta-transcriptomics, involve samples containing ...
  • Deep sequencing approaches to investigate the dynamics and evolution of interaction networks of Candida pathogens and the human host
    Thuer, Ernst, 1986- (Universitat Pompeu Fabra, 2017-09-22)
    This thesis describes the application of Next Generation Sequencing, especially RNA sequencing, on the investigation of the pathogenic yeast Candida parapsilosis. Pathogenic yeasts of the Candida clade are one of the most ...
  • Differential gene retention as/nan evolutionary mechanism to generate biodiversity and adaptation in yeasts
    Morel, Guillaume; Sterck, Lieven; Swennen, Dominique; Marcet Houben, Marina; Onesime, Djamila; Levasseur, Anthony; Jacques, Noémie; Mallet, Sandrine; Couloux, Arnaud; Labadie, Karine; Amselem, Joëlle; Beckerich, Jean-Marie; Henrissat, Bernard; van de Peer, Yves; Wincker, Patrick; Souciet, Jean-Luc; Gabaldón Estevan, Juan Antonio, 1973-; Tinsley, Colin R.; Casaregola, Serge (Nature Publishing Group, 2015)
    The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of ...
  • Discovery of EMRE in fungi resolves the true evolutionary history of the mitochondrial calcium uniporter
    Pittis, Alexandros, 1982-; Goh, Valerie; Cebrián Serrano, Alberto; Wettmarshausen, Jennifer; Perocchi, Fabiana; Gabaldón Estevan, Juan Antonio, 1973- (Nature Research, 2020)
    Calcium (Ca2+) influx into mitochondria occurs through a Ca2+-selective uniporter channel, which regulates essential cellular processes in eukaryotic organisms. Previous evolutionary analyses of its pore-forming subunits ...
  • Echinocandin-induced microevolution of Candida parapsilosis influences virulence and abiotic stress tolerance
    Papp, Csaba; Kocsis, Katica; Tóth, Renáta; Bodai, László; Willis, Jesse R.; Ksiezopolska, Ewa; Lozoya-Pérez, Nancy E.; Vágvölgyi, Csaba; Mora Montes, Hector; Gabaldón Estevan, Juan Antonio, 1973-; Nosanchuk, Joshua D.; Gácser, Attila (American Society for Microbiology, 2018)
    Candida species are a major cause of life-threatening bloodstream infections worldwide. Although Candida albicans is responsible for the vast majority of infections, the clinical relevance of other Candida species has also ...
  • eggNOG v4.0: nested orthology inference across 3686 organisms
    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 ...
  • Eicosanoid biosynthesis influences the virulence of Candida parapsilosis
    Chakraborty, Tanmoy; Thuer, Ernst, 1986-; Heijink, Marieke; Tóth, Renáta; Bodai, László; Vágvölgyi, Csaba; Giera, Martin; Gabaldón Estevan, Juan Antonio, 1973-; Gácser, Attila (Taylor & Francis, 2018)
    Lipid mediators, derived from arachidonic acid metabolism, play an important role in immune regulation. The functions of bioactive eicosanoids range from modulating cytokine signaling and inflammasome formation to ...
  • Eukaryotic transporters for hydroxyderivatives of benzoic acid
    Cillingová, Andrea; Zeman, Igor; Tóth, Renáta; Neboháčová, Martina; Dunčková, Ivana; Hölcová, Mária; Jakúbková, Michaela; Gérecová, Gabriela; Pryszcz, Leszek Piotr, 1985-; Tomáška, L'ubomír; Gabaldón Estevan, Juan Antonio, 1973-; Gácser, Attila; Nosek, Jozef (Nature Publishing Group, 2017)
    Several yeast species catabolize hydroxyderivatives of benzoic acid. However, the nature of carriers responsible for transport of these compounds across the plasma membrane is currently unknown. In this study, we analyzed ...
  • EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes
    Marcet Houben, Marina; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2020)
    MOTIVATION: The evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved ...
  • 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 ...
  • Evolutionary and functional patterns of shared gene neighbourhood in fungi
    Marcet Houben, Marina; Gabaldón Estevan, Juan Antonio, 1973- (Nature Research, 2019)
    Gene clusters comprise genomically co-localized and potentially co-regulated genes that tend to be conserved across species. In eukaryotes, multiple examples of metabolic gene clusters are known, particularly among fungi ...
  • Evolutionary emergence of drug resistance in Candida opportunistic pathogens
    Ksiezopolska, Ewa; Gabaldón Estevan, Juan Antonio, 1973- (MDPI, 2018)
    Fungal infections, such as candidiasis caused by Candida, pose a problem of growing medical concern. In developed countries, the incidence of Candida infections is increasing due to the higher survival of susceptible ...
  • Evolutionary genomics of yeast pathogens in the Saccharomycotina
    Gabaldón Estevan, Juan Antonio, 1973-; Naranjo Ortiz, Miguel Ángel, 1989-; Marcet Houben, Marina (Oxford University Press, 2016)
    Saccharomycotina comprises a diverse group of yeasts that includes numerous species of industrial or clinical relevance. Opportunistic pathogens within this clade are often assigned to the genus Candida but belong to ...