Browsing by Author "Alioto, Tyler"

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  • Kuderna, Lukas F.K.; Laayouni, Hafid, 1968-; García Pérez, Raquel; Povolotskaya, Inna, 1986-; Serres Armero, Aitor; Gómez Garrido, Jèssica; Alioto, Tyler; Navarro i Cuartiellas, Arcadi, 1969-; Bertranpetit, Jaume, 1952-; Marquès i Bonet, Tomàs, 1975- (Oxford University Press, 2017)
    The chimpanzee is arguably the most important species for the study of human origins. A key resource for these studies is a high-quality reference genome assembly; however, as with most mammalian genomes, the current ...
  • Mosca, Elena; Cruz, Fernando; Gómez-Garrido, Jèssica; Gut, Marta; Alioto, Tyler; Neale, David D. (Genetics Society of America, 2019)
    Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. ...
  • Alioto, Tyler; Picardi, Ernesto; Guigó Serra, Roderic; Pesole, Graziano (Hindawi, 2013)
    New genomes are being sequenced at an increasingly rapid rate, far outpacing the rate at which manual gene annotation can be performed. Automated genome annotation is thus necessitated by this growth in genome projects; ...
  • Liedtke, H. Christoph; Gómez Garrido, Jèssica; Esteve-Codina, Anna; Gut, Marta; Alioto, Tyler; Gomez-Mestre, Ivan (Genetics Society of America, 2019)
    Amphibians are highly vulnerable and diverse vertebrates for which we still have modest genomic resources. Amphibian larvae are key components of continental wetlands, where they have strong influences on energy fluxes, ...
  • 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 ...
  • Cruz, Fernando; Julca, Irene; Gómez Garrido, Jèssica; Loska, Damian; Marcet Houben, Marina; Cano, Emilio; Galán Sicilia, Beatriz; Frias, Leonor; Ribeca, Paolo; Derdak, Sophia; Gut, Marta; Sánchez Fernández, Manuel; García, Jose Luis; Gut, Ivo Glynne; Vargas Gómez, Pablo; Alioto, Tyler; Gabaldón Estevan, Juan Antonio, 1973- (BioMed Central, 2016)
    Background: The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive ...
  • Almudí, Isabel; Wyatt, Christopher Douglas Robert, 1988-; Cruz, Fernando; Gómez-Garrido, Jèssica; Gut, Marta; Alioto, Tyler; Irimia, Manuel; Casares, Fernando (Nature Research, 2020)
    The evolution of winged insects revolutionized terrestrial ecosystems and led to the largest animal radiation on Earth. However, we still have an incomplete picture of the genomic changes that underlay this diversification. ...
  • Julca, Irene; Marcet Houben, Marina; Cruz, Fernando; Gómez Garrido, Jèssica; Gaut, Brandon S.; Díez, Concepción M.; Gut, Ivo Glynne; Alioto, Tyler; Vargas Gómez, Pablo; Gabaldón Estevan, Juan Antonio, 1973- (BioMed Central, 2020)
    Background: Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties ...
  • Harrow, Jennifer; Nagy, Alinda; Reymond, Alexandre; Alioto, Tyler; Patthy, Laszlo; Antonarakis, Stylianos E.; Guigó Serra, Roderic (BioMed Central, 2009)
    The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here ...
  • Chaves Pozo, Elena; Valero, Yulema; Esteve-Codina, Anna; Gómez Garrido, Jèssica; Dabad, Marc; Alioto, Tyler; Meseguer, José; Esteban, María Ángeles; Cuesta, Alberto (Nature Publishing Group, 2017)
    Nervous necrosis virus (NNV) causes high mortalities in several marine species. We aimed to evaluate the innate cell-mediated cytotoxic (CMC) activity of head-kidney leucocytes (HKLs) isolated from naïve European sea bass ...
  • Gerdol, Marco; Cruz, Fernando; Gómez-Garrido, Jèssica; Vlasova, Anna; Naranjo Ortiz, Miguel Ángel, 1989-; Corvelo, André; Frias, Leonor; Gut, Marta; Gabaldón Estevan, Juan Antonio, 1973-; Alioto, Tyler; Figueras, Antonio (BioMed Central, 2020)
    Background: The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive ...
  • Julca, Irene; Marcet Houben, Marina; Cruz, Fernando; Vargas-Chavez, Carlos; Johnston, John Spencer; Gómez Garrido, Jèssica; Frias, Leonor; Corvelo, André; Loska, Damian; Cámara, Francisco; Gut, Marta; Alioto, Tyler; Latorre, Amparo; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2020)
    Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications ...
  • Denoeud, France; Kapranov, Philipp; Ucla, Catherine; Frankish, Adam; Castelo Valdueza, Robert; Drenkow, Jorg; Lagarde, Julien; Alioto, Tyler; Manzano, Caroline; Chrast, Jacqueline; Dike, Sujit; Wyss, Carine; Henrichsen, Charlotte N.; Holroyd, Nancy; Dickson, Mark C.; Taylor, Ruth; Hance, Zahra; Foissac, Sylvain; Myers, Richard M.; Rogers, Jane; Hubbard, Tim J.; Harrow, Jennifer; Guigó Serra, Roderic; Gingeras, Thomas R.; Antonarakis, Stylianos E.; Reymond, Alexandre (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
    This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using ...
  • Kuderna, Lukas F.K.; Lizano, Esther; Julià, Eva; Gómez Garrido, Jèssica; Serres Armero, Aitor; Kuhlwilm, Martin; Alandes, Regina Antoni; Alvarez-Estape, Marina; Juan, David; Simon, Heath; Alioto, Tyler; Gut, Marta; Gut, Ivo Glynne; Schierup, Mikkel H.; Fornas Carreño, Oscar; Marquès i Bonet, Tomàs, 1975- (Nature Research, 2019)
    Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions, only a handful of species have their Y chromosome properly ...
  • Alioto, Tyler; Cruz, Fernando; Gómez Garrido, Jèssica; Triyatni, Miriam; Gut, Marta; Frias, Leonor; Esteve-Codina, Anna; Menne, Stephan; Kiialainen, Anna; Kumpesa, Nadine; Birzele, Fabian; Schmucki, Roland; Gut, Ivo Glynne; Spleiss, Olivia (Genetics Society of America, 2019)
    The Eastern woodchuck (Marmota monax) has been extensively used in research of chronic hepatitis B and liver cancer because its infection with the woodchuck hepatitis virus closely resembles a human hepatitis B virus ...
  • Ledoux, Jean-Baptiste; Cruz, Fernando; Gómez Garrido, Jèssica; Antoni, Regina; Blanc, Julie; Gómez Gras, Daniel; Kipson, Silvija; López Sendino, Paula; Antunes, Agostinho; Linares, Cristina; Gut, Marta; Alioto, Tyler; Garrabou, Joaquim (Genetics Society of America, 2020)
    The octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata ...
  • Puerma, Eva; Orengo, Dorcas J.; Cruz, Fernando; Gómez Garrido, Jèssica; Librado, Pablo; Salguero, David; Papaceit, Montserrat; Gut, Marta; Segarra, Carmen; Alioto, Tyler; Aguadé, Montserrat (Oxford University Press, 2018)
    Drosophila guanche is a member of the obscura group that originated in the Canary Islands archipelago upon its colonization by D. subobscura. It evolved into a new species in the laurisilva, a laurel forest present in wet ...
  • Alioto, Tyler; Ngai, John (BioMed Central, 2005)
    Background: Vertebrate odorant receptors comprise three types of G protein-coupled receptors: the OR, V1R and V2R receptors. The OR superfamily contains over 1,000 genes in some mammalian species, representing the largest ...
  • Mudge, Jonathan M.; Frankish, Adam; Fernández Banet, Julio; Alioto, Tyler; Derrien, Thomas; Howald, Cédric; Reymond, Alexandre; Guigó Serra, Roderic; Hubbard, Tim J.; Harrow, Jennifer (Oxford University Press, 2011)
    Alternative splicing (AS) has the potential to greatly expand the functional repertoire of mammalian transcriptomes. However, few variant transcripts have been characterized functionally, making it difficult to assess the ...
  • Alioto, Tyler; Cruz, Fernando; Frias, Leonor; Gómez Garrido, Jèssica; Gut, Marta; Julca, Irene; Ribeca, Paolo; Vlasova, Anna; Gabaldón Estevan, Juan Antonio, 1973-; Arús, Pere (Wiley-VCH Verlag, 2020)
    We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, ...