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Browsing by Author "Alioto, Tyler"

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A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)

Kuderna, Lukas, 1989-; Laayouni, Hafid, 1968-; García Pérez, Raquel, 1989-; Povolotskaya, Inna, 1986-; Serres Armero, Aitor, 1992-; 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 ...
A chromosome‐level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex‐determining gene in the flatfish Solea senegalensis

de la Herrán, Roberto; Gómez-Garrido, Jèssica; Cruz, Fernando; Alioto, Tyler; Martínez, Paulino (Wiley, 2023)

Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and ...
A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

Alioto, Tyler; Derdak, Sophia; Ribeca, Paolo; Castro Giner, Francesc; Beltran, Sergi; Raineri, Emanuele; Dabad, Marc; Heath, Simon; Gut, Marta; Gut, Ivo Glynne (Nature Research, 2015)

As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different ...
A new variant of the aadE-sat4-aphA-3 gene cluster found in a conjugative plasmid from a MDR campylobacter jejuni isolate

Guirado, Pedro; Miró, Elisenda; Iglesias-Torrens, Yaidelis; Navarro, Ferran; Campoy, Susana; Alioto, Tyler; Gómez-Garrido, Jèssica; Madrid, Cristina; Balsalobre, Carlos (MDPI, 2022)

Campylobacter jejuni is a foodborne pathogen causing bacterial gastroenteritis, with the highest incidence reported in Europe. The prevalence of antibiotic resistance in C. jejuni, as well as in many other bacterial ...
A reference genome sequence for the european silver fir (abies alba mill.): a community-generated genomic resource

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. ...
Alteration in the Culex pipiens transcriptome reveals diverse mechanisms of the mosquito immune system implicated upon Rift Valley fever phlebovirus exposure

Núñez, Ana I.; Esteve-Codina, Anna; Gómez-Garrido, Jèssica; Brustolin, Marco; Talavera, Sandra; Berdugo, Miguel; Dabad, Marc; Alioto, Tyler; Bensaid, Albert; Busquets, Núria (Public Library of Science (PLoS), 2020)

Rift Valley fever phlebovirus (RVFV) causes an emerging zoonotic disease and is mainly transmitted by Culex and Aedes mosquitoes. While Aedes aegypti-dengue virus (DENV) is the most studied model, less is known about the ...
ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection

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; ...
Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish

Guerrero-Cózar, Israel; Gómez-Garrido, Jèssica; Berbel, Concha; Martinez-Blanch, Juan F.; Alioto, Tyler; Claros, M. Gonzalo; Gagnaire, Pierre-Alexandre; Manchado, Manuel (Nature Research, 2021)

The integration of physical and high-density genetic maps is a very useful approach to achieve chromosome-level genome assemblies. Here, the genome of a male Senegalese sole (Solea senegalensis) was de novo assembled and ...
Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad

Liedtke, H. Christoph; Cruz, Fernando; Gómez Garrido, Jèssica; Fuentes Palacios, Diego; Marcet Houben, Marina; Gut, Marta; Alioto, Tyler; Gabaldón Estevan, Juan Antonio, 1973-; Gomez-Mestre, Ivan (Oxford University Press, 2022)

Genomic resources for amphibians are still hugely under-represented in vertebrate genomic research, despite being a group of major interest for ecology, evolution and conservation. Amphibians constitute a highly threatened ...
Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)

Gómez Garrido, Jèssica; Cruz, Fernando; Alioto, Tyler; Feiner, Nathalie; Uller, Tobias; Sanchez Escudero, Ignacio; Tavecchia, Giacomo; Rotger, Andreu; Otalora Acevedo, Katherin Eliana; Baldo, Laura (Oxford University Press, 2023)

The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for ...
Chromosome-level genome assembly of Lilford’s wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)

Gómez-Garrido, Jèssica; Cruz, Fernando; Alioto, Tyler; Feiner, Nathalie; Uller, Tobias; Gut, Marta; Sanchez Escudero, Ignacio; Tavecchia, Giacomo; Rotger, Andreu; Otalora Acevedo, Katherin Eliana; Baldo, Laura (Oxford University Press, 2023)

The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for ...
Combining nanopore and illumina sequencing permits detailed analysis of insertion mutations and structural variations produced by PEG-Mediated transformation in ostreococcus tauri

Thomy, Julie; Sanchez, Frederic; Gut, Marta; Cruz, Fernando; Alioto, Tyler; Piganeau, Gwenael; Grimsley, Nigel; Yau, Sheree (MDPI, 2021)

Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms ...
De Novo assembly and annotation of the larval transcriptome of two spadefoot toads widely divergent in developmental rate

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, ...
De novo transcriptome sequencing and gene co-expression reveal a genomic basis for drought sensitivity and evidence of a rapid local adaptation on Atlas cedar (Cedrus atlantica)

Cobo-Simón, Irene; Gómez-Garrido, Jèssica; Esteve-Codina, Anna; Dabad, Marc; Alioto, Tyler; Maloof, Julin N.; Méndez-Cea, Belén; Seco, José Ignacio; Linares, Juan Carlos; Gallego, Francisco Javier (Frontiers, 2023)

Introduction: Understanding the adaptive capacity to current climate change of drought-sensitive tree species is mandatory, given their limited prospect of migration and adaptation as long-lived, sessile organisms. Knowledge ...
Developmental RNA-Seq transcriptomics of haploid germ cells and spermatozoa uncovers novel pathways associated with teleost spermiogenesis

Castro-Arnau, Júlia; Chauvigné, François; Gómez-Garrido, Jèssica; Esteve-Codina, Anna; Dabad, Marc; Alioto, Tyler; Finn, Roderick Nigel; Cerdà, Joan (Nature Research, 2022)

In non-mammalian vertebrates, the molecular mechanisms involved in the transformation of haploid germ cells (HGCs) into spermatozoa (spermiogenesis) are largely unknown. Here, we investigated this process in the marine ...
Epigenetic regulation of gene expression in Chinese hamster ovary cells in response to the changing environment of a batch culture

Hernandez, Inmaculada; Dhiman, Heena; Klanert, Gerald; Jadhav, Vaibhav; Auer, Norbert; Hanscho, Michael; Baumann, Martina; Esteve-Codina, Anna; Dabad, Marc; Gómez, Jessica; Alioto, Tyler; Merkel, Angelika; Raineri, Emanuele; Heath, Simon; Rico, Daniel; Borth, Nicole (Wiley, 2019)

The existence of dynamic cellular phenotypes in changing environmental conditions is of major interest for cell biologists who aim to understand the mechanism and sequence of regulation of gene expression. In the context ...
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 ...
Genome sequence of the olive tree, Olea europaea

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 ...
Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings

Almudi, Isabel; Wyatt, Christopher Douglas Robert, 1988-; Cruz, Fernando; Gómez-Garrido, Jèssica; Gut, Marta; Alioto, Tyler; Irimia Martínez, 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. ...
Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.)

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 ...

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