Visualitza per autoria "Marquès i Bonet, Tomàs, 1975-"

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  • Circular DNA intermediates in the generation of large human segmental duplications
    Chicote, Javier U.; López Sánchez, Marcos, 1986-; Marquès i Bonet, Tomàs, 1975-; Callizo, José; Pérez Jurado, Luis Alberto; García-España, Antonio (BioMed Central, 2020)
    Background: Duplications of large genomic segments provide genetic diversity in genome evolution. Despite their importance, how these duplications are generated remains uncertain, particularly for distant duplicated genomic ...
  • Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly
    Warren, Wesley C.; García Pérez, Raquel, 1989-; Xu, Sen; Lampert, Kathrin P.; Chapolin, Domitille; Stöck, Matthias; Loewe, Laurence; Lu, Yuan; Kuderna, Lukas, 1989-; Minx, Patrick; Montague, Michael J.; Tomlinson, Chad; Hillier, LeDeana W.; Murphy, Daniel N.; Wang, John; Wang, Zhongwei; Macias Garcia, Constantino; Thomas, Gregg C. W.; Volff, Jean-Nicolas; Farias, Fabiana; Aken, Bronwen; Walter, Ronald B.; Pruitt, Kim D.; Marquès i Bonet, Tomàs, 1975-; Hahn, Matthew W.; Kneitz, Susanne; Lynch, Michael; Schartl, Manfred (Nature Publishing Group, 2018)
    The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual ...
  • The common marmoset genome provides insight into primate biology and evolution
    Worley, Kim C.; Lorente-Galdós, Belén, 1981-; Marquès i Bonet, Tomàs, 1975-; Wilson, Richard K.; The Marmoset Genome Sequencing and Analysis Consortium (Nature Publishing Group, 2014)
    We report the whole-genome sequence of the common marmoset (Callithrix jacchus). The 2.26-Gb genome of a female marmoset was assembled using Sanger read data (6×) and a whole-genome shotgun strategy. A first analysis has ...
  • Comparative genomics reveals the hybrid origin of a macaque group
    Zhang, Bao-Lin; Marquès i Bonet, Tomàs, 1975-; Wu, Dong-Dong (American Association for the Advancement of Science (AAAS), 2023)
    Although species can arise through hybridization, compelling evidence for hybrid speciation has been reported only rarely in animals. Here, we present phylogenomic analyses on genomes from 12 macaque species and show that ...
  • Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
    Mak, Sarah Siu Tze; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel Holger S.; Kuderna, Lukas, 1989-; Zhang, Wenwei; Fu, Shujin; Vieira, Filipe Garrett; Germonpré, Mietje; Bocherens, Hervé; Fedorov, Sergey E.; Petersen, Bent; Sicheritz-Ponten, Thomas; Marquès i Bonet, Tomàs, 1975-; Zhang, Guojie; Jiang, Hui; Gilbert, M Thomas (Oxford University Press, 2017)
    Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant ...
  • Complex evolutionary history with extensive ancestral gene flow in an African primate radiation
    Jensen, Axel; Swift, Frances; de Vries, Dorien; Beck, Robin M. D.; Kuderna, Lukas, 1989-; Knauf, Sascha; Chuma, Idrissa S.; Keyyu, Julius D.; Kitchener, Andrew C.; Farh, Kyle; Rogers, Jeffrey; Marquès i Bonet, Tomàs, 1975-; Detwiler, Kate M.; Roos, Christian; Guschanski, Katerina (Oxford University Press, 2023)
    Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons ...
  • Comprehensive identification of somatic nucleotide variants in human brain tissue
    Wang, Yifan; Lobon, Irene; Juan, David; Lizano González, Esther, 1974-; Marquès i Bonet, Tomàs, 1975-; Abyzov, Alexej (BioMed Central, 2021)
    Background: Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. ...
  • Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta)
    Brasó-Vives, Marina, 1990-; Povolotskaya, Inna, 1986-; Hartasánchez Frenk, Diego Andrés, 1982-; Farré, Xavier; Fernández Callejo, Marcos; Raveendran, Muthuswamy; Harris, R. Alan; Rosene, Douglas L.; Lorente Galdós, Maria Belén; Navarro i Cuartiellas, Arcadi, 1969-; Marquès i Bonet, Tomàs, 1975-; Rogers, Jeffrey; Juan Sopeña, David Alejandro, 1975- (Public Library of Science (PLoS), 2020)
    The rhesus macaque is an abundant species of Old World monkeys and a valuable model organism for biomedical research due to its close phylogenetic relationship to humans. Copy number variation is one of the main sources ...
  • Copy number variation analysis in the great apes reveals species-specific patterns of structural variation
    Gazave, Elodie; Darre, Fleur; Morcillo Suárez, Carlos, 1969-; Petit, Natalia; Carreño Torres, Angel; Marigorta, Urko M.; Ryder, Oliver A.; Blancher, Antoine; Rocchi, Mariano; Bosch Fusté, Elena; Baker, Carl; Marquès i Bonet, Tomàs, 1975-; Eichler, Evan E.; Navarro i Cuartiellas, Arcadi, 1969- (Cold Spring Harbor Laboratory Press (CSHL Press), 2011)
    Copy number variants (CNVs) are increasingly acknowledged as an important source of evolutionary novelties in the human lineage. However, our understanding of their significance is still hindered by the lack of primate CNV ...
  • Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
    Serres Armero, Aitor, 1992-; Davis, Brian W.; Povolotskaya, Inna, 1986-; Morcillo Suárez, Carlos, 1969-; Plassais, Jocelyn; Juan, David; Ostrander, Elaine A.; Marquès i Bonet, Tomàs, 1975- (Cold Spring Harbor Laboratory Press (CSHL Press), 2021)
    Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant ...
  • Death and resurrection of the human IRGM gene
    Bekpen, Cemalettin; Marquès i Bonet, Tomàs, 1975-; Alkan, Can; Antonacci, Francesca; Leogrande, Maria Bruna; Ventura, Mario; Kidd, Jeffrey M.; Siswara, Priscillia; Howard, Jonathan C.; Eichler, Evan E. (Public Library of Science (PLoS), 2009)
    Immunity-related GTPases (IRG) play an important role in defense against intracellular pathogens. One member of this gene family in humans, IRGM, has been recently implicated as a risk factor for Crohn's disease. We analyzed ...
  • Demographic history of the genus Pan inferred from whole mitochondrial genome reconstructions
    Lobón, Irene; Tucci, Serena; de Manuel, Marc; Ghirotto, Silvia; Benazzo, Andrea; Prado Martínez, Javier, 1987-; Lorente-Galdós, Belén, 1981-; Nam, Kiwoong; Dabad, Marc; Hernández Rodríguez, Jéssica, 1983-; Comas, David, 1969-; Navarro i Cuartiellas, Arcadi, 1969-; Schierup, Mikkel H.; Andrés Morán, Aida, 1976-; Barbujani, Guido; Hvilsom, Christina; Marquès i Bonet, Tomàs, 1975- (Oxford University Press, 2016)
    The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan ...
  • Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European
    Olalde Marquínez, Íñigo, 1987-; Sánchez Quinto, Federico A, 1985-; Santpere Baró, Gabriel, 1981-; Rodríguez Pérez, Juan Antonio, 1985-; Quilez Oliete, Javier; Ramírez, Oscar; Marigorta, Urko M.; Fernández Callejo, Marcos; Marquès i Bonet, Tomàs, 1975-; Navarro i Cuartiellas, Arcadi, 1969-; Lalueza Fox, Carles, 1965- (Nature Research, 2014)
    Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe. The adoption of farming, stock breeding and sedentary societies during the ...
  • Differential DNA methylation of vocal and facial anatomy genes in modern humans
    Gokhman, David; García Pérez, Raquel, 1989-; Lizano González, Esther, 1974-; Ferrando-Bernal, Manuel, 1990-; Gelabert Xirinachs, Pere, 1991-; Lalueza Fox, Carles, 1965-; Marquès i Bonet, Tomàs, 1975-; Carmel, Liran (Nature Research, 2020)
    Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, ...
  • Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences
    Meyer, Kyle A.; Marquès i Bonet, Tomàs, 1975-; Sestan, Nenad (Oxford University Press, 2017)
    Previous studies have found that genes which are differentially expressed within the developing human brain disproportionately neighbor conserved noncoding sequences (CNSs) that have an elevated substitution rate in humans ...
  • Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories
    Bentley, Blair P.; Pawar, Harvinder; Kuhlwilm, Martin; Marquès i Bonet, Tomàs, 1975-; Komoroske, Lisa M. (National Academy of Sciences, 2023)
    Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in ...
  • DNA methylation contributes to natural human variation
    Heyn, Holger; Moran, Sebastian; Hernando Herráez, Irene, 1985-; Sayols, Sergi; Gómez, Antonio; Sandoval, Juan; Monk, Dave; Hata, Kenichiro; Marquès i Bonet, Tomàs, 1975-; Wang, Liewei; Esteller, Manel (Cold Spring Harbor Laboratory Press (CSHL Press), 2013)
    DNA methylation patterns are important for establishing cell, tissue, and organism phenotypes, but little is known about their contribution to natural human variation. To determine their contribution to variability, we ...
  • DNA methylation: insights into human evolution
    Hernando Herráez, Irene, 1985-; García Pérez, Raquel, 1989-; Sharp, Andrew J.; Marquès i Bonet, Tomàs, 1975- (Public Library of Science (PLoS), 2015)
    A fundamental initiative for evolutionary biologists is to understand the molecular basis underlying phenotypic diversity. A long-standing hypothesis states that species-specific traits may be explained by differences in ...
  • Dynamics of DNA methylation in recent human and great ape evolution
    Hernando Herráez, Irene, 1985-; Prado Martínez, Javier, 1987-; Garg, Paras; Fernández Callejo, Marcos; Heyn, Holger; Hvilsom, Christina; Navarro i Cuartiellas, Arcadi, 1969-; Esteller, Manel; Sharp, Andrew J.; Marquès i Bonet, Tomàs, 1975- (Public Library of Science (PLoS), 2013)
    DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex disease. However, ...
  • Elephant shark genome provides unique insights into gnathostome evolution
    Venkatesh, Byrappa; Lorente-Galdós, Belén, 1981-; Quilez Oliete, Javier; Marquès i Bonet, Tomàs, 1975-; Warren, Wesley C. (Nature Publishing Group, 2014)
    The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. ...

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