Browsing by Author "Marquès i Bonet, Tomàs, 1975-"

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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 ...
  • Marquès i Bonet, Tomàs, 1975-; Kidd, Jeffrey M.; Ventura, Mario; Graves, Tina A.; Cheng, Ze; Hillier, LeDeana W.; Jiang, Zhaoshi; Baker, Carl; Malfavon-Borja, Ray; Fulton, Lucinda; Alkan, Can; Aksay, Gozde; Girirajan, Santhosh; Siswara, Priscillia; Chen, Lin; Cardone, Maria Francesca; Navarro i Cuartiellas, Arcadi, 1969-; Mardis, Elaine R.; Wilson, Richard K.; Eichler, Evan E. (Nature Publishing Group, 2009)
    It is generally accepted that the extent of phenotypic change between human and great apes is dissonant with the rate of molecular change. Between these two groups, proteins are virtually identical, cytogenetically there ...
  • Olalde Marquínez, Íñigo, 1987-; Lobón, Irene; Ramírez, Oscar; Marquès i Bonet, Tomàs, 1975-; Lalueza Fox, Carles, 1965- (Oxford University Press, 2015)
    The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: An initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; ...
  • Blake, Lauren E.; Roux, Julien; Hernando Herráez, Irene, 1985-; Banovich, Nicholas E.; García Pérez, Raquel, 1989-; Hsiao, Chiaowen Joyce; Eres, Ittai; Cuevas, Claudia; Marquès i Bonet, Tomàs, 1975-; Gilad, Yoav (Cold Spring Harbor Laboratory Press (CSHL Press), 2020)
    Previously published comparative functional genomic data sets from primates using frozen tissue samples, including many data sets from our own group, were often collected and analyzed using nonoptimal study designs and ...
  • Gallego Romero, Irene; Hernando Herráez, Irene, 1985-; Marquès i Bonet, Tomàs, 1975-; Gilad, Yoav (eLife, 2015)
    Comparative genomics studies in primates are restricted due to our limited access to samples. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must ...
  • Lorente-Galdós, Belén, 1981-; Bleyhl, Jonathan; Santpere Baró, Gabriel, 1981-; Vives, Laura; Ramírez, Oscar; Hernández Rodríguez, Jéssica, 1983-; Anglada Busquets, Roger; Cooper, Gregory M.; Navarro i Cuartiellas, Arcadi, 1969-; Eichler, Evan E.; Marquès i Bonet, Tomàs, 1975- (BioMed Central, 2013)
    BACKGROUND: The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most ...
  • Steely, Cody J.; Walker, Jerilyn A.; Jordan, Vallmer E.; Beckstrom, Thomas O.; McDaniel, Cullen L.; St Romain, Corey P.; Bennett, Emily C.; Robichaux, Arianna; Clement, Brooke N.; Raveendran, Muthuswamy; Baboon Genome Analysis Consortium; Marquès i Bonet, Tomàs, 1975-; Worley, Kim C.; Phillips-Conroy, Jane; Jolly, Clifford J.; Rogers, Jeffrey; Konkel, Miriam K.; Batzer, Mark A. (Oxford University Press, 2017)
    Male dispersal from the natal group at or near maturity is a feature of most baboon (Papio) species. It potentially has profound effects upon population structure and evolutionary processes, but dispersal, especially for ...
  • Ramírez, Oscar; Olalde Marquínez, Íñigo, 1987-; Berglund, Jonas; Lorente-Galdós, Belén, 1981-; Hernández Rodríguez, Jéssica, 1983-; Quilez Oliete, Javier; Webster, Matthew T; Wayne, Robert K.; Lalueza Fox, Carles, 1965-; Vilà, Carles; Marquès i Bonet, Tomàs, 1975- (BioMed Central, 2014)
    Background: Although a variety of genetic changes have been implicated in causing phenotypic differences among dogs, the role of copy number variants (CNVs) and their impact on phenotypic variation is still poorly understood. ...
  • Kuhlwilm, Martin; Prado Martínez, Javier, 1987-; Lalueza Fox, Carles, 1965-; Marquès i Bonet, Tomàs, 1975-; Castellano Hereza, Sergi (Nature Research, 2016)
    It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000-65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together ...
  • Tamazian, Gaik; Simonov, Serguei; Dobrynin, Pavel; Makunin, Alexey; Logachev, Anton; Komissarov, Aleksey; Shevchenko, Andrey; Brukhin, Vladimir; Cherkasov, Nikolay; Svitin, Anton; Goldman, David B. (David Benjamin); Antunes, Agostinho; Quilez Oliete, Javier; Lorente-Galdós, Belén, 1981-; Alkan, Can; Marquès i Bonet, Tomàs, 1975-; Menotti-Raymond, Marylin; David, Victor A; Narfström, Kristina; O’Brien, Stephen J. (BioMed Central, 2014)
    Background. Domestic cats enjoy an extensive veterinary medical surveillance which has described nearly 250 genetic diseases analogous to human disorders. Feline infectious agents offer powerful natural models of deadly ...
  • Kuderna, Lukas, 1989- (Universitat Pompeu Fabra, 2020-01-24)
    Genomic analyses are at the center of contemporary biology. These studies heavily rely on reference genome assemblies, yet those are typically highly fragmented. Having accurate representations of complex genomes, or parts ...
  • Han, Sojung, 1984- (Universitat Pompeu Fabra, 2019-10-16)
    Bonobos are an interesting species to study due to their unique evolutionary features such as a peaceful social nature and hypersexual behavior. The prolonged exaggerated sexual swelling in females is a notable difference ...
  • de Manuel, Marc; Kuhlwilm, Martin; Sousa, Victor C.; Prado Martínez, Javier, 1987-; Hernández Rodríguez, Jéssica, 1983-; Dupanloup, Isabelle; Lao Grueso, Oscar, 1976-; Heredia Genestar, José María; Kuderna, Lukas F.K.; Casals López, Ferran; Angedakin, Samuel; Arandjelovic, Mimi; Boesch, Christophe; Kühl, Hjalmar S.; Vigilant, Linda; Navarro i Cuartiellas, Arcadi, 1969-; Excoffier, Laurent; Marquès i Bonet, Tomàs, 1975- (American Association for the Advancement of Science (AAAS), 2016)
    Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that ...
  • Warren, Wesley C.; García Pérez, Raquel; Xu, Sen; Lampert, Kathrin P.; Chapolin, Domitille; Stöck, Matthias; Loewe, Laurence; Lu, Yuan; Kuderna, Lukas F.K.; 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 ...
  • 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 ...
  • Mak, Sarah Siu Tze; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel Holger S.; Kuderna, Lukas F.K.; 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...