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

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  • A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)
    Kuderna, Lukas F.K.; 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 burst of segmental duplications in the genome of the African great ape ancestor
    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 ...
  • A common genetic origin for early farmers from mediterranean cardial and central european LBK cultures
    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; ...
  • A comparative genomics multitool for scientific discovery and conservation
    Zoonomia Consortium; Serres Armero, Aitor, 1992-; Juan, David; Kuderna, Lukas F.K.; Marquès i Bonet, Tomàs, 1975- (Nature Research, 2020)
    The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe ...
  • A comparison of gene expression and DNA methylation patterns across tissues and species
    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 ...
  • A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives
    Westbury, Michael V.; Barnett, Ross; Sandoval Velasco, Marcela; Gower, Graham; Garrett Vieira, Filipe; Manuel Montero, Marc de, 1991-; Hansen, Anders J.; Yamaguchi, Nobuyuki; Werdelin, Lars; Marquès i Bonet, Tomàs, 1975-; Gilbert, M Thomas; Lorenzen, Eline D. (UNLISTED PUBLISHER, 2021)
    Background: The evolutionary relationships of Felidae during their Early–Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is ...
  • A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)
    Palmada-Flores, Marc; Orkin, Joseph D.; Haase, Bettina; Mountcastle, Jacquelyn; Bertelsen, Mads F.; Fedrigo, Olivier; Kuderna, Lukas F.K.; Jarvis, Erich D.; Marquès i Bonet, Tomàs, 1975- (Oxford University Press, 2022)
    Background: The ring-tailed lemur (Lemur catta) is a charismatic strepsirrhine primate endemic to Madagascar. These lemurs are of particular interest, given their status as a flagship species and widespread publicity in ...
  • A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics
    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 ...
  • Accelerated exon evolution within primate segmental duplications
    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 ...
  • Alu insertion polymorphisms as evidence for population structure in baboons
    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 ...
  • Analysis of structural diversity in wolf-like canids reveals post-domestication variants
    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. ...
  • Ancient and modern genomes unravel the evolutionary history of the rhinoceros family
    Liu, Shanlin; Marquès i Bonet, Tomàs, 1975-; Gilbert, M Thomas (Elsevier, 2021)
    Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct ...
  • Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum
    Boubli, Jean P.; Ruiz-Gartzia, Irune; Kuderna, Lukas F.K.; Marquès i Bonet, Tomàs, 1975-; Roos, Christian (Science Press, 2021)
    The pygmy marmoset, the smallest of the anthropoid primates, has a broad distribution in Western Amazonia. Recent studies using molecular and morphological data have identified two distinct species separated by the Napo ...
  • Ancient gene flow from early modern humans into Eastern Neanderthals
    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 ...
  • Annotated features of domestic cat – Felis catus genome
    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 ...
  • Application of genome assembly methods to human and non-human primate genomics
    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 ...
  • Assessment of the gene mosaicism burden in blood and its implications for immune disorders
    Solís Moruno, Manuel; Mensa Vilaró, Anna; Batlle Masó, Laura, 1993-; Lobón, Irene; Bonet, Núria; Marquès i Bonet, Tomàs, 1975-; Aróstegui, Juan Ignacio; Casals López, Ferran (Nature Research, 2021)
    There are increasing evidences showing the contribution of somatic genetic variants to non-cancer diseases. However, their detection using massive parallel sequencing methods still has important limitations. In addition, ...
  • Characterization of nuclear mitochondrial insertions in the whole genomes of primates
    Dayama, Gargi; Zhou, Weichen; Prado Martínez, Javier, 1987-; Marquès i Bonet, Tomàs, 1975-; Mills, Ryan E. (Oxford University Press, 2020)
    The transfer and integration of whole and partial mitochondrial genomes into the nuclear genomes of eukaryotes is an ongoing process that has facilitated the transfer of genes and contributed to the evolution of various ...
  • Chimpanzee genomic diversity reveals ancient admixture with bonobos
    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, 1985-; 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 ...
  • 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 ...