Browsing by Author "García Pérez, Raquel, 1989-"

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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 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 ...
  • 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 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 ...
  • 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, ...
  • 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 ...
  • Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures
    García Pérez, Raquel, 1989-; Esteller-Cucala, Paula; Mas, Glòria; Lobón, Irene; Di Carlo, Valerio; Riera, Meritxell; Kuhlwilm, Martin; Navarro i Cuartiellas, Arcadi, 1969-; Blancher, Antoine; Di Croce, Luciano; Gómez Skarmeta, José Luis; Juan, David; Marquès i Bonet, Tomàs, 1975- (Nature Research, 2021)
    Changes in the epigenetic regulation of gene expression have a central role in evolution. Here, we extensively profiled a panel of human, chimpanzee, gorilla, orangutan, and macaque lymphoblastoid cell lines (LCLs), using ...
  • Evolutionary interplay between epigenetic regulation and gene expression dynamics in human and other primates
    García Pérez, Raquel, 1989- (Universitat Pompeu Fabra, 2019-01-29)
    The evolution of the human phenotype involved gene regulatory innovations. Comparative functional epigenomic studies are a powerful tool with potential to shed light on many long-standing questions regarding human evolution. ...
  • Genomic legacy of the African cheetah, Acinonyx jubatus
    Dobrynin, Pavel; Kuderna, Lukas F.K.; García Pérez, Raquel, 1989-; de Manuel, Marc; Marquès i Bonet, Tomàs, 1975-; O’Brien, Stephen J. (BioMed Central, 2015)
    BACKGROUND: Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. RESULTS: Here the genome sequence of wild-born African cheetahs ...
  • Genomic legacy of the African cheetah, Acinonyx jubatus
    Dobrynin, Pavel; Liu, Shiping; Tamazian, Gaik; Xiong, Zijun; Yurchenko, Andrey A.; Krasheninnikova, Ksenia; Kliver, Sergey; Schmidt-Küntzel, Anne; Koepfli, Klaus-Peter; Johnson, Warren; Kuderna, Lukas F.K.; García Pérez, Raquel, 1989-; de Manuel, Marc; Godinez, Ricardo; Komissarov, Aleksey; Makunin, Alexey; Brukhin, Vladimir; Qiu, Weilin; Zhou, Long; Li, Fang; Yi, Jian; Driscoll, Carlos; Antunes, Agostinho; Oleksyk, Taras K.; Eizirik, Eduardo; Perelman, Polina; Roelke, Melody; Wildt, David; Diekhans, Mark; Marquès i Bonet, Tomàs, 1975-; Marker, Laurie; Bhak, Jong; Wang, Jun; Zhang, Guojie; O'Brien, Stephen J. (BioMed Central, 2015)
    BACKGROUND: Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. RESULTS: Here the genome sequence of wild-born African cheetahs ...
  • Molecular and cellular reorganization of neural circuits in the human lineage
    Sousa, André M. M.; Zhu, Ying; Raghanti, Mary Ann; Kitchen, Robert R.; Onorati, Marco; Tebbenkamp, Andrew T. N.; Stutz, Bernardo; Meyer, Kyle A.; Li, Mingfeng; Kawasawa, Yuka Imamura; Liu, Fuchen; García Pérez, Raquel, 1989-; Mele, Marta; Carvalho, Tiago Loureiro de, 1987-; Skarica, Mario; Gulden, Forrest O.; Pletikos, Mihovil; Shibata, Akemi; Stephenson, Alexa R.; Edler, Melissa K.; Ely, John J.; Elsworth, John D.; Horvath, Tamas L.; Hof, Patrick R.; Hyde, Thomas M.; Kleinman, Joel E.; Weinberger, Daniel R.; Reimers, Mark; Lifton, Richard P.; Mane, Shrikant M.; Noonan, James P.; State, Matthew W.; Lein, Ed S.; Knowles, James A.; Marquès i Bonet, Tomàs, 1975-; Sherwood, Chet C.; Gerstein, Mark B.; Sestan, Nenad (American Association for the Advancement of Science (AAAS), 2017)
    To better understand the molecular and cellular differences in brain organization between human and nonhuman primates, we performed transcriptome sequencing of 16 regions of adult human, chimpanzee, and macaque brains. ...
  • The genome of the vervet (Chlorocebus aethiops sabaeus)
    Warren, Wesley C.; García Pérez, Raquel, 1989-; Marquès i Bonet, Tomàs, 1975-; Freimer, Nelson B. (Cold Spring Harbor Laboratory Press (CSHL Press), 2015)
    We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency ...
  • The landscape of expression and alternative splicing variation across human traits
    García Pérez, Raquel, 1989-; Ramirez, Jose Miguel; Ripoll Cladellas, Aida; Chazarra-Gil, Ruben; Oliveros, Winona; Soldatkina, Oleksandra; Bosio, Mattia; Rognon, Paul Joris; Capella Gutiérrez, Salvador Jesús, 1985-; Calvo, Miquel (Calvo Llorca); Reverter, Ferran; Guigó Serra, Roderic; Aguet, François; Ferreira, Pedro G.; Ardlie, Kristin G.; Melé Messeguer, Marta, 1982- (Elsevier, 2022)
    Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as ...
  • Transcriptome innovations in primates revealed by single-molecule long-read sequencing
    Ferrández Peral, Luis, 1991-; Zhan, Xiaoyu; Zhan, Xiaoyu; Alvarez-Estape, Marina; Chiva, Cristina; Esteller-Cucala, Paula; García Pérez, Raquel, 1989-; Julià, Eva; Lizano González, Esther, 1974-; Fornas Carreño, Oscar; Sabidó Aguadé, Eduard, 1981-; Li, Qiye; Marquès i Bonet, Tomàs, 1975-; Juan, David; Zhang, Guojie (Cold Spring Harbor Laboratory Press (CSHL Press), 2022)
    Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution ...