Browsing by Author "Eichler, Evan E."

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  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • Evolution and diversity of copy number variation in the great ape lineage
    Sudmant, Peter H.; Huddleston, John; Catacchio, Claudia R.; Malig, Maika; Hillier, LeDeana W.; Baker, Carl; Mohajeri, Kiana; Kondova, Ivanela; Bontrop, Ronald E.; Persengiev, Stephan; Antonacci, Francesca; Ventura, Mario; Prado Martínez, Javier, 1987-; Marquès i Bonet, Tomàs, 1975-; Eichler, Evan E.; Project Great Ape Genome (Cold Spring Harbor Laboratory Press (CSHL Press), 2013)
    Copy number variation (CNV) contributes to disease and has restructured the genomes of great apes. The diversity and rate of this process, however, have not been extensively explored among great ape lineages. We analyzed ...
  • Evolutionary dynamism of the primate LRRC37 gene family
    Giannuzzi, Giuliana; Siswara, Priscillia; Malig, Maika; Marquès i Bonet, Tomàs, 1975-; Mullikin, James C.; Ventura, Mario; Eichler, Evan E.; NISC Comparative Sequencing Program (Cold Spring Harbor Laboratory Press (CSHL Press), 2013)
    Core duplicons in the human genome represent ancestral duplication modules shared by the majority of intrachromosomal duplication blocks within a given chromosome. These cores are associated with the emergence of novel ...
  • Global diversity, population stratification, and selection of human copy-number variation
    Sudmant, Peter H.; Eichler, Evan E.; Comas, David, 1969- (American Association for the Advancement of Science (AAAS), 2015)
    In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications ...
  • Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee
    Ventura, Mario; Catacchio, Claudia R.; Alkan, Can; Marquès i Bonet, Tomàs, 1975-; Saijadian, Saba; Graves, Tina A.; Hormozdiari, Fereydoun; Navarro i Cuartiellas, Arcadi, 1969-; Malig, Maika; Baker, Carl; Lee, Choli; Turner, Emily H.; Chen, Lin; Kidd, Jeffrey M.; Archidiacono, Nicoletta; Shendure, Jay; Wilson, Richard K.; Eichler, Evan E. (Cold Spring Harbor Laboratory Press-CSHL Press, 2011)
    Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. Recent analyses have suggested that the genomes of chimpanzee and human have been particularly enriched ...
  • Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21
    Lyle, Robert; Prandini, Paola; Osoegawa, Kazutoyo; Ten Hallers, Boudewijn; Humphray, Sean; Zhu, Baoli; Eyras Jiménez, Eduardo; Castelo Valdueza, Robert; Bird, Christine P.; Gagos, Sarantos; Scott, Carol; Cox, Antony; Deutsch, Samuel; Ucla, Catherine; Cruts, Marc; Dahoun, Sophie; She, Xinwei; Bena, Frederique; Wang, Sheng-Yue; Broeckhoven, Christine van; Eichler, Evan E.; Guigó Serra, Roderic; Rogers, Jane; De Jong, Pieter J.; Reymond, Alexandre; Antonarakis, Stylianos E. (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
    The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p), estimated to be 10% of 21p. ...
  • Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders
    Wang, Tianyun; Pérez Jurado, Luis Alberto; Eichler, Evan E. (Nature Research, 2020)
    Most genes associated with neurodevelopmental disorders (NDDs) were identified with an excess of de novo mutations (DNMs) but the significance in case-control mutation burden analysis is unestablished. Here, we sequence ...
  • Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses
    Hurle, Belen; Marquès i Bonet, Tomàs, 1975-; Antonacci, Francesca; Hughes, Inna; Ryan, Joseph F.; NISC Comparative Sequencing Program; Eichler, Evan E.; Ornitz, David M.; Green, Eric D. (BioMed Central, 2011)
    Background: Mutations in the Otopetrin 1 gene (Otop1) in mice and fish produce an unusual bilateral vestibular pathology that involves the absence of otoconia without hearing impairment. The encoded protein, Otop1, is the ...
  • Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites
    Girirajan, Santhosh; Chen, Lin; Graves, Tina A.; Marquès i Bonet, Tomàs, 1975-; Ventura, Mario; Fronick, Catrina; Fulton, Lucinda; Rocchi, Mariano; Fulton, Robert S.; Wilson, Richard K.; Mardis, Elaine R.; Eichler, Evan E. (Cold Spring Harbor Laboratory Press-CSHL Press, 2009)
    The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of these rearrangement ...
  • Sequencing primate genomes: what have we learned?
    Marquès i Bonet, Tomàs, 1975-; Ryder, Oliver A.; Eichler, Evan E. (Annual Reviews Inc, 2009)
    We summarize the progress in whole-genome sequencing and analyses of primate genomes. These emerging genome datasets have broadened our understanding of primate genome evolution revealing unexpected and complex patterns ...
  • The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2
    Ventura, Mario; Catacchio, Claudia R.; Saijadian, Saba; Vives, Laura; Sudmant, Peter H.; Marquès i Bonet, Tomàs, 1975-; Graves, Tina A.; Wilson, Richard K.; Eichler, Evan E. (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Chimpanzee and gorilla chromosomes differ from human chromosomes by the presence of large blocks of subterminal heterochromatin thought to be composed primarily of arrays of tandem satellite sequence. We explore their ...
  • The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild
    Prado Martínez, Javier, 1987-; Hernando Herráez, Irene, 1985-; Lorente-Galdós, Belén, 1981-; Dabad, Marc; Ramírez, Oscar; Baeza Delgado, Carlos; Morcillo Suárez, Carlos, 1969-; Alkan, Can; Hormozdiari, Fereydoun; Raineri, Emanuele; Estellé, Jordi; Fernández Callejo, Marcos; Vallès, Mònica; Ritscher, Lars; Schöneberg, Torsten; Calle Mustienes, Elisa de la; Casillas, Sònia; Rubio Acero, Raquel; Melé Messeguer, Marta, 1982-; Engelken, Johannes; Cáceres Aguilar, Mario; Gómez Skarmeta, José Luis; Gut, Marta; Bertranpetit, Jaume, 1952-; Gut, Ivo Glynne; Abelló, Teresa; Eichler, Evan E.; Mingarro, Ismael; Lalueza Fox, Carles, 1965-; Navarro i Cuartiellas, Arcadi, 1969-; Marquès i Bonet, Tomàs, 1975- (BioMed Central, 2013)
    BACKGROUND: The only known albino gorilla, named Snowflake, was a male wild born individual from Equatorial Guinea who lived at the Barcelona Zoo for almost 40 years. He was diagnosed with non-syndromic oculocutaneous ...
  • The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
    Marquès i Bonet, Tomàs, 1975-; Cheng, Ze; She, Xinwei; Eichler, Evan E.; Navarro i Cuartiellas, Arcadi, 1969- (BioMed Central, 2008)
    Background: It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of ...
  • The origins and impact of primate segmental duplications
    Marquès i Bonet, Tomàs, 1975-; Girirajan, Santhosh; Eichler, Evan E. (Elsevier, 2009)
    Duplicated sequences are substrates for the emergence of new genes and are an important source of genetic instability associated with rare and common diseases. Analyses of primate genomes have shown an increase in the ...