Now showing items 1-13 of 13

    • 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. 

      Lowe, Craig B; Haussler, David (PloS one, 2012-01)
      Recent research supports the view that changes in gene regulation, as opposed to changes in the genes themselves, play a significant role in morphological evolution. Gene regulation is largely dependent on transcription ...
    • A high-resolution map of human evolutionary constraint using 29 mammals. 

      Lindblad-Toh, Kerstin; Garber, Manuel; Zuk, Or; Lin, Michael F; Parker, Brian J; Washietl, Stefan; Kheradpour, Pouya; ... (89 authors) (Nature, 2011-10-12)
      The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome ...
    • Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. 

      Bradnam, Keith R; Fass, Joseph N; Alexandrov, Anton; Baranay, Paul; Bechner, Michael; Birol, Inanç; Boisvert, Sébastien; ... (92 authors) (Gigascience, 2013-07-22)
      BACKGROUND: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many ...
    • Comparative genomics reveals insights into avian genome evolution and adaptation. 

      Alfaro-Núñez, A; Alström, P; An, N; Antunes, A; Avian Genome Consortium; Bertelsen, MF; Borges, R; ... (106 authors) (Science, 2014-12-12)
      Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. ...
    • Endangered species hold clues to human evolution. 

      Lowe, Craig B; Bejerano, Gill; Salama, Sofie R; Haussler, David (The Journal of heredity, 2010-07)
      We report that 18 conserved, and by extension functional, elements in the human genome are the result of retroposon insertions that are evolving under purifying selection in mammals. We show evidence that 1 of the 18 elements ...
    • Feather development genes and associated regulatory innovation predate the origin of Dinosauria. 

      Lowe, Craig B; Clarke, Julia A; Baker, Allan J; Haussler, David; Edwards, Scott V (Molecular biology and evolution, 2015-01)
      The evolution of avian feathers has recently been illuminated by fossils and the identification of genes involved in feather patterning and morphogenesis. However, molecular studies have focused mainly on protein-coding ...
    • Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53 

      Wang, Ting; Zeng, Jue; Lowe, Craig B; Sellers, Robert G; Salama, Sofie R; Yang, Min; Burgess, Shawn M; ... (9 authors) (Proceedings of the National Academy of Sciences, 2007-11-20)
    • The birds of Genome10K 

      OBrien, Stephen J; Haussler, David; Ryder, Oliver (GigaScience, 2014)
    • The genome of the green anole lizard and a comparative analysis with birds and mammals. 

      Alföldi, Jessica; Di Palma, Federica; Grabherr, Manfred; Williams, Christina; Kong, Lesheng; Mauceli, Evan; Russell, Pamela; ... (50 authors) (Nature, 2011-08-31)
      The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. ...
    • Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. 

      Lowe, Craig B; Bejerano, Gill; Haussler, David (Proceedings of the National Academy of Sciences of the United States of America, 2007-05)
      At least 5% of the human genome predating the mammalian radiation is thought to have evolved under purifying selection, yet protein-coding and related untranslated exons occupy at most 2% of the genome. Thus, the majority ...
    • Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. 

      Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; ... (55 authors) (Science, 2014-12-12)
      To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), ...
    • Three periods of regulatory innovation during vertebrate evolution. 

      Lowe, Craig B; Kellis, Manolis; Siepel, Adam; Raney, Brian J; Clamp, Michele; Salama, Sofie R; Kingsley, David M; ... (9 authors) (Science (New York, N.Y.), 2011-08)
      The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, ...
    • Whole-genome analyses resolve early branches in the tree of life of modern birds. 

      Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon YW; ... (106 authors) (Science, 2014-12-12)
      To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered ...