Now showing items 1-10 of 10

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

      Lowe, Craig; 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. 

      Lowe, Craig; Lindblad-Toh, Kerstin; Garber, Manuel; Zuk, Or; Lin, Michael F; Parker, Brian J; Washietl, Stefan; ... (86 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 ...
    • Detecting differential copy number variation between groups of samples 

      Lowe, Craig; Sanchez-Luege, Nicelio; Howes, Timothy R; Brady, Shannon D; Daugherty, Rhea R; Jones, Felicity C; Bell, Michael A; ... (8 authors) (Genome Research, 2018-02)
      © 2018 Lowe et al. We present a method to detect copy number variants (CNVs) that are differentially present between two groups of sequenced samples. We use a finite-state transducer where the emitted read depth is conditioned ...
    • Endangered species hold clues to human evolution. 

      Lowe, Craig; 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; 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 ...
    • GREAT improves functional interpretation of cis-regulatory regions. 

      Lowe, Craig; McLean, Cory Y; Bristor, Dave; Hiller, Michael; Clarke, Shoa L; Schaar, Bruce T; Wenger, Aaron M; ... (8 authors) (Nature biotechnology, 2010-05-02)
      We developed the Genomic Regions Enrichment of Annotations Tool (GREAT) to analyze the functional significance of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. ...
    • Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53 

      Lowe, Craig; Wang, T; Zeng, J; Sellers, RG; Salama, SR; Yang, M; Burgess, SM; ... (9 authors) (Proceedings of the National Academy of Sciences, 2007-11-20)
    • The genome of the green anole lizard and a comparative analysis with birds and mammals. 

      Lowe, Craig; Alföldi, Jessica; Di Palma, Federica; Grabherr, Manfred; Williams, Christina; Kong, Lesheng; Mauceli, Evan; ... (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; 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 periods of regulatory innovation during vertebrate evolution. 

      Lowe, Craig; 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, ...