Now showing items 1-20 of 44

    • 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 ...
    • An Exploration into Fern Genome Space. 

      Banks, JA; Der, JP; Gitzendanner, MA; Li, FW; Marchant, DB; Pryer, Kathleen M; Rothfels, CJ; ... (13 authors) (Genome Biol Evol, 2015-08-26)
      Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, ...
    • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. 

      Adachi, J; Aizawa, K; Arakawa, T; Baldarelli, R; Batalov, S; Beisel, KW; Birney, E; ... (139 authors) (Nature, 2002-12-05)
      Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure ...
    • Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements. 

      Lekprasert, P; Mayhew, M; Ohler, Uwe (PLoS One, 2011)
      BACKGROUND: Many computational microRNA target prediction tools are focused on several key features, including complementarity to 5'seed of miRNAs and evolutionary conservation. While these features allow for successful ...
    • Avian genomes. A flock of genomes. Introduction. 

      Gilbert, M Thomas P; Jarvis, Erich David; Zhang, G (Science, 2014-12-12)
    • Avianbase: a community resource for bird genomics. 

      Aken, BL; Archibald, A; Burt, DW; Eöry, L; Flicek, P; Gilbert, M Thomas P; Jarvis, Erich David; ... (10 authors) (Genome Biol, 2015-01-29)
      Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore ...
    • Behavior genetics and postgenomics. 

      Charney, Evan (Behav Brain Sci, 2012-10)
      The science of genetics is undergoing a paradigm shift. Recent discoveries, including the activity of retrotransposons, the extent of copy number variations, somatic and chromosomal mosaicism, and the nature of the epigenome ...
    • Between two fern genomes. 

      Banks, JA; Barker, MS; Der, JP; Duffy, AM; Graham, SW; Hasebe, M; Langdale, J; ... (19 authors) (Gigascience, 2014)
      Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution ...
    • Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler. 

      Haines, A; Hudak, K; Kepler, TB; Ramsburg, Elizabeth A; Roach, J; Sample, C; Walsh, A (BMC Genomics, 2010-07-21)
      BACKGROUND: The rate of emergence of human pathogens is steadily increasing; most of these novel agents originate in wildlife. Bats, remarkably, are the natural reservoirs of many of the most pathogenic viruses in humans. ...
    • 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. ...
    • Comparative genomics reveals molecular features unique to the songbird lineage. 

      Jarvis, Erich David; Lovell, PV; Mello, CV; Wirthlin, M (BMC Genomics, 2014-12-13)
      BACKGROUND: Songbirds (oscine Passeriformes) are among the most diverse and successful vertebrate groups, comprising almost half of all known bird species. Identifying the genomic innovations that might be associated with ...
    • Detecting structure of haplotypes and local ancestry. 

      Guan, Yongtao (Genetics, 2014-03)
      We present a two-layer hidden Markov model to detect the structure of haplotypes for unrelated individuals. This allows us to model two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), ...
    • Dissecting the Functional Impacts of Non-Coding Genetic Variation 

      Guo, Cong (2016)
      A large proportion of the variation in traits between individuals can be attributed to variation in the nucleotide sequence of the genome. The most commonly studied traits in human genetics are related to disease and disease ...
    • DOK2 inhibits EGFR-mutated lung adenocarcinoma. 

      Chen, Ming; Berger, Alice H; Morotti, Alessandro; Janas, Justyna A; Niki, Masaru; Bronson, Roderick T; Taylor, Barry S; ... (12 authors) (PloS one, 2013-01)
      Somatic mutations in the EGFR proto-oncogene occur in ~15% of human lung adenocarcinomas and the importance of EGFR mutations for the initiation and maintenance of lung cancer is well established from mouse models and cancer ...
    • Dynamic evolution of base composition: causes and consequences in avian phylogenomics. 

      Ellegren, Hans; Jarvis, Erich David; Künstner, A; Nabholz, B; Wang, R (Mol Biol Evol, 2011-08)
      Resolving the phylogenetic relationships among birds is a classical problem in systematics, and this is particularly so when it comes to understanding the relationships among Neoaves. Previous phylogenetic inference of birds ...
    • Educating future providers of personalized medicine. 

      Gilliss, Catherine; Dungan, Jennifer; Ginsburg, Geoffrey; Katsanis, Sara (North Carolina medical journal, 2013-11)
    • Evidence for a single loss of mineralized teeth in the common avian ancestor. 

      Gilbert, M Thomas P; Jarvis, Erich David; Meredith, RW; Springer, MS; Zhang, G (Science, 2014-12-12)
      Edentulism, the absence of teeth, has evolved convergently among vertebrates, including birds, turtles, and several lineages of mammals. Instead of teeth, modern birds (Neornithes) use a horny beak (rhamphotheca) and a muscular ...
    • Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates. 

      Antunes, A; Gilbert, M Thomas P; Jarvis, Erich David; Johnson, WE; O'Brien, Stephen J; Pereira, J; Vasconcelos, V; ... (8 authors) (PLoS One, 2014)
      The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems ...
    • 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 ...
    • Finding our way through phenotypes. 

      Anzaldo, SS; Ashburner, M; Balhoff, JP; Blackburn, DC; Blake, JA; Burleigh, JG; Chanet, B; ... (74 authors) (PLoS Biol, 2015-01)
      Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable ...