Now showing items 1-20 of 34

    • 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 genome-wide RNAi screen reveals multiple regulators of caspase activation. 

      Yi, Caroline H; Sogah, Dodzie K; Boyce, Michael; Degterev, Alexei; Christofferson, Dana E; Yuan, Junying (The Journal of cell biology, 2007-11-12)
      Apoptosis is an evolutionally conserved cellular suicide mechanism that can be activated in response to a variety of stressful stimuli. Increasing evidence suggests that apoptotic regulation relies on specialized cell death ...
    • 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 ...
    • Avian genomes. A flock of genomes. Introduction. 

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

      Eöry, Lél; Gilbert, M Thomas P; Li, Cai; Li, Bo; Archibald, Alan; Aken, Bronwen L; Zhang, Guojie; ... (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 ...
    • Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler. 

      Kepler, Thomas B; Sample, Christopher; Hudak, Kathryn; Roach, Jeffrey; Haines, Albert; Walsh, Allyson; Ramsburg, Elizabeth 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. ...
    • Comparison of pattern detection methods in microarray time series of the segmentation clock. 

      Dequéant, Mary-Lee; Ahnert, Sebastian; Edelsbrunner, Herbert; Fink, Thomas MA; Glynn, Earl F; Hattem, Gaye; Kudlicki, Andrzej; ... (15 authors) (PLoS One, 2008-08-06)
      While genome-wide gene expression data are generated at an increasing rate, the repertoire of approaches for pattern discovery in these data is still limited. Identifying subtle patterns of interest in large amounts of data ...
    • Core and region-enriched networks of behaviorally regulated genes and the singing genome. 

      Whitney, Osceola; Pfenning, Andreas R; Howard, Jason T; Blatti, Charles A; Liu, Fang; Ward, James M; Wang, Rui; ... (14 authors) (Science, 2014-12-12)
      Songbirds represent an important model organism for elucidating molecular mechanisms that link genes with complex behaviors, in part because they have discrete vocal learning circuits that have parallels with those that ...
    • EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. 

      Janies, Daniel A; Witter, Zach; Linchangco, Gregorio V; Foltz, David W; Miller, Allison K; Kerr, Alexander M; Jay, Jeremy; ... (9 authors) (BMC Bioinformatics, 2016-01-22)
      BACKGROUND: One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation transcriptome data. The current dataset is the ...
    • Evidence for a single loss of mineralized teeth in the common avian ancestor. 

      Meredith, Robert W; Zhang, Guojie; Gilbert, M Thomas P; Jarvis, Erich D; Springer, Mark S (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 ...
    • Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. 

      Weber, Claudia C; Boussau, Bastien; Romiguier, Jonathan; Jarvis, Erich D; Ellegren, Hans (Genome Biol, 2014)
      BACKGROUND: While effective population size (Ne) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC ...
    • Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds. 

      Borges, Rui; Borges, Rui; Khan, Imran; Johnson, Warren E; Gilbert, M Thomas P; Zhang, Guojie; Jarvis, Erich D; ... (9 authors) (BMC Genomics, 2015-10-06)
      BACKGROUND: The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the ...
    • Genome-wide identification of autosomal genes with allelic imbalance of chromatin state. 

      Savol, Andrej J; Wang, Peggy I; Jeon, Yesu; Colognori, David; Yildirim, Eda; Pinter, Stefan F; Payer, Bernhard; ... (9 authors) (PloS one, 2017-01)
      In mammals, monoallelic gene expression can result from X-chromosome inactivation, genomic imprinting, and random monoallelic expression (RMAE). Epigenetic regulation of RMAE is not fully understood. Here we analyze allelic ...
    • Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. 

      Carey, HV; Chang, L; Chen, C; Chen, T; Cheng, C; Gilbert, M Thomas P; Guo, Y; ... (33 authors) (Genome Biol, 2014)
      BACKGROUND: Nearly one-quarter of all avian species is either threatened or nearly threatened. Of these, 73 species are currently being rescued from going extinct in wildlife sanctuaries. One of the previously most ...
    • GREAT improves functional interpretation of cis-regulatory regions. 

      McLean, Cory Y; Bristor, Dave; Hiller, Michael; Clarke, Shoa L; Schaar, Bruce T; Lowe, Craig B; 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. ...
    • Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). 

      Larsen, Peter A; Harris, R Alan; Liu, Yue; Murali, Shwetha C; Campbell, C Ryan; Brown, Adam D; Sullivan, Beth A; ... (20 authors) (BMC biology, 2017-11-16)
      The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications. Here, we present an ...
    • Low frequency of paleoviral infiltration across the avian phylogeny. 

      Cui, Jie; Zhao, Wei; Huang, Zhiyong; Jarvis, Erich D; Gilbert, M Thomas P; Walker, Peter J; Holmes, Edward C; ... (8 authors) (Genome Biol, 2014)
      BACKGROUND: Mammalian genomes commonly harbor endogenous viral elements. Due to a lack of comparable genome-scale sequence data, far less is known about endogenous viral elements in avian species, even though their small ...
    • Mitochondrial DNA polymorphism A4917G is independently associated with age-related macular degeneration. 

      Canter, Jeffrey A; Olson, Lana M; Spencer, Kylee; Schnetz-Boutaud, Nathalie; Anderson, Brent; Hauser, Michael A; Schmidt, Silke; ... (12 authors) (PLoS One, 2008-05-07)
      The objective of this study was to determine if MTND2*LHON4917G (4917G), a specific non-synonymous polymorphism in the mitochondrial genome previously associated with neurodegenerative phenotypes, is associated with increased ...
    • Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida. 

      Khan, Imran; Yang, Zhikai; Maldonado, Emanuel; Li, Cai; Zhang, Guojie; Gilbert, M Thomas P; Jarvis, Erich D; ... (10 authors) (Mol Biol Evol, 2015-11)
      Olfactory receptors (ORs) govern a prime sensory function. Extant birds have distinct olfactory abilities, but the molecular mechanisms underlining diversification and specialization remain mostly unknown. We explored OR ...