Now showing items 1-20 of 51

    • A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses. 

      Koelle, K; Mattingly, Jonathan Christopher; Pasour, Virginia B; Rasmussen, DA; Ratmann, O (Proc Biol Sci, 2011-12-22)
      Antigenically variable RNA viruses are significant contributors to the burden of infectious disease worldwide. One reason for their ubiquity is their ability to escape herd immunity through rapid antigenic evolution and ...
    • 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 ...
    • A modular switch for spatial Ca2+ selectivity in the calmodulin regulation of CaV channels. 

      Dick, IE; Tadross, Michael Raphael; Liang, H; Tay, LH; Yang, W; Yue, DT (Nature, 2008-02-14)
      Ca2+/calmodulin-dependent regulation of voltage-gated CaV1-2 Ca2+ channels shows extraordinary modes of spatial Ca2+ decoding and channel modulation, vital for many biological functions. A single calmodulin (CaM) molecule ...
    • A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis. 

      Bertelsen, MF; da Fonseca, RR; Gilbert, M Thomas P; Jarvis, Erich David; Kristensen, AT; Ribeiro, Ângela M; Zepeda-Mendoza, ML (BMC Evol Biol, 2015-06-30)
      BACKGROUND: Hemostasis is a defense mechanism that enhances an organism's survival by minimizing blood loss upon vascular injury. In vertebrates, hemostasis has been evolving with the cardio-vascular and hemodynamic systems ...
    • 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 ...
    • Beta2-adrenergic receptor gene polymorphisms as systemic determinants of healthy aging in an evolutionary context. 

      Arbeev, Konstantin; Culminskaya, IV; Kulminski, Alexander; Land, Kenneth C; Ukraintseva, Svetlana; Yashin, Anatoli I (Mech Ageing Dev, 2010-05)
      The Gln(27)Glu polymorphism but not the Arg(16)Gly polymorphism of the beta2-adrenergic receptor (ADRB2) gene appears to be associated with a broad range of aging-associated phenotypes, including cancers at different sites, ...
    • Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. 

      Alam, S Munir; Boyd, SD; Cai, Fangping; Chen, S; Chen, Y; Cohen, M; Du, X; ... (45 authors) (Nature, 2013-04-25)
      Current human immunodeficiency virus-1 (HIV-1) vaccines elicit strain-specific neutralizing antibodies. However, cross-reactive neutralizing antibodies arise in approximately 20% of HIV-1-infected individuals, and details ...
    • 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. ...
    • Complex evolutionary trajectories of sex chromosomes across bird taxa. 

      An, N; Bachtrog, D; Gilbert, M Thomas P; Huang, Q; Jarvis, Erich David; Zhang, G; Zhang, J; ... (8 authors) (Science, 2014-12-12)
      Sex-specific chromosomes, like the W of most female birds and the Y of male mammals, usually have lost most genes owing to a lack of recombination. We analyze newly available genomes of 17 bird species representing the avian ...
    • Conservation, duplication, and loss of the Tor signaling pathway in the fungal kingdom. 

      Bastidas, RJ; Cardenas, Maria E; Heitman, Joseph; Li, W; Shertz, CA (BMC Genomics, 2010-09-23)
      BACKGROUND: The nutrient-sensing Tor pathway governs cell growth and is conserved in nearly all eukaryotic organisms from unicellular yeasts to multicellular organisms, including humans. Tor is the target of the immunosuppressive ...
    • Convergent transcriptional specializations in the brains of humans and song-learning birds. 

      Bakken, T; Bernard, A; Bongaarts, A; Ganapathy, G; Gilbert, M Thomas P; Hara, E; Hartemink, Alexander J; ... (25 authors) (Science, 2014-12-12)
      Song-learning birds and humans share independently evolved similarities in brain pathways for vocal learning that are essential for song and speech and are not found in most other species. Comparisons of brain transcriptomes ...
    • Delimiting species without nuclear monophyly in Madagascar's mouse lemurs. 

      Fiorentino, I; Goodman, SM; Kappeler, PM; Ralison, JM; Rasoloarison, RM; Weisrock, DW; Yoder, Anne Daphne (PLoS One, 2010-03-31)
      BACKGROUND: Speciation begins when populations become genetically separated through a substantial reduction in gene flow, and it is at this point that a genetically cohesive set of populations attain the sole property of ...
    • 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), ...
    • Distinctive variation in the U3R region of the 5' Long Terminal Repeat from diverse HIV-1 strains. 

      Anderson, Lettie; Denny, Thomas; Mbondji-Wonje, Christelle; Dong, Ming; Wang, Xue; Zhao, Jiangqin; Ragupathy, Viswanath; ... (9 authors) (PloS one, 2018-01)
      Functional mapping of the 5'LTR has shown that the U3 and the R regions (U3R) contain a cluster of regulatory elements involved in the control of HIV-1 transcription and expression. As the HIV-1 genome is characterized by ...
    • 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 ...
    • Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles. 

      Bao, W; Gilbert, M Thomas P; Greenwold, MJ; Hu, H; Jarvis, Erich David; Li, C; Sawyer, RH; ... (8 authors) (BMC Evol Biol, 2014-12-12)
      BACKGROUND: Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We ...
    • 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 ...
    • 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 ...
    • Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. 

      Boussau, B; Ellegren, Hans; Jarvis, Erich David; Romiguier, J; Weber, Claudia C (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 ...
    • Evidence that the human pathogenic fungus Cryptococcus neoformans var. grubii may have evolved in Africa. 

      Carbone, I; Govender, NP; Litvintseva, AP; Mitchell, Thomas Greenfield; Rossouw, J; Thakur, R (PLoS One, 2011-05-11)
      Most of the species of fungi that cause disease in mammals, including Cryptococcus neoformans var. grubii (serotype A), are exogenous and non-contagious. Cryptococcus neoformans var. grubii is associated worldwide with avian ...