Now showing items 1-20 of 73

    • A Genocentric Approach to Discovery of Mendelian Disorders. 

      Hansen, Adam W; Murugan, Mullai; Li, He; Khayat, Michael M; Wang, Liwen; Rosenfeld, Jill; Andrews, B Kim; ... (25 authors) (American journal of human genetics, 2019-11)
      The advent of inexpensive, clinical exome sequencing (ES) has led to the accumulation of genetic data from thousands of samples from individuals affected with a wide range of diseases, but for whom the underlying genetic ...
    • A genome-wide association study of upper aerodigestive tract cancers conducted within the INHANCE consortium. 

      McKay, James D; Truong, Therese; Gaborieau, Valerie; Chabrier, Amelie; Chuang, Shu-Chun; Byrnes, Graham; Zaridze, David; ... (130 authors) (PLoS genetics, 2011-03-17)
      Genome-wide association studies (GWAS) have been successful in identifying common genetic variation involved in susceptibility to etiologically complex disease. We conducted a GWAS to identify common genetic variation involved ...
    • A longitudinal study of epigenetic variation in twins. 

      Wong, Chloe Chung Yi; Caspi, Avshalom; Williams, Benjamin; Craig, Ian W; Houts, Renate; Ambler, Antony; Moffitt, Terrie E; ... (8 authors) (Epigenetics, 2010-08-16)
      DNA methylation is a key epigenetic mechanism involved in the developmental regulation of gene expression. Alterations in DNA methylation are established contributors to inter-individual phenotypic variation and have been ...
    • A molecular phylogeny of the fern family Pteridaceae: assessing overall relationships and the affinities of previously unsampled genera. 

      Schuettpelz, E; Schneider, H; Huiet, L; Windham, MD; Pryer, KM (Molecular phylogenetics and evolution, 2007-09)
      The monophyletic Pteridaceae accounts for roughly 10% of extant fern diversity and occupies an unusually broad range of ecological niches, including terrestrial, epiphytic, xeric-adapted rupestral, and even aquatic species. ...
    • A Quantitative Analysis of Growth and Size Regulation in Manduca sexta: The Physiological Basis of Variation in Size and Age at Metamorphosis. 

      Grunert, Laura W; Clarke, Jameson W; Ahuja, Chaarushi; Eswaran, Harish; Nijhout, H Frederik (PLoS One, 2015)
      Body size and development time are important life history traits because they are often highly correlated with fitness. Although the developmental mechanisms that control growth have been well studied, the mechanisms that ...
    • A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis. 

      Ribeiro, Ângela M; Zepeda-Mendoza, M Lisandra; Bertelsen, Mads F; Kristensen, Annemarie T; Jarvis, Erich D; Gilbert, M Thomas P; da Fonseca, Rute R (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 ...
    • Amino acid-level signal-to-noise analysis of incidentally identified variants in genes associated with long QT syndrome during pediatric whole exome sequencing reflects background genetic noise. 

      Landstrom, Andrew P; Fernandez, Ernesto; Rosenfeld, Jill A; Yang, Yaping; Dailey-Schwartz, Andrew L; Miyake, Christina Y; Allen, Hugh D; ... (9 authors) (Heart rhythm, 2018-07)
      BACKGROUND:Due to rapid expansion of clinical genetic testing, an increasing number of genetic variants of undetermined significance and unclear diagnostic value are being identified in children. Variants found in genes ...
    • An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease. 

      Wang, Liuyang; Pittman, Kelly J; Barker, Jeffrey R; Salinas, Raul E; Stanaway, Ian B; Williams, Graham D; Carroll, Robert J; ... (22 authors) (Cell host & microbe, 2018-08)
      Pathogens have been a strong driving force for natural selection. Therefore, understanding how human genetic differences impact infection-related cellular traits can mechanistically link genetic variation to disease ...
    • Analyses of pediatric isolates of Cryptococcus neoformans from South Africa. 

      Miglia, Kathleen J; Govender, Nelesh P; Rossouw, Jenny; Meiring, Susan; Mitchell, Thomas G; Group for Enteric, Respiratory and Meningeal Disease Surveillance in South Africa (J Clin Microbiol, 2011-01)
      Compared to the incidence in adults, cryptococcosis is inexplicably rare among children, even in sub-Saharan Africa, which has the highest prevalence of coinfection with HIV and Cryptococcus neoformans. To explore any mycological ...
    • Ancestral population genomics: the coalescent hidden Markov model approach. 

      Dutheil, Julien Y; Ganapathy, Ganesh; Hobolth, Asger; Mailund, Thomas; Uyenoyama, Marcy K; Schierup, Mikkel H (Genetics, 2009-09)
      With incomplete lineage sorting (ILS), the genealogy of closely related species differs along their genomes. The amount of ILS depends on population parameters such as the ancestral effective population sizes and ...
    • apex: phylogenetics with multiple genes. 

      Jombart, Thibaut; Archer, Frederick; Schliep, Klaus; Kamvar, Zhian; Harris, Rebecca; Paradis, Emmanuel; Goudet, Jérome; ... (8 authors) (Mol Ecol Resour, 2017-01)
      Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number ...
    • APOL1-G0 protects podocytes in a mouse model of HIV-associated nephropathy. 

      Bruggeman, Leslie A; Wu, Zhenzhen; Luo, Liping; Madhavan, Sethu; Drawz, Paul E; Thomas, David B; Barisoni, Laura; ... (9 authors) (PloS one, 2019-01)
      African polymorphisms in the gene for Apolipoprotein L1 (APOL1) confer a survival advantage against lethal trypanosomiasis but also an increased risk for several chronic kidney diseases (CKD) including HIV-associated nephropathy ...
    • Are the native giant tortoises from the Seychelles really extinct? A genetic perspective based on mtDNA and microsatellite data. 

      Palkovacs, EP; Marschner, M; Ciofi, C; Gerlach, J; Caccone, A (Mol Ecol, 2003-06)
      The extinction of the giant tortoises of the Seychelles Archipelago has long been suspected but is not beyond doubt. A recent morphological study of the giant tortoises of the western Indian Ocean concluded that specimens ...
    • Association of tumor necrosis factor-alpha promoter variants with risk of HPV-associated oral squamous cell carcinoma. 

      Jin, Lei; Sturgis, Erich M; Zhang, Yang; Huang, Zhigang; Song, Xicheng; Li, Chao; Wei, Qingyi; ... (8 authors) (Molecular cancer, 2013-07-19)
      Tumor necrosis factor alpha (TNF-α) plays an important role in inflammation, immunity, and defense against infection and clearance of human papillomavirus (HPV). Thus, genetic variants may modulate individual susceptibility ...
    • Can Genetics Predict Response to Complex Behavioral Interventions? Evidence from a Genetic Analysis of the Fast Track Randomized Control Trial. 

      Albert, Dustin; Belsky, Daniel W; Crowley, D Max; Latendresse, Shawn J; Aliev, Fazil; Riley, Brien; Group, Conduct Problems Prevention Research; ... (9 authors) (J Policy Anal Manage, 2015)
      Early interventions are a preferred method for addressing behavioral problems in high-risk children, but often have only modest effects. Identifying sources of variation in intervention effects can suggest means to improve ...
    • Captivity humanizes the primate microbiome. 

      Clayton, Jonathan B; Vangay, Pajau; Huang, Hu; Ward, Tonya; Hillmann, Benjamin M; Al-Ghalith, Gabriel A; Travis, Dominic A; ... (17 authors) (Proc Natl Acad Sci U S A, 2018-03-01)
      The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and ...
    • Common genetic variation and the control of HIV-1 in humans. 

      Fellay, Jacques; Ge, Dongliang; Shianna, Kevin V; Colombo, Sara; Ledergerber, Bruno; Cirulli, Elizabeth T; Urban, Thomas J; ... (38 authors) (PLoS Genet, 2009-12)
      To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants ...
    • Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana. 

      Chen, Yuan; Litvintseva, Anastasia P; Frazzitta, Aubrey E; Haverkamp, Miriam R; Wang, Liuyang; Fang, Charles; Muthoga, Charles; ... (9 authors) (Mol Ecol, 2015-07)
      Cryptococcus neoformans var. grubii (Cng) is the most common cause of fungal meningitis, and its prevalence is highest in sub-Saharan Africa. Patients become infected by inhaling airborne spores or desiccated yeast cells ...
    • Comparative genomics reveals insights into avian genome evolution and adaptation. 

      Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M; Lee, Chul; Storz, Jay F; ... (107 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. ...
    • 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), ...