Browsing FAS Scholarly Articles by Keyword "genomics"

Now showing items 1-20 of 28

    • America's red gold: multiple lineages of cultivated cochineal in Mexico 

      Campana, Michael G; Robles García, Nelly M; Tuross, Noreen (BlackWell Publishing Ltd, 2015)
      Cultivated cochineal (Dactylopius coccus) produces carminic acid, a valuable red dye used to color textiles, cosmetics, and food. Extant native D. coccus is largely restricted to two populations in the Mexican and the ...

    • Automatic Categorization of Diverse Experimental Information in the Bioscience Literature 

      Fang, Ruihua; Schindelman, Gary; Auken, Kimberly Van; Fernandes, Jolene; Chen, Wen; Wang, Xiaodong; Davis, Paul; Tuli, Mary Ann; Marygold, Steven J; Millburn, Gillian; Matthews, Beverley; Zhang, Haiyan; Brown, Nick; Gelbart, William Martin; Sternberg, Paul W (BioMed Central, 2012)
      Background: Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical ...

    • Bayesian Nonparametric Inference of Population Size Changes from Sequential Genealogies 

      Palacios, Julia A.; Wakeley, John; Ramachandran, Sohini (Genetics Society of America, 2015)
      Sophisticated inferential tools coupled with the coalescent model have recently emerged for estimating past population sizes from genomic data. Recent methods that model recombination require small sample sizes, make ...

    • A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules 

      Zhang, Wei; Zhu, Jun; Schadt, Eric E.; Liu, Jun; Stormo, Gary D. (Public Library of Science, 2010)
      Studies of the relationship between DNA variation and gene expression variation, often referred to as “expression quantitative trait loci (eQTL) mapping”, have been conducted in many species and resulted in many significant ...

    • Burkholderia Xenovorans LB400 Harbors a Multi-Replicon, 9.73-Mbp Genome Shaped for Versatility 

      Konstantinidis, Konstantinos T.; Seeger, Michael; Vergez, Lisa M.; Chain, Patrick S. G.; Malfatti, Stephanie A.; Denef, Vincent J.; Zhulin, Igor B.; Mahenthiralingam, Eshwar; LiPuma, John J.; Lao, Victoria; Larimer, Frank; Cordova, Macarena; Sul, Woo Jun; Tiedje, James M.; Spilker, Theodore; Land, Miriam; Tsoi, Tamara V.; Ulrich, Luke E.; Reyes, Valeria Latorre; Agullo, Loreine; Smith, Daryl; Parnell, J. Jacob; Ramette, Alban; Hauser, Loren; Richardson, Paul; Marx, Christopher; Gonzalez, Myriam; Gomez, Luis (National Academy of Sciences, 2006)
      <i>Burkholderia xenovorans</i> LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic <i>Burkholderia</i> isolate ...

    • A Careful Look at Binding Site Reorganization in the even-skipped Enhancers of Drosophila and Sepsids 

      Hare, Emily E.; Peterson, Brant K.; Eisen, Michael B. (Public Library of Science, 2008)

    • The Case for Selection at CCR5-Δ32 

      Walsh, Emily; Schaffner, Steve F; Varilly, Patrick; Fry, Ben; Hutcheson, Holli B; Cullen, Mike; Mikkelsen, Tarjei S; Roy, Jessica; Patterson, Nick; Sabeti, Pardis Christine; Cooper, Richard; Reich, David Emil; Altshuler, David Matthew; O'Brien, Stephen James; Lander, Eric Steven (Public Library of Science, 2005)
      The C-C chemokine receptor 5, 32 base-pair deletion (CCR5-Δ32) allele confers strong resistance to infection by the AIDS virus HIV. Previous studies have suggested that CCR5-Δ32 arose within the past 1,000 y and rose to ...

    • Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single-Molecule Barcodes 

      Shiroguchi, Katsuyuki; Jia, Tony Z; Sims, Peter A.; Xie, Xiaoliang Sunney (Proceedings of the National Academy of Sciences, 2012)
      RNA sequencing (RNA-Seq) is a powerful tool for transcriptome profiling, but is hampered by sequence-dependent bias and inaccuracy at low copy numbers intrinsic to exponential PCR amplification. We developed a simple ...

    • Discovering Communities through Friendship 

      Morrison, Gregory C.; Mahadevan, Lakshminarayanan (Public Library of Science, 2012)
      We introduce a new method for detecting communities of arbitrary size in an undirected weighted network. Our approach is based on tracing the path of closest‐friendship between nodes in the network using the recently ...

    • Evolutionary Dynamics of Intron Size, Genome Size, and Physiological Correlates in Archosaurs 

      Waltari, Eric; Edwards, Scott (University of Chicago Press, 2002)
      It has been proposed that intron and genome sizes in birds are reduced in comparison with mammals because of the metabolic demands of flight. To test this hypothesis, we examined the sizes of 14 introns in a nonflying ...

    • Expression and Putative Function of Innate Immunity Genes under In Situ Conditions in the Symbiotic Hydrothermal Vent Tubeworm Ridgeia piscesae 

      Nyholm, Spencer V.; Song, Pengfei; Dang, Jeanne; Bunce, Corey; Girguis, Peter R. (Public Library of Science, 2012)
      The relationships between hydrothermal vent tubeworms and sulfide-oxidizing bacteria have served as model associations for understanding chemoautotrophy and endosymbiosis. Numerous studies have focused on the physiological ...

    • Genetic Determinism, Technology Optimism, and Race: Views of the American Public 

      Hochschild, Jennifer L.; Sen, Maya (SAGE Publications, 2015)
      We begin with a typology of Americans’ understanding of the links between genetic inheritance and racial or ethnic groups. The typology has two dimensions: one running from genetic determinism to social construction, and ...

    • Genome Landscapes and Bacteriophage Codon Usage 

      Lucks, Julius B.; Nelson, David R.; Kudla, Grzegorz R.; Plotkin, Joshua B.; Regev, Aviv (Public Library of Science, 2008)
      Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonymous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes ...

    • Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in the Heliconius melpomene Clade 

      Baxter, Simon W.; Nadeau, Nicola J.; Maroja, Luana S.; Wilkinson, Paul; Counterman, Brian A.; Dawson, Anna; Beltran, Margarita; Perez-Espona, Silvia; Ferguson, Laura; Davidson, Claire; Glithero, Rebecca; Mallet, James; Joron, Mathieu; ffrench-Constant, Richard H.; Jiggins, Chris D.; Chamberlain, Nicola L; Clark, Richard; McMillan, W. Owen; Kronforst, Marcus (Public Library of Science, 2010)
      Wing patterning in Heliconius butterflies is a longstanding example of both Müllerian mimicry and phenotypic radiation under strong natural selection. The loci controlling such patterns are “hotspots” for adaptive evolution ...

    • GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units 

      Zandevakili, Pooya; Hu, Ming; Qin, Zhaohui (Public Library of Science, 2012)
      Computational detection of TF binding patterns has become an indispensable tool in functional genomics research. With the rapid advance of new sequencing technologies, large amounts of protein-DNA interaction data have ...

    • High-Resolution Mutation Mapping Reveals Parallel Experimental Evolution in Yeast 

      Segrè, Ayellet V; Murray, Andrew W.; Leu, Jun-Yi (Public Library of Science, 2006)
      Understanding the genetic basis of evolutionary adaptation is limited by our ability to efficiently identify the genomic locations of adaptive mutations. Here we describe a method that can quickly and precisely map the ...

    • Meningioma Genomics: Diagnostic, Prognostic, and Therapeutic Applications 

      Bi, Wenya Linda; Zhang, Michael; Wu, Winona W.; Mei, Yu; Dunn, Ian F. (Frontiers Media S.A., 2016)
      There has been a recent revolution in our understanding of the genetic factors that drive meningioma, punctuating an equilibrium that has existed since Cushing’s germinal studies nearly a century ago. A growing appreciation ...

    • Molecular Organization of Vomeronasal Chemoreception 

      Isogai, Yoh; Si, Sheng; Pont-Lezica, Lorena; Tan, Taralyn Marie; Kapoor, Vikrant; Murthy, Venkatesh N.; Dulac, Catherine (Nature Publishing Group, 2011)
      The vomeronasal organ (VNO) has a key role in mediating the social and defensive responses of many terrestrial vertebrates to species- and sex-specific chemosignals. More than 250 putative pheromone receptors have been ...

    • Phylogenomics of Unusual Histone H2A Variants in Bdelloid Rotifers 

      Van Doninck, Karine; Mandigo, Morgan L.; Hur, Jae H.; Wang, Peter; Guglielmini, Julien; Milinkovitch, Michel C.; Lane, William S.; Meselson, Matthew Stanley; Malik, Harmit S. (Public Library of Science, 2009)
      Rotifers of Class Bdelloidea are remarkable in having evolved for millions of years, apparently without males and meiosis. In addition, they are unusually resistant to desiccation and ionizing radiation and are able to ...

    • Race and IQ in the postgenomic age: The microcephaly case 

      Richardson, Sarah S (Nature Publishing Group, 2011)
      A convergence of contextual factors, technological platforms and research frameworks in the genomics of the human brain and cognition has generated a new postgenomic model for the study of race and IQ. Centered on the case ...