Now showing items 21-40 of 55

    • Genomic variation and evolution of the human malaria parasite Plasmodium falciparum 

      Chang, Hsiao-Han (2013-10-08)
      Malaria is a deadly disease that causes nearly one million deaths each year. Understanding the demographic history of the malaria parasite Plasmodium falciparum and the genetic basis of its adaptations to antimalarial ...
    • Glycophorin B is the Erythrocyte Receptor of Plasmodium Falciparum Erythrocyte-Binding Ligand, EBL-1 

      Mayer, D. C. Ghislaine; Cofie, Joann; Jiang, Lubin; Hartl, Daniel L.; Tracy, Erin; Kabat, Juraj; Mendoza, Laurence H.; Miller, Louis H. (National Academy of Sciences, 2009)
      In the war against Plasmodium, humans have evolved to eliminate or modify proteins on the erythrocyte surface that serve as receptors for parasite invasion, such as the Duffy blood group, a receptor for Plasmodium vivax, ...
    • Harnessing evolutionary fitness in Plasmodium falciparum for drug discovery and suppressing resistance 

      Lukens, Amanda Kathleen; Ross, L. S.; Heidebrecht, Richard W; Javier Gamo, F.; Lafuente-Monasterio, M. J.; Booker, M. L.; Hartl, Daniel L.; Wiegand, R. C.; Wirth, Dyann F. (Proceedings of the National Academy of Sciences, 2013)
      Drug resistance emerges in an ecological context where fitness costs restrict the diversity of escape pathways. These pathways are targets for drug discovery, and here we demonstrate that we can identify small-molecule ...
    • Identification and Functional Validation of the Novel Antimalarial Resistance Locus PF10_0355 in Plasmodium falciparum 

      Van Tyne, Daria Natalie; Park, Daniel John; Schaffner, Stephen; Neafsey, Daniel Edward; Angelino, Elaine Lee; Cortese, Joseph F.; Barnes, Kayla G.; Rosen, David M.; Lukens, Amanda Kathleen; Daniels, Rachel Fath; Milner, Danny Arnold; Johnson, Charles A.; Shlyakhter, Ilya; Grossman, Sharon Rachel; Becker, Justin S.; Yamins, Daniel Louis Kanef; Karlsson, Elinor Kathryn; Ndiaye, Daouda; Sarr, Ousmane; Mboup, Souleymane; Happi, Christian Tientcha; Furlotte, Nicholas A.; Eskin, Eleazar; Kang, Hyun Min; Hartl, Daniel L.; Birren, Bruce W.; Wiegand, Roger C.; Lander, Eric Steven; Wirth, Dyann Fergus; Cooke, Sarah Volkman; Sabeti, Pardis Christine (Public Library of Science, 2011)
      The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis ...
    • Key Considerations for Measuring Allelic Expression on a Genomic Scale Using High-throughput Sequencing 

      Fontanillas, Pierre; Landry, Christian R.; Wittkopp, Patricia J.; Russ, Carsten; Gruber, Jonathan D.; Nusbaum, Chad; Hartl, Daniel L. (Blackwell Publishing, 2010)
      Differences in gene expression are thought to be an important source of phenotypic diversity, so dissecting the genetic components of natural variation in gene expression is important for understanding the evolutionary ...
    • The Latest Buzz in Comparative Genomics 

      Kulathinal, Rob J; Hartl, Daniel L. (BioMed Central, 2005)
      A second species of fruit fly has just been added to the growing list of organisms with complete and annotated genome sequences. The publication of the Drosophila pseudoobscura sequence provides a snapshot of how genomes ...
    • Malaria Life Cycle Intensifies Both Natural Selection and Random Genetic Drift 

      Chang, Hsiao-Han; Moss, Eli L.; Park, Daniel John; Ndiaye, Daouda; Mboup, Souleymane; Cooke, Sarah K.; Sabeti, Pardis Christine; Wirth, Dyann F.; Neafsey, Daniel Edward; Hartl, Daniel L. (Proceedings of the National Academy of Sciences, 2013)
      Analysis of genome sequences of 159 isolates of Plasmodium falciparum from Senegal yields an extraordinarily high proportion (26.85%) of protein-coding genes with the ratio of nonsynonymous to synonymous polymorphism greater ...
    • Meta-Analysis Reveals that Genes Regulated by the Y Chromosome in Drosophila melanogaster Are Preferentially Localized to Repressive Chromatin 

      Sackton, Timothy; Hartl, Daniel L. (Oxford University Press, 2013)
      The Drosophila Y chromosome is a degenerated, heterochromatic chromosome with few functional genes. Despite this, natural variation on the Y chromosome in D. melanogaster has substantial trans-acting effects on the regulation ...
    • Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria 

      Daniels, Rachel; Hamilton, Elizabeth J.; Durfee, Katelyn; Ndiaye, Daouda; Wirth, Dyann F.; Hartl, Daniel L.; Volkman, Sarah K. (MyJove Corporation, 2015)
      Despite decades of eradication efforts, malaria remains a global burden. Recent renewed interest in regional elimination and global eradication has been accompanied by increased genomic information about Plasmodium parasite ...
    • Model Transcriptional Networks with Continuously Varying Expression Levels 

      Carneiro, Mauricio O; Taubes, Clifford H.; Hartl, Daniel L. (BioMed Central, 2011)
      Background: At a time when genomes are being sequenced by the hundreds, much attention has shifted from identifying genes and phenotypes to understanding the networks of interactions among genes. We developed a gene network ...
    • Modeling malaria genomics reveals transmission decline and rebound in Senegal 

      Daniels, Rachel Fath; Schaffner, Stephen; Wenger, Edward A.; Proctor, Joshua L.; Chang, Hsiao-Han; Wong, Wesley Philip; Baro, Nicholas; Ndiaye, Daouda; Fall, Fatou Ba; Ndiop, Medoune; Ba, Mady; Milner, Danny Arnold; Taylor, Terrie E.; Neafsey, Daniel Edward; Cooke, Sarah K.; Eckhoff, Philip A.; Hartl, Daniel L.; Wirth, Dyann F. (Proceedings of the National Academy of Sciences, 2015)
      To study the effects of malaria-control interventions on parasite population genomics, we examined a set of 1,007 samples of the malaria parasite Plasmodium falciparum collected in Thiès, Senegal between 2006 and 2013. The ...
    • Natural Selection Constrains Neutral Diversity across A Wide Range of Species 

      Corbett-Detig, Russell B.; Hartl, Daniel L.; Sackton, Timothy B. (Public Library of Science, 2015)
      The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne ...
    • Natural Variation of the Y Chromosome Suppresses Sex Ratio Distortion and Modulates Testis-Specific Gene Expression in Drosophila Simulans 

      Branco, Alan; Tao, Y; Hartl, Daniel L.; Silva, Bernardo Lemos (Nature Publishing Group, 2013)
      X-linked sex-ratio distorters that disrupt spermatogenesis can cause a deficiency in functional Y-bearing sperm and a female-biased sex ratio. Y-linked modifiers that restore a normal sex ratio might be abundant and favored ...
    • A New Take on John Maynard Smith's Concept of Protein Space for Understanding Molecular Evolution 

      Ogbunugafor, C. Brandon; Hartl, Daniel L. (Public Library of Science, 2016)
      Much of the public lacks a proper understanding of Darwinian evolution, a problem that can be addressed with new learning and teaching approaches to be implemented both inside the classroom and in less formal settings. Few ...
    • Next-Generation Population Genomics: Inversion Polymorphisms, Segregation Distortion and Fitness Epistasis 

      Corbett-Detig, Russ Brendan (2014-06-06)
      Although population genetics has a long history and firm theoretical basis, until recently little data was available for empirical hypothesis testing. The unprecedented growth of sequencing methodologies has transformed ...
    • Novel Genes from Formation to Function 

      Ponce, Rita; Martinsen, Lene; Vicente, Luís M.; Hartl, Daniel L. (Hindawi Publishing Corporation, 2012)
      The study of the evolution of novel genes generally focuses on the formation of new coding sequences. However, equally important in the evolution of novel functional genes are the formation of regulatory regions that allow ...
    • Optimization of Gene Expression by Natural Selection 

      Bedford, Trevor; Hartl, Daniel L. (National Academy of Sciences, 2009)
      It is generally assumed that stabilizing selection promoting a phenotypic optimum acts to shape variation in quantitative traits across individuals and species. Although gene expression represents an intensively studied ...
    • Patterns of molecular evolution and epistasis on a genomic and genic scale 

      Jiang, Pan-Pan (2013-10-08)
      Epistasis describes non-additive interactions which affect gene expression and phenotype. It can happen on multiple levels, including on a genomic level with interactions between genes or even chromosomes affecting global ...
    • Population Genomic Inferences from Sparse High-Throughput Sequencing of Two Populations of Drosophila melanogaster 

      Sackton, Timothy; Kulathinal, Rob J.; Bergman, Casey M.; Quinlan, Aaron R.; Dopman, Erik B.; Carneiro, Mauricio Oliveira; Marth, Gabor T.; Hartl, Daniel L.; Clark, Andrew G. (Oxford University Press, 2009)
      Short-read sequencing techniques provide the opportunity to capture genome-wide sequence data in a single experiment. A current challenge is to identify questions that shallow-depth genomic data can address successfully ...
    • Positive Selection Drives Faster-Z Evolution in Silkmoths 

      Sackton, Timothy; Corbett-Detig, Russell B.; Nagaraju, Javaregowda; Vaishna, Lakshmi; Arunkumar, Kallare P.; Hartl, Daniel L. (Wiley-Blackwell, 2014)
      Genes linked to X or Z chromosomes, which are hemizygous in the heterogametic sex, are predicted to evolve at different rates than those on autosomes. This “faster-X effect” can arise either as a consequence of hemizygosity, ...