Now showing items 1-16 of 16

    • Breakdown in the Process of Incipient Speciation in Anopheles gambiae 

      Nwakanma, Davis C.; Neafsey, Daniel Edward; Jawara, Musa; Adiamoh, Majidah; Lund, Emily; Rodrigues, Amabelia; Loua, Kovana M.; Konate, Lassana; Sy, Ngayo; Dia, Ibrahima; Awolola, T. Samson; Muskavitch, Marc; Conway, David J. (Genetics Society of America, 2013)
      Understanding genetic causes and effects of speciation in sympatric populations of sexually reproducing eukaryotes is challenging, controversial, and of practical importance for controlling rapidly evolving pests and ...
    • Cross-kingdom patterns of alternative splicing and splice recognition 

      McGuire, Abigail M; Pearson, Matthew D; Neafsey, Daniel Edward; Galagan, James E (BioMed Central, 2008)
      Background: Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of splice site recognition ...
    • A General SNP-Based Molecular Barcode for Plasmodium Falciparum Identification and Tracking 

      Mahesh, Nira; Rosen, David; Daniels, Rachel; Volkman, Sarah K.; Milner, Danny Arnold; Neafsey, Daniel Edward; Park, Daniel John; Angelino, Elaine; Sabeti, Pardis Christine; Wirth, Dyann Fergus; Wiegand, Roger C. (BioMed Central, 2008)
      Background: Single nucleotide polymorphism (SNP) genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite using a small amount of DNA. ...
    • Genetic Surveillance Detects Both Clonal and Epidemic Transmission of Malaria following Enhanced Intervention in Senegal 

      Daniels, Rachel Fath; Chang, Hsiao-Han; Séne, Papa Diogoye; Park, Danny C.; Neafsey, Daniel Edward; Schaffner, Stephen; Hamilton, Elizabeth Julia; Lukens, Amanda Kathleen; Van Tyne, Daria Natalie; Mboup, Souleymane; Sabeti, Pardis Christine; Ndiaye, Daouda; Wirth, Dyann Fergus; Hartl, Daniel L.; Cooke, Sarah Volkman (Public Library of Science, 2013)
      Using parasite genotyping tools, we screened patients with mild uncomplicated malaria seeking treatment at a clinic in Thiès, Senegal, from 2006 to 2011. We identified a growing frequency of infections caused by genetically ...
    • Genome-Wide SNP Genotyping Highlights the Role of Natural Selection in Plasmodium Falciparum Population Divergence 

      Wirth, Dyann F.; Sabeti, Pardis C.; Lander, Eric S.; Birren, Bruce W.; Hartl, Daniel; Wiegand, Roger; Chitnis, Chetan E.; Dash, Aditya P.; do Lago Moraes, Sandra; Ferreira, Marcelo U.; Mboup, Soulyemane; Ndir, Omar; Ndiaye, Daouda; Ousmane, Sarr; Stange-Thomann, Nicole; Gates, Casey; Tyndall, Erin; Cortese, Joseph F.; Houde, Nathan; Daniels, Rachel; Rosen, David; Lukens, Amanda; Milner, Danny; Montgomery, Philip; Park, Daniel; Volkman, Sarah K.; Schaffner, Stephen F.; Neafsey, Daniel (BioMed Central, 2008)
      Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun ...
    • A genomic and evolutionary approach reveals non-genetic drug resistance in malaria 

      Herman, Jonathan D; Rice, Daniel P; Ribacke, Ulf; Silterra, Jacob; Deik, Amy A; Moss, Eli L; Broadbent, Kate M; Neafsey, Daniel E; Desai, Michael M; Clish, Clary B; Mazitschek, Ralph; Wirth, Dyann F (BioMed Central, 2014)
      Background: Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis ...
    • Human Cerebral Malaria and Plasmodium falciparum Genotypes in Malawi 

      Milner, Danny Arnold; Vareta, Jimmy; Valim, Clarissa; Montgomery, Jacqui; Daniels, Rachel Fath; Cooke, Sarah Volkman; Neafsey, Daniel Edward; Park, Daniel John; Schaffner, Stephen; Mahesh, Nira C; Barnes, Kayla G; Rosen, David M; Lukens, Amanda Kathleen; Van-Tyne, Daria; Wiegand, Roger C.; Sabeti, Pardis Christine; Seydel, Karl B; Glover, Simon J; Kamiza, Steve; Molyneux, Malcolm E; Taylor, Terrie E; Wirth, Dyann Fergus (BioMed Central, 2012)
      Background: Cerebral malaria, a severe form of Plasmodium falciparum infection, is an important cause of mortality in sub-Saharan African children. A Taqman 24 Single Nucleotide Polymorphisms (SNP) molecular barcode assay ...
    • 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 ...
    • 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 ...
    • Mechanisms of Intron Gain and Loss in Cryptococcus 

      Sharpton, Thomas J; Neafsey, Daniel Edward; Galagan, James E; Taylor, John W (BioMed Central, 2008)
      Background: Genome comparisons across deep phylogenetic divergences have revealed that spliceosomal intron gain and loss are common evolutionary events. However, because of the deep divergences involved in these comparisons, ...
    • 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 ...
    • Patterns of Genomic Differentiation between Ecologically Differentiated M and S Forms of Anopheles gambiae in West and Central Africa 

      Reidenbach, Kyanne R.; Neafsey, Daniel Edward; Costantini, Carlo; Sagnon, N’Fale; Simard, Frédéric; Ragland, Gregory J.; Egan, Scott P.; Feder, Jeffrey L.; Muskavitch, Marc; Besansky, Nora J. (Oxford University Press, 2012)
      Anopheles gambiae M and S are thought to be undergoing ecological speciation by adapting to different larval habitats. Toward an improved understanding of the genetic determinants and evolutionary processes shaping their ...
    • Positive Selection for Unpreferred Codon Usage in Eukaryotic Genomes 

      Neafsey, Daniel Edward; Galagan, James E (BioMed Central, 2007)
      Background: Natural selection has traditionally been understood as a force responsible for pushing genes to states of higher translational efficiency, whereas lower translational efficiency has been explained by neutral ...
    • Sequence-Based Association and Selection Scans Identify Drug Resistance Loci in the Plasmodium Falciparum Malaria Parasite 

      Park, Daniel John; Lukens, Amanda Kathleen; Neafsey, Daniel Edward; Schaffner, Stephen; Chang, Hsiao-Han; Valim, Clarissa; Ribacke, Ulf Erik; Van Tyne, Daria Natalie; Galinsky, Kevin Joseph; Galligan, Meghan; Becker, Justin S.; Ndiaye, Daouda; Mboup, Souleymane; Wiegand, Roger C.; Hartl, Daniel L.; Sabeti, Pardis Christine; Wirth, Dyann F.; Cooke, Sarah K. (Proceedings of the National Academy of Sciences, 2012)
      Through rapid genetic adaptation and natural selection, the Plasmodium falciparum parasite—the deadliest of those that cause malaria—is able to develop resistance to antimalarial drugs, thwarting present efforts to control ...
    • SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites 

      Amambua-Ngwa, Alfred; Barnes, Kayla G.; Sene, Papa; Conway, David J.; Park, Daniel John; Volkman, Sarah; Bei, Amy Kristine; Lukens, Amanda Kathleen; Van Tyne, Daria Natalie; Ndiaye, Daouda; Wirth, Dyann Fergus; Neafsey, Daniel Edward; Schaffner, Stephen (Oxford University Press, 2012)
      We used a high-density single-nucleotide polymorphism array to genotype 75 Plasmodium falciparum isolates recently collected from Senegal and The Gambia to search for signals of selection in this malaria endemic region. ...
    • Stepwise Acquisition of Pyrimethamine Resistance in the Malaria Parasite 

      Lozovsky, Elena; Chookajorn, Thanat; Brown, Kyle M.; Imwong, Mallika; Shaw, Philip J.; Kamchonwongpaisan, Sumalee; Neafsey, Daniel Edward; Weinreich, Daniel M.; Hartl, Daniel L. (National Academy of Sciences, 2009)
      The spread of high-level pyrimethamine resistance in Africa threatens to curtail the therapeutic lifetime of antifolate antimalarials. We studied the possible evolutionary pathways in the evolution of pyrimethamine resistance ...