Browsing by Author "Chang, Hsiao-Han"

Now showing items 1-14 of 14

    • The Distribution of Pairwise Genetic Distances: A Tool for Investigating Disease Transmission 

      Worby, Colin J.; Chang, Hsiao-Han; Hanage, William P.; Lipsitch, Marc (Genetics Society of America, 2014)
      Whole-genome sequencing of pathogens has recently been used to investigate disease outbreaks and is likely to play a growing role in real-time epidemiological studies. Methods to analyze high-resolution genomic data in ...

    • The Evolution and Functional Significance of Nested Gene Structures in Drosophila melanogaster 

      Lee, Yuh Chwen G.; Chang, Hsiao-Han (Oxford University Press, 2013-10-01)
      Nearly ten percent of the genes in the genome of Drosophila melanogaster are in nested structures, in which one gene is completely nested within the intron of another gene (nested and including gene, respectively). Even ...

    • 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 ...

    • 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 ...

    • 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 ...

    • 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 ...

    • Origin and Proliferation of Multiple-Drug Resistance in Bacterial Pathogens 

      Chang, Hsiao-Han; Cohen, Ted; Grad, Yonatan Hagai; Hanage, William P.; O, Thomas F.; Lipsitch, Marc (American Society for Microbiology, 2015)
      SUMMARY: Many studies report the high prevalence of multiply drug-resistant (MDR) strains. Because MDR infections are often significantly harder and more expensive to treat, they represent a growing public health threat. ...

    • Persistence of Plasmodium falciparum parasitemia after artemisinin combination therapy: evidence from a randomized trial in Uganda 

      Chang, Hsiao-Han; Meibalan, Elamaran; Zelin, Justin; Daniels, Rachel; Eziefula, Alice C.; Meyer, Evan C.; Tadesse, Fitsum; Grignard, Lynn; Joice, Regina C.; Drakeley, Chris; Wirth, Dyann F.; Volkman, Sarah K.; Buckee, Caroline; Bousema, Teun; Marti, Matthias (Nature Publishing Group, 2016)
      Artemisinin resistance is rapidly spreading in Southeast Asia. The efficacy of artemisinin-combination therapy (ACT) continues to be excellent across Africa. We performed parasite transcriptional profiling and genotyping ...

    • Recurrent bottlenecks in the malaria life cycle obscure signals of positive selection 

      Chang, Hsiao-Han; Hartl, Daniel L. (Cambridge University Press (CUP), 2014)
      Detecting signals of selection in the genome of malaria parasites is a key to identify targets for drug and vaccine development. Malaria parasites have a unique life cycle alternating between vector and host organism with ...

    • Sequence tag–based analysis of microbial population dynamics 

      Abel, Sören; Abel zur Wiesch, Pia; Chang, Hsiao-Han; Davis, Brigid; Lipsitch, Marc; Waldor, Matthew K (Nature Publishing Group, 2015)
      We describe sequence tag-based analysis of microbial populations (STAMP) for characterization of pathogen population dynamics during infection. STAMP analyzes the frequency changes of genetically 'barcoded' organisms to ...

    • 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 ...

    • STAMP: Sequence tag-based analysis of microbial population dynamics 

      Abel, Sören; zur Wiesch, Pia Abel; Chang, Hsiao-Han; Davis, Brigid M.; Lipsitch, Marc; Waldor, Matthew K. (2014)
      We describe a new method (STAMP) for characterization of pathogen population dynamics during infection. STAMP analyzes the frequency changes of genetically “barcoded” organisms to quantify population bottlenecks and infer ...

    • Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses 

      Chang, Hsiao-Han; Huber, Roland G; Bond, Peter J; Grad, Yonatan Hagai; Camerini, David; Maurer-Stroh, Sebastian; Lipsitch, Marc (WHO Press, 2017)

    • Variation in infection length and superinfection enhance selection efficiency in the human malaria parasite 

      Chang, Hsiao-Han; Childs, Lauren M.; Buckee, Caroline O. (Nature Publishing Group, 2016)
      The capacity for adaptation is central to the evolutionary success of the human malaria parasite Plasmodium falciparum. Malaria epidemiology is characterized by the circulation of multiple, genetically diverse parasite ...