The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC

[1]  R. Irizarry ggplot2 , 2019, Introduction to Data Science.

[2]  E. Legrand,et al.  African isolates show a high proportion of multiple copies of the Plasmodium falciparum plasmepsin-2 gene, a piperaquine resistance marker , 2019, Malaria Journal.

[3]  Caroline O. Buckee,et al.  Estimating Relatedness Between Malaria Parasites , 2019, Genetics.

[4]  V. Sinou,et al.  Prevalence of Plasmodium falciparum parasites resistant to sulfadoxine/pyrimethamine in the Democratic Republic of the Congo: emergence of highly resistant pfdhfr/pfdhps alleles , 2018, The Journal of antimicrobial chemotherapy.

[5]  J. Bailey,et al.  Drug-Resistance and Population Structure of Plasmodium falciparum Across the Democratic Republic of Congo Using High-Throughput Molecular Inversion Probes , 2018, The Journal of infectious diseases.

[6]  P. Lutumba,et al.  Impact of treatment and re-treatment with artemether-lumefantrine and artesunate-amodiaquine on selection of Plasmodium falciparum multidrug resistance gene-1 polymorphisms in the Democratic Republic of Congo and Uganda , 2018, PloS one.

[7]  J. Bailey,et al.  Plasmodium falciparum genetic variation of var2csa in the Democratic Republic of the Congo , 2018, Malaria Journal.

[8]  T. Imir,et al.  Molecular identification of sulfadoxine-pyrimethamine resistance in malaria infected women who received intermittent preventive treatment in the Democratic Republic of Congo , 2018, Malaria Journal.

[9]  A. Ghansah,et al.  Efficacy of Artesunate/Amodiaquine in the Treatment of Uncomplicated Malaria among Children in Ghana. , 2017, The American journal of tropical medicine and hygiene.

[10]  S. Volkman,et al.  Malaria Genomics in the Era of Eradication. , 2017, Cold Spring Harbor perspectives in medicine.

[11]  Peter J. Diggle,et al.  PrevMap:An R Package for Prevalence Mapping , 2017 .

[12]  P. de Mol,et al.  Molecular surveillance of Plasmodium falciparum resistance to artemisinin-based combination therapies in the Democratic Republic of Congo , 2017, PloS one.

[13]  J. Bailey,et al.  Surveillance for sulfadoxine-pyrimethamine resistant malaria parasites in the Lake and Southern Zones, Tanzania, using pooling and next-generation sequencing , 2017, Malaria Journal.

[14]  Dhruviben S. Patel,et al.  Molecular Epidemiology of Plasmodium falciparum kelch13 Mutations in Senegal Determined by Using Targeted Amplicon Deep Sequencing , 2017, Antimicrobial Agents and Chemotherapy.

[15]  Caroline O. Buckee,et al.  THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites , 2017, PLoS Comput. Biol..

[16]  P. Rosenthal,et al.  Changing Antimalarial Drug Resistance Patterns Identified by Surveillance at Three Sites in Uganda , 2016, The Journal of infectious diseases.

[17]  M. Gautier,et al.  rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure , 2016, bioRxiv.

[18]  Nicholas P. J. Day,et al.  Genomic epidemiology of artemisinin resistant malaria. , 2016, eLife.

[19]  P. de Mol,et al.  Falciparum malaria molecular drug resistance in the Democratic Republic of Congo: a systematic review , 2015, Malaria Journal.

[20]  Steve M. Taylor,et al.  The geography of malaria genetics in the Democratic Republic of Congo: A complex and fragmented landscape. , 2015, Social science & medicine.

[21]  Steve M. Taylor,et al.  Absence of putative artemisinin resistance mutations among Plasmodium falciparum in Sub-Saharan Africa: a molecular epidemiologic study. , 2015, The Journal of infectious diseases.

[22]  B. Pradines,et al.  Limited polymorphisms in k13 gene in Plasmodium falciparum isolates from Dakar, Senegal in 2012–2013 , 2014, Malaria Journal.

[23]  Hanspeter Pfister,et al.  UpSet: Visualization of Intersecting Sets , 2014, IEEE Transactions on Visualization and Computer Graphics.

[24]  Samuel A. Assefa,et al.  Whole-Genome Scans Provide Evidence of Adaptive Evolution in Malawian Plasmodium falciparum Isolates , 2014, The Journal of infectious diseases.

[25]  Steve M. Taylor,et al.  A cross-sectional survey of Plasmodium falciparum pfcrt mutant haplotypes in the Democratic Republic of Congo. , 2014, The American journal of tropical medicine and hygiene.

[26]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[27]  Steve M. Taylor,et al.  Plasmodium falciparum sulfadoxine resistance is geographically and genetically clustered within the DR Congo , 2013, Scientific Reports.

[28]  Bradley P. Coe,et al.  Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders , 2012, Science.

[29]  Renaud Vitalis,et al.  rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure , 2012, Bioinform..

[30]  E. Mohammadi,et al.  Barriers and facilitators related to the implementation of a physiological track and trigger system: A systematic review of the qualitative evidence , 2017, International journal for quality in health care : journal of the International Society for Quality in Health Care.

[31]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[32]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[33]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[34]  Jay Shendure,et al.  Massively parallel exon capture and library-free resequencing across 16 genomes , 2009, Nature Methods.

[35]  B. Sharp,et al.  Multiple Origins and Regional Dispersal of Resistant dhps in African Plasmodium falciparum Malaria , 2009, PLoS medicine.

[36]  A. Mårtensson,et al.  Diversity of the sarco/endoplasmic reticulum Ca(2+)-ATPase orthologue of Plasmodium falciparum (PfATP6). , 2008, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[37]  Elena R. Lozovsky,et al.  Duplication, gene conversion, and genetic diversity in the species-specific acyl-CoA synthetase gene family of Plasmodium falciparum. , 2006, Molecular and biochemical parasitology.

[38]  Weltgesundheitsorganisation World malaria report , 2005 .

[39]  S. Meshnick,et al.  Resistance to Antimalarials in Southeast Asia and Genetic Polymorphisms in pfmdr1 , 2003, Antimicrobial Agents and Chemotherapy.

[40]  F. Rousset Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. , 1997, Genetics.

[41]  B. Weir,et al.  ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.

[42]  M. Kimura,et al.  An introduction to population genetics theory , 1971 .

[43]  G. Malécot,et al.  The mathematics of heredity , 1948 .