Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens

Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics

(2018) Annie N. Cowell et al.   SCIENCE

Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal

(2017) Wesley Wong et al.   Genome Medicine

XIBD: software for inferring pairwise identity by descent on the X chromosome

(2016) Lyndal Henden et al.   BIOINFORMATICS

Indels, structural variation, and recombination drive genomic diversity inPlasmodium falciparum

(2016) Alistair Miles et al.   GENOME RESEARCH

Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi

(2016) Matt Ravenhall et al.   MALARIA JOURNAL

Exceptionally long-range haplotypes in Plasmodium falciparum chromosome 6 maintained in an endemic African population

(2016) Alfred Amambua-Ngwa et al.   MALARIA JOURNAL

Globally prevalent PfMDR1 mutations modulate Plasmodium falciparum susceptibility to artemisinin-based combination therapies

(2016) M. Isabel Veiga et al.   Nature Communications

Modeling malaria genomics reveals transmission decline and rebound in Senegal

(2015) Rachel F. Daniels et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia

(2014) Shannon Takala-Harrison et al.   JOURNAL OF INFECTIOUS DISEASES

Spatial and temporal epidemiology of clinical malaria in Cambodia 2004–2013

(2014) Richard J Maude et al.   MALARIA JOURNAL

Detecting and Characterizing Genomic Signatures of Positive Selection in Global Populations

(2013) Xuanyao Liu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Modulation of PF10_0355 (MSPDBL2) Alters Plasmodium falciparum Response to Antimalarial Drugs

(2013) Daria Van Tyne et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

SLiM: Simulating Evolution with Selection and Linkage

(2013) Philipp W. Messer   GENETICS

Identity by Descent: Variation in Meiosis, Across Genomes, and in Populations

(2013) E. A. Thompson   GENETICS

A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

(2013) Frédéric Ariey et al.   NATURE

Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia

(2013) Olivo Miotto et al.   NATURE GENETICS

Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

(2013) Kelley Harris et al.   PLoS Genetics

Mitotic Evolution of Plasmodium falciparum Shows a Stable Core Genome but Recombination in Antigen Families

(2013) Selina E. R. Bopp et al.   PLoS Genetics

Identity by Descent Between Distant Relatives: Detection and Applications

(2012) Sharon R. Browning et al.   Annual Review of Genetics

Using identity by descent estimation with dense genotype data to detect positive selection

(2012) Lide Han et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites

(2012) Alfred Amambua-Ngwa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

(2012) Magnus Manske et al.   NATURE

Harnessing genomics and genome biology to understand malaria biology

(2012) Sarah K. Volkman et al.   NATURE REVIEWS GENETICS

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite

(2012) D. J. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Identification and Functional Validation of the Novel Antimalarial Resistance Locus PF10_0355 in Plasmodium falciparum

(2011) Daria Van Tyne et al.   PLoS Genetics

Inference of Unexpected Genetic Relatedness among Individuals in HapMap Phase III

(2010) Trevor J. Pemberton et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Natural Selection and the Distribution of Identity-by-Descent in the Human Genome

(2010) Anders Albrechtsen et al.   GENETICS

Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium

(2008) Anders Albrechtsen et al.   GENETIC EPIDEMIOLOGY

Comparative genomics of the neglected human malaria parasite Plasmodium vivax

(2008) Jane M. Carlton et al.   NATURE

Adaptive Copy Number Evolution in Malaria Parasites

(2008) Shalini Nair et al.   PLoS Genetics

Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

(2008) Daniel E Neafsey et al.   GENOME BIOLOGY