Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago

From high to low malaria transmission in Zanzibar—challenges and opportunities to achieve elimination

(2019) A. Björkman et al.   BMC Medicine

Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa

(2019) Sofonias Tessema et al.   eLife

Dramatic Changes in Malaria Population Genetic Complexity in Dielmo and Ndiop, Senegal, Revealed Using Genomic Surveillance

(2018) Amy K Bei et al.   JOURNAL OF INFECTIOUS DISEASES

hmmIBD: software to infer pairwise identity by descent between haploid genotypes

(2018) Stephen F. Schaffner et al.   MALARIA JOURNAL

Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics

(2018) Sarah Auburn et al.   Nature Communications

Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission

(2018) Wesley Wong et al.   PLoS Computational Biology

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

(2018) Lyndal Henden et al.   PLoS Genetics

Mapping malaria by combining parasite genomic and epidemiologic data

(2018) Amy Wesolowski et al.   BMC Medicine

malariaAtlas: an R interface to global malariometric data hosted by the Malaria Atlas Project

(2018) Daniel A. Pfeffer et al.   MALARIA JOURNAL

Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data

(2017) Paula Tataru et al.   GENETICS

Surveillance for sulfadoxine-pyrimethamine resistant malaria parasites in the Lake and Southern Zones, Tanzania, using pooling and next-generation sequencing

(2017) Jeremiah M. Ngondi et al.   MALARIA JOURNAL

Malaria Genomics in the Era of Eradication

(2017) Daniel E. Neafsey et al.   Cold Spring Harbor Perspectives in Medicine

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

(2017) Wesley Wong et al.   Genome Medicine

Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent

(2017) Aimee R. Taylor et al.   PLoS Genetics

Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data

(2017) Paula Tataru et al.   GENETICS

AKT: ancestry and kinship toolkit

(2016) Rudy Arthur et al.   BIOINFORMATICS

Admixture, Population Structure, and F-Statistics

(2016) B. M. Peter   GENETICS

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

(2016) Alistair Miles et al.   GENOME RESEARCH

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

(2016) Samuel O. Oyola et al.   MALARIA JOURNAL

Molecular monitoring of Plasmodium falciparum super-resistance to sulfadoxine–pyrimethamine in Tanzania

(2016) Reginald A. Kavishe et al.   MALARIA JOURNAL

Approaches to estimating inbreeding coefficients in clinical isolates of Plasmodium falciparum from genomic sequence data

(2016) John D. O’Brien et al.   MALARIA JOURNAL

Quantitative, model-based estimates of variability in the generation and serial intervals of Plasmodium falciparum malaria

(2016) John H. Huber et al.   MALARIA JOURNAL

Robust and scalable inference of population history from hundreds of unphased whole genomes

(2016) Jonathan Terhorst et al.   NATURE GENETICS

Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria

(2016) Sesh A. Sundararaman et al.   Nature Communications

Genomic epidemiology of artemisinin resistant malaria

(2016)   eLife

Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent

(2015) Sharon R. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

High-level Plasmodium falciparum sulfadoxine-pyrimethamine resistance with the concomitant occurrence of septuple haplotype in Tanzania

(2015) Vito Baraka et al.   MALARIA JOURNAL

hapbin: An Efficient Program for Performing Haplotype-Based Scans for Positive Selection in Large Genomic Datasets: Fig. 1.

(2015) Colin A. Maclean et al.   MOLECULAR BIOLOGY AND EVOLUTION

The effect of malaria control on Plasmodium falciparum in Africa between 2000 and 2015

(2015) S. Bhatt et al.   NATURE

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

Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites

(2015) Hanif Samad et al.   PLoS Genetics

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Relatedness in the post-genomic era: is it still useful?

(2014) Doug Speed et al.   NATURE REVIEWS GENETICS

Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts

(2014) Thomas D. Otto et al.   Nature Communications

Sub-microscopic gametocyte carriage in febrile children living in different areas of Gabon

(2013) Denise Mawili-Mboumba et al.   MALARIA JOURNAL

Malaria life cycle intensifies both natural selection and random genetic drift

(2013) H.-H. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Genomic Sequencing of Plasmodium falciparum Malaria Parasites from Senegal Reveals the Demographic History of the Population

(2012) Hsiao-Han Chang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

(2012) Magnus Manske et al.   NATURE

Close kinship within multiple-genotype malaria parasite infections

(2012) S. C. Nkhoma et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Quantifying the Impact of Human Mobility on Malaria

(2012) A. Wesolowski et al.   SCIENCE

Factors determining the occurrence of submicroscopic malaria infections and their relevance for control

(2012) Lucy C. Okell et al.   Nature Communications

Travel risk, malaria importation and malaria transmission in Zanzibar

(2011) Arnaud Le Menach et al.   Scientific Reports

A Research Agenda for Malaria Eradication: Diagnoses and Diagnostics

(2011)   PLOS MEDICINE

The use of mobile phone data for the estimation of the travel patterns and imported Plasmodium falciparum rates among Zanzibar residents

(2009) Andrew J Tatem et al.   MALARIA JOURNAL

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics