Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa

Assessing Kwa-Zulu-Natal’s progress towards malaria elimination and its readiness for sub-national verification

(2019) Ryleen Balawanth et al.   MALARIA JOURNAL

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

(2019) Sofonias Tessema et al.   eLife

Mapping imported malaria in Bangladesh using parasite genetic and human mobility data

(2019) Hsiao-Han Chang et al.   eLife

High Genetic Diversity of Plasmodium falciparum in the Low-Transmission Setting of the Kingdom of Eswatini

(2019) Michelle E Roh et al.   JOURNAL OF INFECTIOUS DISEASES

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

Drug-Resistance and Population Structure of Plasmodium falciparum Across the Democratic Republic of Congo Using High-Throughput Molecular Inversion Probes

(2018) Ozkan Aydemir et al.   JOURNAL OF INFECTIOUS DISEASES

Molecular approaches to determine the multiplicity of Plasmodium infections

(2018) Daibin Zhong et al.   MALARIA JOURNAL

A review of progress towards sub-national malaria elimination in Matabeleland South Province, Zimbabwe (2011–2015): a qualitative study

(2018) Gladwin Muchena et al.   MALARIA JOURNAL

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

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

De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria

(2018) Seth N Redmond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Host-mediated selection impacts the diversity of Plasmodium falciparum antigens within infections

(2018) Angela M. Early et al.   Nature Communications

Consistent signatures of selection from genomic analysis of pairs of temporal and spatial Plasmodium falciparum populations from The Gambia

(2018) Alfred Amambua-Ngwa et al.   Scientific Reports

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

(2018) Lyndal Henden et al.   PLoS Genetics

Increasingly inbred and fragmented populations of Plasmodium vivax associated with the eastward decline in malaria transmission across the Southwest Pacific

(2018) Andreea Waltmann et al.   PLoS Neglected Tropical Diseases

Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development

(2018) Craig W. Duffy et al.   Scientific Reports

Mapping malaria by combining parasite genomic and epidemiologic data

(2018) Amy Wesolowski et al.   BMC Medicine

Genetic Evidence of Focal Plasmodium falciparum Transmission in a Pre-elimination Setting in Southern Province, Zambia

(2018) Julia C Pringle et al.   JOURNAL OF INFECTIOUS DISEASES

High-Resolution Single-Cell Sequencing of Malaria Parasites

(2017) Simon G Trevino et al.   Genome Biology and Evolution

Dissecting malaria biology and epidemiology using population genetics and genomics

(2017) Sarah Auburn et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Travel patterns and demographic characteristics of malaria cases in Swaziland, 2010–2014

(2017) Natalia Tejedor‐Garavito et al.   MALARIA JOURNAL

A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity

(2017) Robin H. Miller et al.   MALARIA JOURNAL

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

(2017) Nathan D. Grubaugh et al.   NATURE

Virus genomes reveal factors that spread and sustained the Ebola epidemic

(2017) Gytis Dudas et al.   NATURE

SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing

(2017) Nicholas J Hathaway et al.   NUCLEIC ACIDS RESEARCH

Malaria Epidemiology at the Clone Level

(2017) Cristian Koepfli et al.   TRENDS IN PARASITOLOGY

THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites

(2017) Hsiao-Han Chang et al.   PLoS Computational Biology

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

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

Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya

(2017) Brandt Levitt et al.   Scientific Reports

Pooled Amplicon Deep Sequencing of Candidate Plasmodium falciparum Transmission-Blocking Vaccine Antigens

(2016) Jonathan J. Juliano et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Estimating the Number of Subpopulations ( K ) in Structured Populations

(2016) Robert Verity et al.   GENETICS

Genetic diversity and population structure of Plasmodium falciparum over space and time in an African archipelago

(2016) Patrícia Salgueiro et al.   INFECTION GENETICS AND EVOLUTION

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

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

Reviewing South Africa’s malaria elimination strategy (2012–2018): progress, challenges and priorities

(2016) Jaishree Raman et al.   MALARIA JOURNAL

Genomic epidemiology of artemisinin resistant malaria

(2016)   eLife

Estimating the Number of Subpopulations ( K ) in Structured Populations

(2016) Robert Verity et al.   GENETICS

Malaria Molecular Epidemiology: Lessons from the International Centers of Excellence for Malaria Research Network

(2015) Ananias A. Escalante et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Tackling Imported Malaria: An Elimination Endgame

(2015) Hugh J. W. Sturrock et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Comparison of genomic signatures of selection on Plasmodium falciparum between different regions of a country with high malaria endemicity

(2015) Craig W. Duffy et al.   BMC GENOMICS

COIL: a methodology for evaluating malarial complexity of infection using likelihood from single nucleotide polymorphism data

(2015) Kevin Galinsky et al.   MALARIA JOURNAL

Malaria genotyping for epidemiologic surveillance

(2015) Bryan Greenhouse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Malaria genomics: tracking a diverse and evolving parasite population

(2015) D. Kwiatkowski   International Health

Genome-Wide Analysis of Selection on the Malaria Parasite Plasmodium falciparum in West African Populations of Differing Infection Endemicity

(2014) Victor A. Mobegi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population genetic structure of Plasmodium falciparum across a region of diverse endemicity in West Africa

(2012) Victor A Mobegi et al.   MALARIA JOURNAL

Population genetic correlates of declining transmission in a human pathogen

(2012) Standwell C. Nkhoma et al.   MOLECULAR ECOLOGY

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

Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data

(2012) Sarah Auburn et al.   PLoS One

Force of infection is key to understanding the epidemiology of Plasmodium falciparum malaria in Papua New Guinean children

(2012) I. Mueller 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

Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing

(2010) J. J. Juliano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking

(2008) Rachel Daniels et al.   MALARIA JOURNAL

Infecting epidemiology with genetics: a new frontier in disease ecology

(2008) Elizabeth A. Archie et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2008) Daniel E Neafsey et al.   GENOME BIOLOGY