Using deep learning to identify recent positive selection in malaria parasite sequence data

Genetic diversity of the Plasmodium falciparum GTP-cyclohydrolase 1, dihydrofolate reductase and dihydropteroate synthetase genes reveals new insights into sulfadoxine-pyrimethamine antimalarial drug resistance

(2021) Anna Turkiewicz et al.   PLoS Genetics

Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa

(2021) Ernest Diez Benavente et al.   Nature Communications

Evolution of the Plasmodium vivax multidrug resistance 1 gene in the Greater Mekong Subregion during malaria elimination

(2020) Huguette Gaelle Ngassa Mbenda et al.   Parasites & Vectors

A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria

(2020) Ernest Diez Benavente et al.   PLoS Genetics

An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene

(2019) Matt Ravenhall et al.   Scientific Reports

Rapid and iterative genome editing in the malaria parasite Plasmodium knowlesi provides new tools for P. vivax research

(2019) Franziska Mohring et al.   eLife

Genetic Variations Associated with Drug Resistance Markers in Asymptomatic Plasmodium falciparum Infections in Myanmar

(2019) Yan Zhao et al.   Genes

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

(2018) Lyndal Henden et al.   PLoS Genetics

Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development

(2018) Ernest Diez Benavente et al.   Scientific Reports

The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference

(2018) Lex Flagel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure

(2017) Ernest Diez Benavente et al.   PLoS One

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

(2016) Matt Ravenhall et al.   MALARIA JOURNAL

rehh2.0: a reimplementation of the R packagerehhto detect positive selection from haplotype structure

(2016) Mathieu Gautier et al.   Molecular Ecology Resources

Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax

(2016) Daniel N Hupalo et al.   NATURE GENETICS

Plasmodium vivax Reticulocyte Binding Proteins Are Key Targets of Naturally Acquired Immunity in Young Papua New Guinean Children

(2016) Camila T. França et al.   PLoS Neglected Tropical Diseases

Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations

(2015) Marc Pybus et al.   BIOINFORMATICS

Mutations in the Plasmodium falciparum chloroquine resistance transporter, PfCRT, enlarge the parasite’s food vacuole and alter drug sensitivities

(2015) Serena Pulcini et al.   Scientific Reports

Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites

(2015) Hanif Samad et al.   PLoS Genetics

estMOI: estimating multiplicity of infection using parasite deep sequencing data

(2014) Samuel A. Assefa et al.   BIOINFORMATICS

Whole-Genome Scans Provide Evidence of Adaptive Evolution in Malawian Plasmodium falciparum Isolates

(2014) Harold Ocholla et al.   JOURNAL OF INFECTIOUS DISEASES

A HECT Ubiquitin-Protein Ligase as a Novel Candidate Gene for Altered Quinine and Quinidine Responses in Plasmodium falciparum

(2014) Cecilia P. Sanchez et al.   PLoS Genetics

Detecting and Characterizing Genomic Signatures of Positive Selection in Global Populations

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

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

(2013) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets

(2012) N. Alachiotis et al.   BIOINFORMATICS

rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure

(2012) Mathieu Gautier et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

(2011) Fantine Mordelet et al.   BMC BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A flexible forward simulator for populations subject to selection and demography

(2008) R. D. Hernandez   BIOINFORMATICS