Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution

Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates

(2018) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria

(2018) Thomas D. Otto et al.   Nature Microbiology

Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution

(2017) Gavin G. Rutledge et al.   NATURE

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Daniel N Hupalo et al.   NATURE GENETICS

Companion: a web server for annotation and analysis of parasite genomes

(2016) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Role ofPlasmodium vivaxDuffy-binding protein 1 in invasion of Duffy-null Africans

(2016) Karthigayan Gunalan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ape malaria transmission and potential for ape-to-human transfers in Africa

(2016) Boris Makanga et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A New Method for Estimating Species Age Supports the Coexistence of Malaria Parasites and Their Mammalian Hosts

(2015) Joana C. Silva et al.   MOLECULAR BIOLOGY AND EVOLUTION

No Evidence for Ape Plasmodium Infections in Humans in Gabon

(2015) Lucresse Délicat-Loembet et al.   PLoS One

Comparative Analysis of Field-Isolate and Monkey-Adapted Plasmodium vivax Genomes

(2015) Ernest R. Chan et al.   PLoS Neglected Tropical Diseases

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

A comprehensive evaluation of rodent malaria parasite genomes and gene expression

(2014) Thomas D Otto et al.   BMC BIOLOGY

Optimized Whole-Genome Amplification Strategy for Extremely AT-Biased Template

(2014) Samuel O. Oyola et al.   DNA RESEARCH

Distinguishing between Incomplete Lineage Sorting and Genomic Introgressions: Complete Fixation of Allospecific Mitochondrial DNA in a Sexually Reproducing Fish (Cobitis; Teleostei), despite Clonal Reproduction of Hybrids

(2014) Lukas Choleva et al.   PLoS One

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

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

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Diversity, host switching and evolution of Plasmodium vivax infecting African great apes

(2013) F. Prugnolle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

GapFiller: a de novo assembly approach to fill the gap within paired reads

(2012) Francesca Nadalin et al.   BMC BIOINFORMATICS

BamView: visualizing and interpretation of next-generation sequencing read alignments

(2012) T. Carver et al.   BRIEFINGS IN BIOINFORMATICS

Ion and nutrient uptake by malaria parasite-infected erythrocytes

(2012) Sanjay A. Desai   CELLULAR MICROBIOLOGY

Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade

(2012) Shin-Ichiro Tachibana et al.   NATURE GENETICS

Estimating divergence times in large molecular phylogenies

(2012) K. Tamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole Genome Sequencing of Field Isolates Provides Robust Characterization of Genetic Diversity in Plasmodium vivax

(2012) Ernest R. Chan et al.   PLoS Neglected Tropical Diseases

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing

(2011) Sarah Auburn et al.   PLoS One

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Plasmodium falciparum Accompanied the Human Expansion out of Africa

(2010) Kazuyuki Tanabe et al.   CURRENT BIOLOGY

The International Limits and Population at Risk of Plasmodium vivax Transmission in 2009

(2010) Carlos A. Guerra et al.   PLoS Neglected Tropical Diseases

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

(2010) Isheng J Tsai et al.   GENOME BIOLOGY

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

A New Malaria Agent in African Hominids

(2009) Benjamin Ollomo et al.   PLoS Pathogens

The genome of the simian and human malaria parasite Plasmodium knowlesi

(2008) A. Pain et al.   NATURE

Comparative genomics of the neglected human malaria parasite Plasmodium vivax

(2008) Jane M. Carlton et al.   NATURE

Plasmodium knowlesi: The Fifth Human Malaria Parasite

(2007) N. J. White   CLINICAL INFECTIOUS DISEASES