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

Multigenomic Delineation ofPlasmodiumSpecies of theLaveraniaSubgenus Infecting Wild-Living Chimpanzees and Gorillas

(2016) Weimin Liu et al.   Genome Biology 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

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

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

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

The Plasmodium gaboni genome illuminates allelic dimorphism of immunologically important surface antigens in P. falciparum

(2015) Scott William Roy   INFECTION GENETICS AND EVOLUTION

Genetic evidence for contribution of human dispersal to the genetic diversity of EBA-175 in Plasmodium falciparum

(2015) Yoshiki Yasukochi et al.   MALARIA JOURNAL

Diversity of malaria parasites in great apes in Gabon

(2015) Larson Boundenga et al.   MALARIA JOURNAL

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

Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals

(2015) G. W. C. Thomas et al.   MOLECULAR BIOLOGY AND EVOLUTION

A novel locus of resistance to severe malaria in a region of ancient balancing selection

(2015)   NATURE

Hybridization and pre-zygotic reproductive barriers in Plasmodium

(2015) R. S. Ramiro et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ape parasite origins of human malaria virulence genes

(2015) Daniel B. Larremore et al.   Nature Communications

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

STEVOR Is a Plasmodium falciparum Erythrocyte Binding Protein that Mediates Merozoite Invasion and Rosetting

(2014) Makhtar Niang et al.   Cell Host & Microbe

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

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

Genetic diversity of VAR2CSA ID1-DBL2Xb in worldwide Plasmodium falciparum populations: Impact on vaccine design for placental malaria

(2014) Bita Bordbar et al.   INFECTION GENETICS AND EVOLUTION

Structure of malaria invasion protein RH5 with erythrocyte basigin and blocking antibodies

(2014) Katherine E. Wright et al.   NATURE

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

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

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

Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis

(2014) Antoine Claessens et al.   PLoS Genetics

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

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

Maurer's clefts, the enigma of Plasmodium falciparum

(2013) E. Mundwiler-Pachlatko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RH5-Basigin interaction plays a major role in the host tropism of Plasmodium falciparum

(2013) M. Wanaguru et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

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

Isolation of Plasmodium falciparum by flow-cytometry: implications for single-trophozoite genotyping and parasite DNA purification for whole-genome high-throughput sequencing of archival samples

(2012) Anne Boissière et al.   MALARIA JOURNAL

Revising the human mutation rate: implications for understanding human evolution

(2012) Aylwyn Scally et al.   NATURE REVIEWS GENETICS

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

A DOC2 Protein Identified by Mutational Profiling Is Essential for Apicomplexan Parasite Exocytosis

(2012) A. Farrell et al.   SCIENCE

Effective/census population size ratio estimation: a compendium and appraisal

(2012) Friso P. Palstra et al.   Ecology and Evolution

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Timing the origin of human malarias: the lemur puzzle

(2011) M Andreína Pacheco et al.   BMC EVOLUTIONARY BIOLOGY

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

(2011) P. Markova-Raina et al.   GENOME RESEARCH

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

Optimal enzymes for amplifying sequencing libraries

(2011) Michael A Quail et al.   NATURE METHODS

RATT: Rapid Annotation Transfer Tool

(2011) Thomas D. Otto et al.   NUCLEIC ACIDS RESEARCH

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

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

(2010) Thomas D. Otto et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

The pir multigene family of Plasmodium: Antigenic variation and beyond

(2010) Deirdre Cunningham et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Origin of the human malaria parasite Plasmodium falciparum in gorillas

(2010) Weimin Liu et al.   NATURE

African great apes are natural hosts of multiple related malaria species, including Plasmodium falciparum

(2010) F. Prugnolle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes – Divide and Conquer

(2010) Thomas S. Rask et al.   PLoS Computational Biology

SNP-o-matic

(2009) Heinrich Magnus Manske et al.   BIOINFORMATICS

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for an ancient adaptive episode of convergent molecular evolution

(2009) T. A. Castoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A New Malaria Agent in African Hominids

(2009) Benjamin Ollomo et al.   PLoS Pathogens

The Dawn of Human Matrilineal Diversity

(2008) Doron M. Behar et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE