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

Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species

(2016) Hifzur Rahman Ansari et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

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

(2016) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

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

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

Variant Exported Blood-Stage Proteins Encoded by Plasmodium Multigene Families Are Expressed in Liver Stages Where They Are Exported into the Parasitophorous Vacuole

(2016) Aurélie Fougère et al.   PLoS Pathogens

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

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

Structurally conserved erythrocyte-binding domain inPlasmodiumprovides a versatile scaffold for alternate receptor engagement

(2015) Jakub Gruszczyk 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

Natural infection of Plasmodium brasilianum in humans: Man and monkey share quartan malaria parasites in the Venezuelan Amazon

(2015) Albert Lalremruata et al.   EBioMedicine

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

The ears of the African elephant: unexpected high seroprevalence of Plasmodium ovale and Plasmodium malariae in healthy populations in Western Africa

(2014) Cécile Doderer-Lang et al.   MALARIA JOURNAL

The common marmoset genome provides insight into primate biology and evolution

(2014) Kim C Worley et al.   NATURE GENETICS

Asymptomatic malaria infections: detectability, transmissibility and public health relevance

(2014) Teun Bousema et al.   NATURE REVIEWS MICROBIOLOGY

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   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

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

High diversity of West African bat malaria parasites and a tight link with rodent Plasmodium taxa

(2013) J. Schaer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An observational study of malaria in British travellers:Plasmodium ovale wallikeriandPlasmodium ovale curtisidiffer significantly in the duration of latency

(2013) Debbie Nolder et al.   BMJ Open

The Plasmodium Apicoplast Genome: Conserved Structure and Close Relationship of P. ovale to Rodent Malaria Parasites

(2012) N. Arisue et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum

(2011) María J López-Barragán et al.   BMC GENOMICS

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

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

Studying the co-evolution of protein families with the Mirrortree web server

(2010) David Ochoa et al.   BIOINFORMATICS

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

(2010) Thomas D. Otto et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Two Nonrecombining Sympatric Forms of the Human Malaria ParasitePlasmodium ovaleOccur Globally

(2010) Colin J. Sutherland et al.   JOURNAL OF INFECTIOUS DISEASES

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite

(2010) Tracey L. Campbell et al.   PLoS Pathogens

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

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

A New Malaria Agent in African Hominids

(2009) Benjamin Ollomo et al.   PLoS Pathogens

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

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

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY