Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing

Do fitness costs explain the rapid spread of kelch13-C580Y substitutions conferring artemisinin resistance?

(2018) Shalini Nair et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Molecular approaches to determine the multiplicity of Plasmodium infections

(2018) Daibin Zhong et al.   MALARIA JOURNAL

Computational correction of index switching in multiplexed sequencing libraries

(2018) Anton J M Larsson et al.   NATURE METHODS

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

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

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Surveillance for sulfadoxine-pyrimethamine resistant malaria parasites in the Lake and Southern Zones, Tanzania, using pooling and next-generation sequencing

(2017) Jeremiah M. Ngondi et al.   MALARIA JOURNAL

A new method for sequencing the hypervariable Plasmodium falciparum gene var2csa from clinical samples

(2017) Antoine Dara 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

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

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

Increased risk of low birth weight in women with placental malaria associated with P. falciparum VAR2CSA clade

(2017) Jaymin C. Patel et al.   Scientific Reports

Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data

(2016) Thomas S. Rask et al.   BMC BIOINFORMATICS

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data

(2016) Melanie Schirmer et al.   BMC BIOINFORMATICS

A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India

(2016) Pavitra N. Rao et al.   JOURNAL OF CLINICAL MICROBIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Using Amplicon Deep Sequencing to Detect Genetic Signatures ofPlasmodium vivaxRelapse

(2015) Jessica T. Lin et al.   JOURNAL OF INFECTIOUS DISEASES

Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine

(2015) Daniel E. Neafsey et al.   NEW ENGLAND JOURNAL OF MEDICINE

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

A Phase 3 Trial of RTS,S/AS01 Malaria Vaccine in African Infants

(2012)   NEW ENGLAND JOURNAL OF MEDICINE

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

High-Throughput Pooling and Real-Time PCR-Based Strategy for Malaria Detection

(2009) S. M. Taylor et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2008) Rachel Daniels et al.   MALARIA JOURNAL