Hybrid selection for sequencing pathogen genomes from clinical samples

Complete Bacteriophage Transfer in a Bacterial Endosymbiont (Wolbachia) Determined by Targeted Genome Capture

(2011) Bethany N. Kent et al.   Genome Biology and Evolution

Probable Zoonotic Leprosy in the Southern United States

(2011) Richard W. Truman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Identification of a Salmonellosis Outbreak by Means of Molecular Sequencing

(2011) E. Kurt Lienau et al.   NEW ENGLAND JOURNAL OF MEDICINE

Identification and Functional Validation of the Novel Antimalarial Resistance Locus PF10_0355 in Plasmodium falciparum

(2011) Daria Van Tyne et al.   PLoS Genetics

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control

(2010) D. E. Neafsey et al.   GENOME RESEARCH

Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs

(2010) Jianbing Mu et al.   NATURE GENETICS

The Origin of the Haitian Cholera Outbreak Strain

(2010) Chen-Shan Chin et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH