ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data

MindTheGap: integrated detection and assembly of short and long insertions

(2014) G. Rizk et al.   BIOINFORMATICS

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements

(2014) Mariko Nakagome et al.   BMC BIOINFORMATICS

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

(2014) Jeffrey E Barrick et al.   BMC GENOMICS

Mycobacterium tuberculosis expressing phospholipase C subverts PGE2 synthesis and induces necrosis in alveolar macrophages

(2014) Patricia A Assis et al.   BMC MICROBIOLOGY

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

Culture-independent detection and characterisation ofMycobacterium tuberculosisandM. africanumin sputum samples using shotgun metagenomics on a benchtop sequencer

(2014) Emma L. Doughty et al.   PeerJ

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Tn6168, a transposon carrying an ISAba1-activated ampC gene and conferring cephalosporin resistance in Acinetobacter baumannii

(2013) Mohammad Hamidian et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

ISAba1 targets a specific position upstream of the intrinsic ampC gene of Acinetobacter baumannii leading to cephalosporin resistance

(2013) M. Hamidian et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

(2013) Iñaki Comas et al.   NATURE GENETICS

Tracking the establishment of local endemic populations of an emergent enteric pathogen

(2013) K. E. Holt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice

(2013) Sofia M. C. Robb et al.   G3-Genes Genomes Genetics

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer

(2012) Kenneth D Doig et al.   BMC GENOMICS

Horizontal transfer of an ISAba125-activated ampC gene between Acinetobacter baumannii strains leading to cephalosporin resistance

(2012) M. Hamidian et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Deciphering the role of IS6110 in a highly transmissible Mycobacterium tuberculosis Beijing strain, GC1237

(2011) Henar Alonso et al.   TUBERCULOSIS

Genomewide Analysis of Divergence of Antibiotic Resistance Determinants in Closely Related Isolates of Acinetobacter baumannii

(2010) M. D. Adams et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

A generic mechanism inNeisseria meningitidisfor enhanced resistance against bactericidal antibodies

(2008) Maria Jose Uria et al.   JOURNAL OF EXPERIMENTAL MEDICINE

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS