ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing

Differential Requirement for PBP1a and PBP1b inIn VivoandIn VitroFitness of Vibrio cholerae

(2014) Tobias Dörr et al.   INFECTION AND IMMUNITY

Protter: interactive protein feature visualization and integration with experimental proteomic data

(2013) Ulrich Omasits et al.   BIOINFORMATICS

A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data

(2013) Michael A DeJesus et al.   BMC BIOINFORMATICS

Tryptophan Biosynthesis Protects Mycobacteria from CD4 T-Cell-Mediated Killing

(2013) Yanjia J. Zhang et al.   CELL

Tn-Seq Analysis of Vibrio cholerae Intestinal Colonization Reveals a Role for T6SS-Mediated Antibacterial Activity in the Host

(2013) Yang Fu et al.   Cell Host & Microbe

Understanding Barriers to Borrelia burgdorferi Dissemination during Infection Using Massively Parallel Sequencing

(2013) Erin B. Troy et al.   INFECTION AND IMMUNITY

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

(2013) Tim van Opijnen et al.   NATURE REVIEWS MICROBIOLOGY

High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model–based analyses of transposon-insertion sequencing data

(2013) Michael C. Chao et al.   NUCLEIC ACIDS RESEARCH

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium

(2013) Lars Barquist et al.   NUCLEIC ACIDS RESEARCH

Approaches to querying bacterial genomes with transposon-insertion sequencing

(2013) Lars Barquist et al.   RNA Biology

A Comprehensive Analysis of In Vitro and In Vivo Genetic Fitness of Pseudomonas aeruginosa Using High-Throughput Sequencing of Transposon Libraries

(2013) David Skurnik et al.   PLoS Pathogens

Gene Fitness Landscapes of Vibrio cholerae at Important Stages of Its Life Cycle

(2013) Heather D. Kamp et al.   PLoS Pathogens

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis

(2012) Yanjia J. Zhang et al.   PLoS Pathogens

RNA-Seq-Based Monitoring of Infection-Linked Changes in Vibrio cholerae Gene Expression

(2011) Anjali Mandlik et al.   Cell Host & Microbe

Genome-Scale Identification of Resistance Functions in Pseudomonas aeruginosa Using Tn-seq

(2011) L. A. Gallagher et al.   mBio

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms

(2009) Tim van Opijnen et al.   NATURE METHODS

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung

(2009) J. D. Gawronski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA