AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments

Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle

(2019) Prerna Vohra et al.   BMC GENOMICS

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157

(2018) Lauren A. Cowley et al.   mBio

The essential genomic landscape of the commensal Bifidobacterium breve UCC2003

(2017) Lorena Ruiz et al.   Scientific Reports

High-Throughput Analysis of Gene Essentiality and Sporulation in Clostridium difficile

(2015) Marcin Dembek et al.   mBio

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud

(2015) Enis Afgan et al.   PLoS One

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

Cython: The Best of Both Worlds

(2010) Stefan Behnel et al.   COMPUTING IN SCIENCE & ENGINEERING

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

Exposure of Escherichia coli and Salmonella enterica serovar Typhimurium to triclosan induces a species-specific response, including drug detoxification

(2009) A. M. Bailey et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

(2009) Tim van Opijnen 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