Deletion and acquisition of genomic content during early stage adaptation of Pseudomonas aeruginosa to a human host environment

Case Studies of the Spatial Heterogeneity of DNA Viruses in the Cystic Fibrosis Lung

(2011) Dana Willner et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Bacterial adaptation during chronic infection revealed by independent component analysis of transcriptomic data

(2011) Lei Yang et al.   BMC MICROBIOLOGY

Bacteriophages as vehicles of the resistome in cystic fibrosis

(2011) J. M. Rolain et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Insertion Sequence-Driven Evolution of Escherichia coli in Chemostats

(2011) Joël Gaffé et al.   JOURNAL OF MOLECULAR EVOLUTION

Evolutionary dynamics of bacteria in a human host environment

(2011) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes

(2011) Alessandro M Varani et al.   GENOME BIOLOGY

Microindel detection in short-read sequence data

(2010) Peter Krawitz et al.   BIOINFORMATICS

Prevalence, conservation and functional analysis of Yersinia and Escherichia CRISPR regions in clinical Pseudomonas aeruginosa isolates

(2010) K. C. Cady et al.   MICROBIOLOGY-SGM

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes

(2010) G. L. Winsor et al.   NUCLEIC ACIDS RESEARCH

The Early Stage of Bacterial Genome-Reductive Evolution in the Host

(2010) Han Song et al.   PLoS Pathogens

IslandViewer: an integrated interface for computational identification and visualization of genomic islands

(2009) M. G. I. Langille et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

Prophinder: a computational tool for prophage prediction in prokaryotic genomes

(2008) Gipsi Lima-Mendez et al.   BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Interaction between Bacteriophage DMS3 and Host CRISPR Region Inhibits Group Behaviors of Pseudomonas aeruginosa

(2008) M. E. Zegans et al.   JOURNAL OF BACTERIOLOGY