Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Explaining microbial phenotypes on a genomic scale: GWAS for microbes

(2013) B. E. Dutilh et al.   Briefings in Functional Genomics

PhenoLink - a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains

(2012) Jumamurat R Bayjanov et al.   BMC GENOMICS

Complete Genome Sequence of a Sucrose-Nonfermenting Epidemic Strain of Vibrio cholerae O1 from Brazil

(2012) L. L. C. d. S. Morais et al.   JOURNAL OF BACTERIOLOGY

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

A Two-Stage Random Forest-Based Pathway Analysis Method

(2012) Ren-Hua Chung et al.   PLoS One

Genome-Wide Study of the Defective Sucrose Fermenter Strain of Vibrio cholerae from the Latin American Cholera Epidemic

(2012) Daniel Rios Garza et al.   PLoS One

Genomic diversity of 2010 Haitian cholera outbreak strains

(2012) N. A. Hasan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Genome Sequence of the Human Pathogen Vibrio cholerae Amazonia

(2011) C. C. Thompson et al.   JOURNAL OF BACTERIOLOGY

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

(2010) Robert Schmieder et al.   BMC BIOINFORMATICS

Letter to the Editor: Stability of Random Forest importance measures

(2010) M. L. Calle et al.   BRIEFINGS IN BIOINFORMATICS

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Convergent random forest predictor: Methodology for predicting drug response from genome-scale data applied to anti-TNF response

(2009) Jadwiga R. Bienkowska et al.   GENOMICS

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

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

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