Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens

Pangenomic Study of Corynebacterium diphtheriae That Provides Insights into the Genomic Diversity of Pathogenic Isolates from Cases of Classical Diphtheria, Endocarditis, and Pneumonia

(2012) E. Trost et al.   JOURNAL OF BACTERIOLOGY

Going viral: next-generation sequencing applied to phage populations in the human gut

(2012) Alejandro Reyes et al.   NATURE REVIEWS MICROBIOLOGY

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

Metabolic Networks of Sodalis glossinidius: A Systems Biology Approach to Reductive Evolution

(2012) Eugeni Belda et al.   PLoS One

PIPS: Pathogenicity Island Prediction Software

(2012) Siomar C. Soares et al.   PLoS One

Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control

(2012) Sam P. Brown et al.   TRENDS IN MICROBIOLOGY

Evolution of Chlamydia trachomatis

(2011) Ian N. Clarke   Annals of the New York Academy of Sciences

Evolutionarily Conserved Orthologous Families in Phages Are Relatively Rare in Their Prokaryotic Hosts

(2011) D. M. Kristensen et al.   JOURNAL OF BACTERIOLOGY

Characterization of pathogenicity island prophage in clinical and environmental strains of Vibrio cholerae

(2011) H. Mohammadi-Barzelighi et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

BacMap: an up-to-date electronic atlas of annotated bacterial genomes

(2011) J. Cruz et al.   NUCLEIC ACIDS RESEARCH

BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata

(2011) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2011) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Genomic anatomy of Escherichia coli O157:H7 outbreaks

(2011) M. Eppinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Impact of Recombination on dN/dS within Recently Emerged Bacterial Clones

(2011) Santiago Castillo-Ramírez et al.   PLoS Pathogens

Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles

(2011) Maya Botzman et al.   GENOME BIOLOGY

Rickettsial evolution in the light of comparative genomics

(2010) Vicky Merhej et al.   BIOLOGICAL REVIEWS

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

Massive comparative genomic analysis reveals convergent evolution of specialized bacteria

(2009) Vicky Merhej et al.   Biology Direct

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

The Association of Virulence Factors with Genomic Islands

(2009) Shannan J. Ho Sui et al.   PLoS One

The Defective Prophage Pool of Escherichia coli O157: Prophage–Prophage Interactions Potentiate Horizontal Transfer of Virulence Determinants

(2009) Md Asadulghani et al.   PLoS Pathogens