Funded Collaborators

Tyrrell Conway and Joe Grissom at University of Oklahoma

NaCTeM (National Centre for Text Mining) via subcontract to University of Manchester

New City

The SEED/FIG via subcontract to University of Chicago

Driving Biological Project (DBP) Collaborators

  • “Comparative transcriptome and proteome analysis of Clostridium difficile strains”
    • Dr. Yung-Fu Chang, PI, Dept. of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
  • “Fitness Annotation of Bacterial Genomes”
  • “Integrated genomic approaches to elucidating novel virulence factors for bacteria complicating influenza”
  • “Identification of Salmonella-specific Regulatory Networks”
      • Dr. Joseph Wade, PI, Division of Genetics, Wadsworth Center, New York State Department of Health

Full article on 2010 DBP awards.

Scientific Collaborations

Click here for a list of PATRIC 2.0 joint publications with other Scientific Collaborators.



Data Sources Used by PATRIC:

BIND (Berkeley Internet Name Domain)

BioGRID (Biological General Repository for Interaction Datasets)

CTD (Comparative Toxicogenomics Database)

DIP (Database of Interacting Proteins)

EBI (European Bioinformatics Institute)

GAD (Genetic Association Database)

GO (Gene Ontology)


HMP (Human Microbiome Project)

IEDB (Immune Epitope Database)

KEGG (Kyoto Encyclopedia of Genes and Genomes)

MINT (Molecular Interaction Database)

NCBI (National Center for Biotechnology Information)

PDB (Protein Data Bank)

PSICQUIC (Protemics Standard Initiative Common Query Interface)

STITCH (Search Tool for Interactions of Chemicals)

STRING (Search Tool for the Retrieval of Interacting Genes/Proteins)

UniProt (Universal Protein Resource)

VFDB (Virulence Factors Database)

Software and Tools used by PATRIC:

BLAST (Basic Local Alignment Search Tool)







JBrowse via The Holmes Lab


MCL (Markov Cluster Algorithm)

MUSCLE (Multiple Sequence Comparison by Log- Expectation)


PATRIC Data Release Policy