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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

• MG-RAST (Metagenomics Analysis Server)

• RAST (Rapid Annotation using Subsystem Technology)

• The Model SEED

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”
•  Dr. Michael McClelland, PI, Dept. of Pathology and Laboratory Medicine, University of California, Irvine

• “Integrated genomic approaches to elucidating novel virulence factors for bacteria complicating influenza”
• Dr. Jon McCullers and Dr. Jason Rosch, Co-PIs, St. Jude Children’s Research Hospital

• “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.

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Scientific Collaborations

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

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Acknowledgements

 

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)

• ArrayExpress
• PRIDE
• IntAct

GAD (Genetic Association Database)

GO (Gene Ontology)

HealthMap

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)

• BioProject
• CDD
• Genome
• GEO
• MMDB
• PubMed
• RefSeq
• Taxonomy

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)

BLAT

Cluster3

Cytoscape

FastTree

Gblocks

HMMER

JBrowse via The Holmes Lab

Jmol

MCL (Markov Cluster Algorithm)

MUSCLE (Multiple Sequence Comparison by Log- Expectation)

OrthoMCL

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PATRIC Data Release Policy