Transcript To provide the scientific community with a robust point of entry for

NIAID
Bioinformatics Resource Centers
Valentina Di Francesco
Bioinformatics Program Director
Microbial Genomics Program, DMID
Overview and Goals
5 year initiative launched in the summer of 2004 (-> 2 years, 4
months)
To provide the scientific community with a robust point of entry
for access of genomic and related data in a user-friendly
format.
To facilitate the identification of potential targets for the
development of vaccines, therapeutics and diagnostics
The centers cover ALL the organisms listed in the NIAID
Category A-C priority list, invertebrate vectors and
pathogens causing emerging or re-emerging diseases that
are relevant for biodefense
BRCs features
 Database of genomics data types
 Web, GUI, API interfaces to the DB
 Computational annotation, human curation and data
integration
 Comparative genomics
 Development and distribution of open source s/w for
analysis and interpretation of genomics data
 Multidisciplinary teams
 Outreach to the organism experts and developers of
diagnostics, vaccine and therapeutics
 Scientific Working Groups
 Training and Workshops
The Institute for Genomic Research
PI: Dr. Owen White - PATHEMA
Bacillus anthracis, Clostridium botulinum, Burkholderia
mallei, Burkholderia pseudomallei, Clostridium
perfringens, Entamoeba histolytica
University of Pennsylvania; University of Georgia
PI: Dr. David Roos, U-Penn - ApiDB
Apicomplexa species: Toxoplasma gondii, Cryptosporidium
parvum, Plasmodium phylum
University of Notre Dame (UND); European
Bioinformatics Institute; Imperial College of
London; Institute of Molecular Biology and
Biotechnology; Harvard University; Purdue
University; University of California Riverside
PI: Dr. Frank Collins, UND - VectorBase
Invertebrate vectors of human pathogens: Anopheles
gambiae, Aedes aegypti, Culex pipiens, Ixodes scapularis
SRA International; University of Wisconsin Madison
PI: Dr. John Greene, SRA - ERIC
Yersinia pestis, Diarrheagenic E. coli, Yersinia
enterocolitica, Shigella, Salmonella
Virginia Bioinformatics Institute (VBI); Loyola
University Medical Center; Social and Scientific
Systems; University of Maryland
PI: Dr. Bruno Sobral, VBI - PATRIC
Rickettsiae species, Brucella species, Coxiella burnetii,
Calicivirus, Hepatitis A virus, Rabies virus, Lyssavirus,
Coronavirus
University of Alabama Birmingham
(UAB); University of Victoria, Canada
PI: Dr. Elliot Lefkowitz, UAB - VBRC
Variola major virus, Arenavirus, Hanta virus,
Rift Valley fever virus, Ebola virus, Marburg
virus, Dengue virus
California encephalitis group virus, Kyasanar
forest disease virus, Omsk hemorrhagic fever
virus, West Nile virus, Alphavirus, Hantaan
virus, Puumala virus, Crimean-Congo
hemorrhagic fever virus, Yellow fever virus,
Tick-borne encephalitis, Nipah virus, Equine
morbillivirus
Northrop Grumman; University of Texas
Southwestern Medical Center (UTSMC);
Vecna Technologies; Amar International
PI: Dr. Richard Scheuermann, UTSMC BioHealthBase
Francisella tularensis, Giardia lamblia,
Microsporidia, Ricinus communis, Multi-drug
resistant Mycobacterium tuberculosis,
Influenza virus
University of Chicago (UC); Fellowship for
Interpretation of Genomes; University of
Illinois Urbana-Champaign
PI: Prof. Rick Stevens, UC - NMPDR
Staphylococcus aureus, pathogenic vibrios,
Listeria monocytogenes, Campylobacter jejuni,
Streptococcus pyogenes, Streptococcus
pneumoniae
BRC-Central
http://www.brc-central.org/
BRCs services to the scientific community
 Computational Annotation
 Data curation (genes, pathways, literature)
 Comparative genomics and intra-species
variation
 Phylogenic analysis
 Integration with other datasets (genomics,
gene expression, proteomics)
 Training and workshops (ApiDB, NMPDR)
General Challenges for the BRCs
 Demostrate BRCs added value to the scientific
community
 Improvements to the Genbank/EMBL annotations
 Integration of a variety of genomic data types
 Collaborations with developers of ‘products’ in the
biodefense community
 Lists of therapeutic targets
 Outreach to the community of organism experts and
bench scientists
 SWG members can help
 Customize genomics information to meet the needs of
the community – there is a lack of specification and
requirements