Pyres: 2001 UK FMD Outbreak - Photo: Murdo Macleod.  Slides L-R: Smallpox, SARS Coronavirus , Foot and Mouth Disease, West Nile Virus.
Bioinformatics: Pathological Diagnostics
Analytical tools to enhance diagnosis, containment, control and rapid vaccine development.


Stephen M. Apatow
Founder, Director of Research & Development
Humanitarian Resource Institute (UN:NGO:DESA)
Humanitarian University Consortium Graduate Studies
Center for Medicine, Veterinary Medicine & Law
Phone: 203-668-0282

Pathobiologics International

In The Spotlight:
  • The Future of Biodetection Systems - Final Workshop Analysis: The Future of Biodetection Systems Workshop was held last year to bring together industry, academia, national labs, and federal agency personnel in an interactive process, to develop a roadmap for research and development investment in biodetection.  Sponsored by Los Alamos National Laboratory, September 26 & 27 2006. -- Overview: BTACC Pathobiologics International.  Keynote: DNA-based Detection Technologies (Powerpoint): Stephen M.Apatow, Humanitarian University Consortium Graduate Studies Center for Medicine, Veterinary Medicine and Law.
  • Severe acute respiratory syndrome (SARS)—paradigm of an emerging viral infection: Berger, Doerr, Stürmer, Preiser, (Institute for Medical Virology, Johann Wolfgang Goethe University Hospital), Drosten, (Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany).
  • SARS coronavirus: a new challenge for prevention and therapy: The genes of SARS-CoV were compared with the corresponding genes of known coronaviruses of humans, pigs, cattle, dogs, cats, mice, rats, chickens, and turkeys. Each gene of SARS-CoV has only 70% or less identity with the corresponding gene of the known coronaviruses. Thus, SARS-CoV is only dis-tantly related to the known coronaviruses of humans and animals. Phylogenetic analysis suggests that SARS-CoV does not fit within any of the three groups that contain all other known coronaviruses. Holmes, J. Clin. Invest. 111:1605–1609 (2003). doi:10.1172/JCI200318819.
  • Poxvirus Bioinformatics Resource Center. The Center provides a relational database that supports data storage of poxvirus genomic sequences, and annotation and analysis of poxvirus genes; web-based data mining and sequence analysis tools; software for analysis of complete genomes; a poxvirus literature resource; a repository of poxvirus species and strains (at ATCC); and a discussion forum. Monkeypox:  Biodefense and Epidemiological Tracking
  • Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection: Lancet, 5 May 2003.
  • BC: SARS - Coronavirus Sequencing: The current Genome Shotgun Data is available for download and Comparative images generated by the Sockeye genome viewer, developed at the Genome Sciences Centre. The tracks show Blast comparison to (1) avian infectious bronchitis virus, (2) bovine coronavirus, (3) human coronavirus 229E, (4) murine hepatitis virus, (5) porcine epidemic diarrhea virus, (6) transmissible gastroenteritis virus. 
  • CDC: SARS - Coronavirus Sequencing: Sequence information provided by collaborators at National Microbiology Laboratory, Canada, University of California at San Francisco, Erasmus University, Rotterdam and Bernhard-Nocht Institute, Hamburg facilitated this sequencing effort. Includes: Entire Nucleotide Sequence of SARS-CoV (Urbani strain) and Coronavirus Protein Analysis Phylogenetic Trees.
Influenza Genome Databases
  • NCBI Influenza Virus Resource: Presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses.
  • Influenza Virus Database (IVDB): Beijing Institute of Genomics.

Major Centers and Servers

  • Entrez NCBI. The Entrez Interface is the primary gateway into all of the NCBI maintained resources including nucleotide and protein sequence records, protein structure data, and other genetic databases
  • ExPASy Molecular Biology Server SIB. A collection of proteomics tools, software and databases for sequence analysis and structure predictions
  • GenBank NCBI. GenBank is the NIH genetic sequence database providing an annotated collection of all publicly available DNA sequences and the entry site for sequence submission
  • GENOME CENTERS AND DATABASE NCBI. Listings of the major genome centers with links and listings of the key resources supported at each center
  • National Center for Biotechnology Information, NCBI. The main entry point into NCBI with links to the NIH databases in a searchable format through PUBMED, BLAST, ENTREZ and OMIM
  • SRSWWW EMBL. Sequence Retrieval System (SRS) is the main search interface for the EMBL databases
  • TIGR Database TIGR. Collection of genomic databases for multiple species providing sequence, cellular function,tissue specific expression and taxonomic information
  • Whitehead Institute for Biomedical Research/MIT Center for Genome Research WIBR/MIT. Genomic databases, mapping, software and sequencing projects maintained by WIBR/MIT

  • The BioToolKit: An annotated directory of 1129 links to online molecular biology resources, includes basic research tools and advanced applications for genome, transcriptome, and proteome data retrieval, analysis, and visualization. 
  • ExPASy Proteomics Tools. Molecular proteomics analysis tools for nucleotide translation, protein identification, primary sequence analysis, secondary and tertiary structure prediction, transmembrane region detection and sequence alignment 
Additional Resources

Collaborative relationships with College/University research centers are being established worldwide, in support of this initiative. 

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