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Bioinformatics:
Pathological Diagnostics
Analytical tools to enhance diagnosis, containment, control
and
rapid vaccine development.
Contact:
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
Email:
s.m.apatow@humanitarian.net
Internet:
www.humanitarian.net
Pathobiologics
International
Internet:
www.pathobiologics.org
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.
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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
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Toolkits
- 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.
To submit resources for inclusion on
this
site, contact: s.m.apatow@pathobiologics.org
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