NIH
Northeast Biodefense Center [NBC]
1U54AI057158-01 (PI Lipkin)
9/04/03 - 2/29/08
NIH/NIAID
Northeast Biodefense Center
Role: Former Director, Biomedical Informatics Core (Lussier)
Co-investigators: Jeffrey Skolnick, Mark Gerstein
The overall grant is funding for a biodefense
center in the Northeast. The Lussier Research
Group contribution is part of the informatics
core. We proposed to develop a tool to help
with the rapid annotation and
characterization of a newly sequenced
microbial pathogen. Our tool will comprise a
number of modules including large-scale rapid
similarity comparisons, structure and
localization prediction, rapid information
retrieval, and prediction of interactions.
Articles funded by this
grant:
• Cantor MN, Sarkar IN, Bodenreider O,
Lussier YA*.
Genestrace: Phenomic Knowledge
Discovery Via Structured Terminology.
Pacific Symposium on Biocomputing,
2005 (in Press). Computational mapping
prediction between heterogeneous ontologies.
Proof of concept study to compare phenotypes.
(Website) (Abstract)
(Preprint)
• Y Liu, PM Harrison, V Kunin, M Gerstein*.
Comprehensive analysis of pseudogenes
in prokaryotes: widespread gene decay and
failure of putative horizontally transferred
genes. (2004) Genome Biol 5: R64.
(Website) (Abstract)
(Preprint)
• Tao Y, Friedman C, Lussier YA*.
The Use of Information Visualization
Techniques in Bioinformatics during the
Postgenomic Era. Biosilico (in
Press). A review of literature addressing
difficulties of visualizing multiscale
datasets as those observed in host-pathogen
interactions. We propose solutions involving
computational approaches using ontologies.
(Website) (Abstract) (Preprint)
•Tao Y, Friedman C*, Lussier YA*.
Information Visualization of
Heterogeneous Post Genomics Databases. Bioinformatics
(under review for minor revisions). A
novel visualization method involving the use
of ontologies (also an invention report,
below).
(Website) (Abstract)
(Preprint)
• W. Tian, A. Arakaki and J. Skolnick*.
EFICAz: a comprehensive approach to
accurate genome-scale enzyme function
inference. Nucleic Acid
Research (in press).
(Website) (Abstract)
(Preprint)
• H Yu, D Greenbaum, H Xin Lu, X Zhu,
M Gerstein*
(2004). Genomic analysis of
essentiality within protein networks.
Trends Genet 20: 227-31.By merging
data from large-scale phenotypic experiments,
we define the condition of 'marginal
essentiality' and demonstrate a correlation
between essentiality and participation in
protein-protein interaction networks: protein
with a greater degree of marginal
essentiality are more likely to be hubs in
these networks.
(Website) (Abstract)
(Preprint)
Related sites:
Pathogen
Functional Genomics Resource Center
