1U54AI057158-01 (PI Lipkin)
9/04/03 - 2/29/08
Northeast Biodefense Center
Role: informatics core participant (Yves Lussier, core director)

The overall grant is funding for a biodefense center in the Northeast. The Gerstein lab 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.

Related material:

Year 1 report [ html ]

URL: http://www.nbc.columbia.edu/

URL: http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6797830&p_grant_num=5U54AI05715802&p_query=&ticket=12246867&p_audit_session_id=58038221&p_keywords=
Articles funded by this grant:
An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.
Y Liu, J Li, L Sam, CS Goh, M Gerstein, YA Lussier (2006). PLoS Comput Biol 2: e159.

Integration of curated databases to identify genotype-phenotype associations.
CS Goh, TA Gianoulis, Y Liu, J Li, A Paccanaro, YA Lussier, M Gerstein (2006). BMC Genomics 7: 257.

Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes.
Y Liu, PM Harrison, V Kunin, M Gerstein (2004). Genome Biol 5: R64.

Genomic analysis of essentiality within protein networks.
H Yu, D Greenbaum, H Xin Lu, X Zhu, M Gerstein (2004). Trends Genet 20: 227-31.

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