We propose to establish a Center for Computational Biology and Bioinformatics that will serve as a focal point for research and education at Columbia. The center will facilitate the integration of computational methods into different areas of biomedical research through the fostering of collaborations between laboratory and computational scientists, through training programs, workshops and seminars, and by providing the computational infrastructure and support that is necessary for cutting-edge research in this area. In-house research will include areas such as DNA and protein sequence analysis, SNP analysis and its relationship to human disease, protein structure analysis, the analysis of microarrays, the analysis and comparison of complete genomes, functional annotation of proteins, the study of networks of interacting proteins, and the 3D structure-based design of new pharmaceuticals. The center will play a central role in education through the development of joint courses and degree programs with participating departments. An industrial outreach program will also be established in which industrial scientists will be able to attend center lectures, symposia and workshops, spend mini-sabbaticals at the center, and establish research contacts with center scientists.

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Exploratory Grants (P20)
Project #
1P20LM007276-01
Application #
6401952
Study Section
Special Emphasis Panel (ZRG1-SSS-E (01))
Program Officer
Florance, Valerie
Project Start
2001-09-30
Project End
2004-08-31
Budget Start
2001-09-30
Budget End
2002-08-31
Support Year
1
Fiscal Year
2001
Total Cost
$701,157
Indirect Cost
Name
Columbia University (N.Y.)
Department
Biochemistry
Type
Schools of Medicine
DUNS #
167204994
City
New York
State
NY
Country
United States
Zip Code
10032
Kundaje, Anshul; Middendorf, Manuel; Shah, Mihir et al. (2006) A classification-based framework for predicting and analyzing gene regulatory response. BMC Bioinformatics 7 Suppl 1:S5
Kundaje, Anshul; Middendorf, Manuel; Gao, Feng et al. (2005) Combining sequence and time series expression data to learn transcriptional modules. IEEE/ACM Trans Comput Biol Bioinform 2:194-202
Kuang, Rui; Ie, Eugene; Wang, Ke et al. (2005) Profile-based string kernels for remote homology detection and motif extraction. J Bioinform Comput Biol 3:527-50
Foat, Barrett C; Houshmandi, S Sean; Olivas, Wendy M et al. (2005) Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc Natl Acad Sci U S A 102:17675-80
Richards, Stephen; Liu, Yue; Bettencourt, Brian R et al. (2005) Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res 15:1-18
Ziv, Etay; Koytcheff, Robin; Middendorf, Manuel et al. (2005) Systematic identification of statistically significant network measures. Phys Rev E Stat Nonlin Soft Matter Phys 71:016110
Zhang, Xiang H-F; Leslie, Christina S; Chasin, Lawrence A (2005) Dichotomous splicing signals in exon flanks. Genome Res 15:768-79
Middendorf, Manuel; Kundaje, Anshul; Wiggins, Chris et al. (2004) Predicting genetic regulatory response using classification. Bioinformatics 20 Suppl 1:i232-40
Kuang, Rui; Ie, Eugene; Wang, Ke et al. (2004) Profile-based string kernels for remote homology detection and motif extraction. Proc IEEE Comput Syst Bioinform Conf :152-60
Stolc, Viktor; Gauhar, Zareen; Mason, Christopher et al. (2004) A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306:655-60

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