Understanding Transcriptional Regulation of Genes
Biological processes are controlled at various levels in the cell and while these mechanisms are poorly understood, transcriptional control is widely recognized as an important component and a better understanding of which will provide an efficient means for the therapeutic intervention disease processes. We have been focusing on various computational problems pertaining to transcriptional regulation, namely, 1) Computational identification of transcription factor binding sites (TFBS), 2) PolII promoter prediction, 3) Predicting interaction among transcription factors (TF), 4) Transcriptional modeling, i.e. identifying arrangements of TFs that co-regulate a set of transcripts.
Selected Publications
S. Vardhanabhuti, J. Wang, S. Hannenhalli*: Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. NAR 35: 3339-3354, 2007.
Lewinski, M. K., Yamashita, H., Emerman, M., Shinn, P., Leipzig, J., Hannenhalli, S., Berry, C., Ecker, J. R., Bushman, F.D.: Retroviral gag and integrase act synergistically to determine integration target specificity. PLoS Pathogens 2(6): e60, 2006.
S. Hannenhalli, R. P. Middleton, S. Levy, B. Perroud, J. A. Holzwarth, K. McDonald, and S. S. Hannah: Identification and Cross-Species Comparison of Canine Osteoarthritic Gene Regulatory cis-Elements. OSTEOARTHRITIS AND CARTILAGE 14(8): 830-838, 2006.
P. Evans, G. Donahue and S. Hannenhalli*: Conservation patterns in cis-elements reveal compensatory mutations. RECOMB-Comparative Genomics, Lecture Notes in Computer Science. A. McLysaght, J. Lagergren and D. Sankoff (eds.). Springer Berlin 4205: 186-199, 2006.
S. Hannenhalli, M. Putt, J. Gilmore, J. Wang, M. Parmacek, J. Epstein, E. Morrisey, K. Margulies and T. Cappola: Transcriptional genomics associates FOX transcription factors with human heart failure. Circulation 2006.
L. Everett , L.S. Wang, and S. Hannenhalli*: Dense subgraph computation via stochastic search: application to detect transcriptional modules. Bioinformatics 22(14): e117-e123, 2006.
M.B. Keeley, M. Wood, C. Isiegas, J. Stein, K. Hellman, S. Hannenhalli, T. Abel: Differential Transcriptional Response to Non-Associative and Associative Components of Classical Fear Conditioning in the Amygdala and Hippocampus. Memory and Learning 13: 135-142, 2006.
J. Wang and S. Hannenhalli*: A mammalian promoter model links cis elements to genetic networks. Biochem Biophys Res Commun 347(1): 166-177, 2006.
L.S. Wang, S.T. Jensen, S. Hannenhalli*: An Interaction-dependent model for transcription factor binding. RECOMB-Regulation 2005.
J. Wang and S. Hannenhalli*: Generalized Markov models for sequence classification. BMC Bioinformatics 6(1): 219-230, 2005.
F. Bushman, M. Lewinski, A. Ciuffi, S. Barr, J. Leipzig, S. Hannenhalli, C. Hoffmann: Genome-wide analysis of retroviral DNA integration. Nat Rev Microbiol 3(11): 848-58, 2005.
S. Hannenhalli* and L.S. Wang: Enhanced position weight matrices using mixture models. Bioinformatics 21(suppl 1): i204-212 2005.
S. Hannenhalli and S. Levy: Predicting transcription factor synergism. Nucleic Acids Research 30: 4278-4284, 2002.
S. Hannenhalli and S. Levy: Transcriptional regulation of protein complexes and pathways. Mammalian Genome 14: 611-619, 2003.
S. Levy and S. Hannenhalli: Identification of transcription factor binding sites in the human genome. Mammalian Genome 13: 510-514, 2002.
S. Hannenhalli and S. Levy: Promoter prediction in human genome. Bioinformatics 17: S90-S96, 2001.
S. Hannenhalli and R. Russell: Analysis and prediction of protein functional sub-typse from protein sequence alignments. Journal of Molecular Biology 202: 61-76, 2000.
Venter et al: The human genome. Science 291: 1304-1351, 2001.
S. Hannenhalli, W. Hayes, A. Hatzgeorgiou and J. Fickett: Bacterial start site prediction. NAR 27: 3577-3582, 1999.
S. Hannenhalli, C. Chappey, E. Koonin and P. Pevzner: Genome sequence comparison and scenarios for gene rearrangements: A test case. Genomics 30: 299-311, 1995.
S. Hannenhalli and P. Pevzner: Transforming men into mice (polynomial algorithm for genomic distance problem). 36th Annual IEEE Symposium on Foundations of Computer Science Page: 581-592, 1995.
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Last updated: 08/25/2008
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