2007                    Workshop on Algorithms in Bioinformatics (program co-chair)
2004-2006           RECOMB Satellite conference on Transcriptional Regulation program committee
2006-present        Asia Pacific Bioinformatics Conference (APBC) program committee
2001-2006           RECOMB  program committee
2002                     RECOMB Organizing Chair

Research Publications (peer reviewed)

1. K. Hua and S. Hannenhalli: Parallel transitive closure computations using topological sort. Proc. of Intl. conf. on Parallel and Distributed Information Systems, (1991).
2. S. Hannenhalli and K. Perumalla and N. Chandrasekharan and R. Sridhar: A distributed algorithm for ear decomposition. Proc. of Intl. conf. on Computing and Information, (1993): 180-184.
3. N. Chandrasekharan and S. Hannenhalli: Efficient algorithms for computing matching and chromatic polynomials in series-parallel graphs. Journal of Combinatorial Mathematics and Combinatorial Computing, 1994(15): 19-32.
4. M. Borah and S. Hannenhalli and R. Bajwa and M. Irwin A SIMD solution to the sequence comparison problem on the MGAP. Proc. of Intl. conf. on Application Specific Array Processing, (1994): 336-345.
5. S. Hannenhalli and P. Pevzner: Transforming men into mice (polynomial algorithm for genomic distance problem). 36th Annual IEEE Symposium on Foundations of Computer Science, (1995):581-592.
6. S. Hannenhalli and P. Pevzner: Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). Proc. 27th Annual ACM Symposium on the Theory of Computing, (1995):178-189.
7. S. Hannenhalli and C. Chappey and E. Koonin and P. Pevzner: Genome sequence comparison and scenarios for gene rearrangements: A test case. Genomics, 1995(30): 299-311.
8. S. Hannenhalli and P. Pevzner and H. Lewis and S. Skeina and W. Feldman: Positional sequencing by hybridization. CABIOS, 1996(12): 19-24.
9. P. Berman and S. Hannenhalli: Fast sorting by reversal. Combinatorial Pattern Matching, (1996): 168-185.
10. S. Hannenhalli: Polynomial algorithm for computing translocation distance between genomes. Journal of Discrete Applied Math (Special Issue on Computational Molecular Biology) 71(1996): 137-152
11. S. Hannenhalli and P. Pevzner: To cut ... or not to cut (applications of comparative physical maps in molecular evolution). Seventh Annual ACM-SIAM Symposium on Discrete Algorithms, (1996):304-313.
12. R. Agarwala and S. Batzoglou and V. Dancik and S. Decatur and S. Hannenhalli and M. Farach and S. Muthukrishnan and S. Skiena: Local rules for protein folding on a triangular Lattice and generalized hydrophobicity in HP model. Journal of Computational Biology, 4(1997):275-296.
13. V. Dancik and S. Hannenhalli and S. Muthukrishnan: Hardness of flip-cut problems from optical mapping. Journal of Computational Biology, 4(1997):119-125.
14. S. Hannenhalli and W. Hayes and A. Hatzigeorgiou and J. Fickett: Bacterial start site prediction. NAR, 27(1999):3577-3582.
15. V. Bafna and S. Hannenhalli and K. Rice and L. Vawter: Ligand-receptor pairing via tree comparison. Journal of Computational Biology, 7(2000):59-70.
16. S. Hannenhalli and R. Russell: Analysis and prediction of protein functional sub-types from protein sequence alignments. Journal of Molecular Biology, 202(2000):61-76.
17.  J.C. Venter et al.: The human genome. Science, 291 (2001):1304-1351.
18. S. Hannenhalli   and S. Levy: Promoter prediction in human genome. ISMB 2001, Bioinformatics, 17 (2001):S90-S96.
19. S. Levy and S. Hannenhalli and C. Workman: Enrichment of regulatory signals in conserved non-coding genomic sequence. ISB 2001, Bioinformatics, 1 (2001):1-7.
20. P. Berman and S. Hannenhalli and M. Karpinski: 1.375-Approximation algorithm for sorting by reversals. ESA (2002)
21. S. Levy and S. Hannenhalli: Identification of transcription factor binding sites in the human genome. Mammalian Genome, 13(2002):510-514.
22. S. Hannenhalli and S. Levy: Predicting transcription factor synergism. Nucleic Acids Research, 2002 30: 4278-4284.
23. S. Hannenhalli and S. Levy: Transcriptional regulation of protein complexes and pathways. Mammalian Genome, 14(2003):611-619
24. S. Istrail et al.: Whole-genome shotgun assembly and comparison of human genome assemblies. PNAS USA,2004 101(7): 1916-21
25. V. Bafna and D. Gusfield and S. Hannenhalli and S. Yooseph: A Note on Efficient Computation of Haplotypes via Perfect Phylogeny, Journal of Computational Biology, 2004 11(5): 858-866
26. M. K. Lewinski, D. Bisgrove, P. Shinn, H. Chen, S. Hannenhalli, E. Verdin, C. C. Berry, J. R. Ecker, and F. D. Bushman: Genome-wide analysis of chromosomal feature repressing HIV transcription.  J. Virology, 2005 79(11): 6610-6619.
27. S. Hannenhalli and L.S. Wang: Enhanced position weight matrices using mixture models. Bioinformatics, 2005 Vol 21(Suppl 1):i204-212
28. L.S. Wang, S.T. Jensen, S. Hannenhalli: An Interaction-dependent model for transcription factor binding (2005) RECOMB-Regulation, To appear in Lecture Notes in Computer Science.
29. J. Wang and S. Hannenhalli: Generalized Markov models for sequence classification. BMC Bioinformatics, 2005 6:219
30. 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, 2006, 13, 135-142.
31. D. A. Ross, S. Hannenhalli, J. Tobias, N. Cooch, R. Shiekhattar and T. Kadesch: Functional analysis of Hes-1 in preadipocyte. Mol Endocrinol, 2006, 20:698-705.
32. Lewinski, M. K., Yamashita, H., Emerman, M., Shinn, P., Leipzig, J., Hannenhalli, S., Berry, C., Ecker, J. R., Bushman, F.D.: (2006). Retroviral gag and integrase act synergistically to determine integration target specificity. PLoS Pathogens, 2006, 2(6):e60
33. L. Everett , L.S. Wang, and S. Hannenhalli: Dense subgraph computation via stochastic search: application to detect transcriptional modules.Bioinformatics, 2006, 22(14):e117:23
34. 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, 2006, 14(8): 830:8
35. J. Wang and S. Hannenhalli: A mammalian promoter model links cis elements to genetic networks. Biochem Biophys Res Commun, 2006, 347(1):166-177
36. P. Evans, G.  Donahue and S. Hannenhalli: Conservation patterns in cis-elements reveal compensatory mutations ,RECOMB-Comparative Genomics, Lecture Notes in Computer Science, 2006,4205:186-199
37. H. Hinsch and S. Hannenhalli: Recurring genomic breaks in independent lineages support genomic fragility,BMC Evolutionary Biology, 2006,6:90
38. 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, 114(12):1269-76
39. D. Hadley, T. Murphy, O. Valladares, S. Hannenhalli, L. Ungar, J. Kim, M. Bucan: Patterns of Sequence Conservation in Presynaptic Neural Genes. Genome Biology, 2006, 7(11):R105
40. C. Berry, S. Hannenhalli, J. Leipzig and F. Bushman: Selection of Target Sites for Mobile DNA Integration in the Human Genome,  PLoS Comput Biol, 2006, 2(11):e157
41. Y. Zhang, N. Rath, S. Hannenhalli, Z. Wang, T. Cappola, S. Kimura, E. Atochina-Vasserman, M.M. Lu, M. Beers, and E.E. Morrisey: GATA and Nkx factors synergistically regulate tissue specific gene expression and development in vivo. Development, 2007, 134(1):189-98
42. N. Minkah, Y. Hwang, K. Perry, G.D. Van Duyne, R.C. Hendrick, E.J. Lefkowitz, S. Hannenhalli, F. Bushman:: Variola Virus Topoisomerase: DNA Cleavage Specificity and Distribution of Sites in Poxvirus Genomes. Virology, 2007,365(1):60-69
43. S. Vardhanabhuti, J. Wang, S. Hannenhalli:Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. NAR, 2007,35(10):3203-13
44. Y. Zhang, N. Rath, S. Hannenhalli, Z. Wang, T. Cappola, S. Kimura, E. Atochina-Vasserman, M.M. Lu, M. Beers, and E.E. Morrisey:GATA and Nkx factors synergistically regulate tissue specific gene expression and development in vivo. Development, 2007,134(1):189-98
45. J. Wang, S. Hannenhalli, L. Ungar:MetaProm: a neural network based meta-predictor for alternative human promoter prediction. BMC Genomics, 2007,374(8):374-386
46. L.N. Singh, L.S. Wang, S. Hannenhalli:TREMOR – A tool for retrieving transcriptional modules by incorporating motif covariance. NAR, 2007,35(21):7360-71
47. S. Yang, K. Wang, O. Valladares, S. Hannenhalli and M. Bucan:Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. Genome Biology, 2007,8(11):R247
48. L. Singh and S. Hannenhalli:Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression. PLoS ONE, 2008,((in press)

1. S. Hannenhalli and P. Pevzner: Towards a computational theory of genome rearrangements. Lecture Notes in Computer Science,1995, 1000:184-202.
2. S. Hannenhalli, E. Hubbell, R. Lipshutz and P. Pevzner: Combinatorial Anlysis for design of DNA Arrays. Chip Technology (editor J. Hoheisel), Springer-Verlag, 2002:1-19.
3. F. Bushman, M. Lewinski, A. Ciuffi, S. Barr, J. Leipzig, S. Hannenhalli, C. Hoffmann: Genome-wide analysis of retroviral DNA integration. Nat Rev Microbiol, 2005, 3(11):848-58

Invited Lectures/ Workshops (last 5 years)
 

1. Nov 2003.    Transcritional Regulation: Signals, Interactions and  Modules at Penn State University, State College, PA
2. Feb 2004.    Computational analysis of transcriptional regulation,  at Villanova University, Villanova, PA
3. Nov 2004.    Computational analysis of transcriptional regulation, at CHOP, PA
4. Dec 2005.    Transcription regulation analysis: theory and applicaiton, at Thomas Jefferson University, PA
5. Jun 2006.    Transcription factor DNA binding specifcity (or lack thereof), Bertinoro Bioinformatics Meeting, Bertinoro, Italy.
6. Aug 2006.    Deciphering Gene Regulatory Networks by in silico approaches, BIOKDD international conference, Philadelphia, PA
7. Oct 2006.    Deciphering Gene Regulatory Networks by in silico approaches, George Washington University, Washington D.C
8. Nov 2006.    Deciphering Gene Regulatory Networks by in silico approaches, Brown University, Providence
9. Jul  2007.    Signals, interactions and Networks, Center for Gene Regulation, Barcelona, Spain 
10. Aug 2007.    Computational Analysis of Transcriptional Regulation, Emerging Information and Technology Conference, Princeton University, Princeton.
11. Oct 2007.    In silico approaches to transcriptional regulation and evolution. NHGRI, NIH, Bethesda, MD. Nov  2007. In silico approaches to transcriptional regulation and its evolution, Princeton, NJ .
12. Feb 2008.    Computational analysis of eukaryotic transcriptional regulation and its evolution, Center for comp bio and bioinformatics, Indiana University Purdue University, Indianapolis. 
13. Mar 2008.    Computational analysis of eukaryotic transcriptional regulation and its evolution, Carnegie Mellon University, Pittsburgh. 
14. Apr 2008.    Computational analysis of eukaryotic transcriptional regulation and its evolution, J Craig Venter Institute, Rockville.