Publications (updated June 2019)

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Misc contributions

2. Scientific progress -- it takes a village - guest editorial at Current Science Journal, 2019.

1. Transcription - a contribution to the Sciku project, 2017.

Preprints at BioRxiv

5. Assaf Magen, Jia Nie, Thomas Ciucci, Samira Tamoutounour, Yongmei Zhao, Monika Mehta, Bao Tran, Dorian B McGavern, Sridhar Hannenhalli, Remy Bosselut: Single-cell profiling of tumor-reactive CD4+ T-cells reveals unexpected transcriptomic diversity. 2019.

4. Haley Wight, Junhui Zhou, Muzi Li, Sridhar Hannenhalli, Steve Mount, Zhongchi Liu: Draft Genome Assembly and Annotation of Red Raspberry Rubus Idaeus. 2019.

3. Bharath Saravanan, Deepanshu Soota, Zubairul Islam, Ranveer Singh Jayani, Rajat Mann, Umer Farooq, Sweety Meel, Kaivalya Walavalkar, Srimonta Gayen, Anurag Kumar Singh, Sridhar Hannenhalli, Dimple Notani: Ligand dependent gene regulation by transient ERa clustered enhancers. 2019.

2. Seung Gu Park and Sridhar Hannenhalli: First intron length in mammals is associated with 5' exon skipping rate. 2015.

1. Justin Malin, Daphne Ezer, Xiaoyan Ma, Steve Mount, Hiren Karathia, Seung Gu Park, Boris Adryan, and Sridhar Hannenhalli: Crowdsourcing: Spatial clustering of low-affinity binding sites amplifies in vivo transcription factor occupancy. 2015.


123. Nishanth Ulhas Nair, Avinash Das, Vasiliki-Maria Rogkoti, Michiel Fokkelman, Richard Marcotte, Chiaro Jong, Joo Sang Lee, Isaac Meilijson, Sridhar Hannenhalli, Benjamin Neel, Bob van de Water, Sylvia E Le Devedec, Eytan Ruppin: Migration rather than proliferation transcriptomic signatures are strongly associated with breast cancer patient survival. Scientific Reports, 2019 (in press).

122. Magen A., Das A., Lee J.S., Sharmin M., Lugo A., Gutkind S., Shaffer, A., Ruppin E., and Hannenhalli S.: Beyond synthetic lethality: charting the landscape of pairwise gene expression states associated with survival in cancer. Cell Reports, 2019 (in press).

121. Pablo Cordero, Victoria Parikh,..., Sridhar Hannenhalli, ..., Euan Ashley: Pathologic gene network rewiring implicates PPP1R3A as a central regulator in pressure overload heart failure. Nature Communications, 2019 (in press).

120. Alicia D. Howard, Xiaochun Wang, Megana Prasad, Avinash Das Sahu, Radhouane Aniba, Michael Miller, Sridhar Hannenhalli, Yen-Pei Christy Chang: Allele-specific enhancers mediate associations between LCAT and ABCA1 polymorphisms and HDL metabolism. PLoS One, 2019 (in press).

119. Vishaka Datta, Sridhar Hannenhalli, and Rahul Siddharthan: ChIPulate : A comprehensive ChIP-seq simulation pipeline. PLoS Comp Bio, 2019 (in press).

118. Avinash Das, Joo Sang Lee, Zhiyong Wang, Ramiro Iglesias-Bartolome, Noam Ausslander, Livnat Jerby-Arnon, Allon Wagner, Kuoyuan Cheng, Seung Gu Park, Welles Robinson, Arnaud Amzallag, Cyril Benes, Kevin Gardner, Sridhar Hannenhalli, J. Silvio Gutkind, Eytan Ruppin: Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy. Mol Sys Bio, 2019 (in press).


117. M. Senthil Kumar, Eric V. Slud, Kwame Okrah, Stephanie C. Hicks, Sridhar Hannenhalli, Hector Corrada Bravo: Analysis And Correction Of Compositional Bias In Sparse Sequencing Count Data.BMC Genomics, 2018 (in press).

116. Lee JS, Adler L, Karathia H, ..., Samuels Y, Hannenhalli S, Ruppin E, Erez A: Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures. Cell, 174:6, 1559-1570, 2018.

115. Kun Wang, Di Wu, Haoyue Zhang, Avinash Das, Mahashweta Basu, Justin Malin, Kan Cao, Sridhar Hannenhalli: Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases. Scientific Reports, 8:1 10929, 2018

114. Ray Hu, Michael Morley, Jeffrey Brandimarto, Nathan Tucker,Victoria Parsons,Sihai Zhao,Benjamin Meder, Hugo Katus, Frank Rühle, Monika Stoll, Eric Villard, François Cambien, Honghuang Lin, Nicholas Smith, Janine Felix, Ramachandran Vasan,Pim van der Harst, Christopher Newton-Cheh, Jin Li, Cecilia Kim, Hakon Hakonarson, Sridhar Hannenhalli,Euan Ashley, Christine Moravec, WH Tang, Marjorie Maillet, Jeffery Molkentin,Patrick Ellinor, Kenneth Margulies, and Thomas Cappola: Genetic Reduction in Left Ventricular Protein Kinase C alpha and Adverse Ventricular Remodeling in Human Subjects. Circulation: Cardiovascular Genetics11:3 e001901, 2018

113. Joo Sang Lee, Avinash Das, Livnat Jerby-Arnon, Seung Gu Park, Matthew Davidson, Dilka Atias, Arnaud Amzallag, Chani Stossel, Ella Buzhor, Welles Robinson, Kuoyuan Cheng, Joshua Waterfall, Paul S. Meltzer, Sridhar Hannenhalli, Cyrill H. Benes, Talia Golan, Emma Shanks, Eytan Ruppin: Harnessing synthetic lethality to predict clinical outcomes of cancer treatment. Nature Communications, 9:1 2546, 2018.

112. Nishanth Ulhas Nair, Avinash Das, Uri Amit, Welles Robinson, Seung Gu Park, Mahashweta Basu, Alex Lugo, Jonathan Leor, Eytan Ruppin, and Sridhar Hannenhalli: Putative functional genes in idiopathic dilated cardiomyopathy. Scientific Reports, 8:1, 66, 2018.


111. Sushant Patkar, Assaf Maegan, Roded Sharan, and Sridhar Hannenhalli: A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer. PLoS Comp Bio, 13(11):e1005793, 2016.

110. Shrutii Sarda and Sridhar Hannenhalli: Orphan CpG islands as alternative promoters. Transcription, 27(4):553-566, 2017.

109. Mahashweta Basu, Mahfuza Sharmin, Avinash Das, Nishanth Ulhas Nair, Kun Wang, Joo Sang Lee, Yen-Pei Christy Chang, Eytan Ruppin1 Sridhar Hannenhalli1: Prediction and Subtyping of Hypertension from pan-tissue transcriptomic and genetic analyses. Genetics, 2017, doi: 10.1534/genetics.117.300280.

108. Uri Amit et al...,Avinash Das,...,Eytan Ruppin, Sridhar Hannenhalli, and Jonathan Leor: A New Role for Interleukin-13 Receptor in Myocardial Homeostasis and Heart Failure. Journal of the American Heart Association, 2017, doi: 10.1161/JAHA.116.005108.

107. Shrutii Sarda, Avinash Das, Charles Vinson, and Sridhar Hannenhalli: Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal-promoters. Genome Research, 2017, 27(4):553-566.


106. Hiren Karathia, Carl Kingsford, Michelle Girvan, and Sridhar Hannenhalli: A pathway-centric view of spatial proximity in the 3D nucleome across cell lines. Scientific Reports, 2016 (doi:10.1038/srep39279).

105. Mahfuza Sharmin, Hector Corrada Bravo, and Sridhar Hannenhalli: Heterogeneity of Transcription Factor binding specificity models within and across cell lines. Gen Research, 2016 (doi: 10.1101/gr.199166.115).

104. Mahfuza Sharmin, Hector Corrada-Bravo, and Sridhar Hannenhalli: Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer. BMC Cancer, 2016, 16(1):88.


103. M. Senthil Kumar, Joshua B. Plotkin, and Sridhar Hannenhalli: Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution. PLoS Comp Bio, 2015, 11(11).

102. Shrutii Sarda and Sridhar Hannenhalli: High throughput identification of cis-regulatory rewiring events in yeast. Mol Bio Evol, 2015, 32(12):3047-63.

101. Kun Wang, Kan Cao, and Sridhar Hannenhalli: Chromatin and Genomic determinants of alternative splicing. ACM-BCB, 2015.

100. Avinash Das, Michael Morley, Christine Moravec, WH Wilson Tang, Hakon Hakonarson, MAGNet Consortium, Kenneth B. Margulies, Thomas P. Cappola, Shane Jensen, and Sridhar Hannenhalli: Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability. Nat Communications, 2015, 6: 8555.

99. Nivedita Rangarajan, Prakash Kulkarni, and Sridhar Hannenhalli: Evolutionarily conserved network properties of intrinsically disordered proteins. PLoS One, 10(5): e0126729, 2015.


98. Yichuan Liu, Michael Morley, Jeffrey Brandimarto, Sridhar Hannenhalli, Yu Hu, Euan A. Ashley, W.H. Wilson Tang, Christine S. Moravec, Kenneth B. Margulies, Thomas P. Cappola, Mingyao Li: RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure. Genomics, 105(2): 83-89, 2014.

97. Kun Wang, Avinash Das, Zheng-Mei Xiong, Kan Cao and Sridhar Hannenhalli: Phenotype-dependent coexpression gene clusters: application to normal and premature ageing. Transactions on Computational Biology and Bioinformatics(TCBB) (doi: TCBB.2014.2359446), 2014.

96. Seung Gu Park, Sridhar Hannenhalli*, and Sun Shim Choi: Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals. BMC Genomics, 15(526), 2014.

95. Yun Lu, Mary Putt, Sridhar Hannenhalli and Thomas Cappola: An Evaluation of MC Logic and logicFS Motivated by a Study of the Regulation of Gene Expression in Heart Failure. Journal of Applied Statistics , 41(9):1956-75, 2014.

94. Diana K. Darnell, Li S. Zhang, Sridhar Hannenhalli and Sergey Yu. Yaklichkin: Developmental Expression of chicken FOXN1 and putative target genes during feather development. International Journal of Developmental Biology 58(1): 57-64, 2014.

93. Elfalem Alemu, Joseph W. Carl Jr., Hector Corrada-Bravo and Sridhar Hannenhalli: Determinants of expression variability. NAR, 42(6):3503-14, 2014.


92. Shrutii Sarda and Sridhar Hannenhalli: Next Generation Sequencing and Epigenomics research - A hammer in search of nails. Genomics Inform, 12(1):2-11, 2013.

91. Plasschaert, Robert; Vigneau, Sebatien; Tempera, Italo; Gupta, Ravi; Maksimoska, Jasna; Everett, Logan; Davuluri, Ramana; Marmorstein, Ronen; Lieberman, Paul; Schultz, David; Hannenhalli, Sridhar*; Bartolomei, Marisa: CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation.NAR, 42(2): 774-789, 2013.

90. Kun Wang, Avinash Das, Zheng-Mei Xiong, Kan Cao and Sridhar Hannenhalli: Identification of gene clusters with phenotype-dependent expression with application to normal and premature ageing.ACM BCB, 2013.

89. Hao Wang, Geet Duggal, Rob Patro, Michelle Girvan, Sridhar Hannenhalli and Carl Kingsford: Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin.ACM BCB, 2013.

88. Justin Malin, Radhouane Mohamed Aniba, and Sridhar Hannenhalli: Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers. NAR, 41(14): 6828-6838, 2013.

87. Robert Kim, Prakash Kulkarni and Sridhar Hannenhalli: Derepression of Cancer/Testis Antigens in Cancer is Associated with Distinct Patterns of DNA Hypomethylation. BMC Cancer, 13: pp144, 2013.

86. Sun Shim Choi and Sridhar Hannenhelli: Three Independent Determinants of Protein Evolutionary Rate. J Mol Evol, 76(3) 98-111, 2013.

85. R. Mukherjee, L.N.S. Singh, P. Evans, S. Hannenhalli: Correlated evolution of positions within mammalian cis elements. PLoS ONE,8(2): e55521, 2013.


84. Alexander J. Stewart, Sridhar Hannenhalli and Joshua B. Plotkin: Why Transcription Factor Binding Sites Are Ten Nucleotides Long. Genetics, 192(3): 973-985,2012.

83. Gita Mahmoudabadi, Krithika Rajagopalan, Robert H. Getzenberg, Sridhar Hannenhalli, Govindan Rangarajan, and Prakash Kulkarni: Intrinsically Disordered Proteins and Conformational Noise: Implications in Cancer. Cell Cycle, 12(1): 26-31,2012.

82. Jia Zeng and Sridhar Hannenhalli: Inferring Evolution of Gene Duplicates Using Probabilistic Models and Nonparametric Belief Propagation. BMC Genomics 14 Suppl 1: S15, 2012.

81. Joseph Carl, Joanne Trgovcich and Sridhar Hannenhalli: Widespread evidence of viral miRNAs targeting host pathways. BMC Bioinformatics 14 Suppl 2: S3, 2012.

80. Avinash D. Sahu, R. Aniba, Y.C. Chang, S. Hannenhalli: Epigenomic model of cardiac enhancers with application to Genome wideassociation studies. Proceedings of the Pacific Symposium on Biocomputing, 2012.

79. Christopher G. Vecsey, Lucia Peixoto, Jennifer H.K. Choi, Mathieu Wimmer, Devan Jaganath, Pepe J. Hernandez, Jennifer Blackwell, Karuna Meda, Alan J. Park, Sridhar Hannenhalli and Ted Abel: Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus, Physiological Genomics, 44(20): 981-991, 2012.

78. Mugdha Khaladkar, Sridhar Hannenhalli: Functional Divergence of Gene Duplicates: a Domain-centric view, BMC Evolutionary Biology, 12: 126, 2012.

77. Jian Li, Nina Bowens, Lan Cheng, Mary Chen, Sridhar Hannenhalli, Xiaohong Zhu, Thomas P. Cappola, and Michael S. Parmacek: Myocardin-like Protein (MKL)-2 Regulates TGF-beta Signaling in Embryonic Stem Cells and the Developing Vasculature Development, 139(19): 3531-3542, 2012.


76. Dewey, F. E., M. V. Perez, Wheeler, M. T., Watt, C., Spin, J., Langfelder, P., Horvath, S., Hannenhalli, S., Cappola, T. P., Ashley, E. A.: Gene coexpression network topology of cardiac development, hypertrophy, and failure. Circ Cardiovasc Genet 4(1): 26-35, 2011.

75. Yaklichkin, S. Y., D. K. Darnell, Pier, M. V., Antin, P. B. and Hannenhalli, S.: Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1. BMC Evol Biol 11: 302, 2011.

74. Y. Tian, Y. Zhang, L. Hurd, S. Hannenhalli, F. Liu, M.M. Lu, and E. Morrisey: Regulation of lung endoderm progenitor cell behavior by miR302/367 Development, 138(7): 1235-1245, 2011.

73. M. Khaladkar, M. Smyda, and S. Hannenhalli: Epigenomic and RNA Structural Correlates of Polyadenylation. RNA Biology, 8(3): 529-537, 2011.

72. L. Everett, Jensen, S., and Hannenhalli, S.: Transcriptional regulation via TF-modifying enzymes -- an integrative model-based analysis NAR, 39(12):e78, 2011.

71. A. Vishnoi, Praveen Sethupathy, Daniel Simola, Joshua B. Plotkin, and Sridhar Hannenhalli: Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Molecular Biology and Evolution, 28(9): 2615-2627, 2011.

70. Hannenhalli, S.: Modeling regulatory motifs. Bioinformatics for Biologist. Pavel Pevzner and Ron Shamir (eds.). Cambridge University Press, 2011.


69. A.K. Rohlfing, Miteva, Y., Hannenhalli, S. and Lamitina, T.: Genetic and physiological activation of osmosensitive gene expression mimics transcriptional signatures of pathogen infection in C. elegans. PLoS ONE 5(2): e9010, 2010.

68. L. N. Singh and Sridhar Hannenhalli: Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families. NAR 38(3): 738-49, 2010.

67. C.M. Trivedi, W. Zhu, Q. Wang, C. Jia, H.J. Kee, L. Li, S. Hannenhalli, and J.A. Epstein: Hopx and Hdac2 interact to modulate Gata4 acetylation and embryonic cardiac myocyte proliferation. Developmental Cell 19(3): 450-459, 2010.

66. A. Vishnoi, S. Kryazhimskiy, G.A. Bazykin, S. Hannenhalli*, J.B. Plotkin: Young proteins experience more variable selection pressures than old proteins. Genome Research 20(11): 1574-1581, 2010. *co-corresponding author.

65. M. Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli: Mimosa Mixture model of co-expression to detect modulators of regulatory interaction  Algorithms in Mol Biology 5(4), 2010 Notes: Accepted at the conference 'Workshop on Algorithms in Bioinformics.


64. M. Putt, Hannenhalli, S., Lu, Y., Haines, P., Chandruptla, H., Morrisey, E.E., Margulies, K.B., Cappola, T.: Evidence for co-regulation of myocardial gene expression by MEF2 and NFAT in human heart failure. Circulation: Cardiovascular Genetics 2(3): 212-219, 2009.

63. L. Everett, Vo, A., Hannenhalli, S.: PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic Acids Res 37(Database issue): D66-71, 2009.

62. K. Essien, S. Vigneau, S. Apreleva, L.N. Singh, M.S. Bartolomei and S. Hannenhalli: CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features. Genome Biology 10(11): R131, Nov 2009.

61. A.N. Qasim, T.S. Metkus, M. Lehrke, S. Restine, M.L. Wolfe, T. Cappola, S. Hannenhalli, M. Tadesse, D.J. Rader, M.P. Reilly: Resistin Gene Variation is Associated with Systemic Inflammation but not Plasma Adipokine Levels, Metabolic Syndrome or Coronary Atherosclerosis in non-Diabetic Caucasians. Clinical Endocrinology 70(5): 698-705, July 2009.

60. Rui Liu, Sridhar Hannenhalli*, Maja Bucan: Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons  Genome Biology 10(7): R72, June 2009 Notes: *co-corresponding author.

59. R. Shah, Yun Lu, Christine C Hinkle, Fiona C McGillicuddy, Roy Kim, Sridhar Hannenhalli, Thomas Cappola, Sean Heffron, XingMei Wang, Nehal Mehta, Mary Putt, Muredach P. Reilly: Gene profiling of human adipose tissue during evoked inflammation in vivo. Diabetes 58(10): 2211-2219, June 2009.

58. Sridhar Hannenhalli and Klaus Kaestner: The evolution of FOX genes and their role in development and disease. Nature Review Genetics 10: 233-40, April 2009.


57. L.B. Wan, Pan, H., Hannenhalli, S., Cheng, Y., Ma, J., Fedoriw, A., Lobanenkov, V., Latham, K.E., Schultz, R.M. & Bartolomei, M.S.: Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development. Development 135: 2729-2738, 2008.

56. D.R. Fermin, A. Barac, S. Lee, S.P. Polster, S. Hannenhalli, T Bergemann, S.M. Grindle, D.B. Dyke, F.D. Pagani, L.W. Miller, S. Tan, C. dos Remedios, T.P. Cappola, K.B. Margulies, and J.L. Hall1 : Sex and Age Dimorphism of Myocardial Gene Expression in Nonischemic Human Heart Failure. Circulation Cadiovascular Genetics CIRCGENETICS.108.802652, December 2008.

55. P. Sethupathy, H. Giang, J. Plotkin, S. Hannenhalli: Genome-wide analysis of natural selection on human cis-elements. PLoS ONE 3(9): e3137, Aug 2008.

54. K. Essien, S. Hannenhalli, C.J. Stoeckert Jr: Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity. PLoS ONE 3(9): e3122, August 2008.

53. L. Singh and S. Hannenhalli: Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression. PLoS ONE 3(e2345), April 2008.

52. Hannenhalli, S.: Eukaryotic transcription factor binding sites--modeling and integrative search methods. Bioinformatics 24(11): 1325-31, 2008.

51. Praveen Sethupathy and Sridhar Hannenhalli: A tutorial of the Poisson Random Field model in population genetics. Advances in Bioinformatics 2008.


50. 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 134(1): 189-98, 2007.

49. S. Yang, Kai Wang, Otto Valladares, Sridhar Hannenhalli and Maja Bucan: Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. Genome Biology 8(11): R247, 2007.

48. 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.

47. N. Minkah, Hwang, Y., Perry, K., Van Duyne, G. D., Hendrickson, R., Lefkowitz, E. J., Hannenhalli, S., Bushman, F. D.: Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. Virology 365(1): 60-9, 2007.

46. L. N. Singh, Li-San Wang, and Sridhar Hannenhalli: TREMOR - A tool for retrieving transcriptional modules by incorporating motif covariance. NAR 35(21): 7360-71, 2007.

45. J. Wang, L. Ungar, S. Tseng, and S. Hannenhallii: MetaProm: a neural network based meta-predictor for alternative human promoter prediction. BMC Genomics 8: 374-386, 2007.

44. Hannenhalli, S.: Eukaryotic Transcriptional Regulation: Signals, Interactions and Modules. Computational Genomics Stojanovich, N. (eds.). Horizon Bioscience, Page: 55-82, 2007.


43. 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.

42. 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 114(12): 1269-76, 2006.

41. 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.

40. 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.

39. M. K. Lewinski, 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.

38. 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.

37. J. Wang and S. Hannenhalli: A mammalian promoter model links cis elements to genetic networks. Biochem Biophys Res Commun 347(1): 166-177, 2006.

36. H. Hinsch and Sridhar Hannenhalli: Recurring genomic breaks in independent lineages support genomic fragility. BMC Evolutionary Biology 6: 90, 2006.

35. D. Hadley, T. Murphy, O. Valladares, S. Hannenhalli, L. Ungar, J. Kim, M. Bucan: Patterns of Sequence Conservation in Presynaptic Neural Genes. Genome Biology 7(11): R105, 2006.

34. D. A. Ross, S. Hannenhalli, J. Tobias, N. Cooch, R. Shiekhattar and T. Kadesch: Functional analysis of Hes-1 in preadipocyte. Mol Endocrinol 20: 698-705, 2006.

33. C. Berry, S. Hannenhalli, J. Leipzig and F. Bushman : Selection of Target Sites for Mobile DNA Integration in the Human Genome. PLoS Comput Biol 2(11): e157, 2006.

2001-2005 (Celera years and getting to know the Academia)

32. S. Hannenhalli* and L.S. Wang: Enhanced position weight matrices using mixture models. Bioinformatics 21(suppl 1): i204-212  2005. *Corresponding author

31. 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 79(11): 6610-6619, 2005.

30. 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.

29. L.S. Wang, S.T. Jensen, S. Hannenhalli: An Interaction-dependent model for transcription factor binding. RECOMB-Regulation 2005

28. J. Wang and S. Hannenhalli: Generalized Markov models for sequence classification. BMC Bioinformatics 6(1): 219-230, 2005.

27. 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 11(5): 858-866, 2004.

26. Istrail, S., Sutton, G. G., Florea, L., Halpern, A. L., Mobarry, C. M., Lippert, R., Walenz, B., Shatkay, H., Dew, I., Miller, J. R., Flanigan, M. J., Edwards, N. J., Bolanos, R., Fasulo, D., Halldorsson, B. V., Hannenhalli, S., Turner, R., Yooseph, S., Lu, F., Nusskern, D. R., Shue, B. C., Zheng, X. H., Zhong, F., Delcher, A. L., Huson, D. H., Kravitz, S. A., Mouchard, L., Reinert, K., Remington, K. A., Clark, A. G., Waterman, M. S., Eichler, E. E., Adams, M. D., Hunkapiller, M. W., Myers, E. W., and Venter, J. C.: Whole-genome shotgun assembly and comparison of human genome assemblies. PNAS 101(7): 1916-21, 2004.

25. S. Hannenhalli and S. Levy: Transcriptional regulation of protein complexes and pathways. Mammalian Genome 14: 611-619, 2003.

24. S. Levy and S. Hannenhalli: Identification of transcription factor binding sites in the human genome. Mammalian Genome 13: 510-514, 2002.

23. S. Hannenhalli* and S. Levy: Predicting transcription factor synergism. Nucleic Acids Research 30: 4278-4284, 2002. *Corresponding author

22. P. Berman, S. Hannenhalli and M. Karpinski: Approximation algorithm for sorting by reversals. ESA 1: 375, 2002.

21. Venter et al: The human genome. Science 291: 1304-1351, 2001.

20. S. Levy, S. Hannenhalli and C. Workman: Enrichment of regulatory signals in conserved non-coding genomic sequence. Bioinformatics 1: 1-7, 2001.

19. S. Hannenhalli* and S. Levy: Promoter prediction in human genome. Bioinformatics 17: S90-S96, 2001. *Corresponding author

18. S. Hannenhalli, E. Hubbell, R. Lipshutz and P. Pevzner: Combitatorial Analysis for design of DNA Arrays. Chip Technology J. Hoheisel (eds.). Springer-Verlag, Page: 1-19, 2002.

1997-2000 (Random explorations)

17. V. Bafna, S. Hannenhalli, K. Rice and L. Vawter: Ligand-receptor pairing via tree comparison. Journal of Computational Biology 7: 59-70, 2000.

16. 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.

15. S. Hannenhalli, W. Hayes, A. Hatzgeorgiou and J. Fickett: Bacterial start site prediction. NAR 27: 3577-3582, 1999.

14. V. Dancik, S. Hannenhalli and S. Muthukrishnan: Hardness of flip-cut problems from optical mapping. Journal of Computational Biology 4: 119-125, 1997.

13. R. Agarwala, S. Batzoglou, V. Dancik, S. Decatur, S. Hannenhalli, M. farach, 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: 275-296, 1997.

1991-1996 (The early years)

12. S. Hannenhalli and P. Pevzner: Towards a computational theory of genome rearrangements. Lecture Notes in Computer Science 1000: 184-202, 1995

11. S. Hannenhalli, P. Pevzner, H. Lewis, S. Skeina and W. Feldman: Positional sequencing by hybridization. Bioinformatics (formerly CABIOS) 12: 19-24, 1996.

10. 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 Page: 304-313, 1996.

9. S. Hannenhalli: Polynomial algorithm for computing translocation distance between genomes. Journal of Discrete Applied Math (Special Issue on Computational Molecular Biology) 1: 137-152, 1996.

8. P. Berman and S. Hannenhalli: Fast sorting for reversal. Combinatorial Pattern Matching Page: 168-185, 1996.

7. 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.

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 Page: 178-189, 1995.

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 Page: 581-592, 1995.

4. N. Chandrasekharan and S. Hannenhalli: Efficient algorithms for computing matching and chromatic polynomials in series-parallel graphs. Journal of Combinatorial Mathematics and Combinatorial Computing 15: 19-32, 1994.

3. M. Borah, S. Hannenhalli, 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 Page: 336-345, 1994.

2. S. Hannenhalli, K. Perumalla, N. Chandrasekharan and R. Sridhar: A distributed algorithm for ear decomposition. Proc. of Intl. Conf. on Computating and Information Page: 180-184, 1993.

1. K. Hua and S. Hannenhalli: Parallel transitive closure computations using topological sort. Proc. of Intl. Conf. on Parallel and Distributed Information Systems 1991.


S. Hannenhalli and R. Russell: Analysis and prediction of protein functional sub-types from protein sequence alignments,. European Patent Patent Number # EP1096411, 2000