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Hannenhalli S, Pevzner P.  1995.  Towards a computational theory of genome rearrangements. Computer Science TodayComputer Science Today. 1000:184-202.
Hannenhalli S, Putt ME, Gilmore JM, Wang J, Parmacek MS, Epstein JA, Morrisey EE, Margulies KB, Cappola TP.  2006.  Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure. Circulation. 114(12):1269-1276.
Hannenhalli S.  1996.  Polynomial-time algorithm for computing translocation distance between genomes. Discrete Applied Mathematics. 71(1–3):137-151.
Hannenhalli S.  2006.  Invited Talk: Deciphering Gene Regulatory Networks by in silico approaches. 6th International Workshop on Data Mining in Bioinformatics (BIOKDD06). :31-31.
Hannenhalli S.  1995.  Transforming men into mice (a computational theory of genome rearrangements).
Hannenhalli S, Feldman W, Lewis HF, Skiena SS, Pevzner PA.  1996.  Positional sequencing by hybridization. Computer applications in the biosciences : CABIOS. 12(1):19-24.
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77:1-19.
Hannenhalli S, Pevzner P.  1996.  To cut… or not to cut (applications of comparative physical maps in molecular evolution). Proceedings of the seventh annual ACM-SIAM symposium on Discrete algorithms. :304-313.
Hannenhalli S, Kaestner KH.  2009.  The evolution of Fox genes and their role in development and disease. Nature reviews. GeneticsNat Rev Genet. 10(4):233-240.
Hannenhalli S.  1995.  Polynomial-time algorithm for computing translocation distance between genomes. Combinatorial Pattern MatchingCombinatorial Pattern Matching. 937:162-176.
Hannenhalli S, Middleton RP, Levy S, Perroud B, Holzwarth JA, McDonald K, Hannah SS.  2006.  Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements. Osteoarthritis and Cartilage. 14(8):830-838.
Hannenhalli S, Pevzner PA.  1999.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACM. 46(1):1-27.
Hannenhalli S, Pevzner PA.  1995.  Transforming men into mice (polynomial algorithm for genomic distance problem). Foundations of Computer Science, Annual IEEE Symposium on. :581-581.
Hannenhalli S, Hayes WS, Hatzigeorgiou AG, Fickett JW.  1999.  Bacterial Start Site Prediction. Nucleic Acids ResearchNucl. Acids Res.. 27(17):3577-3582.
Hannenhalli S, Perumalla K, Chandrasekharan N, Sridhar R.  1993.  A distributed algorithm for ear decomposition. , Fifth International Conference on Computing and Information, 1993. Proceedings ICCI '93. :180-184.
Hannuksela J, Sangi P, Heikkila J, Liu X, Doermann D.  2007.  Document Image Mosaicing with Mobile Phones. International Conference on Image Analysis and Processing (ICIAP'07). :1-8.
Hansel D, Cleaveland R, Smolka SA.  2004.  Distributed prototyping from validated specifications. Journal of Systems and Software. 70(3):275-298.
Hansen D, Shneiderman B, Smith MA.  2010.  Analyzing Social Media Networks with NodeXL.
Hansen P C, O'Leary DP.  1993.  The Use of the L-Curve in the Regularization of Discrete Ill-Posed Problems. SIAM Journal on Scientific Computing. 14(6):1487-1503.
Hansen M, Everett L, Singh L, Hannenhalli S.  2010.  Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction. Algorithms for Molecular Biology. 5(1):4-4.
Hansen D, Smith MA, Shneiderman B.  2011.  EventGraphs: Charting Collections of Conference Connections. 2011 44th Hawaii International Conference on System Sciences (HICSS). :1-10.
Hansen DL, Jacobs DW, Lewis D, Biswas A, Preece J, Rotman D, Stevens E.  2011.  Odd Leaf Out: Improving Visual Recognition with Games. Privacy, security, risk and trust (passat), 2011 ieee third international conference on and 2011 ieee third international conference on social computing (socialcom). :87-94.
Hansen P C, O'Leary DP.  1997.  Regularization algorithms based on total least squares. Recent advances in total least squares techniques and errors-in-variables modeling (Leuven, 1996)Recent advances in total least squares techniques and errors-in-variables modeling (Leuven, 1996). :127-137.
Hansen M, Everett L, Singh L, Hannenhalli S.  2009.  Mimosa: mixture model of co-expression to detect modulators of regulatory interaction. Proceedings of the 9th international conference on Algorithms in bioinformatics. :133-144.
Hansen D, Shneiderman B, Smith MA.  2010.  Analyzing Social Media Networks with NodeXL: Insights from a Connected World. :302.

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