# ITR project

__Start Date:__

September 1, 2003

__Abstract: __

Advances in information technology have resulted in the generation of voluminous data in every walk of life. Efficient techniques are needed to process these data. The state of the art in information extraction is

the use of disparate ad-hoc application-specific techniques. A major goal of our project is to develop unifying techniques for processing data. Such unifying information extraction techniques could benefit from and be of benefit to the

various communities that deal with massive data.

#### As a part of this project, we have developed a web system called Minimotif Miner (MnM) for motif search. This system is currently under use by numerous biologists worldwide.

__Participants:__

Sanguthevar Rajasekaran(Univ. of Connecticut)Sartaj Sahni (Univ. of Florida)

Tom Cormen (Dartmouth College)

Reda Ammar (Univ. of Connecticut)

Chun-Hsi Huang (Univ. of Connecticut)

__Supported Personnel:__

Geeta Chaudhry (Postdoctoral Researcher, Dartmouth College), 2004-2005.

Sandeep Sen (Prof. of CS, IIT New Delhi), Dec. 2003 to June 2004.

Sudha Balla (Graduate Student, UConn), 2005-2006.

Jaime Davila (Graduate Student, UConn), 2005-2006.

Mingjun Song (Graduate Student, UConn), 2005-2006

Thomas Puzak (Graduate Student, UConn), 2005-2006

Saleh Ibrahim (Graduate Student, UConn), 2005-2006

Sahar Al Seesi (Graduate Student, UConn), 2006-2007

Dragos Trinca (Graduate Student, UConn), 2006-2008

Vamsi Kundeti (Graduate Student,UConn), 2006-2008

E.R. Davidson (Graduate Student,Dartmouth College), 2004-2006

Priya Natarajan (Graduate Student,Dartmouth College), 2006-2007

Y. Li (Graduate Student, Univ. of Florida), 2007-2008

H. Lu (Graduate Student, Univ. of Florida), 2005-2006

W. Lu (Graduate Student, Univ. of Florida), 2005-2006

Tanya Mishra (Graduate Student, Univ. of Florida), 2007-2008

J. Park (Graduate Student, Univ. of Florida), 2005-2006

X. Xu (Graduate Student, Univ. of Florida), 2006-2007

X. Zha (Graduate Student, Univ. of Florida), 2006-2008

ThaiBinh Luong (Undergraduate Student, Univ. of Connecticut), Summer of 2004.

Rick Weinberger (Undergraduate Student, Univ. of Connecticut), Summer of 2004.

Senate Taka (Undergraduate Student, Dartmouth College), 2005-2007

Nick Rubino (Undergraduate Student, Univ. of Connecticut), Summer of 2008

Patrick Gradie (Undergraduate Student, Univ. of Connecticut), Summer of 2008

__PUBLICATIONS__

1. M.F. Ahmed, R.A. Ammar, and S. Rajasekaran, SPENK: adding another level of parallelism on the cell broadband engine, *Proc. IFMT*, 2008.

2. S. Al Seesi, S. Rajasekaran, and R.A. Ammar, RNA Pseudoknot Folding through Inference and Identification Using TAGRNA, *Proc. First International Conference on Bioinformatics and Computational Biology (BICoB)*, 2009, pp. 90-101.

3. S. Al Seesi, S. Rajasekaran, and R.A. Ammar, Pseudoknot Identification through Learning TAGRNA, *Proc. International Symposium on Pattern Recognition in Bioinformatics (PRIB)*, 2008, pp. 132-143.

4. S. Al Seesi, S. Rajasekaran, and R. Ammar, Learning a Subclass of Tree Adjoining Grammars, *Proc. First Southern African Bioinformatics Workshop*, Johannesburg, January 28-30, 2007, pp. 45-48.

5. R.A. Ammar, S. Rajasekaran, A. Hussein, A. Hamdy, Efficient Scheduling of Real-time Tandem Task Graphs on Heterogeneous Clusters with Network Limitations, *Proc. IEEE International Conference on Computers and Communications* (ISCC) 2007, pp. 227-232.

6. S. Balla, J. Davila, and S. Rajasekaran, Sorting and FFT Based Techniques in the Discovery of Biopatterns, in *Bioinformatics Algorithms: Techniques and Applications*, I. Mandoiu and A. Zelikovsky, editors, Wiley Book Series on Bioinformatics, 2008.

7. S. Balla and S.Rajasekaran, Space and Time Efficient Algorithms for Endogenous RNAi Control and Target Discovery In Genomes, Technical Report, BECAT/CSE, University of Connecticut, 2006.

8. S. Balla and S. Rajasekaran, Space and Time Efficient Algorithms for Endogenous RNAi Control and Target Discovery In Genomes, *Proc. International Symposium on Bioinformatics Research and Applications (ISBRA)*, Atlanta, GA, Springer-Verlag Lecture Notes in Bioinformatics 4463, 2007.

9. S. Balla, S. Rajasekaran, An Efficient Algorithm for Minimum Degeneracy Primer Selection, *IEEE Transactions on Nanobioscience (IEEE-TNB),* March 2007, Vol. 6, No. 1, pp 12-17.

10. S. Balla, S. Rajasekaran, I. Mandoiu, Efficient Algorithms for Degenerate Primer Search, *International Journal of Foundations of Computer Science (IJFCS)*, 18, 2007, pp. 899-910.

11. S. Balla, S. Rajasekaran, and I.I. Mandoiu, Faster greedy algorithms for Multiple Degenerate Primer Selection, *Proc. BIBE*, 2008, pp. 1-4.

12. S. Balla, V. Thapar, T. Luong, T. Faghri, C.-H. Huang, S. Rajasekaran, J.J. del Campo, J.H. Shinn, W.A. Mohler, M.W. Maciejewski, M.R. Gryk, B. Piccirillo, S.R. Schiller, and M.R. Schiller, Minimotif Miner, a new tool for investigating protein function, *Nature Methods*, March (2006), pp. 175-177. See also J. Kaiser, NETWATCH, *Science* 311, February 17, 2006, p. 925 and ToolBox, Minimotif Miner, *Journal of Proteome Research,* Vol. 5, No. 4, 2006, pp. 736-737.

13. S. Bandyopadhyay and S. Sahni, Sorting on a Cell Broadband Engine SPU, *Proc. IEEE Symposium on Computers and Communications*, 2009.

14. G. Chaudhry, Parallel Out-Of-Core Sorting: The Third Way, Ph.D. Thesis, Dartmouth College, December

2003.

15. G. Chaudhry and T. H. Cormen, Slabpose Columnsort: A New Oblivious Algorithm for Out-of-Core Sorting on Distributed-Memory Clusters, submitted to *Algorithmica*, 2004.

16. G. Chaudhry and T. H. Cormen, Oblivious vs. Distribution-based Sorting: An Experimental Evaluation, *Proc. 13th Annual European Symposium on Algorithms (ESA)*, 2005, pp. 317-328.

17. S. Chen, M. Song, and S. Sahni, Two techniques for fast computation of constrained shortest paths, *IEEE/ACM Transactions on Networking*, 16(1), 2008, pp. 105-115.

18. T. H. Cormen and E. R. Davidson, FG: A Framework Generator for Hiding Latency in Parallel Programs Running on Clusters, *Proc. 17th International Conference on Parallel and Distributed Computing Systems (PDCS)*, 2004, pp. 137-144.

19. T.H. Cormen, P. Natarajan and E.R. Davidson, When One Pipeline Is Not Enough, *Submitted to SC07*, 2007.

20. E. R. Davidson, The FG Programming Environment: Good and Good **For **You, *Proceedings of the Eighteenth Annual ACM Symposium on Parallel Algorithms and Architectures*, July 2006.

21. E. R. Davidson, Improving Running Time and Programmer Productivity in Pipeline-Structured Applications, submitted to *International Conference on Super Computing*, 2006.

22. E.R. Davidson, Improving Running Time and Programmer Productivity in Pipeline-Structured Applications, *ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming*,March 2007, Poster.

23. E. R. Davidson and T. H. Cormen, Asynchronous Buffered Computational Design and Engineering Framework Generator (ABCDEFG): Tutorial and Reference, CS Department, Dartmouth College, 2006. Available at http://www.cs.dartmouth.edu/FG/

24. E. R. Davidson and T. H. Cormen, Building on a Framework: Using FG for More Flexibility and Improved Performance in Parallel Programs, *Proc. 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS)*, 2005.

25. E. R. Davidson and T. H. Cormen, The FG Programming Environment: Reducing Source Code Size for Parallel Programs Running on Clusters, *Proc. Second Workshop on Productivity and Performance in High-End Computing (P-PHEC)*, 2005.

26. J. Davila, S. Balla, and S. Rajasekaran, Space and Time Efficient Algorithms for Planted Motif Search, *Proc. International Conference on Computational Science (2)*2006, pp.822-829.

27. J. Davila, S. Balla, and S. Rajasekaran, Fast and Practical Algorithms for Planted (*l, d*) Motif Search, *IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)*, 2007, pp. 544-552.

28. J. Davila, S. Balla, and S. Rajasekaran, Fast Algorithms for Selecting Specific siRNA in Complete mRNA Data, to be presented in the *7th International Workshop on Algorithms for Bioinformatics (WABI),* 2007.

29. J. Davila and S. Rajasekaran, Randomized Sorting on the POPS Network, *International Journal of Foundations of Computer Science* 16(1), 2005, pp. 105-116.

30. J. Davila and S. Rajasekaran, Extending Pattern Branching to Handle Challenging Instances, *Proc. IEEE 6th Symposium on Bioinformatics and Bioengineering (BIBE)*, 2006, pp. 65-69.

31. J. Davila and S. Rajasekaran, Randomized Packet Routing, Selection and Sorting on the POPS Network, in *Handbook of Parallel Computing: Models, Algorithms, and Applications*, CRC Press, 2008, pp. 13.1-13.14.

32. S.Demurjian, S. Rajasekaran, R. Ammar, I. Greenshields, T. Doan, and L. He, Applying LSI and Data Reduction to XML for Counter Terrorism, *Proc. 27th IEEE Aerospace Conference,*Big Sky, MT, March 2006.

33. C.-H. Huang, V. Lanza, S. Rajasekaran, and W. Dubitzky, Healthgrid-Bridging Life Science and Information Technology, *Journal of Clinical Monitoring and Computing, *19, 2005, pp. 259-262.

34. C.-H. Huang and S. Rajasekaran, BioGrid: Bridging Life Science and Information Technology, *Proc. of the 5-th IEEE/ACM Cluster Computing and the Grid (3rd BioGrid Workshop)*, May 9-12, 2005, Cardiff, UK.

35. C-H. Huang, S. Rajasekaran, L.T. Yang, and X. He, Finding Hamiltonian paths in tournaments on clusters, *Cluster Computing* 9(3), 2006, pp. 345-353.

36. C.-H. Huang, S. Rajasekaran, and L. Yin, Cooperative Biomedical Knowledge Inference, *Poster Book of the 8-th Annual Int'l Conference on Research in Computational, Molecular Biology (RECOMB)*, 556-557, Mar. 27-31 2004, San Diego, CA.

37. E. Jung, Y. Li, S. Ranka, and S. Sahni, An evaluation of in-advance bandwidth scheduling algorithms for connection-oriented networks, *International Symp. on Parallel Architectures, Algorithms, and Networks* (ISPAN), 2008.

38. E. Jung, Y. Li, S. Ranka, and S. Sahni, Performance evaluation of routing and wavelength assignment algorithms for optical networks, *Proc. IEEE Symposium on Computers and Communications*, 2008.

39. K. Kim and S. Sahni, Efficient construction of pipelined multibit-trie router-tables, *IEEE Transactions on Computers* 56(1), 2007, pp. 32-43.

40. K.M. Konwar, S. Rajasekaran, and A.A. Shvartsman, Robust Network Supercomputing with Malicious Processes, *Proc. 20th International Symposium on Distributed Computing (DISC)*, 2006, pp. 474-488.

41. V. Kundeti, Y. Fei, and S. Rajasekaran, An efficient digital circuit for implementing Sequence Alignment algorithm in an extended processor, *Proc. ASAP*, 2008, pp. 156-161.

42. V. Kundeti and S. Rajasekaran, Efficient Algorithms for Self Assembling Triangular and Other Nano Structures, *Proc. International Symposium on Bioinformatics Research and Applications (ISBRA)*, 2009, pp. 148-158.

43. V. Kundeti and S. Rajasekaran, Efficient PDM Sorting Algorithms, *Proc. International Conference on High Performance Computing (HiPC)*, 2008, pp. 97-107.

44. V. Kundeti and S. Rajasekaran, A local structural alignment algorithm with Variable Length Alignment Fragment Pairs, *Proc. BIBE*, 2008, pp. 1-7.

45. V. Kundeti and S. Rajasekaran, Extending the Four Russian Algorithm to Compute the Edit Script in Linear Space, *Proc. International Conference on Computational Science*, Springer-Verlag LNCS, 2008.

46. Y. Li, S. Ranka, and S. Sahni, In-advance path reservation for file transfers in e-science applications, *Proc. IEEE Symposium on Computers and Communications*, 2009.

47. Y. Li, S. Ranka, S. Sahni, and M. Schmalz, Network centered muliple resource scheduling in e-science applications, *CridNets*, 2009, ICST Series, Springer Verlag.

48. H. Lu and S. Sahni, Conflict detection and resolution in two-dimensional prefix router-tables, *IEEE/ACM Transactions on Networking* 13(6), 2005, pp. 1353-1363.

49. H. Lu and S. Sahni, O(log W) multidimensional packet classification, *IEEE/ACM Transactions on Networking*, 15(2), 2007, pp. 462-472.

50. H. Lu and S. Sahni, Dynamic tree bitmap for IP lookup and update, *Proc. International Conference on Networking*, 2007.

51. W. Lu and S. Sahni, Efficient two-dimensional multibit tries for packet classification, *IEEE Transactions on Computers*, to appear.

52. W. Lu and S. Sahni, Succinct representation of static packet classifiers, *IEEE/ACM Transactions on Networking* 17(3), 2009, pp. 803-816.

53. W. Lu and S. Sahni, Packet classification using two-dimensional multibit tries, *Proc. IEEE Symposium on Computers and Communications*, 2005.

54. W. Lu and S. Sahni, Packet classification using two-dimensional multibit tries, *IEEE Symposium on Computers and Communications*, 2005, pp. 849-854.

55. W. Lu and S. Sahni, Packet forwarding using pipelined multibit tries, *IEEE Symposium on Computers and Communications*, 2006.

56. W. Lu and S. Sahni, Packet classification using pipelined two-dimensional multibit tries, *IEEE Symposium on Computers and Communications*, 2006.

57. W. Lu and S. Sahni,Succinct representation of static packet classifiers, *Proc. IEEE Symposium on Computers and Communications (ISCC),* 2007.

58. W. Lu and S. Sahni, Succinct representation of static packet forwarding tables, *Proc. International Conference on Networking*, 2007.

59. W. Lu and S. Sahni, Recursively partitioned static IP router-tables, *Proc. International Symposium on Computers and Communications (ISCC)*, 2007.

60. W. Lu and S. Sahni, Packet classification using space-efficient pipelined multibit tries, *IEEE Transactions on Computers* 57(5), 2008, pp. 591-605.

61. W. Lu and S. Sahni, Low power TCAMs for very large forwarding tables,* INFOCOM,* 2008.

62. W. Lu and S. Sahni, Packet classification using space-efficient pipelined multibit tries, *IEEE Transactions on Computers*, 57, 5, 2008, 591-605.

63. J. Luo and S. Rajasekaran, A Framework for Mining Association Rules, *International Journal of Computers and Their Applications,*March 2006, pp. 39-49.

64. J. Luo and S. Rajasekaran, FIT: A Fast Algorithm for Discovering Frequent Itemsets in Large Databases, * Proc. 8th International Conference on Knowledge-Based Intelligent Information & Engineering Systems*, Springer-Verlag LNCS, 2004. ABSTRACT

65. T. Mishra and S. Sahni, PETCAM--A power efficient TCAM for forwarding tables, *Proc. IEEE Symposium on Computers and Communications*, 2009.

66. A.A. Mohamed and S. Rajasekaran, A Text Summarizer Based on Meta-Search, *Proc. 5th IEEE Symposium on Signal Processing and Information Technology (ISSPIT),*December 2005, pp. 670-674.

67. J. Park and S. Sahni, Power assignment for symmetric communication in wireless sensor networks, *International Journal on Distributed Sensor Networks* 5(2), 2009, pp. 185-200.

68. J. Park and S. Sahni, An online heuristic for maximum lifetime routing in wireless sensor networks, *IEEE Transactions on Computers* 55(8), 2006, pp. 1048-1056.

69. J. Park and S. Sahni, Maximum lifetime broadcasting in wireless networks, *ACM/IEEE Intl. Conf. on Computer Systems and Applications* (AICCSA), 2005.Invited Paper.

70. J. Park and S. Sahni, Power assignment for symmetric communication in wireless sensor networks, I*EEE Symposium on Computers and Communications*,2006.

71. S. Rajasekaran, Editor, *Bioinformatics and Computational Biology, First International Conference, BICoB* 2009, New Orleans, LA, USA, April 8-10, 2009. Proceedings Springer 2009, Volume LNBI 5462.

72. S. Rajasekaran, Efficient Parallel Hierarchical Clustering Algorithms, *IEEE Transactions on Parallel and Distributed Systems, submitted16(6), June 2005, pp. 497-502.* ABSTRACT

73. S. Rajasekaran, Algorithms for Motif Search, in *Handbook of Computational Molecular Biology, *edited by S. Aluru, Chapman & Hall/CRC, 2006, pp. 37-1--37-21.

74. S. Rajasekaran, Parallel algorithms for motif search, *Proc. ISCA International Conference on Parallel and Distributed Computing Systems* (PDCS) 2007, pp. 175-180.

75. S. Rajasekaran, *Journal of Parallel and Distributed Computing Special Issue on Parallel Techniques for Information Extraction*, 68(1), 2008.

76. S. Rajasekaran, Deterministic and Randomized Sorting Algorithms for Parallel Disk Models, in *Handbook of Parallel Computing: Models, Algorithms, and Applications*, CRC Press, 2008, pp. 6.1-6.18.

77. S. Rajasekaran, S. Al Seesi, R.A. Ammar, Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots, *Proc. International Sympsoium on Bioinformatics Research and Applications (ISBRA)*, 2009, pp. 135-147.

78. S. Rajasekaran, R. Ammar, B. Cheriyan, and L. Loew, Parallel Techniques for the Virtual Cell, *Proc. International Symposium on Signal Processing and Information Technology (ISSPIT)*, 2005.

79. S. Rajasekaran, R. Ammar, S. Demurjian, A. Abdel-Raouf, T. Doan, J. Lian, M. Song, and A. Mohamed, Strategies to process high volumes of data in support of counter-terrorism, *Proc. IEEE Aerospace Conference*, 2005.

80. S. Rajasekaran, R. Ammar, D.-G. Shin, and G. Zhang, Efficient Parallel Algorithms for Processing Biological Sequences, to appear in *International Journal of Computers andtheir Applications in Technology (IJCAT).*Extended Abstract in *Proc. International Symposium on Signal Processing and
Information Technology (ISSPIT)*, 2004. ABSTRACT

81. S. Rajasekaran, S. Balla, and J. Davila, Approximation Algorithms for Primer Selection, Planted Motif Search and Related Problems, in *Approximation Algorithms and Metaheuristics*, T.E. Gonzalez, editor, CRC Press, 2007, pp 75-1 -- 75-25.

82. S. Rajasekaran, S. Balla, P. Gradie, M.R. Gryk, K. Kadaveru, V. Kundeti, M.W. Maciejewski, T. Mi, N. Rubino, J. Vyas, and M.R. Schiller, Minimotif miner 2nd release: a database and web system for motif search, *Nucleic Acids Research* 37 (Database-Issue), 2009, pp. 185-190.

83. S. Rajasekaran, S. Balla, and C.-H. Huang, Exact Algorithms for the Planted Motif Challenge Problems, *Journal of Computational Biology 12(8), 2005, pp. 1117-1128.* ABSTRACT

84. S. Rajasekaran, S. Balla, C.-H. Huang, V. Thapar, Mike Gryk, Mark Maciejewski, and Marty Schiller, High-Performance Exact Algorithms for Motif Search, *Journal of Clinical Monitoring and Computing *19, 2005, pp. 319-328.ABSTRACT

85. S. Rajasekaran and J. Davila, Packet Routing and Selection on the POPS Network, *Journal of Parallel and Distributed Computing* 65(8), 2005, pp. 927-933.

86. S. Rajasekaran, O. Harel, M. Zuba, G. Matthews, and R. Aseltine, Responsible Data Releases, *Proc. Industrial Conference on Data Mining (ICDM)*, 2009, pp. 388-400.

87. S. Rajasekaran, V. Kumar, S. Sahni, and R. Birge, Efficient algorithms for protein-based associative processors and volumetric memories, *Proc. 8th IEEE Conference on Nanotechnology*, 2008.

88. S. Rajasekaran and V. Kundeti, Spectrum Based Techniques for Graph Isomorphism, *International Journal of Foundations of Computer Science* 20(3), 2009, pp. 479-499.

89. S. Rajasekaran and J.H. Reif, *Handbook of Parallel Computing: Models, Applications and Algorithms, *CRC Press, 2008. (1200+ pages).

90. S. Rajasekaran and S. Sen, A generalization of the 0-1 principle for sorting, *Information Processing Letters*94, 2005, pp. 43-47. ABSTRACT

91. S. Rajasekaran and S. Sen, PDM Sorting Algorithms That Take A Small Number Of Passes, *Proc. International Parallel and Distributed Processing Symposium (IPDPS), *2005. ABSTRACT

92. S. Rajasekaran and S. Sen, A Simple Optimal Randomized Algorithm for Sorting on the PDMs, *Proc. International Symposium on Algorithms and Computations (ISAAC) 2005, pp.543-552.* ABSTRACT

93. S. Rajasekaran and S. Sen, Optimal and Practical Algorithms for Sorting on the PDM, *IEEE Transactions on Computers* 57(4), 2008, pp. 547-561.

94. S. Rajasekaran and M. Song, A Novel Scheme for the Parallel Computation of SVDs, *Proc. International Conference on High Performance Computing and Communications (HPCC), Springer-Verlag LNCS 4208,*2006, pp. 129-137.

95. S. Rajasekaran and M. Song, A Relaxation Scheme for Increasing the Parallelism in Jacobi-SVD, *Journal of Parallel and Distributed Computing* 68(6), 2008, pp. 769-777.

96. S. Rajasekaran, V. Thapar, H. Dave, C.-H. Huang, A randomized algorithm for distance matrix calculations in multiple sequence alignment, *Journal of Clinical Monitoring and Computing *19, 2005, pp. 351-359.

97. N.S.V. Rao, C. Glover, M. Shankar, J. Chin, D. Yau, C. Ma, Y. Yang, and S. Sahni, Improved SPRT detection using localization with application to radiation sources, *Fusion*, 2009.

98. N.S.V. Rao, M. Shankar, J. Chin, D. Yau, Y. Yang, J. Hou X. Xu, and S. Sahni, Localization under random measurements with application to radiation sources, *Fusion*, 2008.

99. N. Rao, X. Xu, and S. Sahni, A computational geometry method for DTOA triangulation, *Fusion*, 2007.

100. S. Sahni, N. Rao, S. Ranka, Y. Li, E. Jung, and N. Kamath, Bandwidth scheduling and path computation algorithms for connection-oriented networks, *International Conference on Networking*, 2007, Best Paper Award.

101. D. Sharma, V. Thapar, R.A. Ammar, S. Rajasekaran, and M. Ahmed, Efficient sorting algorithms for the cell broadband engine, *Proc. International Symposium on Computers and Communications (ISCC)*, 2008, pp. 736-741.

102. M. I. Soliman, S. Rajasekaran, and R.A. Ammar, A Block JRS Algorithm for Highly Parallel Computation of SVDs, *Proc. International Conference on High Performance Computing and Communications* (HPCC), 2007, Springer-Verlag LNCS, pp. 346-357.

103. M. Song and S. Rajasekaran, A Novel Scheme for the Detection of an Unknown Class in Classification, *Proc. DMIN,* 2008, pp. 10-13.

104. M. Song and S. Rajasekaran, TM Algorithm for Frequent Itemset Mining, *IEEE Transactions on Knowledge and Data Engineering (TKDE)*18(4), 2006, pp. 472-481. ABSTRACT

105. M. Song and S. Rajasekaran, Fast algorithms for constant approximation k-means clustering, *roc. International Symposium on Algorithms and Computations (ISAAC) 2005.*

106. M. Song and S. Rajasekaran, A Greedy Correlation-Incorporated SVM-Based Algorithm for Gene Selection, *Proc. IEEE International Symposium on Bioinformatics and Life Science Computing (BLSC)*, 2007.

107. M. Song and S. Sahni, Approximation algorithms for multiconstrained quality-of-service routing, *IEEE Transactions on Computers* 55(5), 2006, pp. 603-617.

108. V. Thapar and S. Rajasekaran, A sampling based algorithm for faster and more efficient multiple sequence alignment, BECAT/CSE Technical Report, University of Connecticut, 2008.

109. D. Trinca and S. Rajasekaran, Towards a Collusion-Resistant Algebraic Multi-Party Protocol for Privacy-Preserving Association Rule Mining in Vertically Partitioned Data, *Proc. The 3rd International Workshop on Information Assurance*, 2007.

110. D. Trinca and S. Rajasekaran, Self-Optimizing Parallel Algorithms for Haplotype Reconstruction and Their Evaluation on the JPT and CHB Genotype Data, *Proc. IEEE International Conference on Bioinformatics and Bioengineering* (BIBE) 2007, pp. 1294-1298.

111. D. Trinca and S. Rajasekaran, Fast Cryptographic Multi-party Protocols for Computing Boolean Scalar Products with Applications to Privacy-Preserving Association Rule Mining in Vertically Partitioned Data, *Proc. International Conference on Data Warehousing and Knowledge Discovery* (DaWaK) 2007, Springer-Verlag LNAI 4597, pp. 418-427.

112. X. Xu, N. Rao, and S. Sahni, A computational geometry method for localization using differences of distances,* IEEE Transactions on Sensor Networks*, to appear.

113. X. Xu and S. Sahni, Approximation algorithms for sensor deployment, *Proc. Innovations and Real-Time Applications of Distributed Sensor Network (DSN) Symposium*, 2006.Best Paper Award.

114. X. Xu and S. Sahni, Approximation algorithms for sensor deployment, *IEEE Transactions on Computers*, 56, 2007, pp. 1681-1695.

115. X. Xu, S. Sahni, and N. Rao, Minimum cost sensor coverage of planar regions, *Fusion*, 2008.

116. X. Xu, S. Sahni, and N. Rao, On basic properties of localization using distance-difference measurements, *Fusion*, 2008.

117. L. Yin, C.-H. Huang, and S. Rajasekaran, Parallel Data Mining of Bayesian Networks from Gene Expression Data, *Poster Book of the 8-th Annual Int'l Conference on Research in Computational Molecular Biology (RECOMB),* 122-123, Mar. 27-31 2004, San Diego, CA.

118. X. Zha and S. Sahni, Highly compressed Aho-Corasick automata for intrusion detection, *Proc. IEEE Symposium on Computers and Communications*, 2008.