JOURNAL ARTICLES

 

BIOINFORMATICS AND COMPUTATIONAL BIOLOGY

33) H. Dinh and S. Rajasekaran, A memory-efficient data structure representing exact-match overlap graphs with application for next generation DNA assembly, Bioinformatics 2011; doi:10.1093/bioinformatics/btr321.

32) V. Kundeti and S. Rajasekaran, Efficient algorithms for self-assembling non-rectangular nano structures, Natural Computing, Vol. 10, No. 1, April 2011, pp. 583-605.

31) S. Rajasekaran and H. Dinh, A speedup technique for (l, d)-motif finding algorithms, BMC Research Notes, 4:54, 8 March 2011.

30) V. Kundeti, S. Rajasekaran, H. Dinh, M. Vaughn, and V. Thapar, Efficient Parallel and Out of Core Algorithms for Constructing Large Bi-directed de Bruijn Graphs, BMC Bioinformatics, Highly Accessed, Vol. 11, No. 1, November 2010, pp. 560-588.

29) D. Trinca and S. Rajasekaran, Specialized Compression for Coping with Diffraction Effects in Protein-based Volumetric Memories: Solving Some Challenging Instances, Journal of Nanoelectronics and Optoelectronics (JNO), Vol. 5, No. 3, 2010, pp. 290-294.

28) M. J. Ranaghan, S. Shima, L. Ramos, D. S. Poulin, G. Whited, S. Rajasekaran, J. A. Stuart, A. D. Albert, and R. R. Birge, Photochemical and Thermal Stability of Green and Blue Proteorhodopsins: Implications for Protein-Based Bioelectronic Devices, Journal of Physical Chemistry B, 114, 2010, pp. 14064-14070.

27) S. Rajasekaran, V. Kundeti, V. Kumar, S. Sahni, and R. Birge, Efficient Algorithms for Computing With Protein-based Volumetric Memory Processors, IEEE Transactions on Nanotechnology, to appear.

26) S. Rajasekaran, J.C. Merlin, V. Kundeti, A. Oommen, T. Mi, et al., A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions, Proteins: Structure, Function, and Bioinformatics, Vol. 70, No. 1, October 2010, pp. 153-164.

25) V. Kundeti and S. Rajasekaran, On the hardness of the border length minimization problem on a rectabgular array, International Journal of Foundations of Computer Science, Vol. 21, No. 6, December 2010, pp. 1089-1100.

24) S. Rajasekaran, T. Mi, J.C. Merlin, A. Oommen, P. Gradie, and M.R. Schiller, Partitioning of minimotifs based on function with improved prediction accuracy, PLoS ONE 5(8): e12276, 2010.

23) S. Rajasekaran, S. Al Seesi, and R.A. Ammar, Improved algorithms for parsing ESLTAGs: a grammatical model suitable for RNA pseudoknots, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 7(4), 2010, pp. 619-27.

22) M. Song and S. Rajasekaran, A greedy algorithm for gene selection based on SVM and correlation, International Journal of Bioinformatics Research and Applications (IJBRA) 6(3), 2010, pp. 296-307.

21) J. Vyas, R.J. Nowling, T. Meusburger, D. Sargeant, K. Kadaveru, M.R. Gryk, V. Kundeti, S. Rajasekaran, and M.R. Schiller, MimoSA: a system for minimotif annotation, BMC Bioinformatics, 2010, 11:328.

20) D. Trinca and S. Rajasekaran, Fast local-search-based parallel algorithms for DNA probe placementon oligoneucleotide arrays, Advanced Modeling and Optimization 12(1), 2010, pp. 45-55.

19) J. Vyas, R.J. Nowling, M.W. Maciejewski, S. Rajasekaran, M.R. Gryk, and M.R. Schiller, A proposed syntax for minimotif semantics, version I, BMC Genomics, 2009, 10:360.

18) S. Rajasekaran, Computational techniques for motif search, Frontiers in Bioscience 14, June 1, 2009, pp. 5052-5065.

17) 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, 2009, D185-D190.

16) S. Balla and S. Rajasekaran, An efficient algorithm for minimum degeneracy primer selection, IEEE Transactions on Nanobioscience 6(1), 2007, pp. 12-17.

15) 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.

14) S. Balla, S. Rajasekaran, and I. Mandoiu, Efficient algorithms for degenerate primer search, International Journal of Foundations of Computer Science 18, 2007, pp. 899-910.

13) S. Balla, V. Thapar, S. Verma, 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 Tool for Investigating Protein Function, Nature Methods 3, 2006, pp. 175-177. See also J. Kaiser, NetWatch, Science 311(5763), 2006, p. 925.

12) R. Trumbower, S. Rajasekaran, and P. Faghri, Identifying Offline Muscle Strength Profiles Sufficient for Short-Duration FES-LCE Exercise: A PAC Learning Model Approach, Journal of Clinical Monitoring and Computing 20, 2006, pp. 209-220.

11) S. Rajasekaran, R. Ammar, D.G. Shin, and G. Zhang, Efficient Parallel Algorithms for Processing Biological Sequences, International Journal of Computer Applications in Technology 26(3), 2006, pp. 119-125.

10) S. Rajasekaran, V. Thapar, H. Dave, and C.-H. Huang, Randomized and Parallel Algorithms for Distance Matrix Calculations in Multiple Sequence Alignment, Journal of Clinical Monitoring and Computing 19, 2005, pp. 351-359.

9) S. Rajasekaran, S. Balla, C.-H. Huang, V. Thapar, M. Gryk, M. Maciejewski, and M. Schiller, High-Performance Exact Algorithms for Motif Search, Journal of Clinical Monitoring and Computing 19, 2005, pp. 319-328.

8) 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.

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

6) S. Rajasekaran, R.A. Ammar, B. Cheriyan, and L. Loew, Parallel Techniques for the Virtual Cell, Computing Letters 1(2), 2005, pp. 69-74.

5) C.-H. Huang and S. Rajasekaran, High-Performance Parallel Bio-Computing, Parallel Computing 30(9-10), 2004, pp. 999-1000.

4) C.-H. Huang and S. Rajasekaran, Parallel pattern identification in biological sequences on clusters, IEEE Transactions on Nanobioscience, 2(1), 2003, pp. 29-34.

3) S. Rajasekaran, X. Jin, and J.L. Spouge, The Efficient Computation of Position-Specific Match Scores with the Fast Fourier Transform, Journal of Computational Biology 9(1), 2002, pp. 23-34.

2) S. Rajasekaran, Y. Hu, H. Nick, P.M. Pardalos, S. Sahni, G. Shaw, Efficient Algorithms for Similarity Search, Journal of Combinatorial Optimization, 5(1), 2001, pp. 125-132.

1) S. Rajasekaran, H. Nick, P.M. Pardalos, S. Sahni, G. Shaw, Efficient Algorithms For Local Alignment Search, Journal of Combinatorial Optimization, 5(1), 2001, pp. 117-124.

DATA MINING AND INFORMATION EXTRACTION

8) M. Song and S. Rajasekaran, Fast algorithms for constant approximation k-means clustering, Transactions on Machine Learning and Data Mining, 3(2), October 2010, pp. 67-79.

7) 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.

6) M. Song and S. Rajasekaran, A Transaction Mapping Algorithm for Frequent Itemsets Mining, IEEE Transactions on Knowledge and Data Engineering (TKDE) 18(4), 2006, pp. 472-481.

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

4) A.A. Mohamed and S. Rajasekaran, Efficient Randomized Algorithms for Text Summarization, Advances in Natural Language Processing, Journal of Research in Computing Science, 2006, pp. 195-200.

3) J. Luo and S. Rajasekaran, FIT: A Fast Algorithm for Discovering Frequent Itemsets in Large Databases, Computing Letters 1(3), 2005, pp. 129-136.

2) S. Rajasekaran, Efficient Parallel Hierarchical Clustering Algorithms, IEEE Transactions on Parallel and Distributed Systems 16(6), 2005, pp. 497-502.

1) L. Fu and S. Rajasekaran, Novel Algorithms for Computing Medians and Other Quantiles of Disk Resident Data, Journal of Very Large Data Bases 13(2), 2004, pp. 148-161.

OUT-OF-CORE COMPUTING

4) S. Rajasekaran and S. Sen, Optimal and practical randomized algorithms for sorting on the PDM, IEEE Transactions on Computers 57(4), 2008, pp. 547-561.

3) S. Rajasekaran, Out-of-core Computing on Mesh Connected Computers, Journal of Parallel and Distributed Computing 64(11), 2004, pp. 1311-1317.

2) S. Rajasekaran, A Framework for Simple Sorting Algorithms on Parallel Disk Systems, Theory of Computing Systems, 34(2), 2001, pp. 101-114.

1) S. Rajasekaran, Selection Algorithms for Parallel Disk Systems, Journal of Parallel and Distributed Computing, 61(4), 2001, pp. 536-544.

PARALLEL SORTING, SELECTION, AND PACKET ROUTING

27) 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.

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

25) S. Rajasekaran and S. Sen, A Generalization of the Zero-One Principle for Sorting, Information Processing Letters 94, 2005, pp. 43-47.

24) D.S.L. Wei, S. Rajasekaran, K. Naik, and S-Y. Kuo, Efficient Algorithms for Selection and Sorting of Large Distributed Files on de~Bruijn and Hypercube Structures, International Journal of Foundations of Computer Science, 14(6), 2003, pp. 1129-1146.

23) D.S.L. Wei, S. Rajasekaran, Z. Cheng, K. Naik, and S-Y. Kuo, Efficient Selection and Sorting Schemes Using Corteries for Processing Large Distributed Files, Journal of Parallel and Distributed Computing 62(8), 2002, pp. 1295-1313.

22) J.C. Cogolludo and S. Rajasekaran, Permutation Routing on Reconfigurable Meshes, Algorithmica, 31(1), 2001, pp. 44-57.

21) H. ElGindy and S. Rajasekaran, Sorting and Selection Algorithms on a Linear Array with Optical Bus System, Parallel Processing Letters, 9(3), 1999, pp. 373-383.

20) S. Rajasekaran, Selection on Mesh Connected Computers with Fixed and Reconfigurable Buses, Journal of Algorithms, 29, 1998, pp. 68-81.

19) S. Rajasekaran, An Optimal Parallel Algorithm for Sorting Multisets, Information Processing Letters, 67(3), 1998, pp. 141-143.

18) S. Rajasekaran and T. McKendall, Permutation Routing and Sorting on the Reconfigurable Mesh, International Journal of Foundations of Computer Science 9(2), 1998, pp. 199-211.

17) S. Rajasekaran and S. Sahni, Randomized Routing, Selection and Sorting on the OTIS-Mesh, IEEE Transactions on Parallel and Distributed Systems, 9(9), September 1998, pp. 833-840.

16) S. Rajasekaran, W. Chen, and S. Yooseph, Unifying Themes for Selection on Any Network, Journal of Parallel and Distributed Computing 46(1), 1997, pp. 105-111.

15) S. Rajasekaran and S. Sahni, Deterministic Routing on the Array with Reconfigurable Optical Buses, Parallel Processing Letters 7(3), 1997, pp. 219-224.

14) S. Rajasekaran and S. Sahni, Sorting, Selection, and Routing on the Array with Reconfigurable Optical Buses, IEEE Transactions on Parallel and Distributed Systems 8(11), 1997, pp. 1123-1131.

13) S. Rajasekaran and D.S.L. Wei, Selection, Routing, and Sorting on the Star Graph, Journal of Parallel and Distributed Computing, 41(2), 1997, pp. 225-233.

12) S. Rajasekaran, Randomized Selection on the Hypercube, Journal of Parallel and Distributed Computing, 37(2), 1996, pp. 187-193.

11) S. Rajasekaran, Mesh Connected Computers with Fixed and Reconfigurable Buses: Packet Routing and Sorting, IEEE Transactions on Computers, 45(5), 1996, pp.529-539.

10) S. Rajasekaran and S. Sahni, Sorting and Selection on Distributed Memory Bus Computers, Parallel Algorithms and Applications 8, 1996, pp. 179-193.

9) S. Rajasekaran, k-k  Routing, k-k  Sorting, and Cut Through Routing on the Mesh, Journal of Algorithms 19, 1995, pp. 361-382.

8) M.A. Palis, J.C. Liou, S. Rajasekaran, S. Shende, and D.S.L. Wei, Online Scheduling of Dynamic Trees, Parallel Processing Letters, 5(4), 1995, pp. 635-646.

7) S. Rajasekaran and M. Raghavachari, A Randomized Algorithm for Multipacket Routing on the Mesh, Journal of Parallel and Distributed Computing 26, 1995, pp. 257-260.

6) M.A. Palis, S. Rajasekaran, and D.S.L. Wei, Packet Routing and PRAM Emulation on Star Graphs and Leveled Networks, Journal of Parallel and Distributed Computing 20, 1994, pp. 145-157.

5) D. Krizanc, S. Rajasekaran, and S. Shende, A Comparison of Meshes with Static Buses and Unidirectional Wrap-Arounds, Parallel Processing Letters, 3(2), 1993, pp. 109-114.

4) S. Rajasekaran and S. Sen, On Parallel Integer Sorting, Acta Informatica 29, 1992,  pp. 1-15.

3) S. Rajasekaran and T. Tsantilas, Optimal Routing Algorithms for Mesh-Connected Processor Arrays, Algorithmica 8, 1992, pp. 21-38.

2) S. Rajasekaran and R. Overholt, Constant Queue Routing on a Mesh, Journal of Parallel and Distributed Computing 15, 1992, pp. 160-166.

1) S. Rajasekaran and J.H. Reif, Optimal and Sub-Logarithmic Time Randomized Parallel Sorting Algorithms, SIAM Journal on Computing, 18(3), 1989, pp. 594-607.

COMPUTER SIMULATIONS

3) S. Rajasekaran, R. Ammar, K. Reifsnider, L. Achenie, A. Mohamed, G. Zhang, and M. Ahmed, Efficient Parallel Simulation of Direct Methanol Fuel Cell Models, Journal of Fuel Cell Science and Technology 2, 2005, pp. 141-144.

2) J. Luo and S. Rajasekaran, Parallelizing 1-Dimensional Estuarine Model, International Journal of Foundations of Computer Science, 15(6), 2004, pp. 809-821..

1) S. Rajasekaran and K. Ross, Fast Algorithms for Generating Discrete Random Variates with Changing Distributions, ACM Transactions on Modeling and Computer Simulation, Vol. 3, No. 1, January 1993, pp. 1-19.

MISCELLANEOUS

5) V. Kundeti and S. Rajasekaran, Fast algorithms for permuting large entries along the diagonal of a sparse matrix, Journal of Computational and Applied Mathematics 235(3), 2010, pp. 756-764.

4) S. Rajasekaran and V. Kundeti, Spectrum based techniques for graph isomorphism, International Journal of Foundations of Computer Science 20(3), 2009, pp. 479-499.

3) C.-H. Huang, S. Rajasekaran, L. Yang, and X. He, Finding Hamiltonian Paths in Tournaments on Clusters, Journal of Cluster Computing 9, 2006, pp. 341-348.

2) C.-W. Lee, C.-H. Huang, L. Yang, and S. Rajasekaran, Distributed Path-Based Inference in Semantic Networks, Journal of Supercomputing 29(2), 2004, pp. 211-227.

1) S. Rajasekaran, On the Euclidean Minimum Spanning Tree Problem, Computing Letters 1(1), 2004.

COMPUTATIONAL GEOMETRY AND MOTION PLANNING

3) S. Rajasekaran, Efficient Parallel Algorithms for Template Matching, Parallel Processing Letters, 12(3&4), 2002, pp. 359--364.

2) S. Rajasekaran and S. Ramaswami, Optimal Parallel Randomized Algorithms for the Voronoi Diagram of Line Segments in the Plane and Related Problems, Algorithmica 33(4), 2002, pp. 436--460.

1) S. Rajasekaran and S. Ramaswami, Optimal Mesh Algorithms for the Voronoi Diagram of Line Segments, Visibility Graphs, and Motion Planning in the Plane, Journal of Parallel and Distributed Computing 26, 1995, pp. 99-115.

PARSING ALGORITHMS

2) S. Rajasekaran and S. Yooseph, TAL Parsing in O(M(n2)) Time, Journal of Computer and System Sciences 56(1), 1998, pp. 83-89.

1) S. Rajasekaran, TAL Parsing in o(n6) Time, SIAM Journal on Computing, 25(4), 1996, pp. 862-873.

MODEL CHECKING AND REAL-TIME SYSTEMS

1) S. Rajasekaran and I. Lee, Parallel Algorithms for Relational Coarsest Partition Problems, IEEE Transactions on Parallel and Distributed Systems, 9(7), 1998, pp. 687-699.

OPTIMIZATION

2) S. Rajasekaran, On Simulated Annealing and Nested Annealing, Journal of Global Optimization 16(1), 2000, pp. 43--56.

1) S. Rajasekaran and J.H. Reif, Nested Annealing: A Provable Improvement to Simulated Annealing, Theoretical Computer Science 99, 1992, pp. 157-176.

LEARNING THEORY

1) R. Paturi, S. Rajasekaran, and J.H. Reif, The Light Bulb Problem, Information and Computation 117, 1995, pp. 187-192.