Technical Publications

2008

1. B. Jackson, P.S. Schnable and S. Aluru, \Consensus genetic maps as median orders from inconsistent sources," ACM/IEEE Transactions on Computational Biology and Bioinformatics, in press.
2. A. Sarje and S. Aluru, \Parallel Biological Sequence Alignments on the Cell Broadband Engine," Proc. 22ndIEEE International Parallel and Distributed Processing Symposium (IPDPS), 2008, to appear.

2007

1. S. Aluru, "Text Indexing", In Encyclopedia of Algorithms, Edited by Ming Kao, Springer, to appear.
2. S. Seal and S. Aluru, "Spatial Domain Decomposition Methods for Parallel Scientific Computing", In Handbook of Parallel Computing: Models, Algorithms and Applications, Edited by S. Rajasekaran and J. Reif, Chapman & Hall/CRC Computer and Information Science Series, Chapter 44 (24 pages), 2007.
3. A. Kalyanaraman, S.J. Emrich, P.S. Schnable and S. Aluru, "Assembling genomes on largescale parallel computers," Journal of Parallel and Distributed Computing (special issue on IPDPS best papers), Vol. 67, pp. 1240-1255, 2007.
4. S.J. Emrich, L. Li, T.-J. Wen, M.D. Yandeau-Nelson, Y. Fu, L. Guo, H.-H. Chou, S. Aluru, D.A. Ashlock and P.S. Schanble, "Nearly identical paralogs (NIPs): implications for maize (Zea mays L.) genome evolution," Genetics, Vol. 175, pp. 429-439, 2007. (featured in Science, Vol. 315, No. 5810, pp. 302 in Editor's Choice: Highlights of the recent literature)
5. M. Ott, J. Zola, S. Aluru and A. Stamatakis, "Large-scale maximum likelihood-based phylogenetic analysis on the IBM Blue Gene/L," Proc. ACM/IEEE Supercomputing Conference (SC), 2007. (best paper finalist).
6. P. Ko and S. Aluru, "Optimal self-adjusting suffix tree layout for dynamic string data in secondary storage," Proc. 14th Symposium on String Processing and Information Retrieval (SPIRE), Springer Verlag Lecture Notes in Computer Science, Vol. 4726, pp. 184-194, 2007.
7. J. Zola, X. Yang, A. Rospondek and S. Aluru, "Parallel-TCoffee: A parallel multiple sequence aligner," Proc. ISCA Parallel and Distributed Computing Systems (PDCS), pp. 248-253, 2007.
8. S. Emrich, A. Kalyanaraman and S. Aluru, "Massively parallel expressed sequence tag clustering ," Proc. ISCA Parallel and Distributed Computing Systems (PDCS), pp. 254-261, 2007.
9. S. Seal and S. Aluru, "Communication-aware parallel domain decomposition using space filling curves," ISCA 19th International Conference on Parallel and Distributed Computing Systems (PDCS), pp. 159-164, 2006. (45% acceptance rate)

2006

1. S. Aluru, N. Amato, D. Bader, S. Bhandarkar, L. Kale, D. Marinescu, and N. Samatovan, "Parallel Computational Biology", In Frontiers of Scientific Computing, Edited by Mike Heroux, Padma Raghavan and Horst Simon, SIAM Publishing, pp. 357-378, 2006.
2. S. Aluru, "Bioinformatics," In Handbook of Nature-Inspired and Innovative Computing: Integrating Classical Models with Emerging Technologies, Edited by Albert Y. Zomaya, Springer, Chapter 21, pp. 657-695, 2006.
3. S. Aluru, N. Amato and D.A. Bader, "Editorial: Special section on high performance computational biology," IEEE Transactions on Parallel and Distributed Systems, Vol. 17, No. 8, pp. 737-740, 2006.
4. A. Kalyanaraman and S. Aluru, "Efficient algorithms and software for detection of full-length LTR retrotransposons," Journal of Bioinformatics and Computational Biology, Vol. 4, No. 2, pp. 197-216, 2006.
5. A. Kalyanaraman, S. Aluru and P.S. Schnable, "Turning repeats to advantage: scaffolding genomic contigs using LTR retrotransposons," Proc. Life Sciences Society Computational Systems Bioinformatics (CSB) Conference, pp. 167-178, 2006. (19.2% acceptance rate)
6. S. Tirthapura, S. Seal and S. Aluru, "A formal analysis of space filling curves for parallel domain decomposition," Proc. International Conference on Parallel Processing (ICPP), pp. 505-512, 2006. (32% acceptance rate)
7. P. Ko and S. Aluru, "Obtaining provably good performance from suffix trees in secondary storage," Proc. Combinatorial Pattern Matching (CPM) Conference, Springer Verlag Lecture Notes in Computer Science, Vol. 4009, pp. 72-83, 2006. (38% acceptance rate)
8. A. Kalyanaraman, S.J. Emrich, P.S. Schnable and S. Aluru, "Assembling Genomes on Large- Scale Parallel Computers", Proc. 20thIEEE International Parallel and Distributed Processing Symposium (IPDPS), 2006. (23% acceptance rate; best paper award)

2005

1. S. Aluru (Editor), Handbook of Computational Molecular Biology, Chapman & Hall/CRC Computer and Information Science Series, 2005 (1104 pages). The Editor co-authored 5 chapters: - Pairwise Sequence Alignments (with B. Jackson)
   - Look-up Tables, Suffix Trees and Suffix Arrays (with P. Ko)
   - Suffix Trees Applications in Computational Biology (with P. Ko)
   - Expressed Sequence Tags: Clustering and Applications (with A. Kalyanaraman)
   - Algorithms for Large Scale Sequence Clustering and Assembly (with S.J. Emrich and A. Kalyanaraman)
   
2. R. Sangireddy, N. Futamura, S. Aluru and A.K. Somani, "Scalable, memory efficient, highspeed lookup and update algorithms for IP routing," ACM/IEEE Transactions on Networking, Vol. 13, No. 4, pp. 802-812, 2005.
3. Y. Fu, S.J. Emrich, L. Guo, T.J. Wen, D. Ashlock, S. Aluru, and P.S. Schnable, "Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted novel genes," Proceedings of the National Academy of Sciences USA, Vol. 102, No. 34, pp. 12282-12287, 2005.
4. B. Hariharan and S. Aluru, "Efficient parallel algorithms and software for compressed octrees with applications to hierarchical methods," Parallel Computing, Vol. 31, pp. 311-331, 2005.
5. P. Ko and S. Aluru, "Space efficient linear time construction of suffix arrays," Journal of Discrete Algorithms, Vol. 3, No. 2-4, pp. 143-156, 2005.
6. S. Seal, S. Komarina and S. Aluru, "An optimal hierarchical clustering algorithm for gene expression data," Information Processing Letters, Vol. 93, No. 3, pp. 143-147, 2005.
7. F. Sevilgen, S. Aluru and N. Futamura, "Parallel algorithms for tree accumulations," Journal of Parallel and Distributed Computing, Vol. 65, No.1, pp. 85-93, 2005.
8. Z. Shen, S. Aluru and S. Tirthapura, "Indexing for subscription covering in publish-subscribe systems," Proc. ISCA 18th International Conference on Parallel and Distributed Computing Systems (PDCS), pp. 328-333, 2005.
9. B. Jackson, S. Aluru and P.S. Schnable, "Consensus Genetic Maps: A Graph Theoretic Approach," Proc. IEEE Computational Systems Bioinformatics (CSB) Conference, pp. 35- 43, 2005. (12% acceptance rate)
10. A. Kalyanaraman and S. Aluru, "Efficient Algorithms and Software for Detection of Fulllength LTR Retrotransposons," Proc. IEEE Computational Systems Bioinformatics (CSB) Conference, pp. 56-64, 2005. (12% acceptance rate; best paper award)

2004

1. S. Aluru, "Quad and Oct Trees," In Handbook of Data Structures and Applications, Edited by Dinesh P. Mehta and Sartaj Sahni, Chapman & Hall/CRC Computer and Information Science Series, Chapter 19 (26 pages), 2004.
2. S. Aluru, "Sufix Trees and Sufix Arrays," In Handbook of Data Structures and Applications, Edited by Dinesh P. Mehta and Sartaj Sahni, Chapman & Hall/CRC Computer and Information Science Series, Chapter 29 (21 pages), 2004.
3. S. Rajko and S. Aluru, "Space and time optimal parallel sequence alignments," IEEE Transactions on Parallel and Distributed Systems, Vol. 15, No. 12, pp. 1070-1081, 2004.
4. M. Mitreva, A.A. Elling, M. Dante, A.P. Kloek, A. Kalyanaraman, S. Aluru, S.W. Clifton, D.McK. Bird, T.J. Baum and J.P. McCarter, "A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans," Molecular Genetics and Genomics, Vol. 272, pp. 138-148, 2004.
5. D.A. Bader and S. Aluru, "Special issue: High performance computational biology," Concurrency and Computation: Practice and Experience, Vol. 16, No. 9, pp. 817-821, 2004.
6. S.J. Emrich, S. Aluru, Y. Fu, T.J. Wen, M. Narayanan, L. Guo, D.A. Ashlock, and P.S. Schnable, "A Strategy for Assembling the Maize (Zea mays L.) Genome," Bioinformatics, Vol. 20, No. 2, pp. 140-147, 2004.
7. S. Aluru and F.E. Sevilgen, "Efficient Methods for Database Storage and Retrieval Using Space-filling Curves," Proc. 19th International Symposium on Computer and Information Sciences, Spring Verlag Lecture Notes in Computer Science, Vol. 3280, pp. 503-512, 2004. (31% acceptance rate)
8. P. Ko, M. Narayanan, A. Kalyanaraman, and S. Aluru, "Space-conserving optimal DNAprotein alignment," Proc. IEEE Computational Systems Bioinformatics Conference, pp. 80- 88, 2004. (21% acceptance rate)
9. M.S. Wu, R.A. Kendall, and S. Aluru, "Exploring collective communications on a cluster of SMPs," Proc. IEEE International Conference on High Performance Computing { Asia, pp. 114-117, 2004. (62% acceptance rate)
10. M.S. Wu, R.A. Kendall, and S. Aluru, "A tunable collective communication framework on cluster of SMPs," Proc. IASTED International Conference on Parallel and Distributed Com- puting and Networks, 2004. (58% acceptance rate)
11. S.J. Emrich, S. Aluru, Y. Fu, T.J. Wen, M. Narayanan, L. Guo, D.A. Ashlock, and P.S. Schnable, "A strategy for assembling the maize genome," Plant and Animal Genomes Conference Bioinformatics Workshop, 2004. (28% acceptance rate)

2003

1. N. Futamura, S. Aluru and X. Huang, "Parallel syntenic alignments," Parallel Processing Letters, Vol. 13, No. 4, pp. 689-703, 2003.
2. A. Kalyanaraman, S. Aluru, V. Brendel and S. Kothari, "Space and time efficient parallel algorithms and software for EST clustering," IEEE Transactions on Parallel and Distributed Systems, Vol. 14, No. 12, pp. 1209-1221, 2003.
3. X. Huang, J. Wang, S. Aluru, S.P. Yang and L. Hillier, "PCAP: A whole-genome assembly program," Genome Research, Vol. 13, pp. 2164-2170, 2003.
4. S. Aluru and D.A. Bader, "Guest editors' introduction: Special issue on high performance computational biology," Journal of Parallel and Distributed Computing, Vol. 63, No. 7-8, pp. 671-673, 2003.
5. A. Kalyanaraman, S. Aluru, S. Kothari, and V. Brendel, "Efficient clustering of large EST data sets on parallel computers," Nucleic Acids Research, Vol. 31, No. 11, pp. 2963-2974, 2003.
6. S. Aluru, N. Futamura and K. Mehrotra, "Parallel biological sequence comparison using prefix computations," Journal of Parallel and Distributed Computing, Vol. 63, No. 3, pp. 264-272, 2003.
7. N. Futamura, R. Sangireddy, S. Aluru and A. Somani, "Scalable, memory efficient, highspeed lookup and update algorithms for IP routing," Proc. 12th International Conference on Computer Communications and Networks, pp. 257-263, 2003. (31% acceptance rate)

1991-2002

1. N. Futamura, S. Aluru, D. Ranjan and B. Hariharan, "Efficient parallel algorithms for solvent accessible surface area of proteins," IEEE Transactions on Parallel and Distributed Systems, Vol. 13, No. 6, pp. 544-555, 2002.
2. I. Al-furaih, S. Aluru, S. Goil and S. Ranka, "Parallel construction of multidimensional binary search trees," IEEE Transactions on Parallel and Distributed Systems, Vol. 11, No. 2, pp. 136-148, 2000.
3. S. Aluru, G.M. Prabhu, J. Gustafson and F. Sevilgen, "Distribution-independent hierarchical algorithms for the N-body problem," Journal of Supercomputing, Vol. 12, pp. 303-323, 1998.
4. S. Aluru, "Lagged Fibonacci random number generators for distributed memory parallel computers,", Journal of Parallel and Distributed Computing, Vol. 45, No. 1, pp. 1-12, 1997.
5. I. Al-furaih, S. Aluru, S. Goil and S. Ranka, "Practical algorithms for selection on coarsegrained parallel computers," IEEE Transactions on Parallel and Distributed Systems, Vol. 8, No. 8, pp. 313-324, 1997.
6. J. Gustafson and S. Aluru,"Massively parallel searching for better algorithms or how to do a cross product in five multiplications," Journal of Scientific Programming, pp. 203-217, 1996.
7. S. Aluru, "Greengard's N-body Algorithm is not Order N," SIAM Journal on Scientific Computing, Vol. 17, No. 3, pp. 773-776, 1996.
8. S. Aluru, G.M. Prabhu and J. Gustafson, "A random number generator for parallel computers," Parallel Computing, Vol. 18, pp. 839-847, 1992.
9. S. Aluru, N. Futamura and D. Ranjan, "A parallel Monte Carlo algorithm for protein accessible surface area computation," Proc. 6th IEEE International Conference on High Per- formance Computing, Springer Verlag Lecture Notes in Computer Science, vol. 1745, pp. 339-348, 1999. (18% acceptance rate for regular papers)
10. S. Aluru and F. Sevilgen, "Dynamic compressed hyperoctrees with application to the N-body problem," Proc. 19th International Conference on Foundations of Software Technology and Theoretical Computer Science, Springer Verlag Lecture Notes in Computer Science, vol. 1738, pp. 21-33, 1999. (36% acceptance rate)
11. F. Sevilgen and S. Aluru, "A unifying data structure for hierarchical methods," Proc. IEEE/ACM Supercomputing Conference, http://www.supercomp.org/sc99, 1999. (29% acceptance rate)
12. F. Sevilgen, S. Aluru and N. Futamura, "Distributed memory tree accumulations," Proc. Parallel and Distributed Computing Systems, pp. 389-395, 1999. (46% acceptance rate)
13. K.N.B. Murthy and S. Aluru, "Bidirectional division-free Gaussian elimination algorithm for solving linear equations," Proc. Parallel and Distributed Computing Systems, pp. 520-527, 1999. (46% acceptance rate)
14. S. Aluru and S. Maneewongvatana, "A practical parallel algorithm for line segment visibility," Proc. Parallel and Distributed Processing Technology and Applications, vol. III, pp. 1676- 1682, 1999. (28% acceptance rate)
15. S. Aluru, N. Futamura and K. Mehrotra, "Biological sequence comparison using preffix computations," Proc. 13th IEEE International Parallel Processing Symposium, pp. 653-659, 1999. (45% acceptance rate)
16. S. Aluru and F. Sevilgen,"Parallel domain decomposition and load balancing using space- filling curves," Proc. 4th IEEE International Conference on High Performance Computing, pp. 230-235, 1997. (57% acceptance rate)
17. S. Goil, S. Aluru and S. Ranka, "Concatenated parallelism: a technique for efficient parallel divide and conquer," 8th IEEE Symposium on Parallel and Distributed Processing, pp. 488- 495, 1996. (39% acceptance rate)
18. S. Aluru and S. Maneewongvatana, "Practical parallel algorithms for constructing line arrangements," Proc. International Conference on Parallel and Distributed Processing Tech- niques and Applications, pp. 125-135, 1996.
19. S. Aluru, "Parallel additive lagged Fibonacci random number generators," Proc. 10th ACM International Conference on Supercomputing, pp. 102-108, 1996. (43% acceptance rate)
20. I. Al-furaih, S. Aluru, S. Goil and S. Ranka, "Parallel construction of multidimensional binary search trees,"Proc. 10th ACM International Conference on Supercomputing, pp. 205-212, 1996. (43% acceptance rate)
21. I. Al-furaih, S. Aluru, S. Goil and S. Ranka, "Practical algorithms for selection on coarsegrained parallel computers," Proc. 10th IEEE International Parallel Processing Symposium, pp. 309-313, 1996. (36% acceptance rate)
22. I. Al-furaih, S. Aluru, S. Goil and S. Ranka, "Parallel construction of k-d tree and related problems," Proc. 2nd Workshop on Solving Irregular Problems on Distributed Memory Ma- chines, 1996.
23. S. Aluru, "Properties of binomial coefficients and implications to parallelizing lagged Fibonacci random number generators," Proc. International Conference on Parallel Processing, pp. 25-28, 1995. (28% acceptance rate)
24. S. Aluru, G.M. Prabhu and J. Gustafson, "Truly distribution-independent algorithms for the N-body problem," Proc. IEEE/ACM Supercomputing Conference, pp. 420-428, 1994.
25. S. Aluru and J. Gustafson, "Subtle issues of SIMD tree search," Proc. Parallel Computing, in Parallel Computing: Trends and Applications, Elsevier Publishers, pp. 49-56, 1993.
26. S. Aluru and J. Gustafson, "A massively parallel optimizer for expression evaluation," Proc. 7th ACM International Conference on Supercomputing, pp. 97-106, 1993.
27. S. Aluru and G.M. Prabhu, "Random number generation for parallel computers," Proc. NATO Advanced Study Institute on Parallel Computing on Distributed Memory Multipro- cessors, pp. 315-320, 1991.