Ananth Kalyanaraman

Associate Professor
School of EECS
Washington State University

PEER-REVIEWED PUBLICATIONS
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(2017)

K. Duraisamy, H. Lu, P. Pande, A. Kalyanaraman. Accelerating Graph Community Detection with Approximate Updates via an Energy-Efficient NoC. Proc. Design Automation Conference (DAC), Accepted, June 18-22, 2017.

H. Lu, M. Halappanavar, D. Chavarria-Miranda, A. Gebremedhin, A. Panyala, A. Kalyanaraman. Algorithms for Balanced Colorings with Applications in Parallel Computing. IEEE Transactions on Parallel and Distributed Systems, vol. 28, no. 5, pp. 1240-1256, May 1 2017. doi: 10.1109/TPDS.2016,2620142.
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(2016)

A. Abnousi, S.L. Broschat, A. Kalyanaraman. A Fast Alignment-Free Approach for de novo Detection of Protein Conserved Regions.  PLOS ONE, 11(8), p.e0161338, 2016. doi: 10.1371/journal.pone.0161338.
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P. Pesantez, A. Kalyanaraman. Detecting Communities in Biological Bipartite Networks.  Proc. ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), pp. 98-107, 2016. doi: 10.1145/2975167.2975177.
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P. Ghosh, A. Kalyanaraman. A Fast Sketch-based Assembler for Genomes. Proc. ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), pp. 241-250, 2016. doi: 10.1145/2975167.2975192. Best Student Paper Award.
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M. Kamruzzaman, A. Kalyanaraman, B. Krishnamoorthy. Characterizing the Role of Environment on Phenotypic Traits using Topological Data Analytics. Proc. ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), pp. 487-488, 2016. doi: 10.1145/2975167.2985646.
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K. Duraisamy, H. Lu, P. Pande, A. Kalyanaraman. High performance and energy efficient Network-on-Chip architectures for graph analytics. ACM Transactions on Embedded Computing Systems (TECS), vol. 15, no. 4, p. 66, 2016. doi: 10.1145/2961027.
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J. Daily, A. Kalyanaraman, S. Krishnamoorthy, B. Ren. On the Impact of Widening Vector Registers on Sequence Alignment. Proc. International Conference on Parallel Processing, pp. 506-515, 2016.
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R. Sharpe, T. Koepke, A. Harper, J. Grimes, M. Galli, M. Satoh-Cruz, A. Kalyanaraman, K. Evans, D. Kramer, A. Dhingra. CisSERS: Cutomizable in silico Sequence Evaluation for Restriction Sites. PLOS ONE, 11(4):e0152404, 2016. doi: 10.1371/journal.pone.015404.

A. Kalyanaraman, M. Halappanavar, D. Chavarria-Miranda, H. Lu, K. Duraisamy, P. Pande. Fast uncovering of graph communities on a chip: Toward scalable community detection on multicore and manycore platforms. Foundations and Trends in Electronic Design Automation (FnTEDA), Paperback 118 pages. now Publishers, ISBN-10: 1680831321, ISBN-13: 978-1680831320, 2016.

T. Wu, S.A.N. Sarmadi, V. Venkatasubramanian, A. Pothen, A. Kalyanaraman. Fast SVD computations for synchrophasor algorithms. IEEE Transactions on Power Systems, 31(2):1651-1652, 2016. 
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(2015)

K. Duraisamy, H. Lu, P. Pande, A. Kalyanaraman. High performance and energy efficient wireless NoC-enabled multicore architecture for graph analytics. Proc. International Conference on Compilers, Architectures and Synthesis of Embedded Systems (CASES), pp. 147-156, 2015
(Best Paper Finalist).

A. Abnousi, S.L. Broschat, A. Kalyanaraman. An alignment-free approach to cluster proteins using frequency of conserved k-mers. Proc. ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), pp. 597-606, 2015. DOI: 10.1145/2808719.2812223

T. Majumder, P. Pande, A. Kalyanaraman. On-Chip Network-Enabled Many-Core Architectures for Computational Biology Applications. Proc. Design, Automation and Test in Europe (DATE), 2015, pp. 259-264.
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H. Lu, M. Halappanavar, A. Kalyanaraman. Parallel heuristics for scalable community detection. Parallel Computing, vol. 47, pp. 19-37, 2015,

DOI: 10.1016/j.parco.2015.03.003
(Top Downloaded Article of the journal since August 2015).
Online access PDF

H. Lu, M. Halappanavar, D. Chavarria, A. Gebremedhin, A. Kalyanaraman. Balanced coloring for parallel computing applications. Proc. IEEE International Parallel and Distributed Processing Symposium (IPDPS), May 25-29, 2015, Hyderabad, India, pp. 7-16, DOI: 10.1109/IPDPS.2015/113. 
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J. Daily, A. Kalyanaraman, S. Krishnamoorthy, A. Vishnu. A work stealing based approach for enabling scalable optimal sequence homology detection. Journal of Distributed and Parallel Computing (JPDC), Vol. 79-80, pp. 132-142, May 2015. doi: 10.1016/j.jpdc.2014.08.009.
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(2014)

D. Chavarria, M. Halappanavar, A. Kalyanaraman. Scaling graph community detection on the Tilera Many-core architecture. Proc. IEEE International Conference on High Performance Computing (HiPC), December 17-20, 2014, Goa, India. 11 pages.
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J. Adam et al. BioEarth: Envisioning and developing a new regional earth system model to inform natural and agricultural resource management. Climatic Change, pp. 1-17, 2014.   DOI 10.1007/s10584-014-1115-2.
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H. Lu, M. Halappanavar, A. Kalyanaraman, S. Choudhury. Parallel heuristics for scalable community detection. Proc. International Workshop on Multithreaded Architectures and Applications (MTAAP), IPDPS Workshops, May 23, 2014, Phoenix, AZ, pp. 1375-1385. 
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T. Mullis, M. Liu, A. Kalyanaraman, J. Vaughan, C. Tague, J. Adam. Design and implementation of Kepler workflows for BioEarth. Proc. 2014 International Conference on Computational Science (ICCS), Procedia Computer Science, vol. 29, pp. 1722-1732, 2014. DOI: 10.1016/j.procs.2014.05.157
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T. Majumder, P.P. Pande, A. Kalyanaraman. Hardware Accelerators in Computational Biology: Application, Potential and Challenges. IEEE Design and Test of Computers: Special Issue on Hardware Acceleration, 31(1):8-18, 2014, DOI: 10.1109/MDAT.2013.2290118.

I. Rytsareva, T. Chapman, and A. Kalyanaraman. Parallel algorithms for clustering biological graphs on distributed and shared memory architectures. International Journal of High Performance Computing and Networking: Special issue on Architectures and Algorithms for Irregular Applications (IJHPCN), 7(4):241-257, 2014.
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T. Majumder, P.P. Pande, A. Kalyanaraman. Wireless NoC platforms with dynamic task allocation for maximum likelihood phylogeny reconstruction. IEEE Design and Test of Computers, 31(3):54-64, 2014. DOI: 10.1109/MDAT.2013.2288778.

 

(2013)

M.V. Venkatasubramanian, A. Pothen, A. Kalyanaraman, D.J. Sobajic. Computational challenges in stability monitoring of power systems using large number of PMUs. Proc. National Workshop on Energy Cyber-physical Systems, organized by NSF, Arlington, VA, December 16-17, 2013, pp.1-3.

D. Deford, A. Kalyanaraman. Empirical analysis of space-filling curves for scientific computing applications. Proc. International Conference on Parallel Processing (ICPP), Lyon, France, October 1-4, pp. 170-179, 2013.

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I. Rytsareva, A. Kalyanaraman, K. Konwar, S. Hallam. Scalable heuristics for clustering biological graphs. Proc. IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), New Orleans, LA, June 12-14, 2013, Accepted.
preprint

F. Poursabzi, A. Kalyanaraman. On clustering heterogeneous networks. Proc. SIAM Workshop on Network Science (NetSci13), (held in conjunction with 2013 SIAM Annual Meeting), San Diego, California, July 7-8, 2013, Accepted.
preprint

T. Majumder, P.P. Pande, A. Kalyanaraman. Network-on-chip with long-range wireless links for high-throughput scientific computation. Proc. 3rd Workshop on Communication Architecture for Scalable Systems (CASS), held in conjunction with IPDPS'13, pp. 781-790, 2013. DOI 10.1109/IPDPSW.2013.72
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C. Wu, A. Kalyanaraman. GPU-accelerated protein family identification for metagenomics. Proc. 12th IEEE International Workshop on High Performance Computational Biology (HiCOMB), held in conjunction with IPDPS'13, pp. 559-568, 2013. (invited paper). DOI 10.1109/IPDPSW.2013.185
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N. Dasgupta, Y. Chen, A. Kalyanaraman, S. Daoud. Comparison of clustering algorithms: An example with proteomic data. Advances and Applications in Statistics, 33(1):p63, 2013.
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T. Majumder, P.P. Pande, A. Kalyanaraman. High-throughput, energy-efficient network-on-chip-based hardware accelerators. Sustainable Computing: Informatics and Systems (SUSCOM), 3(1):36-46, 2013. DOI: 10.1016/j.suscom.2013.01.001.
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(2012)

J. Daily, S. Krishnamoorthy, and A. Kalyanaraman. Towards Scalable Optimal Sequence Homology Detection. Proc. Workshop on Parallel Algorithms and Software for Analysis of Massive Graphs (ParGraph'12), Accepted, 2012.
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I. Rytsareva, Q. Le, E. Conner, A. Kalyanaraman, J. Panchal. Evaluating socio-technical coordination in open-source communities: A cluster-based approach. Proc. ASME International Design Engineering Technical Conferences & Computers and Information in Engineering Conference (IDETC/CIE), August 12-15, Chicago, IL, 2012.
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T. Majumder, M. Borgens, P.P. Pande, A. Kalyanaraman. On-Chip network-enabled multi-core platforms targeting maximum likelihood phylogeny reconstruction. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2012, 31(7):1061-1073.
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C. Wu, A. Kalyanaraman, W.R. Cannon. pGraph: Efficient parallel construction of large-scale protein sequence homology graphs. IEEE Transactions on Parallel and Distributed Systems (TPDS), 23(10):1923-1933, 2012, DOI 10.1109/TPDS.2012.19.
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(suppl. material available on publisher's website)

A. Hugo, D.J. Baxter, W.R. Cannon, A. Kalyanaraman, G. Kulkarni, S.J. Callister. Proteotyping of microbial communities using high performance optimization of proteome-spectra matches. Proc. Pacific Symposium on Biocomputing (PSB), 2012.
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T. Majumder, P. Pande, A. Kalyanaraman. NoC-based hardware accelerator for breakpoint phylogeny. IEEE Transactions on Computers, 2012, 61(6):857-869. http://doi.ieeecomputersociety.org/10.1109/TC.2011.100.
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(2011)

I. Rytsareva, A. Kalyanaraman. An efficient MapReduce algorithm for parallelizing large-scale graph clustering. ParGraph - Workshop on Parallel Algorithms and Software for Analysis of Massive Graphs, Held in conjunction with HiPC'11, Bengaluru, India, 2011.
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T. Chapman, A. Kalyanaraman. An OpenMP algorithm and implementation for clustering biological graphs. IA3 - Workshop on Irregular Applications: Architectures & Algorithms (Held in conjunction with SC'11), Seattle, WA, pp. 3-10, 2011. 
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A. Kalyanaraman, W.R. Cannon, B. Latt, D.J. Baxter. MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification. Bioinformatics, 2011, 27(21):3072-3073. doi:10.1093/bioinformatics/btr523.
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T. Majumder, P. Pande, A. Kalyanaraman. Accelerating Maximum Likelihood based phylogenetic kernels using Network-on-chip. Proc. International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD), pp. 17-24, 2011. http://doi.ieeecomputersociety.org/10.1109/SBAC-PAD.2011.17.
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A.O.T. Lau, A. Kalyanaraman, I. Echaide, G.H. Palmer, R. Bock, M.J. Pedroni, M. Rameshkumar, M.B. Ferreira, T.I. Fletcher, T.F. McElwain. Attenuation of virulence in an Apicomplexan hemoparasite results in reduced genomic diversity at the population level. BMC Genomics. 12:410, 2011, doi:10.1186/1471-2164-12-410.
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A. Kalyanaraman. Algorithms for genome assembly. Encyclopedia of Parallel Computing, D. Padua (ed.), Springer Science+Business Media LLC, DOI 10.1007/978-0-387-09766-4, 2011, pp. 755-768.
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(2010)

R. Velasco, A. Zharkikh, J. Affourtit, A. Dhingra, A. Cestaro, A. Kalyanaraman, P. Fontana et al. The genome of the domesticated apple (Malus domestica Borkh.). Nature Genetics, 42:833-839, 2010, doi:10:1038/ng.654.  
(expanded author list)
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C. Wu, A. Kalyanaraman, W. Cannon. A scalable parallel algorithm for large-scale protein sequence homology detection. Proc. International Conference on Parallel Processing (ICPP), 2010, pp. 333-342, doi: 10.1109/ICPP.2010.41.
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T. Majumder, S. Sarkar, P. Pande, A. Kalyanaraman. An optimized NoC architecture for accelerating TSP kernels in breakpoint median problem. Proc. IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP), pp. 89-96, 2010.
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S. Sarkar, T. Majumder, A. Kalyanaraman, P. Pande. Hardware accelerators for biocomputing: A survey. Proc. IEEE International Symposium on Circuits and Systems (ISCAS), pp. 3789-3792, 2010.
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The International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463, 763-768, 2010. doi:10.1038/nature08747.
(expanded author list)
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S. Sarkar, G. Kulkarni, P. Pande, A. Kalyanaraman. Network-on-chip hardware accelerators for biological sequence alignments. IEEE Transactions on Computers, 59(1):29-41, 2010.
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(2009)

A. Kalyanaraman, D. Baxter, W. Cannon. Using clouds for for data-intensive computing in proteomics. Proc. Workshop on Using Clouds for Parallel Computations in Systems Biology, held in conjunction with SC|09, Portland, OR, November 16, 2009.
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P.S. Schnable et al. The B73 Maize Genome: Complexity, diversity and dynamics. Science, 326(5956):1112-1115, 2009.
(expanded author list)
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F. Wei et al. Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genetics, 5(11):e1000728. doi:10.1371/journal.pgen.1000728, 2009.
(expanded author list)
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Md. Muksitul Haque, A. Kalyanaraman, A. Dhingra, N. Abu-lail, K. Graybeal. DNAjig: A new approach for building DNA nanostructures. Proc. IEEE International Conference on Bioinformatics & Biomedicine (BIBM), Washington D.C., November 1-4, pp. 379-383, 2009. DOI 10.1109/BIBM.2009.71
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G. Kulkarni, A. Kalyanaraman, W. Cannon, D. Baxter. A scalable parallel approach for peptide identification from large-scale mass spectrometry data. Proc. International Conference on Parallel Processing Workshops (ICPP-W), pp. 423-430, Vienna, Austria, September 22-25, 2009, DOI 10.1109/ICPPW.2009.41
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(2008)

C. Wu, A. Kalyanaraman. An efficient parallel approach for identifying protein families in large-scale metagenomic data sets. Proc. ACM/IEEE conference on Supercomputing (SC|08), Austin, TX, November 15-21, pp. 1-10, 2008, ISBN 978-1-4244-2835-9, IEEE Press, Piscataway, NJ, USA.
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W. Davis, A. Kalyanaraman, D. Cook. An information theoretic approach for the discovery of irregular and repetitive patterns in genomic data. Proc. IEEE Computational Intelligence in Bioinformatics and Bioengineering (CIBCB'08), Sun Valley, ID, September 15-17, 2008.
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(2007)

A. Kalyanaraman, S.J. Emrich, P.S. Schnable, S. Aluru. Assembling genomes on large-scale parallel computers. Journal of Parallel and Distributed Computing (JPDC), 67(12):1240-1255, 2007.
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S.J. Emrich, A. Kalyanaraman, S. Aluru. Massively parallel clustering of Expressed Sequence Tags, Proc. ISCA 20th International Conference on Parallel and Distributed Computing Systems (PDCS'07), Las Vegas, NV,  September 24-26, 2007.
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(2006)

A. Kalyanaraman, S. Aluru. Efficient algorithms and software for detection of full-length LTR retrotransposons. Journal of Bioinformatics and Computational Biology (JBCB), 4(2):197-216, 2006.
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A. Kalyanaraman, S. Aluru, P.S. Schnable. Turning repeats to advantage: Scaffolding genomic contigs using LTR retrotransposons. Proc. LSS Computational Systems Bioinformatics (CSB'06), 167-178, 2006.
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A. Kalyanaraman, S.J. Emrich, P.S. Schnable, S. Aluru. Assembling genomes on large-scale parallel computers. Proc. IEEE International Parallel and Distributed Processing Symposium (IPDPS'06), 2006. (Best Paper Award)
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(2005 or earlier)

A. Kalyanaraman, S. Aluru. Efficient algorithms and software for detection of full-length LTR retrotransposons. IEEE Computational Systems Bioinformatics Conference (CSB'05), pp. 56-64, 2005. (Best Paper Award)
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A. Kalyanaraman, S. Aluru. "Expressed Sequence Tags: Clustering and applications'' in Handbook of Computational Molecular Biology, Edited by S. Aluru, Chapman & Hall/CRC Computer and Information Science Series, 2005.
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S. Emrich, A. Kalyanaraman, S. Aluru. "Algorithms for large-scale clustering and assembly of biological sequence data'' in Handbook of Computational Molecular Biology, Edited by S. Aluru, Chapman & Hall/CRC Computer and Information Science Series, 2005.
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M. Mitreva, A.A. Elling, M. Dante, A.P. Kloek, A. Kalyanaraman, S. Aluru, S.W. Clifton, D.M. Bird, T.J. Baum, J.P. McCarter.  A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans. Molecular Genetics and Genomics (MGG),  272:138-148, 2004.
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P. Ko, M. Narayanan, A. Kalyanaraman, S. Aluru. Space-conserving optimal DNA-protein alignment. Proc. IEEE Computational Systems Bioinformatics Conference (CSB'04), pp. 77-85, 2004.
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A. Kalyanaraman, S. Aluru, V. Brendel, S. Kothari. Space and time efficient parallel algorithms and software for EST clustering.  IEEE Transactions on Parallel and Distributed Systems (TPDS), 14(12):1209-1221, 2003.
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A. Kalyanaraman, S. Aluru, S. Kothari, V. Brendel. Efficient clustering of large EST data sets on parallel computers. Nucleic Acids Research (NAR), 31(11):2963-2974, 2003.
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A. Kalyanaraman, S. Aluru, S. Kothari. Space and time efficient parallel algorithms and software for EST clustering. Proc. International Conference on Parallel Processing (ICPP'02), 331-339, 2002.
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A. Kalyanaraman, S. Aluru, S. Kothari. Parallel EST clustering. Proc. First International Workshop on High Performance Computational Biology (HiCOMB'02), held in conjunction with IPDPS '02, 2002.
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Ph.D. DISSERTATION

Title:    Large-scale methods in computational genomics
Completed:    Summer 2006
Advisor:    Prof. Srinivas Aluru
Institution:    Iowa State University

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