PUBLICATIONS
REFEREED JOURNAL ARTICLES
(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.
(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.
(2004) 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.
(2003) 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) 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.
REFEREED CONFERENCE PUBLICATIONS
(2008) C. Wu, A. Kalyanaraman. An efficient parallel approach for identifying protein families in large-scale metagenomic data sets. To appear in Proc. IEEE/ACM Supercomputing Conference (SC08), Austin, TX, November 15-21.
(2008) W. Davis, A. Kalyanaraman, D. Cook. An information theoretic approach for the discovery of irregular and repetitive patterns in genomic data. To appear in Proc. IEEE Computational Intelligence in Bioinformatics and Bioengineering (CIBCB'08), Sun Valley, ID, September 15-17.
(2007) 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.
(2006) 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) 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). (Best Paper Award)
(2005) A. Kalyanaraman, S. Aluru. Efficient algorithms and software for detection of full-length LTR retrotransposons. IEEE Computational Systems Bioinformatics Conference (CSB'05), 56-64. (Best Paper Award)
(2004) P. Ko, M. Narayanan, A. Kalyanaraman, S. Aluru. Space-conserving optimal DNA-protein alignment. Proc. IEEE Computational Systems Bioinformatics Conference (CSB'04), 77-85.
(2002) 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.
REFEREED WORKSHOP PUBLICATIONS
(2002) 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.
EXTENDED ABSTRACTS AND POSTERS
(2008) C. Wu, A. Kalyanaraman, A. Dhingra. Enabling cost-effective sequencing of arbitrarily long conserved DNA sequences. Proc. Plant & Animal Genomes XVI Conference (PAG'08), San Diego, January 12-16.
(2007) C. Wu, A. Kalyanaraman, A. Dhingra. An efficient computational framework for amplifying arbitrarily long conserved DNA sequences. Proc. LSS Computational Systems Bioinformatics (CSB'07), UC San Diego, August 13-17.
(2007) W. Davis, A. Kalyanaraman, D. Cook. An information theoretic approach for the discovery of irregular and repetitive patterns in genomic data. Proc. LSS Computational Systems Bioinformatics (CSB'07), UC San Diego, August 13-17.
BOOK CHAPTERS
(2005) 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) 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.
CONFERENCE TUTORIALS
(2007) S. Aluru, D.A. Bader, A. Kalyanaraman. High-performance Computing Methods for Computational Genomics. Proc. IEEE International Parallel and Distributed Processing Symposium (IPDPS'07).
(2006) S. Aluru, D.A. Bader, A. Kalyanaraman. High-performance Computing Methods for Computational Genomics. Proc. IEEE/ACM Supercomputing Conference (SC'06).
Ph.D. DISSERTATION
Title:
Large-scale methods in computational genomics
Completed: Summer 2006
Advisor:
Prof. Srinivas Aluru
Institution:
Iowa
State University