PEER-REVIEWED
PUBLICATIONS
(For a more comprehensive, up to date list, please refer to the CV.)
(2012)
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), Accepted, to be held: August 12-15, Chicago, IL, 2012.
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), In Press, 2012.
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), Preprint, 2012, DOI http://doi.ieeecomputersociety.org/10.1109/TPDS.2012.19.
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.
(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. Accepted.
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, 2011. Accepted.
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, Advance online access, 2011. doi:10.1093/bioinformatics/btr523.
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.
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.
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, In Press, 2011.
T. Majumder, P. Pande, A. Kalyanaraman. NoC-based hardware accelerator for breakpoint phylogeny. IEEE Transactions on Computers, In Press, 2011, http://doi.ieeecomputersociety.org/10.1109/TC.2011.100.
(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)
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.
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.
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.
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)
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.
(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.
P.S. Schnable et al.
The B73
Maize Genome: Complexity, diversity and dynamics. Science,
326(5956):1112-1115, 2009.
(expanded
author list)
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)
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
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
(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.
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.
(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.
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.
(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.
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), 2006. (Best Paper Award)
(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)
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, 2005.
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.
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.
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, 2003.
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.
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.
Ph.D. DISSERTATION
Title:
Large-scale methods in computational genomics
Completed: Summer 2006
Advisor:
Prof. Srinivas Aluru
Institution:
Iowa
State University