Publications

2014
 
Miller, J.H., B.T. Schrom and L.J. Kangas, “Artificial Neural Network for Charge Prediction in Metabolite Identification by Mass Spectrometry,” In: Artificial Neural Networks: 2nd Edition, Springer (in press).
 
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), Dec. 17-20, 2014, Goa, India (accepted).
 
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.
 
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.

 

2013
 
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, 2013, In Press, DOI: 10.1109/MDAT.2013.2288778.
 
Cilingir, G., A.O.T. Lau, and S.L. Broschat, "ApicoAMP: The first computational model for identifying apicoplast targeted transmembrane proteins in Apicomplexa," Journal of Microbiological Methods, vol. 95, pp. 313-319, 2013.
 
Zhou, Y., D.R. Call, and S.L. Broschat, "Whole-proteome analysis of twelve species of Alphaproteobacteria links four pathogens," Pathogens, vol. 2, pp. 627-635, 2013. doi: 10.3390/pathogens2040627.
 
Zhou, Y., D.R. Call, and S.L. Broschat, ``Using protein clusters from whole proteomes to construct and augment a dendrogram,’’ Advances in Bioinformatics, vol. 2013, Article ID 191586.
 
Rytsareva, I., A. Kalyanaraman, K. Konwar, and 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, pp. 1-6.
 
Poursabzi, F., and A. Kalyanaraman, ``On clustering heterogeneous networks,’’ Proc. SIAM Workshop on Network Science (NetSci13), San Diego, California, July 7-8, 2013, pp. 1-2.
 
Deford D., and A. Kalyanaraman, ``Empirical analysis of space-filling curves for scientific computing applications,’’ Proc. International Conference on Parallel Processing (ICPP), Lyon, France, October 1-4, 2013.
 
Majumder, T., P.P. Pande, and 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), pp. 781-790, 2013. DOI 10.1109/IPDPSW.2013.72.
 
Wu, C.,  and A. Kalyanaraman, ``GPU-accelerated protein family identification for metagenomics,’’ Proc. 12th IEEE International Workshop on High Performance Computational Biology (HiCOMB), DOI 10.1109/IPDPSW.2013.185.
 
Dasgupta, N., Y. Chen, A. Kalyanaraman, and S. Daoud, ``Comparison of clustering algorithms: An example with proteomic data,’’ Advances and Applications in Statistics, In Press, 2013.
 
Majumder, T., 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.
 
Rytsareva, I., 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), In Press, 2013.
 

2012
 
Kangas, L.J., T.O. Metz, G.L. Mezengie, B.T. Schrom, B.J. Genovska, R.D. Smith, L. Tan, R.R. Lewis and J.H. Miller, “Metabolite In Silico Identification Software (Met ISIS): “A Machine Learning Approach to Tandem Mass Spectral Identification of Metabolites,” Bioinformatics, doi: 10.1093/bioinformatics/bts194, 2012.
 
Miller, J.H., W.B. Chrisler, X. Wang and M.B. Sowa, “Confocal Microscopy for Modeling Electron Microbeam Irradiation of Skin,” Radiat. Environ. Biophys. 10.1007/s00411-011-0371, 2012.
 
Kangas, L.J., T.O. Metz, G. Isaac, B.T, Schrom, B. Ginovska-Pangovska, L. Wang, L. Tan, R.R. Lewis, and J.H. Miller, ``In Silico Identification Software (ISIS): a machine learning approach to tandem mass spectral identification of lipids,’’ Bioinformatics, vol. 28, no. 13, pp. 1705-1713, 2012.
 
Ueti, M., Y. Tan, S.L. Broschat, E. Castaneda-Ortiz, M. Camacho-Nuez, J. Mosqueda, G. Scoles, M. Grimes, K. Brayton, and G. Palmer, ``Expansion of variant diversity associated with high prevalence of pathogen strain superinfection under conditions of natural transmission,’’ Infection and Immunity, 2012, doi: 10.1128/​IAI.00341-12.
 
Zhou, Y., D.R. Call, and S.L. Broschat, ``Genetic relationships among 527 Gram-negative bacterial plasmids,’’ Plasmid, 2012, http://dx.doi.org/10.1016/j.plasmid.2012.05.002.
 
Cilingir, G., S.L. Broschat, and A.O.T. Lau, ``ApicoAP: The first computational model for predicting apicoplast-targeted proteins for multiple species of Apicomplexa,’’ PLoS ONE, vol. 7, no. 5, e36598.
 
Majumder, T., M. Borgens, P.P. Pande, and 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, vol. 31, no. 7, pp. 1061-1073, 2012.
 
Wu, C., A. Kalyanaraman, and W.R. Cannon, ``pGraph: Efficient parallel construction of large-scale protein sequence homology graphs,’’ IEEE Transactions on Parallel and Distributed Systems, Preprint, 2012, DOI http://doi.ieeecomputersociety.org/10.1109/TPDS.2012.19.
 
Hugo, A., D.J. Baxter, W.R. Cannon, A. Kalyanaraman, G. Kulkarni, and S.J. Callister, ``Proteotyping of microbial communities using high performance optimization of proteome-spectra matches,’’ Proc. Pacific Symposium on Biocomputing, 2012.
 
Daily, J., 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.
 
Rytsareva, I., Q. Le, E. Conner, A. Kalyanaraman, and 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.
 

2011
 
Schrom, B.T., L.J. Kangas, B.J. Ginovska, T.O. Metz, and J.H. Miller, “Charge prediction of lipid fragments in mass spectroscopy,” Proceedings of the 10th International Conference on Machine Learning and Applications, Honolulu Hawaii, December 18-21, 2011.
 
Rytsareva, I., and 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.
 
Chapman, T., and 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.
 
Kalyanaraman, A., W.R. Cannon, B. Latt, and D.J. Baxter, ``MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification,’’ Bioinformatics, 2011. doi:10.1093/bioinformatics/btr523.
 
Majumder, T., P. Pande, and A. Kalyanaraman, ``Accelerating Maximum Likelihood based phylogenetic kernels using Network-on-chip,’’ Proc. International Symposium on Computer Architecture and High Performance Computing, pp. 17-24, 2011. http://doi.ieeecomputersociety.org/10.1109/SBAC-PAD.2011.17.
 
Lau, A.O.T., A. Kalyanaraman, I. Echaide, G.H. Palmer, R. Bock, M.J. Pedroni, M. Rameshkumar, M.B. Ferreira, T.I. Fletcher, and 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.
 
Kalyanaraman, A., ``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.
 
Majumder, T., P. Pande, and A. Kalyanaraman, ``NoC-based hardware accelerator for breakpoint phylogeny,’’ IEEE Transactions on Computers, 2011, http://doi.ieeecomputersociety.org/10.1109/TC.2011.100.
 
Lockwood, S., D.E. Voth, K.A. Brayton, P.A. Beare, W.C. Brown, R.A. Heinzen, and S.L. Broschat, ``Identification of Anaplasma marginale type IV secretion system effector proteins,’’ PLoS ONE, vol. 6, no. 11, e7724, Nov. 2011.
 
Davis, M.A., T.E. Besser, L.H. Orfe, K.N.K. Baker, A.S. Lanier, S.L. Broschat, D. New, and D.R. Call, ``Genotypic-phenotypic discrepancies between antibiotic resistance characteristics of Escherichia coli from calves in high and low antibiotic use management settings,’’ Applied and Environmental Microbiology, vol. 77, no. 10, pp. 3293-99, May 2011.
 

2010
 
Yang, F., K.M. Waters, J.H. Miller, M.A. Gristenko, R. Zhao, X. Du, E. Livesay, S.O. Purvine, M.E. Monroe, Y. Wang, D.G. Camp, R.D. Smith, and D.L. Stenoien, Phosphoproteomic profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation, PLoS ONE 5(11), e14152 (2010).
 
Velasco, R., 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)
 
Wu, C., A. Kalyanaraman, and W. Cannon, ``A scalable parallel algorithm for large-scale protein sequence homology detection,’’ Proc. International Conference on Parallel Processing, 2010, pp. 333-342, doi: 10.1109/ICPP.2010.41.
 
Majumder, T., S. Sarkar, P. Pande, and 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, pp. 89-96, 2010.
 
Sarkar, S., T. Majumder, A. Kalyanaraman, and P. Pande, ``Hardware accelerators for biocomputing: A survey,’’ Proc. IEEE International Symposium on Circuits and Systems, 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)
 
Sarkar, S., G. Kulkarni, P. Pande, and A. Kalyanaraman, ``Network-on-chip hardware accelerators for biological sequence alignments,’’ IEEE Transactions on Computers, 59(1):29-41, 2010.
 
Broschat, S.L., D.R. Call, M.A. Davis, D. Meng, S. Lockwood, R. Ahmed, and T.E. Besser, ``Improved identification of epidemiologically related strains of Salmonella enterica by use of a fusion algorithm based on pulsed-field gel electrophoresis and multiple-locus variable-number tandem-repeat analysis,’’ J.  Clinical Microbiology, vol. 48, no. 11, pp. 4072-82, Nov. 2010.
 
Call, D.R., R.S. Singer, D. Meng, S.L. Broschat, L.H. Orfe, J.M. Anderson, D.R. Herndon, L.S. Kappmeyer, J.B. Daniels, and T.E. Besser, ``BlaCMY-2 positive Inc A/C plasmids from Escherichia coli and Salmonella enterica are a distinct component of a larger lineage of plasmids,’’ Antimicrobial Agents and Chemotherapy, online: Nov. 2009; print: vol. 54, no. 2, pp. 590-596, Feb. 2010.

 

2009

 
Springer, D.L., J.H. Miller, S.L. Spinelli, L. Pasa-Tolic, S.L. Purvine, D.S. Daly, R.C. Zangar, S. Jin, N. Blumberg, C.W. Francis, M.B. Taubman, A.E. Casey, S.D. Wittlin, and R.P. Phipps, ``Platelet proteome changes associated with diabetes and during platelet storage for transfusion,’’ J. Proteome Res, 8, 2261-2272, 2009.
 
Kalyanaraman, A., D. Baxter, and W.R. 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.
 
Schnable, P.S., et al., ``The B73 Maize Genome: Complexity, diversity and dynamics,’’ Science, 326(5956):1112-1115, 2009.
(expanded author list)
 
Wei, F.,  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)
 
Haque, M., A. Kalyanaraman, A. Dhingra, N. Abu-lail, and K. Graybeal, ``DNAjig: A new approach for building DNA nanostructures,’’ Proc. IEEE International Conference on Bioinformatics & Biomedicine, Washington D.C., November 1-4, pp. 379-383, 2009. DOI 10.1109/BIBM.2009.71
 
Kulkarni, G., A. Kalyanaraman, W. Cannon, and D. Baxter, ``A scalable parallel approach for peptide identification from large-scale mass spectrometry data,’’ Proc. International Conference on Parallel Processing Workshops, pp. 423-430, Vienna, Austria, September 22-25, 2009, DOI 10.1109/ICPPW.2009.41
 

2008
 
Jin, S, DS Daly, DL Springer, and JH Miller, The effects of shared peptides on protein quantitation in label-free proteomics by LC/MS/MS, J. Proteome Res. 7, 164-169 (2008).
 
Miller, JH, S Jin, WF Morgan, A Yang, Y Wan, U Aypar, JS Peters, and DL Springer, Profiling mitochondrial proteins in radiation-induced genome unstable cell lines with persistent oxidative stress by mass spectrometry. Radiat. Res. 169, 700-706 (2008).
 
Wu, C., and A. Kalyanaraman, ``An efficient parallel approach for identifying protein families in large-scale metagenomic data sets,’’ Proc. ACM/IEEE conference on Supercomputing, Austin, TX, November 15-21, pp. 1-10, 2008, ISBN 978-1-4244-2835-9, IEEE Press, Piscataway, NJ, USA.
 
Davis, W., A. Kalyanaraman, and 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, Sun Valley, ID, September 15-17, 2008.
 
Meng, D., S.L. Broschat, and D.R. Call, ``A Java-based tool for the design of classification microarrays,’’ BMC Bioinformatics, 9:328, Aug. 2008.
 
Leach, M.D., S.L. Broschat, and D.R. Call, ``A discrete, stochastic model and correction method for bacterial source tracking,'' Environmental Science & Technology, online: Dec. 2007, print: vol. 42, no. 2, pp. 524-529, Jan. 2008.

 

2007 and earlier
 
Harańczyk, M, JH Miller, and M Gutowski, Differences in electrostatic potential around DNA fragments containing adenine and 8-oxo-adenine: An analysis based on regular cylindrical projection. J. Molecular Graphics and Modeling 26, 282-289 (2007).
 
Kalyanaraman, A., S.J. Emrich, P.S. Schnable, and S. Aluru, ``Assembling genomes on large-scale parallel computers,’’ Journal of Parallel and Distributed Computing, 67(12):1240-1255, 2007.
 
Emrich, S.J., A. Kalyanaraman, and S. Aluru, ``Massively parallel clustering of Expressed Sequence Tags,’’ Proc. ISCA 20th International Conference on Parallel and Distributed Computing Systems, Las Vegas, NV,  September 24-26, 2007.
 
Wan, Y., S.L. Broschat, and D.R. Call, ``Validation of mixed-genome microarrays as a method for genetic discrimination,'' Applied and Environmental Microbiology, vol. 73, no. 5, pp. 1425-1432, Mar. 2007.
 
Kalyanaraman, A., and S. Aluru, ``Efficient algorithms and software for detection of full-length LTR retrotransposons,’’ Journal of Bioinformatics and Computational Biology, 4(2):197-216, 2006.
 
Kalyanaraman, A., S. Aluru, and P.S. Schnable, ``Turning repeats to advantage: Scaffolding genomic contigs using LTR retrotransposons,’’ Proc. LSS Computational Systems Bioinformatics, 167-178, 2006.
 
Kalyanaraman, A., S.J. Emrich, P.S. Schnable, and S. Aluru, ``Assembling genomes on large-scale parallel computers,’’ Proc. IEEE International Parallel and Distributed Processing Symposium, 2006. (Best Paper Award)
 
Ahram, M, EF Strittmatter, ME Monroe, JN Adkins, JC Hunter, JH Miller, and DL Springer, Identification of shed proteins from CHO cells: Application of statistical confidence using human and mouse protein databases. Proteomics 5, 1815-1826 (2005).
 
Kalyanaraman, A., and S. Aluru, ``Efficient algorithms and software for detection of full-length LTR retrotransposons,’’ IEEE Computational Systems Bioinformatics Conference, pp. 56-64, 2005. (Best Paper Award)
 
Kalyanaraman, A., and 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.
 
Emrich, S.J., A. Kalyanaraman, and 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.
 
Broschat, S.L., D.R. Call, E.A. Kuhn, and F.J. Loge, ``Comparison of the reflectance and Crystal Violet assays for measurement of biofilm formation by Enterococcus,’’ Biofilms, vol. 2, no. 3, pp. 177-181, Jul. 2005.
 
Broschat, S.L., F.J. Loge, J.D. Peppin, D. White, D.R.Call, and E. Kuhn, ``Optical reflectance assay for the detection of biofilm formation,’’ J. Biomedical Optics, vol. 10, no. 4, 044027: pp. 1-6, Jul./Aug. 2005.
 
Miller, JH, and F Zheng, 2004. Large-Scale Simulations of Cellular Signaling Processes. Parallel Computing 30:1137-1149.
 
Mitreva, M., A.A. Elling, M. Dante, A.P. Kloek, A. Kalyanaraman, S. Aluru, S.W. Clifton, D.M. 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,  272:138-148, 2004.
 
Ko, P., M. Narayanan, and A. Kalyanaraman, and S. Aluru, ``Space-conserving optimal DNA-protein alignment,’’ Proc. IEEE Computational Systems Bioinformatics Conference, pp. 77-85, 2004.
 
Miller, JH, CP Fan-Chiang, TP Straatsma, and MA Kennedy, 2003. 8-Oxoguanine Enhances Bending of DNA that Favors Binding to Glycosylases.  J. Am Chem. Soc. 125:6331-6336.
 
Rittenhouse RC, WK Apostoluk, JH Miller, and TP Straatsma, 2003. Characterization of the Active Site of DNA Polymerase b by Molecular Dynamics and Quantum Chemical Calculations. Proteins: Structure, Function and Genetics 53:667-682.
 
Kalyanaraman, A., 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, 14(12):1209-1221, 2003.
 
Kalyanaraman, A., S. Aluru, S. Kothari, and V. Brendel, ``Efficient clustering of large EST data sets on parallel computers,’’ Nucleic Acids Research, 31(11):2963-2974, 2003.
 
Kalyanaraman, A., S. Aluru, and S. Kothari, ``Space and time efficient parallel algorithms and software for EST clustering,’’ Proc. International Conference on Parallel Processing, 331-339, 2002.
 
Kalyanaraman, A., S. Aluru, and S. Kothari, ``Parallel EST clustering,’’ Proc. First International Workshop on High Performance Computational Biology, held in conjunction with IPDPS '02, 2002.
 
Resat, H, TP Straatsma, DA Dixon, and JH Miller, 2001. The arginine finger of RasGAP helps Gln61 align the nucleophilic water in GAP-stimulated hydrolysis of GTP. Proc. Natl. Acad. Sci. USA 98:6033-6038.
 
Soares, TA, JH Miller, and TP Straatsma, 2001. Revisiting the structural dynamics of the complex p21ras-GTP: The Catalytic Conformation of the Molecular Switch II. Proteins: Structure, Function and Genetics 45:297-312.