Srinivas Aluru

Xiao Yang, Sriram P. Chockalingam, Srinivas Aluru: A survey of error-correction methods for next-generation sequencing. Briefings in Bioinformatics 14(1): 56-66 (2013)

Xiao Yang, Jaroslaw Zola, Srinivas Aluru: Large-Scale metagenomic sequence Clustering on Map-Reduce Clusters. J. Bioinformatics and Computational Biology 11(1) (2013)

Abhinav Sarje, Srinivas Aluru: All-pairs computations on many-core graphics processors. Parallel Computing 39(2): 79-93 (2013)

Srinivas Aluru: Invited: Reverse engineering whole-genome networks. ICCABS 2012: 1

Srinivas Aluru: Workshop: Taxonomic clustering of large-scale metagnomic data. ICCABS 2012: 1

Ankit Shah, Sriram P. Chockalingam, Srinivas Aluru: A Parallel Algorithm for Spectrum-based Short Read Error Correction. IPDPS 2012: 60-70

Mark J. Clement, Quinn Snell, Srinivas Aluru, David A. Bader: HiCOMB Introduction. IPDPS Workshops 2012: 663-664

Olga Nikolova, Srinivas Aluru: Parallel Bayesian network structure learning with application to gene networks. SC 2012: 63

Xiao Yang, Florian Sikora, Guillaume Blin, Sylvie Hamel, Romeo Rizzi, Srinivas Aluru: An Algorithmic View on Multi-Related-Segments: A Unifying Model for Approximate Common Interval. TAMC 2012: 319-329

Xiao Yang, Srinivas Aluru, Karin S. Dorman: Repeat-aware modeling and correction of short read errors. BMC Bioinformatics 12(S-1): S52 (2011)

Abhinav Sarje, Jaroslaw Zola, Srinivas Aluru: Accelerating Pairwise Computations on Cell Processors. IEEE Trans. Parallel Distrib. Syst. 22(1): 69-77 (2011)

Aditya Varma, Abhiram Ranade, Srinivas Aluru: An improved maximum likelihood formulation for accurate genome assembly. ICCABS 2011: 165-170

Xiao Yang, Karin S. Dorman, Srinivas Aluru: Workshop: Flexible read decomposition for improved short read error correction. ICCABS 2011: 277

Olga Nikolova, Srinivas Aluru: Parallel Discovery of Direct Causal Relations and Markov Boundaries with Applications to Gene Networks. ICPP 2011: 512-521

Ananth Kalyanaraman, Srinivas Aluru, David A. Bader: HiCOMB Introduction. IPDPS Workshops 2011: 426-427

Xiao Yang, Jaroslaw Zola, Srinivas Aluru: Parallel Metagenomic Sequence Clustering Via Sketching and Maximal Quasi-clique Enumeration on Map-Reduce Clouds. IPDPS 2011: 1223-1233

Srinivas Aluru: Bioinformatics. Encyclopedia of Parallel Computing 2011: 134-136

Jaroslaw Zola, Srinivas Aluru, Srinivas Aluru: Systems Biology, Network Inference in. Encyclopedia of Parallel Computing 2011: 1997-2002

Jaroslaw Zola, Srinivas Aluru, Srinivas Aluru: Systems Biology, Network Inference in. Encyclopedia of Parallel Computing 2011: 1997-2002

Srinivas Aluru, Sanghamitra Bandyopadhyay, Ümit V. Çatalyürek, Devdatt P. Dubhashi, Phillip H. Jones, Manish Parashar, Bertil Schmidt (Eds.): Contemporary Computing - 4th International Conference, IC3 2011, Noida, India, August 8-10, 2011. Proceedings. Communications in Computer and Information Science 168, Springer 2011, isbn 978-3-642-22605-2

Xiao Yang, Karin S. Dorman, Srinivas Aluru: Reptile: representative tiling for short read error correction. Bioinformatics 26(20): 2526-2533 (2010)

André Wehe, Wen-Chieh Chang, Oliver Eulenstein, Srinivas Aluru: A scalable parallelization of the gene duplication problem. J. Parallel Distrib. Comput. 70(3): 237-244 (2010)

Jaroslaw Zola, Maneesha Aluru, Abhinav Sarje, Srinivas Aluru: Parallel Information-Theory-Based Construction of Genome-Wide Gene Regulatory Networks. IEEE Trans. Parallel Distrib. Syst. 21(12): 1721-1733 (2010)

Xiao Yang, Srinivas Aluru: An Improved Model for Gene Cluster Inference. BICoB 2010: 190-195

William Sarje, Srinivas Aluru: A MapReduce Style Framework for Computations on Trees. ICPP 2010: 343-352

Benjamin G. Jackson, Matthew Regennitter, Xiao Yang, Patrick S. Schnable, Srinivas Aluru: Parallel de novo assembly of large genomes from high-throughput short reads. IPDPS 2010: 1-10

George Karypis, Srinivas Aluru, David A. Bader: Message from the workshop chairs. IPDPS Workshops 2010: 1-2

Abhinav Sarje, Srinivas Aluru: Parallel applications employing pairwise computations on emerging architectures. IPDPS Workshops 2010: 1-4

Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru: Parallel short sequence assembly of transcriptomes. BMC Bioinformatics 10(S-1) (2009)

Abhinav Sarje, Srinivas Aluru: Parallel Genomic Alignments on the Cell Broadband Engine. IEEE Trans. Parallel Distrib. Syst. 20(11): 1600-1610 (2009)

Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru: Assembly of Large Genomes from Paired Short Reads. BICoB 2009: 30-43

Olga Nikolova, Jaroslaw Zola, Srinivas Aluru: A parallel algorithm for exact Bayesian network inference. HiPC 2009: 342-349

Jaroslaw Zola, Abhinav Sarje, Srinivas Aluru: Constructing Gene Regulatory Networks on Clusters of Cell Processors. ICPP 2009: 108-115

Melapudi Vikram, Andrew Baczewzki, B. Shanker, Srinivas Aluru: Parallel accelerated cartesian expansions for particle dynamics simulations. IPDPS 2009: 1-11

Sanjay Ranka, Srinivas Aluru, Rajkumar Buyya, Yeh-Ching Chung, Sumeet Dua, Ananth Grama, Sandeep K. S. Gupta, Rajeev Kumar, Vir V. Phoha (Eds.): Contemporary Computing - Second International Conference, IC3 2009, Noida, India, August 17-19, 2009. Proceedings. Communications in Computer and Information Science 40, Springer 2009, isbn 978-3-642-03546-3

David A. Bader, Srinivas Aluru: High-performance computational biology. Parallel Computing 34(11): 613-615 (2008)

Michael Ott, Jaroslaw Zola, Srinivas Aluru, Andrew D. Johnson, Daniel Janies, Alexandros Stamatakis: Large-scale phylogenetic analysis on current HPC architectures. Scientific Programming 16(2-3): 255-270 (2008)

Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru: Consensus Genetic Maps as Median Orders from Inconsistent Sources. IEEE/ACM Trans. Comput. Biology Bioinform. 5(2): 161-171 (2008)

Jaroslaw Zola, Maneesha Aluru, Srinivas Aluru: Parallel Information Theory Based Construction of Gene Regulatory Networks. HiPC 2008: 336-349

Sudip Seal, Michael Moody, Anna Ceguerra, Simon Ringer, Krishna Rajan, Srinivas Aluru: Tracking Nanostructural Evolution in Alloys: Large-Scale Analysis of Atom Probe Tomography Data on Blue Gene/L. ICPP 2008: 338-345

Benjamin G. Jackson, Srinivas Aluru: Parallel Construction of Bidirected String Graphs for Genome Assembly. ICPP 2008: 346-353

Andrew Janowczyk, Sharat Chandran, Srinivas Aluru: Fast, Processor-Cardinality Agnostic PRNG with a Tracking Application. ICVGIP 2008: 171-178

Abhinav Sarje, Srinivas Aluru: Parallel biological sequence alignments on the Cell Broadband Engine. IPDPS 2008: 1-11

Srinivas Aluru: Text Indexing. Encyclopedia of Algorithms 2008

Anantharaman Kalyanaraman, Scott J. Emrich, Patrick S. Schnable, Srinivas Aluru: Assembling genomes on large-scale parallel computers. J. Parallel Distrib. Comput. 67(12): 1240-1255 (2007)

Jaroslaw Zola, Xiao Yang, Adrian Rospondek, Srinivas Aluru: PARALLEL-TCOFFEE: A parallel multiple sequence aligner. ISCA PDCS 2007: 248-253

Scott J. Emrich, Anantharaman Kalyanaraman, Srinivas Aluru: Massively parallel expressed sequence tag clustering. ISCA PDCS 2007: 254-261

Srinivas Aluru: The Combinatorics of Sequencing the Corn Genome. COCOON 2007: 1

Srinivas Aluru, David A. Bader, Anantharaman Kalyanaraman: Symposium Evening Tutorial: High-performance Computing Methods for Computational Genomics. IPDPS 2007: 13

Michael Ott, Jaroslaw Zola, Alexandros Stamatakis, Srinivas Aluru: Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. SC 2007: 4

Pang Ko, Srinivas Aluru: Optimal Self-adjusting Trees for Dynamic String Data in Secondary Storage. SPIRE 2007: 184-194

Srinivas Aluru, Manish Parashar, Ramamurthy Badrinath, Viktor K. Prasanna (Eds.): High Performance Computing - HiPC 2007, 14th International Conference, Goa, India, December 18-21, 2007, Proceedings. Lecture Notes in Computer Science 4873, Springer 2007, isbn 978-3-540-77219-4

Anantharaman Kalyanaraman, Srinivas Aluru: Efficient Algorithms and Software for Detection of Full-length Ltr Retrotransposons. J. Bioinformatics and Computational Biology 4(2): 197-216 (2006)

Srinivas Aluru, Nancy M. Amato, David A. Bader: Editorial: Special Section on High-Performance Computational Biology. IEEE Trans. Parallel Distrib. Syst. 17(8): 737-739 (2006)

Sudip Seal, Srinivas Aluru: Communication-aware Parallel Domain Decomposition using Space Filling Curves. ISCA PDCS 2006: 159-164

Pang Ko, Srinivas Aluru: Obtaining Provably Good Performance from Suffix Trees in Secondary Storage. CPM 2006: 72-83

Srikanta Tirthapura, Sudip Seal, Srinivas Aluru: A Formal Analysis of Space Filling Curves for Parallel Domain Decomposition. ICPP 2006: 505-512

Anantharaman Kalyanaraman, Scott J. Emrich, Patrick S. Schnable, Srinivas Aluru: Assembling genomes on large-scale parallel computers. IPDPS 2006

Srinivas Aluru, David A. Bader, Anantharaman Kalyanaraman: M11 - High-performance computing methods for computational genomics. SC 2006: 225

Sudip Seal, Srikanth Komarina, Srinivas Aluru: An optimal hierarchical clustering algorithm for gene expression data. Inf. Process. Lett. 93(3): 143-147 (2005)

Pang Ko, Srinivas Aluru: Space efficient linear time construction of suffix arrays. J. Discrete Algorithms 3(2-4): 143-156 (2005)

Fatih Erdogan Sevilgen, Srinivas Aluru, Natsuhiko Futamura: Parallel algorithms for tree accumulations. J. Parallel Distrib. Comput. 65(1): 85-93 (2005)

Bhanu Hariharan, Srinivas Aluru: Efficient parallel algorithms and software for compressed octrees with applications to hierarchical methods. Parallel Computing 31(3-4): 311-331 (2005)

Rama Sangireddy, Natsuhiko Futamura, Srinivas Aluru, Arun K. Somani: Scalable, memory efficient, high-speed IP lookup algorithms. IEEE/ACM Trans. Netw. 13(4): 802-812 (2005)

Zhenhui Shen, Srinivas Aluru, Srikanta Tirthapura: Indexing for Subscription Covering in Publish-Subscribe Systems. ISCA PDCS 2005: 328-333

Benjamin G. Jackson, Srinivas Aluru, Patrick S. Schnable: Consensus Genetic Maps: A Graph Theoretic Approach. CSB 2005: 35-43

Anantharaman Kalyanaraman, Srinivas Aluru: Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons. CSB 2005: 56-64

Scott J. Emrich, Srinivas Aluru, Yan Fu, Tsui-Jung Wen, Mahesh Narayanan, Ling Guo, Daniel A. Ashlock, Patrick S. Schnable: A strategy for assembling the maize (Zea mays L.) genome. Bioinformatics 20(2): 140-147 (2004)

David A. Bader, Srinivas Aluru: Special Issue: High Performance Computational Biology. Concurrency - Practice and Experience 16(9): 817-821 (2004)

Stjepan Rajko, Srinivas Aluru: Space and Time Optimal Parallel Sequence Alignments. IEEE Trans. Parallel Distrib. Syst. 15(12): 1070-1081 (2004)

Pang Ko, Mahesh Narayanan, Anantharaman Kalyanaraman, Srinivas Aluru: Space-Conserving Optimal DNA-Protein Alignment . CSB 2004: 80-88

Srinivas Aluru, Fatih Erdogan Sevilgen: Efficient Methods for Database Storage and Retrieval Using Space-Filling Curves. ISCIS 2004: 503-512

Meng-Shiou Wu, Ricky A. Kendall, Srinivas Aluru: A tunable collective communication framework on a cluster of SMPS. Parallel and Distributed Computing and Networks 2004: 56-63

Srinivas Aluru, Natsuhiko Futamura, Kishan Mehrotra: Parallel biological sequence comparison using prefix computations. J. Parallel Distrib. Comput. 63(3): 264-272 (2003)

Srinivas Aluru, David A. Bader: Guest Editor's Introduction: Special issue on high-performance computational biology. J. Parallel Distrib. Comput. 63(7-8): 671-673 (2003)

Natsuhiko Futamura, Srinivas Aluru, Xiaoqiu Huang: Parallel Syntenic Alignments. Parallel Processing Letters 13(4): 689-703 (2003)

Pang Ko, Srinivas Aluru: Space Efficient Linear Time Construction of Suffix Arrays. CPM 2003: 200-210

Stjepan Rajko, Srinivas Aluru: Space and Time Optimal Parallel Sequence Alignments. ICPP 2003: 39-47

Natsuhiko Futamura, Srinivas Aluru, Desh Ranjan, Bhanu Hariharan: Efficient Parallel Algorithms for Solvent Accessible Surface Area of Proteins. IEEE Trans. Parallel Distrib. Syst. 13(6): 544-555 (2002)

Meng-Shiou Wu, Srinivas Aluru, Ricky A. Kendall: Mixed Mode Matrix Multiplication. CLUSTER 2002: 195-

Natsuhiko Futamura, Srinivas Aluru, Xiaoqiu Huang: Parallel Syntenic Alignments. HiPC 2002: 420-430

Anantharaman Kalyanaraman, Srinivas Aluru, Suresh C. Kothari: Space and Time Efficient Parallel Algorithms and Software for EST Clustering. ICPP 2002: 331-

David A. Bader, Srinivas Aluru: Workshop Introduction. IPDPS 2002

Anantharaman Kalyanaraman, Srinivas Aluru, Suresh C. Kothari: Parallel EST Clustering. IPDPS 2002

Bhanu Hariharan, Srinivas Aluru, Balasubramaniam Shanker: A scalable parallel fast multipole method for analysis of scattering from perfect electrically conducting surfaces. SC 2002: 1-17

Bhanu Hariharan, Srinivas Aluru: Efficient Parallel Algorithms and Software for Compressed Octrees with Applications to Hierarchical Methods. HiPC 2001: 125-136

Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka: Parallel Construction of Multidimensional Binary Search Trees. IEEE Trans. Parallel Distrib. Syst. 11(2): 136-148 (2000)

Fatih Erdogan Sevilgen, Natsuhiko Futamura, Srinivas Aluru: A Provably Optimal, Distribution-Independent Parallel Fast Multipole Method. IPDPS 2000: 77-84

Srinivas Aluru, Fatih Erdogan Sevilgen: Dynamic Compressed Hypertoctrees with Application to the N-Body Problem. FSTTCS 1999: 21-33

Srinivas Aluru, Desh Ranjan, Natsuhiko Futamura: A Parallel Monte Carlo Algorithm for Protein Accessible Surface Area Computation. HiPC 1999: 339-348

Srinivas Aluru, Natsuhiko Futamura, Kishan Mehrotra: Parallel Biological Sequence Comparison Using Prefix Computations. IPPS/SPDP 1999: 653-659

Srinivas Aluru, Songrit Maneewongvatana: A Practical Parallel Algorithm for Line Segment Visibility. PDPTA 1999: 1676-1682

Fatih Erdogan Sevilgen, Srinivas Aluru: A Unifying Data Structure for Hierarchical Methods. SC 1999: 24

Srinivas Aluru, John L. Gustafson, Gurpur M. Prabhu, Fatih Erdogan Sevilgen: Distribution-Independent Hierarchical Algorithms for the N-body Problem. The Journal of Supercomputing 12(4): 303-323 (1998)

Srinivas Aluru: Lagged Fibonacci Random Number Generators for Distributed Memory Parallel Computers. J. Parallel Distrib. Comput. 45(1): 1-12 (1997)

Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka: Practical Algorithms for Selection on Coarse-Grained Parallel Computers. IEEE Trans. Parallel Distrib. Syst. 8(8): 813-824 (1997)

John L. Gustafson, Srinivas Aluru: Massively Parallel Searching for Better Algorithms or How to Do a Cross Product with Five Multiplications. Scientific Programming 5(3): 203-217 (1996)

Srinivas Aluru: Parallel Additive Lagged Fibonacci Random Number Generators. International Conference on Supercomputing 1996: 102-108

Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka: Parallel Construction of Multidimensional Binary Search Trees. International Conference on Supercomputing 1996: 205-212

Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka: Practical Algorithms for Selection on Coarse-Grained Parallel Computers. IPPS 1996: 309-313

Srinivas Aluru, Songrit Maneewongvatana: Practical Paralle1 Algorithm for Constructing Line Arrangements. PDPTA 1996: 125-135

Srinivas Aluru: Properties of Binomial Coefficients and Implications to Parallelizing Lagged Fibonacci Random Number Generators. ICPP (3) 1995: 25-28

Srinivas Aluru, Gurpur M. Prabhu, John L. Gustafson: Truly distribution-independent algorithms for the N-body problem. SC 1994: 420-428

Srinivas Aluru, John L. Gustafson: A Massively Parallel Optimizer for Expression Evaluation. International Conference on Supercomputing 1993: 97-106

Srinivas Aluru, John L. Gustafson: Subtle Issues of SIMD Tree Search. PARCO 1993: 49-56

Srinivas Aluru, Gurpur M. Prabhu, John L. Gustafson: A random number generator for parallel computers. Parallel Computing 18(8): 839-847 (1992)