Srinivas Aluru
According to our database^{1},
Srinivas Aluru
authored at least 180 papers
between 1992 and 2020.
Collaborative distances:
Collaborative distances:
Awards
IEEE Fellow
IEEE Fellow 2010, "For contributions to computational biology".
Timeline
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Homepages:

at orcid.org
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Bibliography
2020
Fast de Bruijn Graph Compaction in Distributed Memory Environments.
IEEE/ACM Trans. Comput. Biology Bioinform., 2020
Interval stabbing on the Automata Processor.
J. Parallel Distributed Comput., 2020
2019
Kmerind: A Flexible Parallel Library for Kmer Indexing of Biological Sequences on Distributed Memory Systems.
IEEE/ACM Trans. Comput. Biology Bioinform., 2019
Evaluating High Performance Pattern Matching on the Automata Processor.
IEEE Trans. Computers, 2019
GLAD: Learning Sparse Graph Recovery.
CoRR, 2019
Validating PairedEnd Read Alignments in Sequence Graphs.
Proceedings of the 19th International Workshop on Algorithms in Bioinformatics, 2019
Distributed enhanced suffix arrays: efficient algorithms for construction and querying.
Proceedings of the International Conference for High Performance Computing, 2019
On the Complexity of Sequence to Graph Alignment.
Proceedings of the Research in Computational Molecular Biology, 2019
Efficient ArchitectureAware Acceleration of BWAMEM for Multicore Systems.
Proceedings of the 2019 IEEE International Parallel and Distributed Processing Symposium, 2019
Accelerating Sequence Alignment to Graphs.
Proceedings of the 2019 IEEE International Parallel and Distributed Processing Symposium, 2019
ParRefCom: Parallel Referencebased Compression of Pairedend Genomics Read Datasets.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019
2018
A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.
Journal of Computational Biology, 2018
An SVMbased method for assessment of transcription factorDNA complex models.
BMC Bioinformatics, 2018
A fast adaptive algorithm for computing wholegenome homology maps.
Bioinformatics, 2018
Optimizing high performance distributed memory parallel hash tables for DNA kmer counting.
Proceedings of the International Conference for High Performance Computing, 2018
Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis.
Proceedings of the Research in Computational Molecular Biology, 2018
Cooperative neural networks (CoNN): Exploiting prior independence structure for improved classification.
Proceedings of the Advances in Neural Information Processing Systems 31: Annual Conference on Neural Information Processing Systems 2018, 2018
A Parallel Algorithm for Bayesian Network Inference Using Arithmetic Circuits.
Proceedings of the 2018 IEEE International Parallel and Distributed Processing Symposium, 2018
Introduction to HiCOMB 2018.
Proceedings of the 2018 IEEE International Parallel and Distributed Processing Symposium Workshops, 2018
Faster Computation of Genome Mappability with one Mismatch.
Proceedings of the 8th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2018
An Alignmentfree Heuristic for Fast Sequence Comparisons with Applications to Phylogeny Reconstruction.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018
Faster Computation of Genome Mappability.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018
Performance extraction and suitability analysis of multi and manycore architectures for next generation sequencing secondary analysis.
Proceedings of the 27th International Conference on Parallel Architectures and Compilation Techniques, 2018
2017
An Adaptive Parallel Algorithm for Computing Connected Components.
IEEE Trans. Parallel Distrib. Syst., 2017
Reprint of "A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications".
Parallel Comput., 2017
Parallelized Kendall's Tau Coefficient Computation via SIMD Vectorized Sorting On ManyIntegratedCore Processors.
CoRR, 2017
A greedy alignmentfree distance estimator for phylogenetic inference.
BMC Bioinformatics, 2017
Parallel Construction of Suffix Trees and the AllNearestSmallerValues Problem.
Proceedings of the 2017 IEEE International Parallel and Distributed Processing Symposium, 2017
Parallel Exact Dynamic Bayesian Network Structure Learning with Application to Gene Networks.
Proceedings of the 24th IEEE International Conference on High Performance Computing, 2017
Probabilistic estimation of overlap graphs for large sequence datasets.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
Confidence assessment of proteinDNA complex models.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
Distributed Memory Partitioning of HighThroughput Sequencing Datasets for Enabling Parallel Genomics Analyses.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017
Reverse Engineering Gene Networks: A Comparative Study at Genomescale.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017
2016
Text Indexing.
Encyclopedia of Algorithms, 2016
Discovering Motifs in Biological Sequences Using the Micron Automata Processor.
IEEE/ACM Trans. Comput. Biology Bioinform., 2016
ALFRED: A Practical Method for AlignmentFree Distance Computation.
Journal of Computational Biology, 2016
A Provably Efficient Algorithm for the kMismatch Average Common Substring Problem.
Journal of Computational Biology, 2016
LightScan: Faster Scan Primitive on CUDA Compatible Manycore Processors.
CoRR, 2016
An Adaptive Parallel Algorithm for Computing Connectivity.
CoRR, 2016
SNVSniffer: an integrated caller for germline and somatic singlenucleotide and indel mutations.
BMC Systems Biology, 2016
Parallel Interval Stabbing on the Automata Processor.
Proceedings of the 6th Workshop on Irregular Applications: Architecture and Algorithms, 2016
A parallel algorithm for finding all pairs kmismatch maximal common substrings.
Proceedings of the International Conference for High Performance Computing, 2016
Parallel Pairwise Correlation Computation on Intel Xeon Phi Clusters.
Proceedings of the 28th International Symposium on Computer Architecture and High Performance Computing, 2016
An Efficient Algorithm for Finding All Pairs kMismatch Maximal Common Substrings.
Proceedings of the Bioinformatics Research and Applications  12th International Symposium, 2016
A Memory and Time Scalable Parallelization of the Reptile ErrorCorrection Code.
Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium Workshops, 2016
High Performance Pattern Matching Using the Automata Processor.
Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium, 2016
Algorithmic Techniques for Solving Graph Problems on the Automata Processor.
Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium, 2016
HiCOMB Introduction and Committees.
Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium Workshops, 2016
Programming Techniques for the Automata Processor.
Proceedings of the 45th International Conference on Parallel Processing, 2016
Genomes Galore: Big Data Challenges in the Life Sciences.
Proceedings of the 23rd IEEE International Conference on High Performance Computing, 2016
Effective Utilization of Paired Reads to Improve Length and Accuracy of Contigs in Genome Assembly.
Proceedings of the 7th ACM International Conference on Bioinformatics, 2016
2015
Parallel Mutual Information Based Construction of GenomeScale Networks on the Intel®Xeon Phi™ Coprocessor.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015
Guest Editors' Introduction: Selected Papers from ACMBCB 2013.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015
Parallel Framework for Dimensionality Reduction of LargeScale Datasets.
Scientific Programming, 2015
Editorial: Scalable Systems for Big Data Management and Analytics.
J. Parallel Distributed Comput., 2015
Dtree: Dynamic Task Scheduling at Petascale.
Proceedings of the High Performance Computing  30th International Conference, 2015
A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications.
Proceedings of the International Conference for High Performance Computing, 2015
Parallel distributed memory construction of suffix and longest common prefix arrays.
Proceedings of the International Conference for High Performance Computing, 2015
Efficient Alignment Free Sequence Comparison with Bounded Mismatches.
Proceedings of the Research in Computational Molecular Biology, 2015
HiCOMB Introduction and Committees.
Proceedings of the 2015 IEEE International Parallel and Distributed Processing Symposium Workshop, 2015
A greedy alignmentfree distance estimator for phylogenetic inference (extended abstract).
Proceedings of the 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2015
Efficient detection of viral transmission with thresholdbased methods.
Proceedings of the 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2015
Parallel Read Error Correction for Big Genomic Datasets.
Proceedings of the 22nd IEEE International Conference on High Performance Computing, 2015
Information Theory Based GenomeScale Gene Networks Construction Using MapReduce.
Proceedings of the 22nd IEEE International Conference on High Performance Computing, 2015
Big data in life sciences and public health.
Proceedings of the 22nd IEEE International Conference on High Performance Computing Workshops, 2015
SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
Parallel machine learning approaches for reverse engineering genomescale networks.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
2014
A Review of Hardware Acceleration for Computational Genomics.
IEEE Design & Test, 2014
A Parallel Algorithm for Exact Bayesian Structure Discovery in Bayesian Networks.
CoRR, 2014
Parallel Bayesian Network Structure Learning for GenomeScale Gene Networks.
Proceedings of the International Conference for High Performance Computing, 2014
Finding Motifs in Biological Sequences Using the Micron Automata Processor.
Proceedings of the 2014 IEEE 28th International Parallel and Distributed Processing Symposium, 2014
Parallel Mutual Information Based Construction of WholeGenome Networks on the Intel (R) Xeon Phi (TM) Coprocessor.
Proceedings of the 2014 IEEE 28th International Parallel and Distributed Processing Symposium, 2014
HiCOMB Introduction and Committees.
Proceedings of the 2014 IEEE International Parallel & Distributed Processing Symposium Workshops, 2014
In search of perfect reads.
Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, 2014
2013
Allpairs computations on manycore graphics processors.
Parallel Comput., 2013
Parallel globally optimal structure learning of Bayesian networks.
J. Parallel Distributed Comput., 2013
LargeScale metagenomic sequence Clustering on MapReduce Clusters.
J. Bioinformatics and Computational Biology, 2013
A survey of errorcorrection methods for nextgeneration sequencing.
Briefings in Bioinformatics, 2013
HiCOMB Introduction.
Proceedings of the 2013 IEEE International Symposium on Parallel & Distributed Processing, 2013
Largescale metagenomic clustering via quasi clique enumeration and read assignment ambiguity resolution.
Proceedings of the IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, 2013
2012
An Algorithmic View on MultiRelatedSegments: A Unifying Model for Approximate Common Interval.
Proceedings of the Theory and Applications of Models of Computation, 2012
Parallel Bayesian network structure learning with application to gene networks.
Proceedings of the SC Conference on High Performance Computing Networking, 2012
A Parallel Algorithm for Spectrumbased Short Read Error Correction.
Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium, 2012
HiCOMB Introduction.
Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012
Workshop: Taxonomic clustering of largescale metagnomic data.
Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012
Invited: Reverse engineering wholegenome networks.
Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012
2011
Systems Biology, Network Inference in.
Proceedings of the Encyclopedia of Parallel Computing, 2011
Bioinformatics.
Proceedings of the Encyclopedia of Parallel Computing, 2011
Accelerating Pairwise Computations on Cell Processors.
IEEE Trans. Parallel Distrib. Syst., 2011
Repeataware modeling and correction of short read errors.
BMC Bioinformatics, 2011
Parallel Metagenomic Sequence Clustering Via Sketching and Maximal Quasiclique Enumeration on MapReduce Clouds.
Proceedings of the 25th IEEE International Symposium on Parallel and Distributed Processing, 2011
HiCOMB Introduction.
Proceedings of the 25th IEEE International Symposium on Parallel and Distributed Processing, 2011
Parallel Discovery of Direct Causal Relations and Markov Boundaries with Applications to Gene Networks.
Proceedings of the International Conference on Parallel Processing, 2011
Workshop: Flexible read decomposition for improved short read error correction.
Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011
An improved maximum likelihood formulation for accurate genome assembly.
Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011
2010
Parallel InformationTheoryBased Construction of GenomeWide Gene Regulatory Networks.
IEEE Trans. Parallel Distrib. Syst., 2010
A scalable parallelization of the gene duplication problem.
J. Parallel Distributed Comput., 2010
Reptile: representative tiling for short read error correction.
Bioinformatics, 2010
Parallel applications employing pairwise computations on emerging architectures.
Proceedings of the 24th IEEE International Symposium on Parallel and Distributed Processing, 2010
Message from the workshop chairs.
Proceedings of the 24th IEEE International Symposium on Parallel and Distributed Processing, 2010
Parallel de novo assembly of large genomes from highthroughput short reads.
Proceedings of the 24th IEEE International Symposium on Parallel and Distributed Processing, 2010
A MapReduce Style Framework for Computations on Trees.
Proceedings of the 39th International Conference on Parallel Processing, 2010
An Improved Model for Gene Cluster Inference.
Proceedings of the ISCA 2nd International Conference on Bioinformatics and Computational Biology, 2010
Pairwise Computations on the Cell Processor.
Proceedings of the Scientific Computing with Multicore and Accelerators., 2010
2009
Parallel Genomic Alignments on the Cell Broadband Engine.
IEEE Trans. Parallel Distrib. Syst., 2009
Parallel short sequence assembly of transcriptomes.
BMC Bioinformatics, 2009
Parallel accelerated cartesian expansions for particle dynamics simulations.
Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009
Constructing Gene Regulatory Networks on Clusters of Cell Processors.
Proceedings of the ICPP 2009, 2009
A parallel algorithm for exact Bayesian network inference.
Proceedings of the 16th International Conference on High Performance Computing, 2009
Assembly of Large Genomes from Paired Short Reads.
Proceedings of the Bioinformatics and Computational Biology, 2009
2008
Text Indexing.
Proceedings of the Encyclopedia of Algorithms  2008 Edition, 2008
Consensus Genetic Maps as Median Orders from Inconsistent Sources.
IEEE/ACM Trans. Comput. Biology Bioinform., 2008
Largescale phylogenetic analysis on current HPC architectures.
Scientific Programming, 2008
Highperformance computational biology.
Parallel Comput., 2008
Parallel biological sequence alignments on the Cell Broadband Engine.
Proceedings of the 22nd IEEE International Symposium on Parallel and Distributed Processing, 2008
Fast, ProcessorCardinality Agnostic PRNG with a Tracking Application.
Proceedings of the Sixth Indian Conference on Computer Vision, Graphics & Image Processing, 2008
Tracking Nanostructural Evolution in Alloys: LargeScale Analysis of Atom Probe Tomography Data on Blue Gene/L.
Proceedings of the 2008 International Conference on Parallel Processing, 2008
Parallel Construction of Bidirected String Graphs for Genome Assembly.
Proceedings of the 2008 International Conference on Parallel Processing, 2008
Parallel Information Theory Based Construction of Gene Regulatory Networks.
Proceedings of the High Performance Computing, 2008
2007
Spatial Domain Decomposition Methods in Parallel Scientific Computing.
Proceedings of the Handbook of Parallel Computing  Models, Algorithms and Applications., 2007
Assembling genomes on largescale parallel computers.
J. Parallel Distributed Comput., 2007
Optimal Selfadjusting Trees for Dynamic String Data in Secondary Storage.
Proceedings of the String Processing and Information Retrieval, 2007
Largescale maximum likelihoodbased phylogenetic analysis on the IBM BlueGene/L.
Proceedings of the ACM/IEEE Conference on High Performance Networking and Computing, 2007
Symposium Evening Tutorial: Highperformance Computing Methods for Computational Genomics.
Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), 2007
The Combinatorics of Sequencing the Corn Genome.
Proceedings of the Computing and Combinatorics, 13th Annual International Conference, 2007
PARALLELTCOFFEE: A parallel multiple sequence aligner.
Proceedings of the ISCA 20th International Conference on Parallel and Distributed Computing Systems, 2007
Massively parallel expressed sequence tag clustering.
Proceedings of the ISCA 20th International Conference on Parallel and Distributed Computing Systems, 2007
2006
Editorial: Special Section on HighPerformance Computational Biology.
IEEE Trans. Parallel Distrib. Syst., 2006
Efficient Algorithms and Software for Detection of Fulllength Ltr Retrotransposons.
J. Bioinformatics and Computational Biology, 2006
M11  Highperformance computing methods for computational genomics.
Proceedings of the ACM/IEEE SC2006 Conference on High Performance Networking and Computing, 2006
A Formal Analysis of Space Filling Curves for Parallel Domain Decomposition.
Proceedings of the 2006 International Conference on Parallel Processing (ICPP 2006), 2006
Obtaining Provably Good Performance from Suffix Trees in Secondary Storage.
Proceedings of the Combinatorial Pattern Matching, 17th Annual Symposium, 2006
Communicationaware Parallel Domain Decomposition using Space Filling Curves.
Proceedings of the ISCA 19th International Conference on Parallel and Distributed Computing Systems, 2006
Parallel Computational Biology.
Proceedings of the Parallel Processing for Scientific Computing, 2006
Bioinformatics.
Proceedings of the Handbook of NatureInspired and Innovative Computing, 2006
2005
Scalable, memory efficient, highspeed IP lookup algorithms.
IEEE/ACM Trans. Netw., 2005
Efficient parallel algorithms and software for compressed octrees with applications to hierarchical methods.
Parallel Comput., 2005
Parallel algorithms for tree accumulations.
J. Parallel Distributed Comput., 2005
Space efficient linear time construction of suffix arrays.
J. Discrete Algorithms, 2005
An optimal hierarchical clustering algorithm for gene expression data.
Inf. Process. Lett., 2005
Consensus Genetic Maps: A Graph Theoretic Approach.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005
Indexing for Subscription Covering in PublishSubscribe Systems.
Proceedings of the ISCA 18th International Conference on Parallel and Distributed Computing Systems, 2005
2004
Suffix Trees and Suffix Arrays.
Proceedings of the Handbook of Data Structures and Applications., 2004
Quadtrees and Octrees.
Proceedings of the Handbook of Data Structures and Applications., 2004
Space and Time Optimal Parallel Sequence Alignments.
IEEE Trans. Parallel Distrib. Syst., 2004
Special Issue: High Performance Computational Biology.
Concurrency  Practice and Experience, 2004
A strategy for assembling the maize (Zea mays L.) genome.
Bioinformatics, 2004
A tunable collective communication framework on a cluster of SMPS.
Proceedings of the IASTED International Conference on Parallel and Distributed Computing and Networks, 2004
Efficient Methods for Database Storage and Retrieval Using SpaceFilling Curves.
Proceedings of the Computer and Information Sciences, 2004
SpaceConserving Optimal DNAProtein Alignment .
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
2003
Parallel Syntenic Alignments.
Parallel Processing Letters, 2003
Parallel biological sequence comparison using prefix computations.
J. Parallel Distributed Comput., 2003
Guest Editor's Introduction: Special issue on highperformance computational biology.
J. Parallel Distributed Comput., 2003
Scalable, memory efficient, highspeed lookup and update algorithms for IP routing.
Proceedings of the 12th International Conference on Computer Communications and Networks, 2003
2002
Efficient Parallel Algorithms for Solvent Accessible Surface Area of Proteins.
IEEE Trans. Parallel Distrib. Syst., 2002
A scalable parallel fast multipole method for analysis of scattering from perfect electrically conducting surfaces.
Proceedings of the 2002 ACM/IEEE conference on Supercomputing, 2002
Parallel EST Clustering.
Proceedings of the 16th International Parallel and Distributed Processing Symposium (IPDPS 2002), 2002
Workshop Introduction.
Proceedings of the 16th International Parallel and Distributed Processing Symposium (IPDPS 2002), 2002
Space and Time Efficient Parallel Algorithms and Software for EST Clustering.
Proceedings of the 31st International Conference on Parallel Processing (ICPP 2002), 2002
Mixed Mode Matrix Multiplication.
Proceedings of the 2002 IEEE International Conference on Cluster Computing (CLUSTER 2002), 2002
2000
Parallel Construction of Multidimensional Binary Search Trees.
IEEE Trans. Parallel Distrib. Syst., 2000
A Provably Optimal, DistributionIndependent Parallel Fast Multipole Method.
Proceedings of the 14th International Parallel & Distributed Processing Symposium (IPDPS'00), 2000
1999
A Unifying Data Structure for Hierarchical Methods.
Proceedings of the ACM/IEEE Conference on Supercomputing, 1999
A Practical Parallel Algorithm for Line Segment Visibility.
Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, 1999
A Parallel Monte Carlo Algorithm for Protein Accessible Surface Area Computation.
Proceedings of the High Performance Computing, 1999
Dynamic Compressed Hypertoctrees with Application to the NBody Problem.
Proceedings of the Foundations of Software Technology and Theoretical Computer Science, 1999
1998
DistributionIndependent Hierarchical Algorithms for the Nbody Problem.
The Journal of Supercomputing, 1998
1997
Practical Algorithms for Selection on CoarseGrained Parallel Computers.
IEEE Trans. Parallel Distrib. Syst., 1997
Lagged Fibonacci Random Number Generators for Distributed Memory Parallel Computers.
J. Parallel Distributed Comput., 1997
Parallel domain decomposition and load balancing using spacefilling curves.
Proceedings of the Fourth International on HighPerformance Computing, 1997
1996
Massively Parallel Searching for Better Algorithms or How to Do a Cross Product with Five Multiplications.
Scientific Programming, 1996
Greengard's NBody Algorithm is not Order N.
SIAM J. Scientific Computing, 1996
Concatenated parallelism: a technique for efficient parallel divide and conquer.
Proceedings of the Eighth IEEE Symposium on Parallel and Distributed Processing, 1996
Practical Paralle1 Algorithm for Constructing Line Arrangements.
Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, 1996
Parallel Additive Lagged Fibonacci Random Number Generators.
Proceedings of the 10th international conference on Supercomputing, 1996
1995
Properties of Binomial Coefficients and Implications to Parallelizing Lagged Fibonacci Random Number Generators.
Proceedings of the 1995 International Conference on Parallel Processing, 1995
1994
Truly distributionindependent algorithms for the Nbody problem.
Proceedings of the Proceedings Supercomputing '94, 1994
1993
Subtle Issues of SIMD Tree Search.
Proceedings of the Parallel Computing: Trends and Applications, 1993
A Massively Parallel Optimizer for Expression Evaluation.
Proceedings of the 7th international conference on Supercomputing, 1993
1992
A random number generator for parallel computers.
Parallel Comput., 1992