Srinivas Aluru

According to our database1, Srinivas Aluru authored at least 183 papers between 1992 and 2020.

Collaborative distances:

Awards

IEEE Fellow

IEEE Fellow 2010, "For contributions to computational biology".

Timeline

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Bibliography

2020
Fast de Bruijn Graph Compaction in Distributed Memory Environments.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

Interval stabbing on the Automata Processor.
J. Parallel Distributed Comput., 2020

Sequential and parallel algorithms for all-pair k-mismatch maximal common substrings.
J. Parallel Distributed Comput., 2020

GLAD: Learning Sparse Graph Recovery.
Proceedings of the 8th International Conference on Learning Representations, 2020

2019
Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Evaluating High Performance Pattern Matching on the Automata Processor.
IEEE Trans. Computers, 2019

GLAD: Learning Sparse Graph Recovery.
CoRR, 2019

Validating Paired-End 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 Architecture-Aware Acceleration of BWA-MEM 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 Reference-based Compression of Paired-end 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.
J. Comput. Biol., 2018

An SVM-based method for assessment of transcription factor-DNA complex models.
BMC Bioinform., 2018

A fast adaptive algorithm for computing whole-genome homology maps.
Bioinform., 2018

Optimizing high performance distributed memory parallel hash tables for DNA <i>k</i>-mer 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 Alignment-free 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 many-core 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 Many-Integrated-Core Processors.
CoRR, 2017

A greedy alignment-free distance estimator for phylogenetic inference.
BMC Bioinform., 2017

Parallel Construction of Suffix Trees and the All-Nearest-Smaller-Values 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 protein-DNA complex models.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

Distributed Memory Partitioning of High-Throughput 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 Genome-scale.
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. Biol. Bioinform., 2016

ALFRED: A Practical Method for Alignment-Free Distance Computation.
J. Comput. Biol., 2016

A Provably Efficient Algorithm for the <i>k</i>-Mismatch Average Common Substring Problem.
J. Comput. Biol., 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 single-nucleotide and indel mutations.
BMC Syst. Biol., 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 <i>k</i>-mismatch 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 k-Mismatch Maximal Common Substrings.
Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016

A Memory and Time Scalable Parallelization of the Reptile Error-Correction 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 Genome-Scale Networks on the Intel®Xeon Phi™ Coprocessor.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Guest Editors' Introduction: Selected Papers from ACM-BCB 2013.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Parallel Framework for Dimensionality Reduction of Large-Scale Datasets.
Sci. Program., 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 alignment-free 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 threshold-based 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 Genome-Scale 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 genome-scale networks.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

2014
A Review of Hardware Acceleration for Computational Genomics.
IEEE Des. Test, 2014

A Parallel Algorithm for Exact Bayesian Structure Discovery in Bayesian Networks.
CoRR, 2014

Parallel Bayesian Network Structure Learning for Genome-Scale 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 Whole-Genome 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
All-pairs computations on many-core graphics processors.
Parallel Comput., 2013

Parallel globally optimal structure learning of Bayesian networks.
J. Parallel Distributed Comput., 2013

Large-Scale metagenomic sequence Clustering on Map-Reduce Clusters.
J. Bioinform. Comput. Biol., 2013

A survey of error-correction methods for next-generation sequencing.
Briefings Bioinform., 2013

HiCOMB Introduction.
Proceedings of the 2013 IEEE International Symposium on Parallel & Distributed Processing, 2013

Large-scale 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 Multi-Related-Segments: 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 Spectrum-based 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 large-scale metagnomic data.
Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

Invited: Reverse engineering whole-genome 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

Repeat-aware modeling and correction of short read errors.
BMC Bioinform., 2011

Parallel Metagenomic Sequence Clustering Via Sketching and Maximal Quasi-clique Enumeration on Map-Reduce 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 Information-Theory-Based Construction of Genome-Wide 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.
Bioinform., 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 high-throughput 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 Bioinform., 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. Biol. Bioinform., 2008

Large-scale phylogenetic analysis on current HPC architectures.
Sci. Program., 2008

High-performance 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, Processor-Cardinality Agnostic PRNG with a Tracking Application.
Proceedings of the Sixth Indian Conference on Computer Vision, Graphics & Image Processing, 2008

Tracking Nanostructural Evolution in Alloys: Large-Scale 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 large-scale parallel computers.
J. Parallel Distributed Comput., 2007

Optimal Self-adjusting Trees for Dynamic String Data in Secondary Storage.
Proceedings of the String Processing and Information Retrieval, 2007

Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L.
Proceedings of the ACM/IEEE Conference on High Performance Networking and Computing, 2007

Symposium Evening Tutorial: High-performance 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

PARALLEL-TCOFFEE: 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 High-Performance Computational Biology.
IEEE Trans. Parallel Distrib. Syst., 2006

Efficient Algorithms and Software for Detection of Full-length Ltr Retrotransposons.
J. Bioinform. Comput. Biol., 2006

M11 - High-performance 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

Communication-aware 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 Nature-Inspired and Innovative Computing, 2006

2005
Scalable, memory efficient, high-speed 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 Publish-Subscribe 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.
Concurr. Pract. Exp., 2004

A strategy for assembling the maize (Zea mays L.) genome.
Bioinform., 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 Space-Filling Curves.
Proceedings of the Computer and Information Sciences, 2004

Space-Conserving Optimal DNA-Protein Alignment .
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2003
Space and time efficient parallel algorithms and software for EST clustering.
IEEE Trans. Parallel Distrib. Syst., 2003

Parallel Syntenic Alignments.
Parallel Process. Lett., 2003

Parallel biological sequence comparison using prefix computations.
J. Parallel Distributed Comput., 2003

Guest Editor's Introduction: Special issue on high-performance computational biology.
J. Parallel Distributed Comput., 2003

Scalable, memory efficient, high-speed 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, Distribution-Independent 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 N-Body Problem.
Proceedings of the Foundations of Software Technology and Theoretical Computer Science, 1999

1998
Distribution-Independent Hierarchical Algorithms for the N-body Problem.
J. Supercomput., 1998

1997
Practical Algorithms for Selection on Coarse-Grained 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 space-filling curves.
Proceedings of the Fourth International on High-Performance Computing, 1997

1996
Massively Parallel Searching for Better Algorithms or How to Do a Cross Product with Five Multiplications.
Sci. Program., 1996

Greengard's <i>N</i>-Body Algorithm is not Order <i>N</i>.
SIAM J. Sci. Comput., 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 distribution-independent algorithms for the N-body 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


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