# Srinivas Aluru

American computer scientist

## Srinivas Aluru's AcademicInfluence.com Rankings

## Download Badge

Computer Science

## Srinivas Aluru's Degrees

- Bachelors Computer Science and Engineering IIT Madras

## Why Is Srinivas Aluru Influential?

(Suggest an Edit or Addition)According to Wikipedia, Srinivas Aluru is a professor in the School of Computational Science and Engineering at Georgia Institute of Technology, and co-Executive Director for the Georgia Tech Interdisciplinary Research Institute in Data Engineering and Science. His main areas of research are high performance computing, data science, bioinformatics and systems biology, combinatorial methods in scientific computing, and string algorithms. Aluru is a Fellow of the American Association for the Advancement of Science and the Institute for Electrical and Electronic Engineers . He is best known for his research contributions in parallel algorithms and applications, interdisciplinary research in bioinformatics and computational biology, and particularly the intersection of these two fields.

## Srinivas Aluru's Published Works

### Published Works

- The B73 Maize Genome: Complexity, Diversity, and Dynamics (2009) (3594)
- High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries (2018) (1841)
- A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana. (2011) (513)
- Space efficient linear time construction of suffix arrays (2003) (429)
- PCAP: a whole-genome assembly program. (2003) (317)
- A survey of error-correction methods for next-generation sequencing (2013) (254)
- Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems (2019) (212)
- Reptile: representative tiling for short read error correction (2010) (174)
- Handbook Of Computational Molecular Biology (2010) (170)
- Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L (2007) (156)
- RD26 mediates crosstalk between drought and brassinosteroid signalling pathways (2017) (145)
- Mechanisms and networks for brassinosteroid regulated gene expression. (2013) (140)
- Efficient clustering of large EST data sets on parallel computers. (2003) (101)
- Parallel biological sequence comparison using prefix computations (1999) (99)
- Parallel domain decomposition and load balancing using space-filling curves (1997) (95)
- Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes. (2005) (82)
- A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases (2017) (81)
- A fast adaptive algorithm for computing whole-genome homology maps (2018) (79)
- Finding Motifs in Biological Sequences Using the Micron Automata Processor (2014) (72)
- Space and time optimal parallel sequence alignments (2004) (72)
- Proceedings of the 25th annual conference on Computer graphics and interactive techniques (1998) (71)
- A comprehensive evaluation of long read error correction methods (2019) (67)
- Nearly Identical Paralogs: Implications for Maize (Zea mays L.) Genome Evolution (2007) (67)
- A Review of Hardware Acceleration for Computational Genomics (2014) (64)
- A strategy for assembling the maize (Zea mays L.) genome (2004) (62)
- Parallel construction of multidimensional binary search trees (2000) (50)
- Scalable, memory efficient, high-speed IP lookup algorithms (2005) (49)
- A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans (2004) (48)
- Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome (2009) (47)
- Parallel de novo assembly of large genomes from high-throughput short reads (2010) (45)
- Parallel short sequence assembly of transcriptomes (2009) (43)
- Space and time efficient parallel algorithms and software for EST clustering (2002) (43)
- Efficient algorithms and software for detection of full-length LTR retrotransposons (2006) (43)
- Consensus Genetic Maps as Median Orders from Inconsistent Sources (2008) (43)
- PARALLEL-TCOFFEE: A parallel multiple sequence aligner (2007) (42)
- On the Complexity of Sequence to Graph Alignment (2019) (41)
- A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem (2016) (41)
- Assembling genomes on large-scale parallel computers (2006) (41)
- A random number generator for parallel computers (1992) (40)
- Parallel Information-Theory-Based Construction of Genome-Wide Gene Regulatory Networks (2010) (39)
- Greengard's N-Body Algorithm is not Order N (1996) (38)
- Reverse engineering and analysis of large genome-scale gene networks (2012) (38)
- A Scalable Parallel Fast Multipole Method for Analysis of Scattering from Perfect Electrically Conducting Surfaces (2002) (37)
- A greedy alignment-free distance estimator for phylogenetic inference (2015) (36)
- Handbook of Computational Molecular Biology (Chapman & All/Crc Computer and Information Science Series) (2005) (33)
- Repeat-aware modeling and correction of short read errors (2011) (33)
- Discovering Motifs in Biological Sequences Using the Micron Automata Processor (2016) (31)
- Accelerating Sequence Alignment to Graphs (2019) (31)
- High Performance Pattern Matching Using the Automata Processor (2016) (31)
- Two-Phase Analysis in Consensus Genetic Mapping (2012) (30)
- Parallel distributed memory construction of suffix and longest common prefix arrays (2015) (30)
- Parallel biological sequence alignments on the Cell Broadband Engine (2008) (29)
- High Performance Computing - HiPC 2007, 14th International Conference, Goa, India, December 18-21, 2007, Proceedings (2007) (28)
- Parallel Genomic Alignments on the Cell Broadband Engine (2009) (28)
- Efficient parallel algorithms and software for compressed octrees with applications to hierarchical methods (2001) (28)
- Real-time mapping of nanopore raw signals (2021) (28)
- High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries (2017) (27)
- Parallel suffix sorting (2001) (27)
- ALFRED: A Practical Method for Alignment-Free Distance Computation (2016) (27)
- Fast, parallel, GPU-based construction of space filling curves and octrees (2008) (26)
- Indexing for Subscription Covering in Publish-Subscribe Systems (2005) (26)
- A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications (2015) (26)
- A Formal Analysis of Space Filling Curves for Parallel Domain Decomposition (2006) (25)
- Parallel Metagenomic Sequence Clustering Via Sketching and Maximal Quasi-clique Enumeration on Map-Reduce Clouds (2011) (25)
- SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations (2016) (24)
- An optimal hierarchical clustering algorithm for gene expression data (2005) (23)
- Parallel Construction of Bidirected String Graphs for Genome Assembly (2008) (23)
- Lagged Fibonacci Random Number Generators for Distributed Memory Parallel Computers (1997) (23)
- Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems (2016) (23)
- Consensus genetic maps: a graph theoretic approach (2005) (22)
- Quadtrees and Octrees (2004) (22)
- An Adaptive Parallel Algorithm for Computing Connected Components (2016) (21)
- Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis (2018) (21)
- Parallel algorithms for tree accumulations (2005) (21)
- Dynamic Compressed Hypertoctrees with Application to the N-Body Problem (1999) (21)
- Practical algorithms for selection on coarse-grained parallel computers (1996) (21)
- Pairwise Sequence Alignments (2005) (21)
- Efficient Alignment Free Sequence Comparison with Bounded Mismatches (2015) (20)
- A provably optimal, distribution-independent parallel fast multipole method (2000) (20)
- Reply to: “Re-evaluating the evidence for a universal genetic boundary among microbial species” (2021) (19)
- Distribution-Independent Hierarchical Algorithms for the N-body Problem (1998) (18)
- Parallel globally optimal structure learning of Bayesian networks (2013) (18)
- Efficient Parallel Algorithms for Solvent Accessible Surface Area of Proteins (2002) (17)
- Space and time optimal parallel sequence alignments (2003) (17)
- Large-scale phylogenetic analysis on current HPC architectures (2008) (17)
- Parallel Bayesian network structure learning with application to gene networks (2012) (16)
- Optimizing High Performance Distributed Memory Parallel Hash Tables for DNA k-mer Counting (2018) (15)
- Algorithmic Techniques for Solving Graph Problems on the Automata Processor (2016) (15)
- Parallel information theory based construction of gene regulatory networks (2008) (15)
- Parallel Bayesian Network Structure Learning for Genome-Scale Gene Networks (2014) (15)
- Parallel Pairwise Correlation Computation on Intel Xeon Phi Clusters (2016) (14)
- Parallel methods for short read assembly (2009) (14)
- A parallel algorithm for exact Bayesian network inference (2009) (14)
- Parallel Framework for Dimensionality Reduction of Large-Scale Datasets (2015) (13)
- Accelerating Pairwise Computations on Cell Processors (2011) (13)
- Truly distribution-independent algorithms for the N-body problem (1994) (13)
- Fast alignment and preprocessing of chromatin profiles with Chromap (2021) (13)
- Parallel Mutual Information Based Construction of Whole-Genome Networks on the Intel (R) Xeon Phi (TM) Coprocessor (2014) (13)
- An SVM-based method for assessment of transcription factor-DNA complex models (2018) (12)
- Parallel Syntenic Alignments (2002) (12)
- Optimal Self-adjusting Trees for Dynamic String Data in Secondary Storage (2007) (12)
- Large-Scale metagenomic sequence Clustering on Map-Reduce Clusters (2013) (12)
- Concatenated parallelism: a technique for efficient parallel divide and conquer (1996) (12)
- Assembly of Large Genomes from Paired Short Reads (2009) (12)
- Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel®Xeon Phi™ Coprocessor (2015) (12)
- Mixed mode matrix multiplication (2002) (11)
- Parallel Discovery of Direct Causal Relations and Markov Boundaries with Applications to Gene Networks (2011) (11)
- Obtaining Provably Good Performance from Suffix Trees in Secondary Storage (2006) (11)
- An improved maximum likelihood formulation for accurate genome assembly (2011) (10)
- A Parallel Algorithm for Spectrum-based Short Read Error Correction (2012) (10)
- GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks (2022) (10)
- Parallel accelerated cartesian expansions for particle dynamics simulations (2009) (10)
- Efficient detection of viral transmissions with Next-Generation Sequencing data (2017) (10)
- All-pairs computations on many-core graphics processors (2013) (10)
- Cooperative neural networks (CoNN): Exploiting prior independence structure for improved classification (2019) (9)
- GRNUlar: Gene Regulatory Network reconstruction using Unrolled algorithm from Single Cell RNA-Sequencing data (2020) (9)
- Lookup Tables, Suffix Trees and Suffix Arrays (2006) (9)
- Fast and Accurate Construction of Ultra-Dense Consensus Genetic Maps Using Evolution Strategy Optimization (2015) (9)
- EnGRaiN: a supervised ensemble learning method for recovery of large-scale gene regulatory networks (2021) (9)
- High Performance Computing - HIPC 2007 (2008) (9)
- A Unifying Data Structure for Hierarchical Methods (1999) (8)
- A MapReduce Style Framework for Computations on Trees (2010) (8)
- Performance extraction and suitability analysis of multi- and many-core architectures for next generation sequencing secondary analysis (2018) (8)
- Exploring collective communications on a cluster of SMPs (2004) (7)
- Fast de Bruijn Graph Compaction in Distributed Memory Environments (2020) (7)
- Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories (2016) (7)
- Distribution-independent hierarchical N-body methods (1995) (7)
- Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons (2005) (7)
- A Special Issue of Journal of Parallel and Distributed Computing: Scalable Systems for Big Data Management and Analytics (2013) (7)
- Algorithms for Large-Scale Clustering and Assembly of Biological Sequence Data (2006) (6)
- A Parallel Algorithm for Bayesian Network Inference Using Arithmetic Circuits (2018) (6)
- Suffix Trees and Suffix Arrays (2018) (6)
- A variant selection framework for genome graphs (2021) (6)
- Space-conserving optimal DNA-protein alignment (2004) (6)
- Constructing Gene Regulatory Networks on Clusters of Cell Processors (2009) (6)
- Scalable, memory efficient, high-speed lookup and update algorithms for IP routing (2003) (6)
- Editorial: Special Section on High-Performance Computational Biology (2006) (6)
- Programming Techniques for the Automata Processor (2016) (6)
- Message from the workshop chairs (2010) (6)
- Validating Paired-end Read Alignments in Sequence Graphs (2019) (6)
- Tracking Nanostructural Evolution in Alloys: Large-Scale Analysis of Atom Probe Tomography Data on Blue Gene/L (2008) (5)
- Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems (2019) (5)
- Fast, Processor-Cardinality Agnostic PRNG with a Tracking Application (2008) (5)
- Parallel Construction of Suffix Trees and the All-Nearest-Smaller-Values Problem (2017) (5)
- In search of perfect reads (2014) (5)
- Parallel EST clustering (2002) (5)
- Parallel additive lagged Fibonacci random number generators (1996) (5)
- Identification of Significant Computational Building Blocks through Comprehensive Investigation of NGS Secondary Analysis Methods (2018) (5)
- LightScan: Faster Scan Primitive on CUDA Compatible Manycore Processors (2016) (4)
- A scalable parallelization of the gene duplication problem (2010) (4)
- Reprint of "A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications" (2017) (4)
- A tunable collective communication framework on a cluster of SMPS (2004) (4)
- Massively Parallel Searching for Better Algorithms or How to Do a Cross Product with Five Multiplications (1996) (3)
- Parallel Exact Dynamic Bayesian Network Structure Learning with Application to Gene Networks (2017) (3)
- Properties of Binomial Coefficients and Implications to Parallelizing Lagged Fibonacci Random Number Generators (1995) (3)
- A Parallel Algorithm for Exact Bayesian Structure Discovery in Bayesian Networks (2014) (3)
- Effective Utilization of Paired Reads to Improve Length and Accuracy of Contigs in Genome Assembly (2016) (3)
- Suffix Tree Applications in Computational Biology (2005) (3)
- Data Mining and Informatics for Quantitative Atom Probe Tomography (2009) (3)
- Text Indexing (2008) (3)
- Dtree: Dynamic Task Scheduling at Petascale (2015) (3)
- An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings (2016) (3)
- Parallelized Kendall's Tau Coefficient Computation via SIMD Vectorized Sorting On Many-Integrated-Core Processors (2017) (3)
- Evaluating High Performance Pattern Matching on the Automata Processor (2019) (3)
- Reverse Engineering Gene Networks: A Comparative Study at Genome-scale (2017) (3)
- Distributed enhanced suffix arrays: efficient algorithms for construction and querying (2019) (3)
- Subtle Issues of SIMD Tree Search (1993) (3)
- Efficient detection of viral transmission with threshold-based methods (2015) (3)
- Scalable, Memory Efficient, High-Speed (2005) (3)
- Computational systems biology (2010) (3)
- An Improved Model for Gene Cluster Inference (2010) (3)
- Fast sequence to graph alignment using the graph wavefront algorithm (2022) (3)
- The Complexity of Approximate Pattern Matching on De Bruijn Graphs (2022) (3)
- Spatial Domain Decomposition Methods in Parallel Scientific Computing (2007) (2)
- A Unified Model for Multi-genome Synteny and Gene Cluster Inference (2009) (2)
- Parallel Read Error Correction for Big Genomic Datasets (2015) (2)
- Editorial: Scalable Systems for Big Data Management and Analytics (2015) (2)
- Efficient Parallel Sparse Symmetric Tucker Decomposition for High-Order Tensors (2021) (2)
- Bulk Synchronous Parallelism (BSP) (2011) (2)
- An Algorithmic View on Multi-Related-Segments: A Unifying Model for Approximate Common Interval (2012) (2)
- Parallel Computational Biology (2006) (2)
- Random Number Generation for Parallel Computers (1993) (2)
- Suffix trees and suffix arrays in primary and secondary storage (2007) (2)
- Scientific Computing with Multicore and Accelerators (2010) (2)
- A massively parallel optimizer for expression evaluation (1993) (2)
- Haplotype-aware variant selection for genome graphs (2022) (2)
- Turning repeats to advantage: scaffolding genomic contigs using LTR retrotransposons. (2006) (2)
- Distributed Memory Partitioning of High-Throughput Sequencing Datasets for Enabling Parallel Genomics Analyses (2017) (2)
- A Parallel Algorithm for Exact Structure Learning of Bayesian Networks (2010) (2)
- Comparative Genomics: Algorithms and Applications (2010) (2)
- Contemporary Computing - Second International Conference, IC3 2009, Noida, India, August 17-19, 2009. Proceedings (2009) (2)
- High-performance computational biology (2008) (2)
- Efficient Methods for Database Storage and Retrieval Using Space-Filling Curves (2004) (2)
- Interval stabbing on the Automata Processor (2018) (2)
- A Parallel Framework for Constraint-Based Bayesian Network Learning via Markov Blanket Discovery (2020) (2)
- Information Theory Based Genome-Scale Gene Networks Construction Using MapReduce (2015) (2)
- Feasibility of Flow Decomposition with Subpath Constraints in Linear Time (2022) (2)
- Confidence assessment of protein-DNA complex models (2017) (1)
- Faster Computation of Genome Mappability (2018) (1)
- On the Hardness of Sequence Alignment on De Bruijn Graphs (2022) (1)
- Guest editors' introduction: selected papers from ACM-BCB 2013 (2015) (1)
- A Parallel Algorithm for Finding All Pairs κ-Mismatch Maximal Common Substrings (2016) (1)
- An Adaptive Parallel Algorithm for Computing Connectivity (2016) (1)
- Applications on emerging paradigms in parallel computing (2010) (1)
- ParBaum: Large-Scale Maximum Likelihood-Based Phylogenetic Analyses (2009) (1)
- Faster Computation of Genome Mappability with one Mismatch (2018) (1)
- SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models (2015) (1)
- High-performance Computing Methods for Computational Genomics (2006) (1)
- An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction (2018) (1)
- A greedy alignment-free distance estimator for phylogenetic inference (2017) (1)
- Parallel Interval Stabbing on the Automata Processor (2016) (1)
- Systems Biology, Network Inference in (2011) (1)
- A Memory and Time Scalable Parallelization of the Reptile Error-Correction Code (2016) (1)
- Parallel applications employing pairwise computations on emerging architectures (2010) (1)
- Genomes Galore: Big Data Challenges in the Life Sciences (2016) (1)
- Massively parallel searching for better algorithms (1992) (1)
- Computational biology on parallel computers (2003) (1)
- State Space Search (2011) (1)
- Large Scale Metagenomic Sequence Clustering via Sketching and Maximal Quasi-clique Enumeration on MapReduce Clusters (2012) (1)
- Practical Paralle1 Algorithm for Constructing Line Arrangements (1996) (1)
- Parallel machine learning approaches for reverse engineering genome-scale networks (2015) (0)
- Symposium Evening Tutorial: High-performance Computing Methods for Computational Genomics (2007) (0)
- Guest Editor's Introduction: Special issue on high-performance computational biology (2003) (0)
- Large-scale metagenomic clustering via quasi clique enumeration and read assignment ambiguity resolution (2013) (0)
- Resolving read assignment ambiguities in metagenomic clustering (2013) (0)
- Parallel Construction of k-d Trees and Related (1996) (0)
- Pairwise Computations on the Cell Processor (2010) (0)
- Workshop Introduction (2002) (0)
- Encyclopedia of Parallel Computing (2011) (0)
- Parallel Construction of Module Networks (2021) (0)
- 7th IEEE International Workshop on High Performance Computational Biology HiCOMB 2008 (2008) (0)
- 2009 Reviewer's List (2010) (0)
- Special Issue: High Performance Computational Biology (2004) (0)
- Supernode Partitioning (2011) (0)
- Special Issue: High Performance Computational Biology: Editorials (2004) (0)
- experimental verification of predicted genes Quality assessment of maize assembled genomic islands ( MAGIs ) and large-scale (2005) (0)
- Sequential and parallel algorithms for all-pair k-mismatch maximal common substrings (2020) (0)
- Parallel Assembly of Large Genomes from Paired Short Reads (2010 JGI/ANL HPC Workshop) (2010) (0)
- Big data in life sciences and public health (2015) (0)
- Ismb/eccb 2019 Proceedings Papers Committee (2019) (0)
- Program Committee (2005) (0)
- The Combinatorics of Sequencing the Corn Genome (2007) (0)
- ParRefCom: Parallel Reference-based Compression of Paired-end Genomics Read Datasets (2019) (0)
- Parallel and Scalable Combinatorial String and Graph Algorithms on Distributed Memory Systems (2018) (0)
- Bsp (2020) (0)
- Invited talk: Automata processor and its applications in bioinformatics (2014) (0)
- Contemporary Computing - 4th International Conference, IC3 2011, Noida, India, August 8-10, 2011. Proceedings (2011) (0)
- Introduction to HiCOMB 2018 (2018) (0)
- Workshop: Taxonomic clustering of large-scale metagnomic data (2012) (0)
- HiCOMB Introduction (2011) (0)
- Workshop: Flexible read decomposition for improved short read error correction (2011) (0)
- MCPNet : A parallel maximum capacity-based genome-scale gene network construction framework (2022) (0)
- HiCOMB Introduction and Committees (2014) (0)
- Proceedings of the 14th international conference on High performance computing (2007) (0)
- Algorithms for large-scale problems in computational biology (2002) (0)
- HiCOMB Introduction (2013) (0)
- HiPCoMB-2005 Reviewers (2005) (0)
- The Complexity of Approximate Pattern Matching (2022) (0)
- A Parallel Monte Carlo Algorithm for Protein Accessible Surface Area Computation (1999) (0)
- A Practical Parallel Algorithm for Line Segment Visibility (1999) (0)
- 6th IEEE International Workshop on High Performance Computational Biology HiCOMB 2007 (2007) (0)
- University of Birmingham Blockchain application in remote condition monitoring (2020) (0)
- Integrated Caller for Germline and Somatic SNV s Based on Bayesian Models (2015) (0)
- Data Infrastructure for Materials and Advanced Manufacturing Workshop : Welcome Address (2016) (0)
- HiCOMB Introduction and Committees (2015) (0)
- Sparse Symmetric Format for Tucker Decomposition (2023) (0)
- Invited: Reverse engineering whole-genome networks (2012) (0)
- Parallel methods for large-scale applications in computational electromagnetics and materials science (2007) (0)
- Distribution independent spatial data structures and algorithms with applications (2000) (0)
- Large-scale methods in computational genomics (2006) (0)
- Computing Methods for Computational Genomics (2006) (0)
- Editorial: From the New Editor-in-Chief (2021) (0)
- Communication-aware Parallel Domain Decomposition using Space Filling Curves (2006) (0)
- ParRefCom (2019) (0)
- Solving Linear Systems on Linear Processor Arrays Using a ∗-Semiring Based Algorithm (2004) (0)
- Special-Purpose Machines (2011) (0)
- Efficient detection of viral transmissions with Next-Generation Sequencing data (2017) (0)
- Parallel Algorithms for Alignments on the Cell BE (2010) (0)
- Organizing & Program Committees (2007) (0)
- Under review for IEEE Transactions on Parallel and Distributed Systems Parallel Construction of Multidimensional Binary Search Trees (2007) (0)
- Massively parallel expressed sequence tag clustering (2007) (0)
- Server Farm (2011) (0)
- Probabilistic estimation of overlap graphs for large sequence datasets (2017) (0)
- An SVM-based method for assessment of transcription factor-DNA complex models (2018) (0)
- Computation of Evolutionary Change Table of Contents Chapter 4. a Framework for Evaluation of Differenc- List of Tables List of Figures (2009) (0)
- Assembly and analysis of complex plant genomes (2007) (0)
- Modeling and Analysis of Gene Networks Using Feedback Control Theory (2005) (0)

This paper list is powered by the following services:

## Other Resources About Srinivas Aluru

## What Schools Are Affiliated With Srinivas Aluru?

Srinivas Aluru is affiliated with the following schools: