Srinivas Aluru

ORCID

Publication Activity (10 Years)

Years Active: 1992-2024
Publications (10 Years): 94

Top Venues

CoRR

IPDPS

BCB

Publications

Neda Tavakoli, Daniel Gibney, Srinivas Aluru
GraphSlimmer: Preserving Read Mappability with the Minimum Number of Variants. J. Comput. Biol. 31 (7) (2024)
Shruti Shivakumar, Jiajia Li, Ramakrishnan Kannan, Srinivas Aluru
Sparse Symmetric Format for Tucker Decomposition. IEEE Trans. Parallel Distributed Syst. 34 (6) (2023)
Shruti Shivakumar, Ilya Amburg, Sinan G. Aksoy, Jiajia Li, Stephen J. Young, Srinivas Aluru
Fast Parallel Tensor Times Same Vector for Hypergraphs. HiPC (2023)
Shruti Shivakumar, Ilya Amburg, Sinan G. Aksoy, Jiajia Li, Stephen J. Young, Srinivas Aluru
Fast Parallel Tensor Times Same Vector for Hypergraphs. CoRR (2023)
Ankit Srivastava, Sriram P. Chockalingam, Srinivas Aluru
A Parallel Framework for Constraint-Based Bayesian Network Learning via Markov Blanket Discovery. IEEE Trans. Parallel Distributed Syst. 34 (6) (2023)
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
The Complexity of Approximate Pattern Matching on de Bruijn Graphs. RECOMB (2022)
Neda Tavakoli, Daniel Gibney, Srinivas Aluru
Haplotype-aware variant selection for genome graphs. BCB (2022)
Harsh Shrivastava, Xiuwei Zhang, Le Song, Srinivas Aluru
GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks. J. Comput. Biol. 29 (1) (2022)
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
On the Hardness of Sequence Alignment on De Bruijn Graphs. J. Comput. Biol. 29 (12) (2022)
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
The Complexity of Approximate Pattern Matching on De Bruijn Graphs. CoRR (2022)
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
Feasibility of Flow Decomposition with Subpath Constraints in Linear Time. WABI (2022)
Maneesha Aluru, Harsh Shrivastava, Sriram P. Chockalingam, Shruti Shivakumar, Srinivas Aluru
EnGRaiN: a supervised ensemble learning method for recovery of large-scale gene regulatory networks. Bioinform. 38 (5) (2022)
Ankit Srivastava, Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru
Parallel construction of module networks. SC (2021)
Srinivas Aluru
Editorial: From the New Editor-in-Chief. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (6) (2021)
Shruti Shivakumar, Jiajia Li, Ramakrishnan Kannan, Srinivas Aluru
Efficient Parallel Sparse Symmetric Tucker Decomposition for High-Order Tensors. ACDA (2021)
Haowen Zhang, Haoran Li, Chirag Jain, Haoyu Cheng, Kin Fai Au, Heng Li, Srinivas Aluru
Real-time mapping of nanopore raw signals. Bioinform. 37 (Supplement) (2021)
Chirag Jain, Neda Tavakoli, Srinivas Aluru
A variant selection framework for genome graphs. Bioinform. 37 (Supplement) (2021)
Sriram P. Chockalingam, Jodh Pannu, Sahar Hooshmand, Sharma V. Thankachan, Srinivas Aluru
An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction. BMC Bioinform. (6) (2020)
Indranil Roy, Ankit Srivastava, Matt Grimm, Srinivas Aluru
Interval stabbing on the Automata Processor. J. Parallel Distributed Comput. 135 (2020)
Ankit Srivastava, Sriram P. Chockalingam, Srinivas Aluru
A parallel framework for constraint-based bayesian network learning via markov blanket discovery. SC (2020)
Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru
On the Complexity of Sequence-to-Graph Alignment. J. Comput. Biol. 27 (4) (2020)
Tony Pan, Rahul Nihalani, Srinivas Aluru
Fast de Bruijn Graph Compaction in Distributed Memory Environments. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (1) (2020)
Harsh Shrivastava, Xinshi Chen, Binghong Chen, Guanghui Lan, Srinivas Aluru, Han Liu, Le Song
GLAD: Learning Sparse Graph Recovery. ICLR (2020)
Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru
Sequential and parallel algorithms for all-pair k-mismatch maximal common substrings. J. Parallel Distributed Comput. 144 (2020)
Chirag Jain, Sanchit Misra, Haowen Zhang, Alexander T. Dilthey, Srinivas Aluru
Accelerating Sequence Alignment to Graphs. IPDPS (2019)
Chirag Jain, Haowen Zhang, Alexander T. Dilthey, Srinivas Aluru
Validating Paired-End Read Alignments in Sequence Graphs. WABI (2019)
Patrick Flick, Srinivas Aluru
Distributed enhanced suffix arrays: efficient algorithms for construction and querying. SC (2019)
Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru
On the Complexity of Sequence to Graph Alignment. RECOMB (2019)
Nagakishore Jammula, Srinivas Aluru
ParRefCom: Parallel Reference-based Compression of Paired-end Genomics Read Datasets. BCB (2019)
Indranil Roy, Ankit Srivastava, Matt Grimm, Marziyeh Nourian, Michela Becchi, Srinivas Aluru
Evaluating High Performance Pattern Matching on the Automata Processor. IEEE Trans. Computers 68 (8) (2019)
Harsh Shrivastava, Eugene Bart, Bob Price, Hanjun Dai, Bo Dai, Srinivas Aluru
Cooperative neural networks (CoNN): Exploiting prior independence structure for improved classification. CoRR (2019)
Md. Vasimuddin, Sanchit Misra, Heng Li, Srinivas Aluru
Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IPDPS (2019)
Md. Vasimuddin, Sanchit Misra, Heng Li, Srinivas Aluru
Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. CoRR (2019)
Tony Pan, Patrick Flick, Chirag Jain, Yongchao Liu, Srinivas Aluru
Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (4) (2019)
Harsh Shrivastava, Xinshi Chen, Binghong Chen, Guanghui Lan, Srinivas Aluru, Le Song
GLAD: Learning Sparse Graph Recovery. CoRR (2019)
Jodh Pannu, Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru
An Alignment-free Heuristic for Fast Sequence Comparisons with Applications to Phylogeny Reconstruction. BCB (2018)
Rosario I. Corona, Sanjana Sudarshan, Srinivas Aluru, Jun-tao Guo
An SVM-based method for assessment of transcription factor-DNA complex models. BMC Bioinform. (20) (2018)
Srinivas Aluru, David A. Bader, Paul Medvedev
Introduction to HiCOMB 2018. IPDPS Workshops (2018)
Sahar Hooshmand, Paniz Abedin, Daniel Gibney, Srinivas Aluru, Sharma V. Thankachan
Faster Computation of Genome Mappability. BCB (2018)
Harsh Shrivastava, Eugene Bart, Bob Price, Hanjun Dai, Bo Dai, Srinivas Aluru
Cooperative neural networks (CoNN): Exploiting prior independence structure for improved classification. NeurIPS (2018)
Md. Vasimuddin, Sriram P. Chockalingam, Srinivas Aluru
A Parallel Algorithm for Bayesian Network Inference Using Arithmetic Circuits. IPDPS (2018)
Chirag Jain, Sergey Koren, Alexander T. Dilthey, Adam M. Phillippy, Srinivas Aluru
A fast adaptive algorithm for computing whole-genome homology maps. Bioinform. 34 (17) (2018)
Sahar Hooshmand, Paniz Abedin, Daniel Gibney, Srinivas Aluru, Sharma V. Thankachan
Faster Computation of Genome Mappability with one Mismatch. ICCABS (2018)
Chirag Jain, Alexander T. Dilthey, Sergey Koren, Srinivas Aluru, Adam M. Phillippy
A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases. J. Comput. Biol. 25 (7) (2018)
Sharma V. Thankachan, Chaitanya Aluru, Sriram P. Chockalingam, Srinivas Aluru
Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis. RECOMB (2018)
Tony C. Pan, Sanchit Misra, Srinivas Aluru
-mer counting. SC (2018)
Sanchit Misra, Tony C. Pan, Kanak Mahadik, George Powley, Priya N. Vaidya, Md. Vasimuddin, Srinivas Aluru
Performance extraction and suitability analysis of multi- and many-core architectures for next generation sequencing secondary analysis. PACT (2018)
Yongchao Liu, Tony Pan, Oded Green, Srinivas Aluru
Parallelized Kendall's Tau Coefficient Computation via SIMD Vectorized Sorting On Many-Integrated-Core Processors. CoRR (2017)
Rosario I. Corona, Sanjana Sudarshan, Jun-tao Guo, Srinivas Aluru
Confidence assessment of protein-DNA complex models. BIBM (2017)
Sriram P. Chockalingam, Maneesha Aluru, Hongqing Guo, Yanhai Yin, Srinivas Aluru
Reverse Engineering Gene Networks: A Comparative Study at Genome-scale. BCB (2017)
Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Ambujam Krishnan, Srinivas Aluru
A greedy alignment-free distance estimator for phylogenetic inference. BMC Bioinform. 18 (8) (2017)
Nagakishore Jammula, Sriram P. Chockalingam, Srinivas Aluru
Distributed Memory Partitioning of High-Throughput Sequencing Datasets for Enabling Parallel Genomics Analyses. BCB (2017)
Patrick Flick, Chirag Jain, Tony Pan, Srinivas Aluru
Reprint of "A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications". Parallel Comput. 70 (2017)
Chirag Jain, Alexander T. Dilthey, Sergey Koren, Srinivas Aluru, Adam M. Phillippy
A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases. RECOMB (2017)
Md. Vasimuddin, Srinivas Aluru
Parallel Exact Dynamic Bayesian Network Structure Learning with Application to Gene Networks. HiPC (2017)
Patrick Flick, Srinivas Aluru
Parallel Construction of Suffix Trees and the All-Nearest-Smaller-Values Problem. IPDPS (2017)
Chirag Jain, Patrick Flick, Tony Pan, Oded Green, Srinivas Aluru
An Adaptive Parallel Algorithm for Computing Connected Components. IEEE Trans. Parallel Distributed Syst. 28 (9) (2017)
Rahul Nihalani, Sriram P. Chockalingam, Shaowei Zhu, Vijay V. Vazirani, Srinivas Aluru
Probabilistic estimation of overlap graphs for large sequence datasets. BIBM (2017)
Tony Pan, Patrick Flick, Chirag Jain, Yongchao Liu, Srinivas Aluru
Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems. BCB (2016)
Srinivas Aluru, David A. Bader, Ananth Kalyanaraman, Jaroslaw Zola
HiCOMB Introduction and Committees. IPDPS Workshops (2016)
Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Alberto Apostolico, Srinivas Aluru
ALFRED: A Practical Method for Alignment-Free Distance Computation. J. Comput. Biol. 23 (6) (2016)
Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt
SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations. BMC Syst. Biol. 10 (S-2) (2016)
Indranil Roy, Nagakishore Jammula, Srinivas Aluru
Algorithmic Techniques for Solving Graph Problems on the Automata Processor. IPDPS (2016)
Chirag Jain, Patrick Flick, Tony Pan, Oded Green, Srinivas Aluru
An Adaptive Parallel Algorithm for Computing Connectivity. CoRR (2016)
Srinivas Aluru
Genomes Galore: Big Data Challenges in the Life Sciences. HiPC (2016)
Indranil Roy, Srinivas Aluru
Discovering Motifs in Biological Sequences Using the Micron Automata Processor. IEEE ACM Trans. Comput. Biol. Bioinform. 13 (1) (2016)
Indranil Roy, Ankit Srivastava, Matt Grimm, Srinivas Aluru
Parallel Interval Stabbing on the Automata Processor. IA3@SC (2016)
Sharma V. Thankachan, Alberto Apostolico, Srinivas Aluru
-Mismatch Average Common Substring Problem. J. Comput. Biol. 23 (6) (2016)
Indranil Roy, Ankit Srivastava, Marziyeh Nourian, Michela Becchi, Srinivas Aluru
High Performance Pattern Matching Using the Automata Processor. IPDPS (2016)
Indranil Roy, Ankit Srivastava, Srinivas Aluru
Programming Techniques for the Automata Processor. ICPP (2016)
Yongchao Liu, Tony Pan, Srinivas Aluru
Parallel Pairwise Correlation Computation on Intel Xeon Phi Clusters. SBAC-PAD (2016)
Rahul Nihalani, Srinivas Aluru
Effective Utilization of Paired Reads to Improve Length and Accuracy of Contigs in Genome Assembly. BCB (2016)
Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru
-mismatch maximal common substrings. SC (2016)
Yongchao Liu, Srinivas Aluru
LightScan: Faster Scan Primitive on CUDA Compatible Manycore Processors. CoRR (2016)
Sharma V. Thankachan, Sriram P. Chockalingam, Srinivas Aluru
An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings. ISBRA (2016)
Vipin Sachdeva, Srinivas Aluru, David A. Bader
A Memory and Time Scalable Parallelization of the Reptile Error-Correction Code. IPDPS Workshops (2016)
Yongchao Liu, Tony Pan, Srinivas Aluru
Parallel Pairwise Correlation Computation On Intel Xeon Phi Clusters. CoRR (2016)
Srinivas Aluru
Big data in life sciences and public health. HiPC Workshops (2015)
Nagakishore Jammula, Sriram P. Chockalingam, Srinivas Aluru
Parallel Read Error Correction for Big Genomic Datasets. HiPC (2015)
Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt
SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models. BIBM (2015)
Srinivas Aluru, Donna K. Slonim
Guest Editors' Introduction: Selected Papers from ACM-BCB 2013. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (1) (2015)
Soumitra Pal, Srinivas Aluru
In search of perfect reads. BMC Bioinform. 16 (S17) (2015)
Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Ambujam Krishnan, Srinivas Aluru
A greedy alignment-free distance estimator for phylogenetic inference (extended abstract). ICCABS (2015)
Patrick Flick, Srinivas Aluru
Parallel distributed memory construction of suffix and longest common prefix arrays. SC (2015)
Inna Rytsareva, Seth Sims, Sriram P. Chockalingam, Srinivas Aluru, David S. Campo, Cansu Tetik, Sharma V. Thankachan, Yury Khudyakov, Yueli Zheng, Chirag Jain, Amanda Sue
Efficient detection of viral transmission with threshold-based methods. ICCABS (2015)
Srinivas Aluru, Alberto Apostolico, Sharma V. Thankachan
Efficient Alignment Free Sequence Comparison with Bounded Mismatches. RECOMB (2015)
Sanchit Misra, Kiran Pamnany, Srinivas Aluru
Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel®Xeon Phi™ Coprocessor. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (5) (2015)
Sai Kiranmayee Samudrala, Jaroslaw Zola, Srinivas Aluru, Baskar Ganapathysubramanian
Parallel Framework for Dimensionality Reduction of Large-Scale Datasets. Sci. Program. 2015 (2015)
Sanguthevar Rajasekaran, Srinivas Aluru, David A. Bader
HiCOMB Introduction and Committees. IPDPS Workshops (2015)
Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru
Information Theory Based Genome-Scale Gene Networks Construction Using MapReduce. HiPC (2015)
Srinivas Aluru
Parallel machine learning approaches for reverse engineering genome-scale networks. BIBM (2015)
Kiran Pamnany, Sanchit Misra, Md. Vasimuddin, Xing Liu, Edmond Chow, Srinivas Aluru
Dtree: Dynamic Task Scheduling at Petascale. ISC (2015)
Patrick Flick, Chirag Jain, Tony Pan, Srinivas Aluru
A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications. SC (2015)
Srinivas Aluru, Yogesh Simmhan
Editorial: Scalable Systems for Big Data Management and Analytics. J. Parallel Distributed Comput. (2015)
Yetian Chen, Jin Tian, Olga Nikolova, Srinivas Aluru
A Parallel Algorithm for Exact Bayesian Structure Discovery in Bayesian Networks. CoRR (2014)
Alba Cristina Magalhaes Alves de Melo, Srinivas Aluru, David A. Bader
HiCOMB Introduction and Committees. IPDPS Workshops (2014)
Sanchit Misra, Md. Vasimuddin, Kiran Pamnany, Sriram P. Chockalingam, Yong Dong, Min Xie, Maneesha R. Aluru, Srinivas Aluru
Parallel Bayesian Network Structure Learning for Genome-Scale Gene Networks. SC (2014)
Indranil Roy, Srinivas Aluru
Finding Motifs in Biological Sequences Using the Micron Automata Processor. IPDPS (2014)
Srinivas Aluru, Nagakishore Jammula
A Review of Hardware Acceleration for Computational Genomics. IEEE Des. Test 31 (1) (2014)
Sanchit Misra, Kiran Pamnany, Srinivas Aluru
Parallel Mutual Information Based Construction of Whole-Genome Networks on the Intel (R) Xeon Phi (TM) Coprocessor. IPDPS (2014)

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Publication Activity (10 Years)

Top Topics

Top Venues

Srinivas Aluru