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ORCIDSrinivas Aluru
Person information
- affiliation: Georgia Institute of Technology, Atlanta, GA, USA
- affiliation (1999 - 2013): Iowa State University, Ames, Iowa, USA
- affiliation (1996 - 1999): New Mexico State University, Las Cruces, NM, USA
- affiliation (1994 - 1996): Syracuse University, NY, USA
- affiliation (former): Indian Institute of Technology, Madras, India
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2020 – today
- 2024
[j69]Neda Tavakoli
, Daniel Gibney, Srinivas Aluru:
GraphSlimmer: Preserving Read Mappability with the Minimum Number of Variants. J. Comput. Biol. 31(7): 616-637 (2024)- 2023
- [j68]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): 1699-1715 (2023) - [j67]Shruti Shivakumar, Jiajia Li, Ramakrishnan Kannan, Srinivas Aluru:
Sparse Symmetric Format for Tucker Decomposition. IEEE Trans. Parallel Distributed Syst. 34(6): 1743-1756 (2023) - [c130]Shruti Shivakumar, Ilya Amburg, Sinan G. Aksoy, Jiajia Li, Stephen J. Young, Srinivas Aluru:
Fast Parallel Tensor Times Same Vector for Hypergraphs. HiPC 2023: 324-334 - [i10]Shruti Shivakumar, Ilya Amburg, Sinan G. Aksoy, Jiajia Li, Stephen J. Young, Srinivas Aluru:
Fast Parallel Tensor Times Same Vector for Hypergraphs. CoRR abs/2311.08595 (2023) - 2022
- [j66]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): 1312-1319 (2022) - [j65]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): 27-44 (2022) - [j64]Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru:
On the Hardness of Sequence Alignment on De Bruijn Graphs. J. Comput. Biol. 29(12): 1377-1396 (2022) - [c129]Neda Tavakoli, Daniel Gibney, Srinivas Aluru:
Haplotype-aware variant selection for genome graphs. BCB 2022: 51:1-51:9 - [c128]Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru:
The Complexity of Approximate Pattern Matching on de Bruijn Graphs. RECOMB 2022: 263-278 - [c127]Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru:
Feasibility of Flow Decomposition with Subpath Constraints in Linear Time. WABI 2022: 17:1-17:16 - [e8]Donald A. Adjeroh, Qi Long, Xinghua Mindy Shi, Fei Guo, Xiaohua Hu, Srinivas Aluru, Giri Narasimhan, Jianxin Wang, Mingon Kang, Ananda Mondal, Jin Liu:
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022, Las Vegas, NV, USA, December 6-8, 2022. IEEE 2022, ISBN 978-1-6654-6819-0 [contents] - [i9]Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru:
The Complexity of Approximate Pattern Matching on De Bruijn Graphs. CoRR abs/2201.12454 (2022) - 2021
- [j63]Chirag Jain, Neda Tavakoli, Srinivas Aluru:
A variant selection framework for genome graphs. Bioinform. 37(Supplement): 460-467 (2021) - [j62]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): 477-483 (2021) - [j61]Srinivas Aluru:
Editorial: From the New Editor-in-Chief. IEEE ACM Trans. Comput. Biol. Bioinform. 18(6): 2058 (2021) - [c126]Shruti Shivakumar, Jiajia Li, Ramakrishnan Kannan, Srinivas Aluru:
Efficient Parallel Sparse Symmetric Tucker Decomposition for High-Order Tensors. ACDA 2021: 193-204 - [c125]Ankit Srivastava, Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru:
Parallel construction of module networks. SC 2021: 26 - 2020
- [j60]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. 21-S(6): 404 (2020) - [j59]Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru:
On the Complexity of Sequence-to-Graph Alignment. J. Comput. Biol. 27(4): 640-654 (2020) - [j58]Indranil Roy, Ankit Srivastava, Matt Grimm, Srinivas Aluru:
Interval stabbing on the Automata Processor. J. Parallel Distributed Comput. 135: 234-245 (2020) - [j57]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: 68-79 (2020) - [j56]Tony Pan, Rahul Nihalani, Srinivas Aluru:
Fast de Bruijn Graph Compaction in Distributed Memory Environments. IEEE ACM Trans. Comput. Biol. Bioinform. 17(1): 136-148 (2020) - [c124]Harsh Shrivastava, Xinshi Chen, Binghong Chen, Guanghui Lan, Srinivas Aluru, Han Liu, Le Song:
GLAD: Learning Sparse Graph Recovery. ICLR 2020 - [c123]Ankit Srivastava, Sriram P. Chockalingam, Srinivas Aluru:
A parallel framework for constraint-based bayesian network learning via markov blanket discovery. SC 2020: 7 - [e7]Xintao Wu, Chris Jermaine, Li Xiong, Xiaohua Hu, Olivera Kotevska, Siyuan Lu, Weija Xu, Srinivas Aluru, Chengxiang Zhai, Eyhab Al-Masri, Zhiyuan Chen, Jeff Saltz:
2020 IEEE International Conference on Big Data (IEEE BigData 2020), Atlanta, GA, USA, December 10-13, 2020. IEEE 2020, ISBN 978-1-7281-6251-5 [contents]
2010 – 2019
- 2019
- [j55]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): 1201-1212 (2019) - [j54]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): 1117-1131 (2019) - [c122]Nagakishore Jammula, Srinivas Aluru:
ParRefCom: Parallel Reference-based Compression of Paired-end Genomics Read Datasets. BCB 2019: 447-456 - [c121]Md. Vasimuddin, Sanchit Misra, Heng Li, Srinivas Aluru:
Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IPDPS 2019: 314-324 - [c120]Chirag Jain, Sanchit Misra, Haowen Zhang, Alexander T. Dilthey, Srinivas Aluru:
Accelerating Sequence Alignment to Graphs. IPDPS 2019: 451-461 - [c119]Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru:
On the Complexity of Sequence to Graph Alignment. RECOMB 2019: 85-100 - [c118]Patrick Flick, Srinivas Aluru:
Distributed enhanced suffix arrays: efficient algorithms for construction and querying. SC 2019: 72:1-72:17 - [c117]Chirag Jain, Haowen Zhang, Alexander T. Dilthey, Srinivas Aluru:
Validating Paired-End Read Alignments in Sequence Graphs. WABI 2019: 17:1-17:13 - [i8]Harsh Shrivastava, Xinshi Chen, Binghong Chen, Guanghui Lan, Srinivas Aluru, Le Song:
GLAD: Learning Sparse Graph Recovery. CoRR abs/1906.00271 (2019) - [i7]Harsh Shrivastava, Eugene Bart, Bob Price, Hanjun Dai, Bo Dai, Srinivas Aluru:
Cooperative neural networks (CoNN): Exploiting prior independence structure for improved classification. CoRR abs/1906.00291 (2019) - [i6]Md. Vasimuddin, Sanchit Misra, Heng Li, Srinivas Aluru:
Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. CoRR abs/1907.12931 (2019) - 2018
- [j53]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): i748-i756 (2018) - [j52]Rosario I. Corona, Sanjana Sudarshan, Srinivas Aluru, Jun-tao Guo:
An SVM-based method for assessment of transcription factor-DNA complex models. BMC Bioinform. 19-S(20): 49-57 (2018) - [j51]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): 766-779 (2018) - [c116]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: 3:1-3:14 - [c115]Sahar Hooshmand, Paniz Abedin, Daniel Gibney, Srinivas Aluru, Sharma V. Thankachan:
Faster Computation of Genome Mappability. BCB 2018: 537 - [c114]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: 540 - [c113]Sahar Hooshmand, Paniz Abedin, Daniel Gibney, Srinivas Aluru, Sharma V. Thankachan:
Faster Computation of Genome Mappability with one Mismatch. ICCABS 2018: 1 - [c112]Md. Vasimuddin, Sriram P. Chockalingam, Srinivas Aluru:
A Parallel Algorithm for Bayesian Network Inference Using Arithmetic Circuits. IPDPS 2018: 34-43 - [c111]Srinivas Aluru, David A. Bader, Paul Medvedev:
Introduction to HiCOMB 2018. IPDPS Workshops 2018: 226 - [c110]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: 4130-4140 - [c109]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: 211-224 - [c108]Tony C. Pan, Sanchit Misra, Srinivas Aluru:
Optimizing high performance distributed memory parallel hash tables for DNA k-mer counting. SC 2018: 11:1-11:13 - [e6]Srinivas Aluru, Ananth Kalyanaraman, Debajyoti Bera, Kishore Kothapalli, David Abramson, Ilkay Altintas, Sanjukta Bhowmick, Madhu Govindaraju, Smruti Ranjan Sarangi, Sushil K. Prasad, Steven Bogaerts, Vikas Saxena, Sanjay Goel:
2018 Eleventh International Conference on Contemporary Computing, IC3 2018, Noida, India, August 2-4, 2018. IEEE Computer Society 2018, ISBN 978-1-5386-6834-4 [contents] - 2017
- [j50]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): 238:1-238:8 (2017) - [j49]Patrick Flick, Chirag Jain, Tony Pan, Srinivas Aluru:
Reprint of "A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications". Parallel Comput. 70: 54-65 (2017) - [j48]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): 2428-2439 (2017) - [c107]Nagakishore Jammula, Sriram P. Chockalingam, Srinivas Aluru:
Distributed Memory Partitioning of High-Throughput Sequencing Datasets for Enabling Parallel Genomics Analyses. BCB 2017: 417-424 - [c106]Sriram P. Chockalingam, Maneesha Aluru, Hongqing Guo, Yanhai Yin, Srinivas Aluru:
Reverse Engineering Gene Networks: A Comparative Study at Genome-scale. BCB 2017: 480-490 - [c105]Rosario I. Corona, Sanjana Sudarshan, Jun-tao Guo, Srinivas Aluru:
Confidence assessment of protein-DNA complex models. BIBM 2017: 9-15 - [c104]Rahul Nihalani, Sriram P. Chockalingam, Shaowei Zhu, Vijay V. Vazirani, Srinivas Aluru:
Probabilistic estimation of overlap graphs for large sequence datasets. BIBM 2017: 247-252 - [c103]Md. Vasimuddin, Srinivas Aluru:
Parallel Exact Dynamic Bayesian Network Structure Learning with Application to Gene Networks. HiPC 2017: 42-51 - [c102]Patrick Flick, Srinivas Aluru:
Parallel Construction of Suffix Trees and the All-Nearest-Smaller-Values Problem. IPDPS 2017: 12-21 - [c101]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: 66-81 - [e5]Vijay Raghavan, Srinivas Aluru, George Karypis, Lucio Miele, Xindong Wu:
2017 IEEE International Conference on Data Mining, ICDM 2017, New Orleans, LA, USA, November 18-21, 2017. IEEE Computer Society 2017, ISBN 978-1-5386-3835-4 [contents] - [e4]Raju Gottumukkala, Xia Ning, Guozhu Dong, Vijay Raghavan, Srinivas Aluru, George Karypis, Lucio Miele, Xindong Wu:
2017 IEEE International Conference on Data Mining Workshops, ICDM Workshops 2017, New Orleans, LA, USA, November 18-21, 2017. IEEE Computer Society 2017, ISBN 978-1-5386-3800-2 [contents] - [i5]Yongchao Liu, Tony Pan, Oded Green, Srinivas Aluru:
Parallelized Kendall's Tau Coefficient Computation via SIMD Vectorized Sorting On Many-Integrated-Core Processors. CoRR abs/1704.03767 (2017) - 2016
- [j47]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): 47 (2016) - [j46]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): 452-460 (2016) - [j45]Sharma V. Thankachan, Alberto Apostolico, Srinivas Aluru:
A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem. J. Comput. Biol. 23(6): 472-482 (2016) - [j44]Indranil Roy, Srinivas Aluru:
Discovering Motifs in Biological Sequences Using the Micron Automata Processor. IEEE ACM Trans. Comput. Biol. Bioinform. 13(1): 99-111 (2016) - [c100]Rahul Nihalani, Srinivas Aluru:
Effective Utilization of Paired Reads to Improve Length and Accuracy of Contigs in Genome Assembly. BCB 2016: 355-363 - [c99]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: 422-433 - [c98]Srinivas Aluru:
Genomes Galore: Big Data Challenges in the Life Sciences. HiPC 2016: 1 - [c97]Indranil Roy, Ankit Srivastava, Srinivas Aluru:
Programming Techniques for the Automata Processor. ICPP 2016: 205-210 - [c96]Indranil Roy, Nagakishore Jammula, Srinivas Aluru:
Algorithmic Techniques for Solving Graph Problems on the Automata Processor. IPDPS 2016: 283-292 - [c95]Srinivas Aluru, David A. Bader, Ananth Kalyanaraman, Jaroslaw Zola:
HiCOMB Introduction and Committees. IPDPS Workshops 2016: 407 - [c94]Vipin Sachdeva, Srinivas Aluru, David A. Bader:
A Memory and Time Scalable Parallelization of the Reptile Error-Correction Code. IPDPS Workshops 2016: 453-462 - [c93]Indranil Roy, Ankit Srivastava, Marziyeh Nourian, Michela Becchi, Srinivas Aluru:
High Performance Pattern Matching Using the Automata Processor. IPDPS 2016: 1123-1132 - [c92]Sharma V. Thankachan, Sriram P. Chockalingam, Srinivas Aluru:
An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings. ISBRA 2016: 3-14 - [c91]Yongchao Liu, Tony Pan, Srinivas Aluru:
Parallel Pairwise Correlation Computation on Intel Xeon Phi Clusters. SBAC-PAD 2016: 141-149 - [c90]Indranil Roy, Ankit Srivastava, Matt Grimm, Srinivas Aluru:
Parallel Interval Stabbing on the Automata Processor. IA3@SC 2016: 10-17 - [c89]Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru:
A parallel algorithm for finding all pairs k-mismatch maximal common substrings. SC 2016: 784-794 - [r7]Srinivas Aluru:
Text Indexing. Encyclopedia of Algorithms 2016: 2226-2231 - [i4]Yongchao Liu, Srinivas Aluru:
LightScan: Faster Scan Primitive on CUDA Compatible Manycore Processors. CoRR abs/1604.04815 (2016) - [i3]Yongchao Liu, Tony Pan, Srinivas Aluru:
Parallel Pairwise Correlation Computation On Intel Xeon Phi Clusters. CoRR abs/1605.01584 (2016) - [i2]Chirag Jain, Patrick Flick, Tony Pan, Oded Green, Srinivas Aluru:
An Adaptive Parallel Algorithm for Computing Connectivity. CoRR abs/1607.06156 (2016) - 2015
- [j43]Soumitra Pal, Srinivas Aluru:
In search of perfect reads. BMC Bioinform. 16(S17): S7 (2015) - [j42]Srinivas Aluru, Yogesh Simmhan:
Editorial: Scalable Systems for Big Data Management and Analytics. J. Parallel Distributed Comput. 79-80: 1-2 (2015) - [j41]Sai Kiranmayee Samudrala, Jaroslaw Zola, Srinivas Aluru, Baskar Ganapathysubramanian:
Parallel Framework for Dimensionality Reduction of Large-Scale Datasets. Sci. Program. 2015: 180214:1-180214:12 (2015) - [j40]Srinivas Aluru, Donna K. Slonim:
Guest Editors' Introduction: Selected Papers from ACM-BCB 2013. IEEE ACM Trans. Comput. Biol. Bioinform. 12(1): 2-3 (2015) - [j39]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): 1008-1020 (2015) - [c88]Srinivas Aluru:
Parallel machine learning approaches for reverse engineering genome-scale networks. BIBM 2015: 3 - [c87]Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt:
SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models. BIBM 2015: 83-90 - [c86]Srinivas Aluru:
Big data in life sciences and public health. HiPC Workshops 2015: 25 - [c85]Nagakishore Jammula, Sriram P. Chockalingam, Srinivas Aluru:
Parallel Read Error Correction for Big Genomic Datasets. HiPC 2015: 446-455 - [c84]Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru:
Information Theory Based Genome-Scale Gene Networks Construction Using MapReduce. HiPC 2015: 464-473 - [c83]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: 1-6 - [c82]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: 1 - [c81]Sanguthevar Rajasekaran, Srinivas Aluru, David A. Bader:
HiCOMB Introduction and Committees. IPDPS Workshops 2015: 329-330 - [c80]Srinivas Aluru, Alberto Apostolico, Sharma V. Thankachan:
Efficient Alignment Free Sequence Comparison with Bounded Mismatches. RECOMB 2015: 1-12 - [c79]Patrick Flick, Chirag Jain, Tony Pan, Srinivas Aluru:
A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications. SC 2015: 15:1-15:11 - [c78]Patrick Flick, Srinivas Aluru:
Parallel distributed memory construction of suffix and longest common prefix arrays. SC 2015: 16:1-16:10 - [c77]Kiran Pamnany, Sanchit Misra, Md. Vasimuddin, Xing Liu, Edmond Chow, Srinivas Aluru:
Dtree: Dynamic Task Scheduling at Petascale. ISC 2015: 122-138 - 2014
- [j38]Srinivas Aluru, Nagakishore Jammula:
A Review of Hardware Acceleration for Computational Genomics. IEEE Des. Test 31(1): 19-30 (2014) - [c76]Soumitra Pal, Srinivas Aluru:
In search of perfect reads. ICCABS 2014: 1-2 - [c75]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: 241-250 - [c74]Indranil Roy, Srinivas Aluru:
Finding Motifs in Biological Sequences Using the Micron Automata Processor. IPDPS 2014: 415-424 - [c73]Alba Cristina Magalhaes Alves de Melo, Srinivas Aluru, David A. Bader:
HiCOMB Introduction and Committees. IPDPS Workshops 2014: 497-498 - [c72]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: 461-472 - [i1]Yetian Chen, Jin Tian, Olga Nikolova, Srinivas Aluru:
A Parallel Algorithm for Exact Bayesian Structure Discovery in Bayesian Networks. CoRR abs/1408.1664 (2014) - 2013
- [j37]Xiao Yang, Sriram P. Chockalingam, Srinivas Aluru:
A survey of error-correction methods for next-generation sequencing. Briefings Bioinform. 14(1): 56-66 (2013) - [j36]Xiao Yang, Jaroslaw Zola, Srinivas Aluru:
Large-Scale metagenomic sequence Clustering on Map-Reduce Clusters. J. Bioinform. Comput. Biol. 11(1) (2013) - [j35]Olga Nikolova, Jaroslaw Zola, Srinivas Aluru:
Parallel globally optimal structure learning of Bayesian networks. J. Parallel Distributed Comput. 73(8): 1039-1048 (2013) - [j34]Abhinav Sarje, Srinivas Aluru:
All-pairs computations on many-core graphics processors. Parallel Comput. 39(2): 79-93 (2013) - [c71]Srinivas Aluru:
Large-scale metagenomic clustering via quasi clique enumeration and read assignment ambiguity resolution. ICCABS 2013: 1 - [c70]Jaroslaw Zola, David A. Bader, Srinivas Aluru:
HiCOMB Introduction. IPDPS Workshops 2013: 499-500 - 2012
- [c69]Srinivas Aluru:
Invited: Reverse engineering whole-genome networks. ICCABS 2012: 1 - [c68]Srinivas Aluru:
Workshop: Taxonomic clustering of large-scale metagnomic data. ICCABS 2012: 1 - [c67]Ankit Shah, Sriram P. Chockalingam, Srinivas Aluru:
A Parallel Algorithm for Spectrum-based Short Read Error Correction. IPDPS 2012: 60-70 - [c66]Mark J. Clement, Quinn Snell, Srinivas Aluru, David A. Bader:
HiCOMB Introduction. IPDPS Workshops 2012: 663-664 - [c65]Olga Nikolova, Srinivas Aluru:
Parallel Bayesian network structure learning with application to gene networks. SC 2012: 63 - [c64]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 - 2011
- [j33]Xiao Yang, Srinivas Aluru, Karin S. Dorman:
Repeat-aware modeling and correction of short read errors. BMC Bioinform. 12(S-1): S52 (2011) - [j32]Abhinav Sarje, Jaroslaw Zola, Srinivas Aluru:
Accelerating Pairwise Computations on Cell Processors. IEEE Trans. Parallel Distributed Syst. 22(1): 69-77 (2011) - [c63]Aditya Varma, Abhiram Ranade, Srinivas Aluru:
An improved maximum likelihood formulation for accurate genome assembly. ICCABS 2011: 165-170 - [c62]Xiao Yang, Karin S. Dorman, Srinivas Aluru:
Workshop: Flexible read decomposition for improved short read error correction. ICCABS 2011: 277 - [c61]Olga Nikolova, Srinivas Aluru:
Parallel Discovery of Direct Causal Relations and Markov Boundaries with Applications to Gene Networks. ICPP 2011: 512-521 - [c60]Ananth Kalyanaraman, Srinivas Aluru, David A. Bader:
HiCOMB Introduction. IPDPS Workshops 2011: 426-427 - [c59]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 - [e3]Srinivas Aluru, Sanghamitra Bandyopadhyay, Ümit V. Çatalyürek, Devdatt P. Dubhashi, Phillip H. Jones, Manish Parashar, Bertil Schmidt:
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 [contents] - [r6]Srinivas Aluru:
Bioinformatics. Encyclopedia of Parallel Computing 2011: 134-136 - [r5]Jaroslaw Zola, Srinivas Aluru:
Systems Biology, Network Inference in. Encyclopedia of Parallel Computing 2011: 1997-2002 - 2010
- [j31]Xiao Yang, Karin S. Dorman, Srinivas Aluru:
Reptile: representative tiling for short read error correction. Bioinform. 26(20): 2526-2533 (2010) - [j30]André Wehe, Wen-Chieh Chang, Oliver Eulenstein, Srinivas Aluru:
A scalable parallelization of the gene duplication problem. J. Parallel Distributed Comput. 70(3): 237-244 (2010) - [j29]Jaroslaw Zola, Maneesha Aluru, Abhinav Sarje, Srinivas Aluru:
Parallel Information-Theory-Based Construction of Genome-Wide Gene Regulatory Networks. IEEE Trans. Parallel Distributed Syst. 21(12): 1721-1733 (2010) - [c58]Xiao Yang, Srinivas Aluru:
An Improved Model for Gene Cluster Inference. BICoB 2010: 190-195 - [c57]William Sarje, Srinivas Aluru:
A MapReduce Style Framework for Computations on Trees. ICPP 2010: 343-352 - [c56]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 - [c55]George Karypis, Srinivas Aluru, David A. Bader:
Message from the workshop chairs. IPDPS Workshops 2010: 1-2 - [c54]Abhinav Sarje, Srinivas Aluru:
Parallel applications employing pairwise computations on emerging architectures. IPDPS Workshops 2010: 1-4 - [p3]Abhinav Sarje, Jaroslaw Zola, Srinivas Aluru:
Pairwise Computations on the Cell Processor. Scientific Computing with Multicore and Accelerators 2010: 297-327
2000 – 2009
- 2009
- [j28]Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru:
Parallel short sequence assembly of transcriptomes. BMC Bioinform. 10(S-1) (2009) - [j27]Abhinav Sarje, Srinivas Aluru:
Parallel Genomic Alignments on the Cell Broadband Engine. IEEE Trans. Parallel Distributed Syst. 20(11): 1600-1610 (2009) - [c53]Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru:
Assembly of Large Genomes from Paired Short Reads. BICoB 2009: 30-43 - [c52]Olga Nikolova, Jaroslaw Zola, Srinivas Aluru:
A parallel algorithm for exact Bayesian network inference. HiPC 2009: 342-349 - [c51]Jaroslaw Zola, Abhinav Sarje, Srinivas Aluru:
Constructing Gene Regulatory Networks on Clusters of Cell Processors. ICPP 2009: 108-115 - [c50]Melapudi Vikram, Andrew Baczewzki, Balasubramaniam Shanker, Srinivas Aluru:
Parallel accelerated cartesian expansions for particle dynamics simulations. IPDPS 2009: 1-11 - [e2]Sanjay Ranka, Srinivas Aluru, Rajkumar Buyya, Yeh-Ching Chung, Sumeet Dua, Ananth Grama, Sandeep K. S. Gupta, Rajeev Kumar, Vir V. Phoha:
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 [contents] - 2008
- [j26]David A. Bader, Srinivas Aluru:
High-performance computational biology. Parallel Comput. 34(11): 613-615 (2008) - [j25]Michael Ott, Jaroslaw Zola, Srinivas Aluru, Andrew D. Johnson, Daniel Janies, Alexandros Stamatakis:
Large-scale phylogenetic analysis on current HPC architectures. Sci. Program. 16(2-3): 255-270 (2008) - [j24]Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru:
Consensus Genetic Maps as Median Orders from Inconsistent Sources. IEEE ACM Trans. Comput. Biol. Bioinform. 5(2): 161-171 (2008) - [c49]Jaroslaw Zola, Maneesha Aluru, Srinivas Aluru:
Parallel Information Theory Based Construction of Gene Regulatory Networks. HiPC 2008: 336-349 - [c48]Sudip Seal, Michael Moody, Anna Ceguerra, Simon P. 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 - [c47]Benjamin G. Jackson, Srinivas Aluru:
Parallel Construction of Bidirected String Graphs for Genome Assembly. ICPP 2008: 346-353 - [c46]Andrew Janowczyk, Sharat Chandran, Srinivas Aluru:
Fast, Processor-Cardinality Agnostic PRNG with a Tracking Application. ICVGIP 2008: 171-178 - [c45]Abhinav Sarje, Srinivas Aluru:
Parallel biological sequence alignments on the Cell Broadband Engine. IPDPS 2008: 1-11 - [r4]Srinivas Aluru:
Text Indexing. Encyclopedia of Algorithms 2008 - 2007
- [j23]Anantharaman Kalyanaraman, Scott J. Emrich, Patrick S. Schnable, Srinivas Aluru:
Assembling genomes on large-scale parallel computers. J. Parallel Distributed Comput. 67(12): 1240-1255 (2007) - [c44]Jaroslaw Zola, Xiao Yang, Adrian Rospondek, Srinivas Aluru:
PARALLEL-TCOFFEE: A parallel multiple sequence aligner. PDCS 2007: 248-253 - [c43]Scott J. Emrich, Anantharaman Kalyanaraman, Srinivas Aluru:
Massively parallel expressed sequence tag clustering. PDCS 2007: 254-261 - [c42]Srinivas Aluru:
The Combinatorics of Sequencing the Corn Genome. COCOON 2007: 1 - [c41]Srinivas Aluru, David A. Bader, Anantharaman Kalyanaraman:
Symposium Evening Tutorial: High-performance Computing Methods for Computational Genomics. IPDPS 2007: 13 - [c40]Michael Ott, Jaroslaw Zola, Alexandros Stamatakis, Srinivas Aluru:
Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. SC 2007: 4 - [c39]Pang Ko, Srinivas Aluru:
Optimal Self-adjusting Trees for Dynamic String Data in Secondary Storage. SPIRE 2007: 184-194 - [e1]Srinivas Aluru, Manish Parashar, Ramamurthy Badrinath, Viktor K. Prasanna:
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 [contents] - [r3]Srinivas Aluru, Sudip Seal:
Spatial Domain Decomposition Methods in Parallel Scientific Computing. Handbook of Parallel Computing 2007 - 2006
- [j22]Anantharaman Kalyanaraman, Srinivas Aluru:
Efficient Algorithms and Software for Detection of Full-length Ltr Retrotransposons. J. Bioinform. Comput. Biol. 4(2): 197-216 (2006) - [j21]Srinivas Aluru, Nancy M. Amato, David A. Bader:
Editorial: Special Section on High-Performance Computational Biology. IEEE Trans. Parallel Distributed Syst. 17(8): 737-739 (2006) - [c38]Sudip Seal, Srinivas Aluru:
Communication-aware Parallel Domain Decomposition using Space Filling Curves. PDCS 2006: 159-164 - [c37]Pang Ko, Srinivas Aluru:
Obtaining Provably Good Performance from Suffix Trees in Secondary Storage. CPM 2006: 72-83 - [c36]Srikanta Tirthapura, Sudip Seal, Srinivas Aluru:
A Formal Analysis of Space Filling Curves for Parallel Domain Decomposition. ICPP 2006: 505-512 - [c35]Anantharaman Kalyanaraman, Scott J. Emrich, Patrick S. Schnable, Srinivas Aluru:
Assembling genomes on large-scale parallel computers. IPDPS 2006 - [c34]Srinivas Aluru, David A. Bader, Anantharaman Kalyanaraman:
M11 - High-performance computing methods for computational genomics. SC 2006: 225 - [p2]Srinivas Aluru:
Bioinformatics. Handbook of Nature-Inspired and Innovative Computing 2006: 657-695 - [p1]Srinivas Aluru, Nancy M. Amato, David A. Bader, Suchindra Bhandarkar, Laxmikant V. Kalé, Dan C. Marinescu:
Parallel Computational Biology. Parallel Processing for Scientific Computing 2006: 357-378 - 2005
- [j20]Sudip Seal, Srikanth Komarina, Srinivas Aluru:
An optimal hierarchical clustering algorithm for gene expression data. Inf. Process. Lett. 93(3): 143-147 (2005) - [j19]Pang Ko, Srinivas Aluru:
Space efficient linear time construction of suffix arrays. J. Discrete Algorithms 3(2-4): 143-156 (2005) - [j18]Fatih Erdogan Sevilgen, Srinivas Aluru, Natsuhiko Futamura:
Parallel algorithms for tree accumulations. J. Parallel Distributed Comput. 65(1): 85-93 (2005) - [j17]Bhanu Hariharan, Srinivas Aluru:
Efficient parallel algorithms and software for compressed octrees with applications to hierarchical methods. Parallel Comput. 31(3-4): 311-331 (2005) - [j16]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) - [c33]Zhenhui Shen, Srinivas Aluru, Srikanta Tirthapura:
Indexing for Subscription Covering in Publish-Subscribe Systems. PDCS 2005: 328-333 - [c32]Benjamin G. Jackson, Srinivas Aluru, Patrick S. Schnable:
Consensus Genetic Maps: A Graph Theoretic Approach. CSB 2005: 35-43 - [c31]Anantharaman Kalyanaraman, Srinivas Aluru:
Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons. CSB 2005: 56-64 - 2004
- [j15]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. Bioinform. 20(2): 140-147 (2004) - [j14]David A. Bader, Srinivas Aluru:
Special Issue: High Performance Computational Biology. Concurr. Pract. Exp. 16(9): 817-821 (2004) - [j13]Stjepan Rajko, Srinivas Aluru:
Space and Time Optimal Parallel Sequence Alignments. IEEE Trans. Parallel Distributed Syst. 15(12): 1070-1081 (2004) - [c30]Pang Ko, Mahesh Narayanan, Anantharaman Kalyanaraman, Srinivas Aluru:
Space-Conserving Optimal DNA-Protein Alignment . CSB 2004: 80-88 - [c29]Srinivas Aluru, Fatih Erdogan Sevilgen:
Efficient Methods for Database Storage and Retrieval Using Space-Filling Curves. ISCIS 2004: 503-512 - [c28]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 - [r2]Srinivas Aluru:
Quadtrees and Octrees. Handbook of Data Structures and Applications 2004 - [r1]Srinivas Aluru:
Suffix Trees and Suffix Arrays. Handbook of Data Structures and Applications 2004 - 2003
- [j12]Srinivas Aluru, Natsuhiko Futamura, Kishan Mehrotra:
Parallel biological sequence comparison using prefix computations. J. Parallel Distributed Comput. 63(3): 264-272 (2003) - [j11]Srinivas Aluru, David A. Bader:
Guest Editor's Introduction: Special issue on high-performance computational biology. J. Parallel Distributed Comput. 63(7-8): 671-673 (2003) - [j10]Natsuhiko Futamura, Srinivas Aluru, Xiaoqiu Huang:
Parallel Syntenic Alignments. Parallel Process. Lett. 13(4): 689-703 (2003) - [j9]Anantharaman Kalyanaraman, Srinivas Aluru, Volker Brendel, Suresh C. Kothari:
Space and time efficient parallel algorithms and software for EST clustering. IEEE Trans. Parallel Distributed Syst. 14(12): 1209-1221 (2003) - [c27]Pang Ko, Srinivas Aluru:
Space Efficient Linear Time Construction of Suffix Arrays. CPM 2003: 200-210 - [c26]Srinivas Aluru:
Computational biology on parallel computers. ECC 2003: 3370-3377 - [c25]Natsuhiko Futamura, Rama Sangireddy, Srinivas Aluru, Arun K. Somani:
Scalable, memory efficient, high-speed lookup and update algorithms for IP routing. ICCCN 2003: 257-263 - [c24]Stjepan Rajko, Srinivas Aluru:
Space and Time Optimal Parallel Sequence Alignments. ICPP 2003: 39-47 - 2002
- [j8]Natsuhiko Futamura, Srinivas Aluru, Desh Ranjan, Bhanu Hariharan:
Efficient Parallel Algorithms for Solvent Accessible Surface Area of Proteins. IEEE Trans. Parallel Distributed Syst. 13(6): 544-555 (2002) - [c23]Meng-Shiou Wu, Srinivas Aluru, Ricky A. Kendall:
Mixed Mode Matrix Multiplication. CLUSTER 2002: 195- - [c22]Natsuhiko Futamura, Srinivas Aluru, Xiaoqiu Huang:
Parallel Syntenic Alignments. HiPC 2002: 420-430 - [c21]Anantharaman Kalyanaraman, Srinivas Aluru, Suresh C. Kothari:
Space and Time Efficient Parallel Algorithms and Software for EST Clustering. ICPP 2002: 331-342 - [c20]David A. Bader, Srinivas Aluru:
Workshop Introduction. IPDPS 2002 - [c19]Anantharaman Kalyanaraman, Srinivas Aluru, Suresh C. Kothari:
Parallel EST Clustering. IPDPS 2002 - [c18]Bhanu Hariharan, Srinivas Aluru, Balasubramaniam Shanker:
A scalable parallel fast multipole method for analysis of scattering from perfect electrically conducting surfaces. SC 2002: 16:1-16:17 - 2001
- [c17]Bhanu Hariharan, Srinivas Aluru:
Efficient Parallel Algorithms and Software for Compressed Octrees with Applications to Hierarchical Methods. HiPC 2001: 125-136 - 2000
- [j7]Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka:
Parallel Construction of Multidimensional Binary Search Trees. IEEE Trans. Parallel Distributed Syst. 11(2): 136-148 (2000) - [c16]Fatih Erdogan Sevilgen, Natsuhiko Futamura, Srinivas Aluru:
A Provably Optimal, Distribution-Independent Parallel Fast Multipole Method. IPDPS 2000: 77-84
1990 – 1999
- 1999
- [c15]Srinivas Aluru, Fatih Erdogan Sevilgen:
Dynamic Compressed Hypertoctrees with Application to the N-Body Problem. FSTTCS 1999: 21-33 - [c14]Srinivas Aluru, Desh Ranjan, Natsuhiko Futamura:
A Parallel Monte Carlo Algorithm for Protein Accessible Surface Area Computation. HiPC 1999: 339-348 - [c13]Srinivas Aluru, Natsuhiko Futamura, Kishan Mehrotra:
Parallel Biological Sequence Comparison Using Prefix Computations. IPPS/SPDP 1999: 653-659 - [c12]Srinivas Aluru, Songrit Maneewongvatana:
A Practical Parallel Algorithm for Line Segment Visibility. PDPTA 1999: 1676-1682 - [c11]Fatih Erdogan Sevilgen, Srinivas Aluru:
A Unifying Data Structure for Hierarchical Methods. SC 1999: 24 - 1998
- [j6]Srinivas Aluru, John L. Gustafson, Gurpur M. Prabhu, Fatih Erdogan Sevilgen:
Distribution-Independent Hierarchical Algorithms for the N-body Problem. J. Supercomput. 12(4): 303-323 (1998) - 1997
- [j5]Srinivas Aluru:
Lagged Fibonacci Random Number Generators for Distributed Memory Parallel Computers. J. Parallel Distributed Comput. 45(1): 1-12 (1997) - [j4]Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka:
Practical Algorithms for Selection on Coarse-Grained Parallel Computers. IEEE Trans. Parallel Distributed Syst. 8(8): 813-824 (1997) - [c10]Srinivas Aluru, Fatih Erdogan Sevilgen:
Parallel domain decomposition and load balancing using space-filling curves. HiPC 1997: 230-235 - 1996
- [j3]Srinivas Aluru:
Greengard's N-Body Algorithm is not Order N. SIAM J. Sci. Comput. 17(3): 773-776 (1996) - [j2]John L. Gustafson, Srinivas Aluru:
Massively Parallel Searching for Better Algorithms or How to Do a Cross Product with Five Multiplications. Sci. Program. 5(3): 203-217 (1996) - [c9]Srinivas Aluru:
Parallel Additive Lagged Fibonacci Random Number Generators. International Conference on Supercomputing 1996: 102-108 - [c8]Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka:
Parallel Construction of Multidimensional Binary Search Trees. International Conference on Supercomputing 1996: 205-212 - [c7]Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka:
Practical Algorithms for Selection on Coarse-Grained Parallel Computers. IPPS 1996: 309-313 - [c6]Srinivas Aluru, Songrit Maneewongvatana:
Practical Paralle1 Algorithm for Constructing Line Arrangements. PDPTA 1996: 125-135 - [c5]Sanjay Goil, Srinivas Aluru, Sanjay Ranka:
Concatenated parallelism: a technique for efficient parallel divide and conquer. SPDP 1996: 488-495 - 1995
- [c4]Srinivas Aluru:
Properties of Binomial Coefficients and Implications to Parallelizing Lagged Fibonacci Random Number Generators. ICPP (3) 1995: 25-28 - 1994
- [c3]Srinivas Aluru, Gurpur M. Prabhu, John L. Gustafson:
Truly distribution-independent algorithms for the N-body problem. SC 1994: 420-428 - 1993
- [c2]Srinivas Aluru, John L. Gustafson:
A Massively Parallel Optimizer for Expression Evaluation. International Conference on Supercomputing 1993: 97-106 - [c1]Srinivas Aluru, John L. Gustafson:
Subtle Issues of SIMD Tree Search. PARCO 1993: 49-56 - 1992
- [j1]Srinivas Aluru, Gurpur M. Prabhu, John L. Gustafson:
A random number generator for parallel computers. Parallel Comput. 18(8): 839-847 (1992)
Coauthor Index
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