Srinivas Aluru

234 papers A* 3A 37B 18C 7Misc 15Journal 82Unranked 55
YearRankTypeTitle / Venue / Authors
2025 A conf
A Work-Optimal Parallel Algorithm for Aligning Sequences to Genome Graphs.
IPDPS
Aranya Banerjee, Daniel Gibney, Helen Xu, Srinivas Aluru
2025 J jnl
Disambiguating a Soft Metagenomic Clustering.
J. Comput. Biol.
Rahul Nihalani, Jaroslaw Zola, Srinivas Aluru
2025 — conf
Efficient and effective methods for variant selection.
BCB
Srinivas Aluru, Anne Benoit, Bora Uçar
2025 J jnl
SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data.
Bioinform.
Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru
2025 A conf
The Power of Parallelism: Accelerating Discovery in the Biosciences.
IPDPS
Srinivas Aluru
2024 J jnl
GraphSlimmer: Preserving Read Mappability with the Minimum Number of Variants.
J. Comput. Biol.
Neda Tavakoli, Daniel Gibney, Srinivas Aluru
2023 J jnl
A Parallel Framework for Constraint-Based Bayesian Network Learning via Markov Blanket Discovery.
IEEE Trans. Parallel Distributed Syst.
Ankit Srivastava, Sriram P. Chockalingam, Srinivas Aluru
2023 Misc conf
Fast Parallel Tensor Times Same Vector for Hypergraphs.
HiPC
Shruti Shivakumar, Ilya Amburg, Sinan G. Aksoy, Jiajia Li, Stephen J. Young, Srinivas Aluru
2023 J jnl
Fast Parallel Tensor Times Same Vector for Hypergraphs.
CoRR
Shruti Shivakumar, Ilya Amburg, Sinan G. Aksoy, Jiajia Li, Stephen J. Young, Srinivas Aluru
2023 J jnl
MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework.
Bioinform.
Tony C. Pan, Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru
2023 J jnl
Sparse Symmetric Format for Tucker Decomposition.
IEEE Trans. Parallel Distributed Syst.
Shruti Shivakumar, Jiajia Li, Ramakrishnan Kannan, Srinivas Aluru
2022 J jnl
EnGRaiN: a supervised ensemble learning method for recovery of large-scale gene regulatory networks.
Bioinform.
Maneesha Aluru, Harsh Shrivastava, Sriram P. Chockalingam, Shruti Shivakumar, Srinivas Aluru
2022 C conf
Feasibility of Flow Decomposition with Subpath Constraints in Linear Time.
WABI
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
2022 J jnl
GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks.
J. Comput. Biol.
Harsh Shrivastava, Xiuwei Zhang, Le Song, Srinivas Aluru
2022 — conf
Haplotype-aware variant selection for genome graphs.
BCB
Neda Tavakoli, Daniel Gibney, Srinivas Aluru
2022 — ed.
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022, Las Vegas, NV, USA, December 6-8, 2022
BIBM
Donald A. Adjeroh, Qi Long, Xinghua Mindy Shi, Fei Guo, Xiaohua Hu, Srinivas Aluru, Giri Narasimhan, Jianxin Wang, Mingon Kang, Ananda Mondal, Jin Liu
2022 J jnl
On the Hardness of Sequence Alignment on De Bruijn Graphs.
J. Comput. Biol.
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
2022 J jnl
The Complexity of Approximate Pattern Matching on De Bruijn Graphs.
CoRR
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
2022 B conf
The Complexity of Approximate Pattern Matching on de Bruijn Graphs.
RECOMB
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
2021 J jnl
A variant selection framework for genome graphs.
Bioinform.
Chirag Jain, Neda Tavakoli, Srinivas Aluru
2021 J jnl
Editorial: From the New Editor-in-Chief.
IEEE ACM Trans. Comput. Biol. Bioinform.
Srinivas Aluru
2021 — conf
Efficient Parallel Sparse Symmetric Tucker Decomposition for High-Order Tensors.
ACDA
Shruti Shivakumar, Jiajia Li, Ramakrishnan Kannan, Srinivas Aluru
2021 A conf
Parallel construction of module networks.
SC
Ankit Srivastava, Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru
2021 J jnl
Real-time mapping of nanopore raw signals.
Bioinform.
Haowen Zhang, Haoran Li, Chirag Jain, Haoyu Cheng, Kin Fai Au, Heng Li, Srinivas Aluru
2020 — ed.
2020 IEEE International Conference on Big Data (IEEE BigData 2020), Atlanta, GA, USA, December 10-13, 2020
IEEE BigData
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 A conf
A parallel framework for constraint-based bayesian network learning via markov blanket discovery.
SC
Ankit Srivastava, Sriram P. Chockalingam, Srinivas Aluru
2020 J jnl
An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction.
BMC Bioinform.
Sriram P. Chockalingam, Jodh Pannu, Sahar Hooshmand, Sharma V. Thankachan, Srinivas Aluru
2020 J jnl
Fast de Bruijn Graph Compaction in Distributed Memory Environments.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tony Pan, Rahul Nihalani, Srinivas Aluru
2020 A* conf
GLAD: Learning Sparse Graph Recovery.
ICLR
Harsh Shrivastava, Xinshi Chen, Binghong Chen, Guanghui Lan, Srinivas Aluru, Han Liu, Le Song
2020 J jnl
Interval stabbing on the Automata Processor.
J. Parallel Distributed Comput.
Indranil Roy, Ankit Srivastava, Matt Grimm, Srinivas Aluru
2020 J jnl
On the Complexity of Sequence-to-Graph Alignment.
J. Comput. Biol.
Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru
2020 J jnl
Sequential and parallel algorithms for all-pair k-mismatch maximal common substrings.
J. Parallel Distributed Comput.
Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru
2019 A conf
Accelerating Sequence Alignment to Graphs.
IPDPS
Chirag Jain, Sanchit Misra, Haowen Zhang, Alexander T. Dilthey, Srinivas Aluru
2019 J jnl
Cooperative neural networks (CoNN): Exploiting prior independence structure for improved classification.
CoRR
Harsh Shrivastava, Eugene Bart, Bob Price, Hanjun Dai, Bo Dai, Srinivas Aluru
2019 A conf
Distributed enhanced suffix arrays: efficient algorithms for construction and querying.
SC
Patrick Flick, Srinivas Aluru
2019 A conf
Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems.
IPDPS
Md. Vasimuddin, Sanchit Misra, Heng Li, Srinivas Aluru
2019 J jnl
Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems.
CoRR
Md. Vasimuddin, Sanchit Misra, Heng Li, Srinivas Aluru
2019 J jnl
Evaluating High Performance Pattern Matching on the Automata Processor.
IEEE Trans. Computers
Indranil Roy, Ankit Srivastava, Matt Grimm, Marziyeh Nourian, Michela Becchi, Srinivas Aluru
2019 J jnl
GLAD: Learning Sparse Graph Recovery.
CoRR
Harsh Shrivastava, Xinshi Chen, Binghong Chen, Guanghui Lan, Srinivas Aluru, Le Song
2019 J jnl
Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tony Pan, Patrick Flick, Chirag Jain, Yongchao Liu, Srinivas Aluru
2019 B conf
On the Complexity of Sequence to Graph Alignment.
RECOMB
Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru
2019 — conf
ParRefCom: Parallel Reference-based Compression of Paired-end Genomics Read Datasets.
BCB
Nagakishore Jammula, Srinivas Aluru
2019 C conf
Validating Paired-End Read Alignments in Sequence Graphs.
WABI
Chirag Jain, Haowen Zhang, Alexander T. Dilthey, Srinivas Aluru
2018 — ed.
2018 Eleventh International Conference on Contemporary Computing, IC3 2018, Noida, India, August 2-4, 2018
IC3
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 J jnl
A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.
J. Comput. Biol.
Chirag Jain, Alexander T. Dilthey, Sergey Koren, Srinivas Aluru, Adam M. Phillippy
2018 A conf
A Parallel Algorithm for Bayesian Network Inference Using Arithmetic Circuits.
IPDPS
Md. Vasimuddin, Sriram P. Chockalingam, Srinivas Aluru
2018 J jnl
A fast adaptive algorithm for computing whole-genome homology maps.
Bioinform.
Chirag Jain, Sergey Koren, Alexander T. Dilthey, Adam M. Phillippy, Srinivas Aluru
2018 B conf
Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis.
RECOMB
Sharma V. Thankachan, Chaitanya Aluru, Sriram P. Chockalingam, Srinivas Aluru
2018 — conf
An Alignment-free Heuristic for Fast Sequence Comparisons with Applications to Phylogeny Reconstruction.
BCB
Jodh Pannu, Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru
2018 J jnl
An SVM-based method for assessment of transcription factor-DNA complex models.
BMC Bioinform.
Rosario I. Corona, Sanjana Sudarshan, Srinivas Aluru, Jun-tao Guo
2018 A* conf
Cooperative neural networks (CoNN): Exploiting prior independence structure for improved classification.
NeurIPS
Harsh Shrivastava, Eugene Bart, Bob Price, Hanjun Dai, Bo Dai, Srinivas Aluru
2018 — conf
Faster Computation of Genome Mappability with one Mismatch.
ICCABS
Sahar Hooshmand, Paniz Abedin, Daniel Gibney, Srinivas Aluru, Sharma V. Thankachan
2018 — conf
Faster Computation of Genome Mappability.
BCB
Sahar Hooshmand, Paniz Abedin, Daniel Gibney, Srinivas Aluru, Sharma V. Thankachan
2018 — conf
Introduction to HiCOMB 2018.
IPDPS Workshops
Srinivas Aluru, David A. Bader, Paul Medvedev
2018 A conf
Optimizing high performance distributed memory parallel hash tables for DNA
SC
Tony C. Pan, Sanchit Misra, Srinivas Aluru
2018 B conf
Performance extraction and suitability analysis of multi- and many-core architectures for next generation sequencing secondary analysis.
PACT
Sanchit Misra, Tony C. Pan, Kanak Mahadik, George Powley, Priya N. Vaidya, Md. Vasimuddin, Srinivas Aluru
2017 — ed.
2017 IEEE International Conference on Data Mining Workshops, ICDM Workshops 2017, New Orleans, LA, USA, November 18-21, 2017
ICDM Workshops
Raju Gottumukkala, Xia Ning, Guozhu Dong, Vijay Raghavan, Srinivas Aluru, George Karypis, Lucio Miele, Xindong Wu
2017 A* ed.
2017 IEEE International Conference on Data Mining, ICDM 2017, New Orleans, LA, USA, November 18-21, 2017
ICDM
Vijay Raghavan, Srinivas Aluru, George Karypis, Lucio Miele, Xindong Wu
2017 B conf
A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.
RECOMB
Chirag Jain, Alexander T. Dilthey, Sergey Koren, Srinivas Aluru, Adam M. Phillippy
2017 J jnl
A greedy alignment-free distance estimator for phylogenetic inference.
BMC Bioinform.
Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Ambujam Krishnan, Srinivas Aluru
2017 J jnl
An Adaptive Parallel Algorithm for Computing Connected Components.
IEEE Trans. Parallel Distributed Syst.
Chirag Jain, Patrick Flick, Tony Pan, Oded Green, Srinivas Aluru
2017 — conf
Confidence assessment of protein-DNA complex models.
BIBM
Rosario I. Corona, Sanjana Sudarshan, Jun-tao Guo, Srinivas Aluru
2017 — conf
Distributed Memory Partitioning of High-Throughput Sequencing Datasets for Enabling Parallel Genomics Analyses.
BCB
Nagakishore Jammula, Sriram P. Chockalingam, Srinivas Aluru
2017 A conf
Parallel Construction of Suffix Trees and the All-Nearest-Smaller-Values Problem.
IPDPS
Patrick Flick, Srinivas Aluru
2017 Misc conf
Parallel Exact Dynamic Bayesian Network Structure Learning with Application to Gene Networks.
HiPC
Md. Vasimuddin, Srinivas Aluru
2017 J jnl
Parallelized Kendall's Tau Coefficient Computation via SIMD Vectorized Sorting On Many-Integrated-Core Processors.
CoRR
Yongchao Liu, Tony Pan, Oded Green, Srinivas Aluru
2017 — conf
Probabilistic estimation of overlap graphs for large sequence datasets.
BIBM
Rahul Nihalani, Sriram P. Chockalingam, Shaowei Zhu, Vijay V. Vazirani, Srinivas Aluru
2017 J jnl
Reprint of "A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications".
Parallel Comput.
Patrick Flick, Chirag Jain, Tony Pan, Srinivas Aluru
2017 — conf
Reverse Engineering Gene Networks: A Comparative Study at Genome-scale.
BCB
Sriram P. Chockalingam, Maneesha Aluru, Hongqing Guo, Yanhai Yin, Srinivas Aluru
2016 — conf
A Memory and Time Scalable Parallelization of the Reptile Error-Correction Code.
IPDPS Workshops
Vipin Sachdeva, Srinivas Aluru, David A. Bader
2016 J jnl
A Provably Efficient Algorithm for the
J. Comput. Biol.
Sharma V. Thankachan, Alberto Apostolico, Srinivas Aluru
2016 A conf
A parallel algorithm for finding all pairs
SC
Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru
2016 J jnl
ALFRED: A Practical Method for Alignment-Free Distance Computation.
J. Comput. Biol.
Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Alberto Apostolico, Srinivas Aluru
2016 A conf
Algorithmic Techniques for Solving Graph Problems on the Automata Processor.
IPDPS
Indranil Roy, Nagakishore Jammula, Srinivas Aluru
2016 J jnl
An Adaptive Parallel Algorithm for Computing Connectivity.
CoRR
Chirag Jain, Patrick Flick, Tony Pan, Oded Green, Srinivas Aluru
2016 — conf
An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings.
ISBRA
Sharma V. Thankachan, Sriram P. Chockalingam, Srinivas Aluru
2016 J jnl
Discovering Motifs in Biological Sequences Using the Micron Automata Processor.
IEEE ACM Trans. Comput. Biol. Bioinform.
Indranil Roy, Srinivas Aluru
2016 — conf
Effective Utilization of Paired Reads to Improve Length and Accuracy of Contigs in Genome Assembly.
BCB
Rahul Nihalani, Srinivas Aluru
2016 Misc conf
Genomes Galore: Big Data Challenges in the Life Sciences.
HiPC
Srinivas Aluru
2016 — conf
HiCOMB Introduction and Committees.
IPDPS Workshops
Srinivas Aluru, David A. Bader, Ananth Kalyanaraman, Jaroslaw Zola
2016 A conf
High Performance Pattern Matching Using the Automata Processor.
IPDPS
Indranil Roy, Ankit Srivastava, Marziyeh Nourian, Michela Becchi, Srinivas Aluru
2016 — conf
Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems.
BCB
Tony Pan, Patrick Flick, Chirag Jain, Yongchao Liu, Srinivas Aluru
2016 J jnl
LightScan: Faster Scan Primitive on CUDA Compatible Manycore Processors.
CoRR
Yongchao Liu, Srinivas Aluru
2016 — conf
Parallel Interval Stabbing on the Automata Processor.
IA3@SC
Indranil Roy, Ankit Srivastava, Matt Grimm, Srinivas Aluru
2016 J jnl
Parallel Pairwise Correlation Computation On Intel Xeon Phi Clusters.
CoRR
Yongchao Liu, Tony Pan, Srinivas Aluru
2016 C conf
Parallel Pairwise Correlation Computation on Intel Xeon Phi Clusters.
SBAC-PAD
Yongchao Liu, Tony Pan, Srinivas Aluru
2016 B conf
Programming Techniques for the Automata Processor.
ICPP
Indranil Roy, Ankit Srivastava, Srinivas Aluru
2016 J jnl
SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations.
BMC Syst. Biol.
Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt
2016 — ch.
Text Indexing.
Encyclopedia of Algorithms
Srinivas Aluru
2015 — conf
A greedy alignment-free distance estimator for phylogenetic inference (extended abstract).
ICCABS
Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Ambujam Krishnan, Srinivas Aluru
2015 A conf
A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications.
SC
Patrick Flick, Chirag Jain, Tony Pan, Srinivas Aluru
2015 — conf
Big data in life sciences and public health.
HiPC Workshops
Srinivas Aluru
2015 C conf
Dtree: Dynamic Task Scheduling at Petascale.
ISC
Kiran Pamnany, Sanchit Misra, Md. Vasimuddin, Xing Liu, Edmond Chow, Srinivas Aluru
2015 J jnl
Editorial: Scalable Systems for Big Data Management and Analytics.
J. Parallel Distributed Comput.
Srinivas Aluru, Yogesh Simmhan
2015 B conf
Efficient Alignment Free Sequence Comparison with Bounded Mismatches.
RECOMB
Srinivas Aluru, Alberto Apostolico, Sharma V. Thankachan
2015 — conf
Efficient detection of viral transmission with threshold-based methods.
ICCABS
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
2015 J jnl
Guest Editors' Introduction: Selected Papers from ACM-BCB 2013.
IEEE ACM Trans. Comput. Biol. Bioinform.
Srinivas Aluru, Donna K. Slonim
2015 — conf
HiCOMB Introduction and Committees.
IPDPS Workshops
Sanguthevar Rajasekaran, Srinivas Aluru, David A. Bader
2015 J jnl
In search of perfect reads.
BMC Bioinform.
Soumitra Pal, Srinivas Aluru
2015 Misc conf
Information Theory Based Genome-Scale Gene Networks Construction Using MapReduce.
HiPC
Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru
2015 J jnl
Parallel Framework for Dimensionality Reduction of Large-Scale Datasets.
Sci. Program.
Sai Kiranmayee Samudrala, Jaroslaw Zola, Srinivas Aluru, Baskar Ganapathysubramanian
2015 J jnl
Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel®Xeon Phi™ Coprocessor.
IEEE ACM Trans. Comput. Biol. Bioinform.
Sanchit Misra, Kiran Pamnany, Srinivas Aluru
2015 Misc conf
Parallel Read Error Correction for Big Genomic Datasets.
HiPC
Nagakishore Jammula, Sriram P. Chockalingam, Srinivas Aluru
2015 A conf
Parallel distributed memory construction of suffix and longest common prefix arrays.
SC
Patrick Flick, Srinivas Aluru
2015 — conf
Parallel machine learning approaches for reverse engineering genome-scale networks.
BIBM
Srinivas Aluru
2015 — conf
SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models.
BIBM
Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt
2014 J jnl
A Parallel Algorithm for Exact Bayesian Structure Discovery in Bayesian Networks.
CoRR
Yetian Chen, Jin Tian, Olga Nikolova, Srinivas Aluru
2014 J jnl
A Review of Hardware Acceleration for Computational Genomics.
IEEE Des. Test
Srinivas Aluru, Nagakishore Jammula
2014 A conf
Finding Motifs in Biological Sequences Using the Micron Automata Processor.
IPDPS
Indranil Roy, Srinivas Aluru
2014 — conf
HiCOMB Introduction and Committees.
IPDPS Workshops
Alba Cristina Magalhaes Alves de Melo, Srinivas Aluru, David A. Bader
2014 — conf
In search of perfect reads.
ICCABS
Soumitra Pal, Srinivas Aluru
2014 A conf
Parallel Bayesian Network Structure Learning for Genome-Scale Gene Networks.
SC
Sanchit Misra, Md. Vasimuddin, Kiran Pamnany, Sriram P. Chockalingam, Yong Dong, Min Xie, Maneesha R. Aluru, Srinivas Aluru
2014 A conf
Parallel Mutual Information Based Construction of Whole-Genome Networks on the Intel (R) Xeon Phi (TM) Coprocessor.
IPDPS
Sanchit Misra, Kiran Pamnany, Srinivas Aluru
2013 J jnl
A survey of error-correction methods for next-generation sequencing.
Briefings Bioinform.
Xiao Yang, Sriram P. Chockalingam, Srinivas Aluru
2013 J jnl
All-pairs computations on many-core graphics processors.
Parallel Comput.
Abhinav Sarje, Srinivas Aluru
2013 — conf
HiCOMB Introduction.
IPDPS Workshops
Jaroslaw Zola, David A. Bader, Srinivas Aluru
2013 J jnl
Large-Scale metagenomic sequence Clustering on Map-Reduce Clusters.
J. Bioinform. Comput. Biol.
Xiao Yang, Jaroslaw Zola, Srinivas Aluru
2013 — conf
Large-scale metagenomic clustering via quasi clique enumeration and read assignment ambiguity resolution.
ICCABS
Srinivas Aluru
2013 J jnl
Parallel globally optimal structure learning of Bayesian networks.
J. Parallel Distributed Comput.
Olga Nikolova, Jaroslaw Zola, Srinivas Aluru
2012 A conf
A Parallel Algorithm for Spectrum-based Short Read Error Correction.
IPDPS
Ankit Shah, Sriram P. Chockalingam, Srinivas Aluru
2012 C conf
An Algorithmic View on Multi-Related-Segments: A Unifying Model for Approximate Common Interval.
TAMC
Xiao Yang, Florian Sikora, Guillaume Blin, Sylvie Hamel, Romeo Rizzi, Srinivas Aluru
2012 — conf
HiCOMB Introduction.
IPDPS Workshops
Mark J. Clement, Quinn Snell, Srinivas Aluru, David A. Bader
2012 — conf
Invited: Reverse engineering whole-genome networks.
ICCABS
Srinivas Aluru
2012 A conf
Parallel Bayesian network structure learning with application to gene networks.
SC
Olga Nikolova, Srinivas Aluru
2012 — conf
Workshop: Taxonomic clustering of large-scale metagnomic data.
ICCABS
Srinivas Aluru
2011 J jnl
Accelerating Pairwise Computations on Cell Processors.
IEEE Trans. Parallel Distributed Syst.
Abhinav Sarje, Jaroslaw Zola, Srinivas Aluru
2011 — conf
An improved maximum likelihood formulation for accurate genome assembly.
ICCABS
Aditya Varma, Abhiram Ranade, Srinivas Aluru
2011 — ch.
Bioinformatics.
Encyclopedia of Parallel Computing
Srinivas Aluru
2011 — ed.
Contemporary Computing - 4th International Conference, IC3 2011, Noida, India, August 8-10, 2011. Proceedings
IC3
Srinivas Aluru, Sanghamitra Bandyopadhyay, Ümit V. Çatalyürek, Devdatt P. Dubhashi, Phillip H. Jones, Manish Parashar, Bertil Schmidt
2011 — conf
HiCOMB Introduction.
IPDPS Workshops
Ananth Kalyanaraman, Srinivas Aluru, David A. Bader
2011 B conf
Parallel Discovery of Direct Causal Relations and Markov Boundaries with Applications to Gene Networks.
ICPP
Olga Nikolova, Srinivas Aluru
2011 A conf
Parallel Metagenomic Sequence Clustering Via Sketching and Maximal Quasi-clique Enumeration on Map-Reduce Clouds.
IPDPS
Xiao Yang, Jaroslaw Zola, Srinivas Aluru
2011 J jnl
Repeat-aware modeling and correction of short read errors.
BMC Bioinform.
Xiao Yang, Srinivas Aluru, Karin S. Dorman
2011 — ch.
Systems Biology, Network Inference in.
Encyclopedia of Parallel Computing
Jaroslaw Zola, Srinivas Aluru
2011 — conf
Workshop: Flexible read decomposition for improved short read error correction.
ICCABS
Xiao Yang, Karin S. Dorman, Srinivas Aluru
2010 B conf
A MapReduce Style Framework for Computations on Trees.
ICPP
William Sarje, Srinivas Aluru
2010 J jnl
A scalable parallelization of the gene duplication problem.
J. Parallel Distributed Comput.
André Wehe, Wen-Chieh Chang, Oliver Eulenstein, Srinivas Aluru
2010 — conf
An Improved Model for Gene Cluster Inference.
BICoB
Xiao Yang, Srinivas Aluru
2010 — conf
Message from the workshop chairs.
IPDPS Workshops
George Karypis, Srinivas Aluru, David A. Bader
2010 — ch.
Pairwise Computations on the Cell Processor.
Scientific Computing with Multicore and Accelerators
Abhinav Sarje, Jaroslaw Zola, Srinivas Aluru
2010 J jnl
Parallel Information-Theory-Based Construction of Genome-Wide Gene Regulatory Networks.
IEEE Trans. Parallel Distributed Syst.
Jaroslaw Zola, Maneesha Aluru, Abhinav Sarje, Srinivas Aluru
2010 — conf
Parallel applications employing pairwise computations on emerging architectures.
IPDPS Workshops
Abhinav Sarje, Srinivas Aluru
2010 A conf
Parallel de novo assembly of large genomes from high-throughput short reads.
IPDPS
Benjamin G. Jackson, Matthew Regennitter, Xiao Yang, Patrick S. Schnable, Srinivas Aluru
2010 J jnl
Reptile: representative tiling for short read error correction.
Bioinform.
Xiao Yang, Karin S. Dorman, Srinivas Aluru
2009 Misc conf
A parallel algorithm for exact Bayesian network inference.
HiPC
Olga Nikolova, Jaroslaw Zola, Srinivas Aluru
2009 — conf
Assembly of Large Genomes from Paired Short Reads.
BICoB
Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru
2009 B conf
Constructing Gene Regulatory Networks on Clusters of Cell Processors.
ICPP
Jaroslaw Zola, Abhinav Sarje, Srinivas Aluru
2009 — ed.
Contemporary Computing - Second International Conference, IC3 2009, Noida, India, August 17-19, 2009. Proceedings
IC3
Sanjay Ranka, Srinivas Aluru, Rajkumar Buyya, Yeh-Ching Chung, Sumeet Dua, Ananth Grama, Sandeep K. S. Gupta, Rajeev Kumar, Vir V. Phoha
2009 J jnl
Parallel Genomic Alignments on the Cell Broadband Engine.
IEEE Trans. Parallel Distributed Syst.
Abhinav Sarje, Srinivas Aluru
2009 A conf
Parallel accelerated cartesian expansions for particle dynamics simulations.
IPDPS
Melapudi Vikram, Andrew Baczewzki, Balasubramaniam Shanker, Srinivas Aluru
2009 J jnl
Parallel short sequence assembly of transcriptomes.
BMC Bioinform.
Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru
2008 J jnl
Consensus Genetic Maps as Median Orders from Inconsistent Sources.
IEEE ACM Trans. Comput. Biol. Bioinform.
Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru
2008 — conf
Fast, Processor-Cardinality Agnostic PRNG with a Tracking Application.
ICVGIP
Andrew Janowczyk, Sharat Chandran, Srinivas Aluru
2008 J jnl
High-performance computational biology.
Parallel Comput.
David A. Bader, Srinivas Aluru
2008 J jnl
Large-scale phylogenetic analysis on current HPC architectures.
Sci. Program.
Michael Ott, Jaroslaw Zola, Srinivas Aluru, Andrew D. Johnson, Daniel Janies, Alexandros Stamatakis
2008 B conf
Parallel Construction of Bidirected String Graphs for Genome Assembly.
ICPP
Benjamin G. Jackson, Srinivas Aluru
2008 Misc conf
Parallel Information Theory Based Construction of Gene Regulatory Networks.
HiPC
Jaroslaw Zola, Maneesha Aluru, Srinivas Aluru
2008 A conf
Parallel biological sequence alignments on the Cell Broadband Engine.
IPDPS
Abhinav Sarje, Srinivas Aluru
2008 — ch.
Text Indexing.
Encyclopedia of Algorithms
Srinivas Aluru
2008 B conf
Tracking Nanostructural Evolution in Alloys: Large-Scale Analysis of Atom Probe Tomography Data on Blue Gene/L.
ICPP
Sudip Seal, Michael Moody, Anna Ceguerra, Simon P. Ringer, Krishna Rajan, Srinivas Aluru
2007 J jnl
Assembling genomes on large-scale parallel computers.
J. Parallel Distributed Comput.
Anantharaman Kalyanaraman, Scott J. Emrich, Patrick S. Schnable, Srinivas Aluru
2007 Misc ed.
High Performance Computing - HiPC 2007, 14th International Conference, Goa, India, December 18-21, 2007, Proceedings
HiPC
Srinivas Aluru, Manish Parashar, Ramamurthy Badrinath, Viktor K. Prasanna
2007 A conf
Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L.
SC
Michael Ott, Jaroslaw Zola, Alexandros Stamatakis, Srinivas Aluru
2007 — conf
Massively parallel expressed sequence tag clustering.
PDCS
Scott J. Emrich, Anantharaman Kalyanaraman, Srinivas Aluru
2007 C conf
Optimal Self-adjusting Trees for Dynamic String Data in Secondary Storage.
SPIRE
Pang Ko, Srinivas Aluru
2007 — conf
PARALLEL-TCOFFEE: A parallel multiple sequence aligner.
PDCS
Jaroslaw Zola, Xiao Yang, Adrian Rospondek, Srinivas Aluru
2007 — ch.
Spatial Domain Decomposition Methods in Parallel Scientific Computing.
Handbook of Parallel Computing
Srinivas Aluru, Sudip Seal
2007 A conf
Symposium Evening Tutorial: High-performance Computing Methods for Computational Genomics.
IPDPS
Srinivas Aluru, David A. Bader, Anantharaman Kalyanaraman
2007 Misc conf
The Combinatorics of Sequencing the Corn Genome.
COCOON
Srinivas Aluru
2006 B conf
A Formal Analysis of Space Filling Curves for Parallel Domain Decomposition.
ICPP
Srikanta Tirthapura, Sudip Seal, Srinivas Aluru
2006 A conf
Assembling genomes on large-scale parallel computers.
IPDPS
Anantharaman Kalyanaraman, Scott J. Emrich, Patrick S. Schnable, Srinivas Aluru
2006 — ch.
Bioinformatics.
Handbook of Nature-Inspired and Innovative Computing
Srinivas Aluru
2006 — conf
Communication-aware Parallel Domain Decomposition using Space Filling Curves.
PDCS
Sudip Seal, Srinivas Aluru
2006 J jnl
Editorial: Special Section on High-Performance Computational Biology.
IEEE Trans. Parallel Distributed Syst.
Srinivas Aluru, Nancy M. Amato, David A. Bader
2006 J jnl
Efficient Algorithms and Software for Detection of Full-length Ltr Retrotransposons.
J. Bioinform. Comput. Biol.
Anantharaman Kalyanaraman, Srinivas Aluru
2006 A conf
M11 - High-performance computing methods for computational genomics.
SC
Srinivas Aluru, David A. Bader, Anantharaman Kalyanaraman
2006 B conf
Obtaining Provably Good Performance from Suffix Trees in Secondary Storage.
CPM
Pang Ko, Srinivas Aluru
2006 — ch.
Parallel Computational Biology.
Parallel Processing for Scientific Computing
Srinivas Aluru, Nancy M. Amato, David A. Bader, Suchindra Bhandarkar, Laxmikant V. Kalé, Dan C. Marinescu
2005 J jnl
An optimal hierarchical clustering algorithm for gene expression data.
Inf. Process. Lett.
Sudip Seal, Srikanth Komarina, Srinivas Aluru
2005 — conf
Consensus Genetic Maps: A Graph Theoretic Approach.
CSB
Benjamin G. Jackson, Srinivas Aluru, Patrick S. Schnable
2005 — conf
Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons.
CSB
Anantharaman Kalyanaraman, Srinivas Aluru
2005 J jnl
Efficient parallel algorithms and software for compressed octrees with applications to hierarchical methods.
Parallel Comput.
Bhanu Hariharan, Srinivas Aluru
2005 — conf
Indexing for Subscription Covering in Publish-Subscribe Systems.
PDCS
Zhenhui Shen, Srinivas Aluru, Srikanta Tirthapura
2005 J jnl
Parallel algorithms for tree accumulations.
J. Parallel Distributed Comput.
Fatih Erdogan Sevilgen, Srinivas Aluru, Natsuhiko Futamura
2005 J jnl
Scalable, memory efficient, high-speed IP lookup algorithms.
IEEE/ACM Trans. Netw.
Rama Sangireddy, Natsuhiko Futamura, Srinivas Aluru, Arun K. Somani
2005 J jnl
Space efficient linear time construction of suffix arrays.
J. Discrete Algorithms
Pang Ko, Srinivas Aluru
2004 J jnl
A strategy for assembling the maize (Zea mays L.) genome.
Bioinform.
Scott J. Emrich, Srinivas Aluru, Yan Fu, Tsui-Jung Wen, Mahesh Narayanan, Ling Guo, Daniel A. Ashlock, Patrick S. Schnable
2004 — conf
A tunable collective communication framework on a cluster of SMPS.
Parallel and Distributed Computing and Networks
Meng-Shiou Wu, Ricky A. Kendall, Srinivas Aluru
2004 — conf
Efficient Methods for Database Storage and Retrieval Using Space-Filling Curves.
ISCIS
Srinivas Aluru, Fatih Erdogan Sevilgen
2004 — ch.
Quadtrees and Octrees.
Handbook of Data Structures and Applications
Srinivas Aluru
2004 J jnl
Space and Time Optimal Parallel Sequence Alignments.
IEEE Trans. Parallel Distributed Syst.
Stjepan Rajko, Srinivas Aluru
2004 — conf
Space-Conserving Optimal DNA-Protein Alignment .
CSB
Pang Ko, Mahesh Narayanan, Anantharaman Kalyanaraman, Srinivas Aluru
2004 J jnl
Special Issue: High Performance Computational Biology.
Concurr. Pract. Exp.
David A. Bader, Srinivas Aluru
2004 — ch.
Suffix Trees and Suffix Arrays.
Handbook of Data Structures and Applications
Srinivas Aluru
2003 — conf
Computational biology on parallel computers.
ECC
Srinivas Aluru
2003 J jnl
Guest Editor's Introduction: Special issue on high-performance computational biology.
J. Parallel Distributed Comput.
Srinivas Aluru, David A. Bader
2003 J jnl
Parallel Syntenic Alignments.
Parallel Process. Lett.
Natsuhiko Futamura, Srinivas Aluru, Xiaoqiu Huang
2003 J jnl
Parallel biological sequence comparison using prefix computations.
J. Parallel Distributed Comput.
Srinivas Aluru, Natsuhiko Futamura, Kishan Mehrotra
2003 B conf
Scalable, memory efficient, high-speed lookup and update algorithms for IP routing.
ICCCN
Natsuhiko Futamura, Rama Sangireddy, Srinivas Aluru, Arun K. Somani
2003 B conf
Space Efficient Linear Time Construction of Suffix Arrays.
CPM
Pang Ko, Srinivas Aluru
2003 B conf
Space and Time Optimal Parallel Sequence Alignments.
ICPP
Stjepan Rajko, Srinivas Aluru
2003 J jnl
Space and time efficient parallel algorithms and software for EST clustering.
IEEE Trans. Parallel Distributed Syst.
Anantharaman Kalyanaraman, Srinivas Aluru, Volker Brendel, Suresh C. Kothari
2002 A conf
A scalable parallel fast multipole method for analysis of scattering from perfect electrically conducting surfaces.
SC
Bhanu Hariharan, Srinivas Aluru, Balasubramaniam Shanker
2002 J jnl
Efficient Parallel Algorithms for Solvent Accessible Surface Area of Proteins.
IEEE Trans. Parallel Distributed Syst.
Natsuhiko Futamura, Srinivas Aluru, Desh Ranjan, Bhanu Hariharan
2002 C conf
Mixed Mode Matrix Multiplication.
CLUSTER
Meng-Shiou Wu, Srinivas Aluru, Ricky A. Kendall
2002 A conf
Parallel EST Clustering.
IPDPS
Anantharaman Kalyanaraman, Srinivas Aluru, Suresh C. Kothari
2002 Misc conf
Parallel Syntenic Alignments.
HiPC
Natsuhiko Futamura, Srinivas Aluru, Xiaoqiu Huang
2002 B conf
Space and Time Efficient Parallel Algorithms and Software for EST Clustering.
ICPP
Anantharaman Kalyanaraman, Srinivas Aluru, Suresh C. Kothari
2002 A conf
Workshop Introduction.
IPDPS
David A. Bader, Srinivas Aluru
2001 Misc conf
Efficient Parallel Algorithms and Software for Compressed Octrees with Applications to Hierarchical Methods.
HiPC
Bhanu Hariharan, Srinivas Aluru
2000 A conf
A Provably Optimal, Distribution-Independent Parallel Fast Multipole Method.
IPDPS
Fatih Erdogan Sevilgen, Natsuhiko Futamura, Srinivas Aluru
2000 J jnl
Parallel Construction of Multidimensional Binary Search Trees.
IEEE Trans. Parallel Distributed Syst.
Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka
1999 Misc conf
A Parallel Monte Carlo Algorithm for Protein Accessible Surface Area Computation.
HiPC
Srinivas Aluru, Desh Ranjan, Natsuhiko Futamura
1999 Misc conf
A Practical Parallel Algorithm for Line Segment Visibility.
PDPTA
Srinivas Aluru, Songrit Maneewongvatana
1999 A conf
A Unifying Data Structure for Hierarchical Methods.
SC
Fatih Erdogan Sevilgen, Srinivas Aluru
1999 — conf
Dynamic Compressed Hypertoctrees with Application to the N-Body Problem.
FSTTCS
Srinivas Aluru, Fatih Erdogan Sevilgen
1999 — conf
Parallel Biological Sequence Comparison Using Prefix Computations.
IPPS/SPDP
Srinivas Aluru, Natsuhiko Futamura, Kishan Mehrotra
1998 J jnl
Distribution-Independent Hierarchical Algorithms for the N-body Problem.
J. Supercomput.
Srinivas Aluru, John L. Gustafson, Gurpur M. Prabhu, Fatih Erdogan Sevilgen
1997 J jnl
Lagged Fibonacci Random Number Generators for Distributed Memory Parallel Computers.
J. Parallel Distributed Comput.
Srinivas Aluru
1997 Misc conf
Parallel domain decomposition and load balancing using space-filling curves.
HiPC
Srinivas Aluru, Fatih Erdogan Sevilgen
1997 J jnl
Practical Algorithms for Selection on Coarse-Grained Parallel Computers.
IEEE Trans. Parallel Distributed Syst.
Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka
1996 — conf
Concatenated parallelism: a technique for efficient parallel divide and conquer.
SPDP
Sanjay Goil, Srinivas Aluru, Sanjay Ranka
1996 J jnl
Greengard's
SIAM J. Sci. Comput.
Srinivas Aluru
1996 J jnl
Massively Parallel Searching for Better Algorithms or How to Do a Cross Product with Five Multiplications.
Sci. Program.
John L. Gustafson, Srinivas Aluru
1996 A conf
Parallel Additive Lagged Fibonacci Random Number Generators.
International Conference on Supercomputing
Srinivas Aluru
1996 A conf
Parallel Construction of Multidimensional Binary Search Trees.
International Conference on Supercomputing
Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka
1996 — conf
Practical Algorithms for Selection on Coarse-Grained Parallel Computers.
IPPS
Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka
1996 Misc conf
Practical Paralle1 Algorithm for Constructing Line Arrangements.
PDPTA
Srinivas Aluru, Songrit Maneewongvatana
1995 — conf
Properties of Binomial Coefficients and Implications to Parallelizing Lagged Fibonacci Random Number Generators.
ICPP (3)
Srinivas Aluru
1994 — —
Distribution-independent hierarchical N-body methods.
Srinivas Aluru
1994 A conf
Truly distribution-independent algorithms for the N-body problem.
SC
Srinivas Aluru, Gurpur M. Prabhu, John L. Gustafson
1993 A conf
A Massively Parallel Optimizer for Expression Evaluation.
International Conference on Supercomputing
Srinivas Aluru, John L. Gustafson
1993 — conf
Subtle Issues of SIMD Tree Search.
PARCO
Srinivas Aluru, John L. Gustafson
1992 J jnl
A random number generator for parallel computers.
Parallel Comput.
Srinivas Aluru, Gurpur M. Prabhu, John L. Gustafson