Publications

Export 21 results:
Author [ Keyword(Asc)] Title Year
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Task Scheduling
Pamnany K, Misra S, Md V, Liu X, Chow E, Aluru S.  2015.  Dtree: Dynamic Task Scheduling at Petascale. International Conference on High Performance Computing.
String Data Structures
Flick P, Aluru S.  2015.  Parallel distributed memory construction of suffix and longest common prefix arrays. Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis.
Sequence Analysis
Rytsareva I, Campo DS, Zheng Y, Sims S, Tetik C, Chirag J, Chockalingam SP, Thankachan SV, Sue A, Aluru S et al..  2015.  Efficient detection of viral transmission with threshold-based methods. Computational Advances in Bio and Medical Sciences (ICCABS), 2015 IEEE 5th International Conference on.
Phylogenetic Inference
Thankachan SV, Chockalingam SP, Liu Y, Krishnan A, Aluru S.  2015.  A greedy alignment-free distance estimator for phylogenetic inference. Computational Advances in Bio and Medical Sciences (ICCABS), 2015 IEEE 5th International Conference on.
Graph Algorithms
Flick P, Jain C, Pan T, Aluru S.  2015.  A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications. Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis.
Automata Processor
Roy I, Aluru S.  2014.  Finding motifs in biological sequences using the micron automata processor. Parallel and Distributed Processing Symposium, 2014 IEEE 28th International.
Roy I, Aluru S.  2016.  Discovering motifs in biological sequences using the micron automata processor. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 13:99–111.
Roy I, Srivastava A, Grimm M, Aluru S.  2016.  Parallel interval stabbing on the automata processor. Proceedings of the Sixth Workshop on Irregular Applications: Architectures and Algorithms.
Roy I, Srivastava A, Nourian M, Becchi M, Aluru S.  2016.  High Performance Pattern Matching using the Automata Processor. Parallel and Distributed Processing Symposium, 2016 IEEE International.
Roy I, Jammula N, Aluru S.  2016.  Algorithmic techniques for solving graph problems on the automata processor. Parallel and Distributed Processing Symposium, 2016 IEEE International.
Roy I, Srivastava A, Aluru S.  2016.  Programming techniques for the Automata Processor. Parallel Processing (ICPP), 2016 45th International Conference on.
Approximate Sequence Matching
Aluru S, Apostolico A, Thankachan SV.  2015.  Efficient alignment free sequence comparison with bounded mismatches. International Conference on Research in Computational Molecular Biology.
Thankachan SV, Chockalingam SP, Liu Y, Krishnan A, Aluru S.  2015.  A greedy alignment-free distance estimator for phylogenetic inference. Computational Advances in Bio and Medical Sciences (ICCABS), 2015 IEEE 5th International Conference on.
Chockalingam SP, Thankachan SV, Aluru S.  2016.  A parallel algorithm for finding all pairs k-mismatch maximal common substrings. Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis.
Thankachan SV, Apostolico A, Aluru S.  2016.  A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem. Journal of Computational Biology. 23:472–482.
Thankachan SV, Chockalingam SP, Aluru S.  2016.  An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings. International Symposium on Bioinformatics Research and Applications.