Publications

Export 23 results:
[ Author(Desc)] Keyword Title Year
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A
Aluru S, Apostolico A, Thankachan SV.  2015.  Efficient alignment free sequence comparison with bounded mismatches. International Conference on Research in Computational Molecular Biology.
Aluru S, Jammula N.  2014.  A review of hardware acceleration for computational genomics. IEEE Design & Test. 31:19–30.
F
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.
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.
J
Jain C, Flick P, Pan T, Green O, Aluru S.  2017.  An Adaptive Parallel Algorithm for Computing Connected Components. IEEE Transactions on Parallel and Distributed Systems.
Jain C, Dilthey A, Koren S, Aluru S, Phillippy AM.  2017.  A fast approximate algorithm for mapping long reads to large reference databases. International Conference on Research in Computational Molecular Biology.
M
Misra S, Vasimuddin M, Pamnany K, Chockalingam SP, Dong Y, Xie M, Aluru MR, Aluru S.  2014.  Parallel bayesian network structure learning for genome-scale gene networks. SC14: International Conference for High Performance Computing, Networking, Storage and Analysis.
N
Nihalani R, Aluru S.  2016.  Effective Utilization of Paired Reads to Improve Length and Accuracy of Contigs in Genome Assembly. Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics.
P
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.
Pan T, Flick P, Jain C, Liu Y, Aluru S.  2016.  Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems. Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics.
R
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, 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, 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, Aluru S.  2014.  Finding motifs in biological sequences using the micron automata processor. Parallel and Distributed Processing Symposium, 2014 IEEE 28th International.
Roy I, Srivastava A, Aluru S.  2016.  Programming techniques for the Automata Processor. Parallel Processing (ICPP), 2016 45th International Conference on.
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.
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.
T
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.
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.
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.