Publications

Export 23 results:
Author Keyword Title [ Year(Desc)]
2014
Roy I, Aluru S.  2014.  Finding motifs in biological sequences using the micron automata processor. Parallel and Distributed Processing Symposium, 2014 IEEE 28th International.
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.
Aluru S, Jammula N.  2014.  A review of hardware acceleration for computational genomics. IEEE Design & Test. 31:19–30.
2015
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.
Aluru S, Apostolico A, Thankachan SV.  2015.  Efficient alignment free sequence comparison with bounded mismatches. International Conference on Research in Computational Molecular Biology.
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.
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.
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.
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.
2016
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.
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.
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.
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.
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.
Chockalingam S, Aluru M, Aluru S.  2016.  Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories. Microarrays. 5:23.
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.
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, Aluru S.  2016.  Programming techniques for the Automata Processor. Parallel Processing (ICPP), 2016 45th 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.
Liu Y, Loewer M, Aluru S, Schmidt B.  2016.  SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations. BMC Systems Biology. 10:47.
2017
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.