Accelerating sequence alignment to graphs. 2019 IEEE 33rd International Symposium on Parallel and Distributed Processing.
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2019. On the complexity of sequence to graph alignment. International Conference on Research in Computational Molecular Biology.
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2019. Algorithmic framework for approximate matching under bounded edits with applications to sequence analysis. International Conference on Research in Computational Molecular Biology.
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2018. Cooperative neural networks (CoNN): Exploiting prior independence structure for improved classification. Advances in Neural Information Processing Systems.
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2018. A fast adaptive algorithm for computing whole-genome homology maps. Bioinformatics. 34:i748-i756.
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2018. Fast de Bruijn Graph Compaction in Distributed Memory Environments. IEEE/ACM transactions on computational biology and bioinformatics.
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2018. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature communications. 9:5114.
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2018. Interval stabbing on the Automata Processor. Journal of Parallel and Distributed Computing.
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2018. Optimizing high performance distributed memory parallel hash tables for DNA k-mer counting. Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis.
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2018. A Parallel Algorithm for Bayesian Network Inference Using Arithmetic Circuits. 2018 IEEE International Parallel and Distributed Processing Symposium (IPDPS).
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2018. Performance extraction and suitability analysis of multi-and many-core architectures for next generation sequencing secondary analysis. Proceedings of the 27th International Conference on Parallel Architectures and Compilation Techniques.
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2018. An Adaptive Parallel Algorithm for Computing Connected Components. IEEE Transactions on Parallel and Distributed Systems.
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2017. Distributed Memory Partitioning of High-Throughput Sequencing Datasets for Enabling Parallel Genomics Analyses. Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics.
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2017. A fast approximate algorithm for mapping long reads to large reference databases. International Conference on Research in Computational Molecular Biology.
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2017. A greedy alignment-free distance estimator for phylogenetic inference. BMC bioinformatics. 18:238.
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2017. Kmerind: A flexible parallel library for k-mer indexing of biological sequences on distributed memory systems. IEEE/ACM transactions on computational biology and bioinformatics.
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2017. Parallel Construction of Suffix Trees and the All-Nearest-Smaller-Values Problem. Parallel and Distributed Processing Symposium (IPDPS), 2017 IEEE International.
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2017. Parallel Exact Dynamic Bayesian Network Structure Learning with Application to Gene Networks. 2017 IEEE 24th International Conference on High Performance Computing (HiPC).
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2017. Probabilistic estimation of overlap graphs for large sequence datasets. Bioinformatics and Biomedicine (BIBM), 2017 IEEE International Conference on.
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2017. Reverse Engineering Gene Networks: A Comparative Study at Genome-scale. Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics.
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2017. Algorithmic techniques for solving graph problems on the automata processor. Parallel and Distributed Processing Symposium, 2016 IEEE International.
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2016. Discovering motifs in biological sequences using the micron automata processor. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 13:99–111.
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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.
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2016. An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings. International Symposium on Bioinformatics Research and Applications.
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2016. High Performance Pattern Matching using the Automata Processor. Parallel and Distributed Processing Symposium, 2016 IEEE International.
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2016.