Accelerating sequence alignment to graphs. 2019 IEEE 33rd International Symposium on Parallel and Distributed Processing.. 2019.
On the complexity of sequence to graph alignment. International Conference on Research in Computational Molecular Biology.. 2019.
Algorithmic framework for approximate matching under bounded edits with applications to sequence analysis. International Conference on Research in Computational Molecular Biology.. 2018.
Cooperative neural networks (CoNN): Exploiting prior independence structure for improved classification. Advances in Neural Information Processing Systems.. 2018.
A fast adaptive algorithm for computing whole-genome homology maps. Bioinformatics. 34:i748-i756.. 2018.
Fast de Bruijn Graph Compaction in Distributed Memory Environments. IEEE/ACM transactions on computational biology and bioinformatics.. 2018.
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature communications. 9:5114.. 2018.
Interval stabbing on the Automata Processor. Journal of Parallel and Distributed Computing.. 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.. 2018.
A Parallel Algorithm for Bayesian Network Inference Using Arithmetic Circuits. 2018 IEEE International Parallel and Distributed Processing Symposium (IPDPS).. 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.. 2018.
An Adaptive Parallel Algorithm for Computing Connected Components. IEEE Transactions on Parallel and Distributed Systems.. 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.. 2017.
A fast approximate algorithm for mapping long reads to large reference databases. International Conference on Research in Computational Molecular Biology.. 2017.
A greedy alignment-free distance estimator for phylogenetic inference. BMC bioinformatics. 18:238.. 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.. 2017.
Parallel Construction of Suffix Trees and the All-Nearest-Smaller-Values Problem. Parallel and Distributed Processing Symposium (IPDPS), 2017 IEEE International.. 2017.
Parallel Exact Dynamic Bayesian Network Structure Learning with Application to Gene Networks. 2017 IEEE 24th International Conference on High Performance Computing (HiPC).. 2017.
Probabilistic estimation of overlap graphs for large sequence datasets. Bioinformatics and Biomedicine (BIBM), 2017 IEEE International Conference on.. 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.. 2017.
Algorithmic techniques for solving graph problems on the automata processor. Parallel and Distributed Processing Symposium, 2016 IEEE International.. 2016.
Discovering motifs in biological sequences using the micron automata processor. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 13:99–111.. 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.. 2016.
An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings. International Symposium on Bioinformatics Research and Applications.. 2016.
High Performance Pattern Matching using the Automata Processor. Parallel and Distributed Processing Symposium, 2016 IEEE International.. 2016.