Publications

(2020). Exact Transcript Quantification Over Splice Graphs. In Proceedings of WABI 2020; journal version in Alg. Mol. Bio. 2021..

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(2019). Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem. 19th International Workshop on Algorithms in Bioinformatics (WABI 2019) 18:1–18:19 (2019); journal version in Alg Mol Bio (2020).

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(2019). Context-Aware Seeds for Read Mapping. 19th International Workshop on Algorithms in Bioinformatics (WABI 2019) 15:1–15:13 (2019) (journal version in Alg Mol Bio).

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(2019). More accurate transcript assembly via parameter advising. The 2019 ICML Workshop on Computational Biology; journal version in Journal of Computational Biology.

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(2017). Theory and A Heuristic for the Minimum Path Flow Decomposition Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics 16(2):658-670.

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(2017). Improved search of large transcriptomic sequencing databases using split sequence bloom trees. International Conference on Research in Computational Molecular Biology, pages 257-271.

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(2016). Teaching Computation to Biologists (book review). Computing in Science & Engineering 18(1):4-5.

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(2016). Compact universal k-mer hitting sets. International Workshop on Algorithms in Bioinformatics, pages 257-268.

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(2015). Semi-nonparametric modeling of topological domain formation from epigenetic data. International Workshop on Algorithms in Bioinformatics, pages 148-161.

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(2015). Rapid, separable compression enables fast analyses of sequence alignments. Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics, pages 194-201.

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(2013). Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, pages 306-315.

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(2013). Multiscale identification of topological domains in chromatin. International Workshop on Algorithms in Bioinformatics, pages 300-312.

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(2012). The missing models: A data-driven approach for learning how networks grow. Proceedings of the 18th ACM SIGKDD international conference on Knowledge discovery and data mining, pages 42-50.

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(2011). Metric labeling and semi-metric embedding for protein annotation prediction. International Conference on Research in Computational Molecular Biology, pages 392-407.

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(2010). Uncovering many views of biological networks using ensembles of near-optimal partitions. MultiClust: 1st International Workshop on Discovering, Summarizing and Using Multiple Clusterings at KDD.

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(2010). Extracting between-pathway models from E-MAP interactions using expected graph compression. Annual International Conference on Research in Computational Molecular Biology, pages 248-262.

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(2010). Exploring biological network dynamics with ensembles of graph partitions. Pacific Symposium on Biocomputing (PSB), pages 166-177.

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(2008). What are decision trees?. Nature Biotechnology 26(9):1011-1013.

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(2008). Uncovering genomic reassortments among influenza strains by enumerating maximal bicliques. 2008 IEEE International Conference on Bioinformatics and Biomedicine, pages 223-230.

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(2006). A compact mathematical programming formulation for DNA motif finding. Annual Symposium on Combinatorial Pattern Matching, pages 233-245.

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(2004). The inapproximability of side-chain positioning. Technical Report. Princeton University, Princeton.

(2003). The side-chain positioning problem: a semidefinite programming formulation with new rounding schemes. Proceedings of the Paris C. Kanellakis memorial workshop on Principles of computing & knowledge: Paris C. Kanellakis memorial workshop on the occasion of his 50th birthday, pages 86-94.