Publications

(2023). Algorithmic Foundations of Genome Graph Construction and Comparison. Ph.D. Thesis CMU-CB-23-101.

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(2023). Novel expression biomarkers via prediction of response to FOLFIRINOX (FFX) treatment for PDAC. Cancer Res (2023) 83 (7_Supplement): 1400.

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(2023). Molecular predictors and immunomodulatory role of dual checkpoint inhibitor blockade using ipilimumab/nivolumab in patients with extensive stage small cell lung cancer. J Clin Oncol 41, 2023 (suppl 16; abstr 8597).

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(2023). Computationally Efficient High-Dimensional Bayesian Optimization via Variable Selection. In Proceedings of AutoML 2023.

(2023). Low density and high conservation pattern-aware sequence sketch. bioRxiv 2022.10.18.512430.

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(2023). Reinforcement Learning for Robotic Liquid Handler Planning. In Proceedings of WABI 2023.

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(2023). Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants. In Proceedings of WABI 2023.

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(2023). Creating and Using Minimizer Sketches in Computational Genomics. J Comp. Biol. (2023).

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(2023). Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and its Variants. arXiv:2305.10577.

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(2022). Algorithms and computational methods for transcriptome analysis. Ph.D. (CMU-CB-22-108).

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(2022). The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance. ISMB 2022.

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(2022). Theory and Practice of Low-Density Minimizer Sketches. Ph.D. Dissertation.

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(2021). DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes. In Proceedings of RECOMB 2022..

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(2021). Personalized neural architecture search for federated learning.. In NeurIPS 2021 Workshop on New Frontiers in Federated Learning 2021..

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(2021). Discovery of a potential predictive marker for eribulin treatment and novel target genes in BRAF V600E mutant metastatic colorectal cancer using an AI-driven RNA-seq analysis platform: Translational research of the BRAVERY study (EPOC1701). Journal of Clinical Oncology 39(15 suppl): e15532 (2021).

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(2021). Constructing small genome graphs via string compression. ISMB 2021.

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(2021). Practical selection of representative sets of RNA-seq samples using a hierarchical approach. ISMB 2021.

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(2021). Sequence-specific minimizers via polar sets. ISMB 2021.

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(2021). Accounting for fragments of unexpected origin improves transcript quantification in RNA-seq simulations focused on increased realism. bioRxiv, doi: https://doi.org/10.1101/2021.01.17.426996.

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(2021). Capturing the complexity of topologically associating domains through multi-feature optimization. bioRxiv.

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(2020). Detecting anomalies in inferred transcript sequences and expression from RNA-seq. Ph.D. Thesis.

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(2020). Probabilistic method corrects previously uncharacterized Hi-C artifact. bioRxiv.

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(2020). Algorithms for the study of chromosomal structure variability. Ph.D. Dissertation.

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

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(2020). Novel target discovery in pembrolizumab-resistant gastric cancer using a comprehensive RNA-seq analysis pipeline. Journal of Clinical Oncology 38(15_suppl), e16541-e16541 (2020).

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(2020). Optimizing Dynamic Structures with Bayesian Generative Search. ICML 2020 (to appear).

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(2020). Harvestman: A framework for hierarchical feature learning and selection from whole genome sequencing data.. BMC Bioinformatics 22:174 (2021).

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(2020). Improved design and analysis of practical minimizers. Proceedings of ISMB 2020 (Bioinformatics).

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(2020). Lower density selection schemes via small universal hitting sets with short remaining path length. Proceedings of RECOMB 2020 (preprint: arXiv:2001.06550 [cs.DS]).

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(2019). VariantStore: A Large-Scale Genomic Variant Search Index. Genome Biology 22: 231 (2021).

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(2019). Finding ranges of optimal transcript expression quantification in cases of non-identifiability. RECOMB 2021.

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(2019). Estimating mutual information under measurement error. bioRxiv 852384.

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(2019). A statistical method for identifying consistently important features across samples. BioRxiv.

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(2019). Detecting, categorizing, and correcting coverage anomalies of RNA-seq quantification. Cell Systems 9:1-11.

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(2019). The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature 574:187-192 (2019).

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(2019). How much data is sufficient to learn high-performing algorithms?. To appear in STOC 2021 (preprint arXiv:1908.02894 cs.LG).

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(2019). Identification of Microbiota-Induced Gene Expression Changes in the Drosophila melanogaster Head. bioRxiv.

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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). Alignment and mapping methodology influence transcript abundance estimation. bioRxiv.

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(2019). Practical universal k-mer sets for minimizer schemes. To appear in ACM-BCB 2019.

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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). Quantifying the Benefit Offered by Transcript Assembly on Single-Molecule Long Reads. Genome Biology 20:287.

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(2019). Collective Model Fusion for Multiple Black-Box Experts. ICML PMLR 97:2742-2750, 2019.

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(2019). Sketching and Sublinear Data Structures in Genomics. Annual Review of Biomedical Data Science 2:93-118.

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(2019). Maximum Likelihood Reconstruction of Ancestral Networks by Integer Linear Programming. bioRxiv.

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(2019). Topological data analysis reveals principles of chromosome structure throughout cellular differentiation. 19th International Workshop on Algorithms in Bioinformatics (WABI 2019) 23:1–23:16 (2019).

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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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(2019). Locality sensitive hashing for the edit distance. Bioinformatics 35(14):i127-i135 (ISMB) 2019.

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(2019). Identification of Microbiota-Induced Gene Expression Changes in the Drosophila melanogaster Head. BioRxiv.

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(2019). Analysis of the structural variability of topologically associated domains as revealed by Hi-C. Nuc. Acids Res. Genomics and Bioinformatics 2(1):lqz008 (2020).

Preprint PDF Project Project DOI PubMed Central

(2018). Using the Ribodeblur pipeline to recover A-sites from yeast ribosome profiling data. Methods 137:67-70.

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(2018). SQUID: transcriptomic structural variation detection from RNA-seq. Genome Biology 19:52.

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(2018). Quantifying the similarity of topological domains across normal and cancer human cell types. Bioinformatics (ISMB) 34(13):i475-i483.

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(2018). Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery. Genome Biology 19:16.

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(2018). Improved search of large transcriptomic sequencing databases using split sequence bloom trees. Journal of Computational Biology 25(7):755-765.

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(2018). Asymptotically optimal minimizers schemes. Bioinformatics (ISMB) 34(13):i13-i22.

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(2018). Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami. HLA Typing, pages 235-247.

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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). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods 14:417-419.

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(2017). Improving the performance of minimizers and winnowing schemes. Bioinformatics (ISMB) 33(14):i110-117.

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(2017). Improving Bloom filter performance on sequence data using k-mer Bloom filters. Journal of Computational Biology 24(6):547-557.

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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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(2017). Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing. PLoS Computational Biology 13(10):e1005777.

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(2017). Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings. Nucleic Acids Research 45(7):3663-3673.

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(2017). Accurate recovery of ribosome positions reveals slow translation of wobble-pairing codons in yeast. Journal of Computational Biology 24(6):486-500.

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(2017). Accurate assembly of transcripts through phase-preserving graph decomposition. Nature Biotechnology 35:1167-1169.

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(2016). The second decade of the international conference on research in computational molecular biology (RECOMB). International Conference on Research in Computational Molecular Biology, pages 3-16.

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

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(2016). Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap. Bioinformatics 32(12):1880-1882.

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(2016). Fast search of thousands of short-read sequencing experiments. Nature Biotechnology 34:300-302.

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(2016). Exploring ribosome positioning on translating transcripts with ribosome profiling. Post-Transcriptional Gene Regulation, pages 71-97.

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(2016). Efficient index maintenance under dynamic genome modification. ArXiv Preprint ArXiv:1604.03132.

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(2016). Diffusion archeology for diffusion progression history reconstruction. Knowledge and Information Systems, pages 1-25.

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(2016). Deconvolution of ensemble chromatin interaction data reveals the latent mixing structures in cell subpopulations. Journal of Computational Biology 23(6):425-438.

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

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(2016). A pathway-centric view of spatial proximity in the 3D nucleome across cell lines. Scientific Reports 6:39279.

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(2016). A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. BMC Bioinformatics 17:155.

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(2015). Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping. Bioinformatics 31(10):1553-1560.

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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). Reference-based compression of short-read sequences using path encoding. Bioinformatics 31(12):1920-1928.

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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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(2015). Optimal seed solver: optimizing seed selection in read mapping. Bioinformatics 32(11):1632-1642.

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(2015). Data-dependent bucketing improves reference-free compression of sequencing reads. Bioinformatics 31(17):2770-2777.

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(2015). Convex risk minimization to infer networks from probabilistic diffusion data at multiple scales. 2015 IEEE 31st International Conference on Data Engineering, pages 663-674.

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(2014). Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology 32:462-464.

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(2014). Identification of alternative topological domains in chromatin. Algorithms for Molecular Biology, 914.

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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). Resolving spatial inconsistencies in chromosome conformation measurements. Algorithms for Molecular Biology 8:8.

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(2013). Predicting protein interactions via parsimonious network history inference. Bioinformatics 29(13):i237-i246.

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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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(2013). Higher-order chromatin domains link eQTLs with the expression of far-away genes. Nucleic Acids Research 42(1):87-96.

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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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(2012). Resolving spatial inconsistencies in chromosome conformation data. International Workshop on Algorithms in Bioinformatics, pages 288-300.

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(2012). Parsimonious reconstruction of network evolution. Algorithms for Molecular Biology 7:25.

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(2012). Graph rigidity reveals well-constrained regions of chromosome conformation embeddings. BMC Bioinformatics 13:241.

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(2012). Global network alignment using multiscale spectral signatures. Bioinformatics 28(23):3105-3114.

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(2012). Dynamic exploration of recording sessions between jazz musicians over time. ASE/IEEE International Conference on Social Computing, pages 368-376.

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(2012). Coral: an integrated suite of visualizations for comparing clusterings. BMC Bioinformatics 13:276.

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(2011). Network archaeology: uncovering ancient networks from present-day interactions. PLoS Computational Biology 7(4):e1001119.

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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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(2011). Extracting between-pathway models from E-MAP interactions using expected graph compression. Journal of Computational Biology 18(3):379-390.

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(2011). Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics 12:95.

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(2011). A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6):764-770.

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(2011). A cost-aggregating integer linear program for motif finding. Journal of Discrete Algorithms 9(4):326-334.

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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). The power of protein interaction networks for associating genes with diseases. Bioinformatics 26(8):1057-1063.

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(2010). Particle swarm optimization for multimodal combinatorial problems and its application to protein design. IEEE Congress on Evolutionary Computation, pages 1-8.

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(2010). GiRaF: robust, computational identification of influenza reassortments via graph mining. Nucleic Acids Research 39(6):e34.

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(2010). Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. Journal of Computational Biology 17(3):503–516.

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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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(2010). Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11:21.

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(2010). Alignment and clustering of phylogenetic markers-implications for microbial diversity studies. BMC Bioinformatics 11:152.

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(2009). Vertices of degree k in edge-minimal, k-edge-connected graphs. ArXiv Preprint ArXiv:0905.1064.

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(2009). Revealing biological modules via graph summarization. Journal of Computational Biology 16(2):253-264.

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(2009). Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. Annual International Conference on Research in Computational Molecular Biology, pages 400-417.

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(2009). A synthesis for exactly 3-edge-connected graphs. ArXiv Preprint ArXiv:0905.1053.

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(2009). A cooperative combinatorial particle swarm optimization algorithm for side-chain packing. 2009 IEEE Swarm Intelligence Symposium, pages 22-29.

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(2009). 2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates. Plos One 4(7):e6402.

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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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(2007). Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biology 8:R22.

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(2007). Genome analysis linking recent European and African influenza (H5N1) viruses. Emerging Infectious Diseases 13(5):713-718.

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(2007). A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes. Molecular Biology and Evolution 24:2091-2098.

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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.

(2004). Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformatics 21:1028-1039.

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(2004). A semidefinite programming approach to side chain positioning with new rounding strategies. INFORMS Journal on Computing 16:380-392.

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(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.

(2001). Experimental construction of very large scale DNA databases with associative search capability. International Workshop on DNA-Based Computers, pages 231-247.

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