Publications
(Google Scholar)

• Wang, Y., Wang, Q., Koehler, H. and Lin, Y., " Query-by-Sketch: Scaling Shortest Path Graph Queries on Very Large Networks", in press, The ACM Special Interest Group on Management of Data SIGMOD'21 (2021).
• Xue, H., Yang, L., Rajan, V., Jiang, W., Wei, Y. and Lin, Y., " Multiplex Bipartite Network Embedding using Dual Hypergraph Convolutional Networks", in press, The Web Conference 2021 WWW'21 (2021).
• Wickramarachchi, A., Lin, Y., " LRBinner: Binning Long Reads in Metagenomics Datasets", accepted, Proc. 21th Workshop on Algorithms in Bioinformatics WABI'21, (2021).
• Mallawaarachchi, V., Wickramarachchi, A., Lin, Y., "Improving metagenomic binning results with overlapped bins using assembly graphs," BMC Algorithms for Molecular Biology 16:3, (2021).
• Wickramarachchi, A., Lin, Y., " GraphPlas: Refined Classification of Plasmid Sequences using Assembly Graphs", The 19th Asia Pacific Bioinformatics Conference APBC'21, in press at IEEE/ACM Trans. on Computational Biology and Bioinformatics (2021).
• Zhao, J., Feng, H., Zhu, D., Lin, Y., " MultiTrans: a novel algorithm for transcriptome assembly through mixed integer linear programming", The 19th Asia Pacific Bioinformatics Conference APBC'21, in press at IEEE/ACM Trans. on Computational Biology and Bioinformatics (2021).
• Li, Y., Patel, H., Lin, Y., " Kmer2SNP: reference-free SNP calling from raw reads based on matching", IEEE International Conference on Bioinformatics and Biomedicine BIBM'20, pp 208-212, (2020).
• Wickramarachchi, A., Mallawaarachchi, V., Rajan V., Lin, Y., " MetaBCC-LR: Metagenomics Binning by Coverage and Composition for Long Reads", Proc. 28th Conf. on Intelligent Systems for Molecular Biology ISMB'20, in Bioinformatics (2020).
• Mallawaarachchi, V., Wickramarachchi, A., Lin, Y., " GraphBin2: refined and overlapped binning of metagenomic contigs using assembly graphs", Proc. 20th Workshop on Algorithms in Bioinformatics WABI'20, (2020).
• Mallawaarachchi, V., Wickramarachchi, A., Lin Y., " GraphBin: refined binning of metagenomic contigs using assembly graphs", Bioinformatics, (2020).
• Li, Y., Lin, Y., " DCHap: A divide-and-conquer haplotype phasing algorithm for third-generation sequencing data", The 18th Asia Pacific Bioinformatics Conference APBC'20, in press, IEEE/ACM Trans. on Computational Biology and Bioinformatics (2020).
• Xue, H., Yang, L., Jiang, W., Wei, Y., Hu, Y., Lin, Y., " Modeling Dynamic Heterogeneous Network for Link Prediction using Hierarchical Attention with Temporal RNN", The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases ECML-PKDD'20 (2020).
• Liany, H., Lin, Y., Jeyasekharan, A., Rajan, V., " Mining Pathway Associations from Networks of Mutual Exclusivity Interactions", 24th International Conference on Research in Computational Molecular Biology, Satellite: Computational Cancer Biology RECOMB-CCB'20 (2020).
• Iftikhar, M., Wang, Q., Lin, Y., " dK-Microaggregation: Anonymizing Graphs with Differential Privacy Guarantees", Pacific-Asia Conference on Knowledge Discovery and Data Mining PAKDD'20 (2020).
• Yang, Y., Liu, X., Shen, Y., Lin, Y., Yang, P., Qiao, L., " In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics", Nature Communications, 11 (1), 1-11, (2020).
• Kolmogorov, M., Yuan, J., Lin, Y., Pevzner, P., " Assembly of Long Error-Prone Reads Using Repeat Graphs", Nature Biotechnology, 37, 540-546, (2019).
• Zhang, Y., Liu, W., Lin, Y., Ng, Y. and Li, S. " Large-scale 3D chromatin reconstruction from chromosomal contacts", BMC Genomics, 20 (Suppl 2) :186 (2019)
• Shao, J., Wang, Q., and Lin, Y., " Skyblocking for entity resolution", Information Systems, 85, pp30-43 (2019).
• Iftikhar, M., Wang, Q., Lin, Y., " Publishing Differentially Private Datasets via Stable Microaggregation", Proc. 22nd Int'l Conference on Extending Database Technology, EDBT'19 (2019).
• Farhan, M., Wang, Q., Lin, Y., Mckay, B. " A Highly Scalable Labelling Approach for Exact Distance Queries in Complex Networks", Proc. 22nd Int'l Conference on Extending Database Technology, EDBT'19 (2019).
• Wong T., Ranjard, L., Lin, Y., Rodrigo, A., " HaploJuice: accurate haplotype assembly from a pool of sequences with known relative concentrations", BMC Bioinformatics, 22;19(1):389 (2018)
• Yang, Y., Lin, Y., and Qiao, L. " Direct MALDI-TOF MS Identification of Bacterial Mixtures", Analytical Chemistry, 90 (17), pp 10400-0408 (2018)
• Pu, L., Lin, Y., and Pevzner, P.A. " Detection and analysis of ancient segmental duplications in mammalian genomes", Genome Research, 28: 901-909 (2018).
• Xia, R., Lin, Y.,, Zhou, J., Feng, B. and Tang, J., " Phylogenetic Reconstruction for Copy-Number Evolution Problems", IEEE/ACM Trans. on Computational Biology and Bioinformatics, (2018).
• Kolmogorov, M., Yuan, J., Lin, Y., and Pevzner, P.A., " Assembly of Long Error-Prone Reads and Repeat Classification", Proc. 22nd Int'l Conf. on Research in Comput. Molecular Bio. RECOMB'18 (2018).
• Xia, R., Lin, Y., Zhou, J., Feng, B., and Tang, J., " A Median Solver and Phylogenetic Inference Based on Double-Cut-and-Join Sorting," Journal of Computational Biology 25, 3 (2018)
• Feng, B., Lin, Y., Zhou, L., Guo, Y., Friedman, R., Xia, R., Hu, F., Liu, C., and Tang, J., " Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data", Scientific Reports 7 (1), 15209 (2017)
• Pu, L., Lin, Y., Zhu, D. and Jiang, H. "Can a breakpoint graph be decomposed into none other than 2-cycles?", Theoretical Computer Science (2017)
• Zhou, L., Lin, Y., Feng, B., Zhao, J., and Tang, J., "Phylogeny analysis from gene-order data with massive duplications," BMC Genomics 18 (7), 13 (2017)
• Yang, Y., Lin, Y., Chen, Z., Gong, T., Yang, P., Girault, H., Liu, B., and Qiao, L. " Bacterial Whole Cell Typing by Mass Spectra Pattern Matching with Bootstrapping Assessment," Analytical Chemistry 89 (22), 12556-12561 (2017).
• Lin, Y., Yuan, J., Shen, M.W., Kolmogorova, M., Chaissonb, M. and Pevzner, P.A., "Assembly of long error-prone reads using de Bruijn graphs," Proc Natl Acad Sci 113 (52) E8396-E8405 (2016).
• Zhou, L., Lin, Y., Feng, B., Zhao, J., and Tang, J., "Phylogeny Reconstruction from Whole-Genome Data Using Variable Length Binary Encoding", Proc. 12th Int'l Symp.Bioinformatics Research & Appls. ISBRA16, 345-346, (2016)
• Zhou, J., Lin, Y., Rajan, V., Hoskins, W., Feng, B., and Tang, J., "Analysis of gene copy number changes in tumor phylogenetics", Algorithms for Molecular Biology 11(1) 26, (2016)
• Lin, Y., Shen, M.W., Yuan, J., and Pevzner, P.A., "Assembly of long error-prone reads using de Bruijn graphs", Proc. 20th Int'l Conf. on Research in Comput. Molecular Bio. RECOMB'16 (2016).
• Nair, N.U., Hunter, L., Shao, M., Grnarova, P., Lin, Y., Bucher, P., and Moret, B.M.E., " A maximum-likelihood approach for building cell-type trees by lifting", Proc. 14th Asia-Pacific Bioinf. Conf. APBC'16, Best Paper Award, in BMC Genomics, 17, 1, 14 (2016).
• Zhou, J., Lin, Y., Rajan, V., Hoskins, W., and Tang. J., " Maximum parsimony analysis of gene copy number changes in tumor phylogenetics," Proc. 15th Workshop on Algorithms in Bioinformatics WABI'15, Lecture Notes in Computer Science 9289, 108-120, Springer Berlin Heidelberg, (2015).
• Zhou, J., Lin, Y., Hoskins, W., and Tang. J., " An iterative approach for phylogenetic analysis of tumor progression using FISH copy number," Int'l Symp.Bioinformatics Research & Appls. ISBRA'15, Lecture Notes in Computer Science 9096, 402-412. Springer International Publishing (2015).
• Shao, M., Lin, Y., and Moret, B.M.E., " An exact algorithm to compute the DCJ distance for genomes with duplicate genes," J. Computational Biology 22, 5 (2015), 425-435.
• Lin, Y. and Pevzner, P.A., "Manifold de Bruijn Graphs," Proc. 14th Workshop on Algorithms in Bioinformatics WABI'14, Lecture Notes in Computer Science 8701, 296-310, Springer Berlin Heidelberg, (2014).
• Lin, Y., Nurk, S., and Pevzner, P.A., " What is the difference between the breakpoint graph and the de Bruijn graph?" BMC Genomics 15(Suppl 6), S6, (2014).
• Hu, F., Lin, Y., and Tang, J., " MLGO: phylogeny reconstruction and ancestral inference from gene-order data, " BMC Bioinformatics, 15:354, (2014).
• Nair, N.U., Lin, Y., Manasovska, A., Antic, J., Grnarova, P., Sahu, A.D., Bucher, P., and Moret, B.M.E., "Study of cell differentiation by phylogenetic analysis using histone modification data," BMC Bioinformatics, 15:269 (2014).
• Shao, M., and Lin, Y., and Moret, B.M.E., "An exact algorithm to compute the DCJ distance for genomes with duplicate genes," Proc. 18th Int'l Conf. on Research in Comput. Molecular Bio. RECOMB'14, in Lecture Notes in Computer Science 8394, 280-292, Springer Verlag (2014).
• Moret, B.M.E., Lin, Y., and Tang, J., "Rearrangements in phylogenetic inference: Compare, model, or encode?", in Models and Algorithms for Genome Evolution, vol. 19 of Computational Biology series, Chauve, C., et al., eds, Springer Verlag (2013), 147-172.
• Lin, Y., Hu, F., Tang, J., and Moret, B.M.E., " Maximum likelihood phylogenetic reconstruction from high-resolution whole-genome data and a tree of 68 eukaryotes," Proc. 18th Pacific Symp. on Biocomputing PSB'13, pp. 285-296, 2013,
• Nair, N.U., Lin, Y., Bucher, P., and Moret, B.M.E., "Phylogenetic analysis of cell types using histone modifications," Proc. 13th Workshop on Algorithms in Bioinformatics WABI'13, in Lecture Notes in Computer Science 8126, 326-337, Springer Verlag (2013).
• Shao, M., and Lin, Y., and Moret, B.M.E., "Sorting genomes with rearrangements and segmental duplications through trajectory graphs," Proc. 11th RECOMB Workshop on Comparative Genomics RECOMB-CG'13, in BMC Bioinformatics 14, Suppl. 15, S9 (2013).
• Lin, Y., Rajan, V., and Moret, B.M.E., "A metric for phylogenetic trees based on matching," IEEE/ACM Trans. on Computational Biology and Bioinformatics, 9, 4 (2012), 1014-1022.
• Lin, Y., Rajan, V., and Moret, B.M.E., "TIBA: A tool for phylogeny inference from rearrangement data with bootstrap analysis," Bioinformatics 28, 24 (2012), 3324-3325.
• Lin, Y., Rajan, V., and Moret, B.M.E., "Bootstrapping phylogenies inferred from rearrangement data," BMC Algorithms for Molecular Biology 7:21, 2012. (selected papers from WABI'11)
• Shao, M., and Lin, Y., " Approximating the edit distance for genomes under DCJ, insertion and deletion," Proc. 10th RECOMB Workshop on Comparative Genomics RECOMB-CG'12, in BMC Bioinformatics 13 (Suppl 19):S13, 2012.
• Lin, Y., Rajan, V., and Moret, B.M.E., "Bootstrapping phylogenies inferred from rearrangement data," Proc. 11th Workshop on Algorithms in Bioinformatics WABI'11, Lecture Notes in Computer Science 6833, 175-187, Springer Verlag (2011).
• Lin, Y., and Moret, B.M.E., "A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes," J. Computational Biology 18(9): 1055-1064 (2011). (special issue on RECOMB-CG'10).
• Lin, Y., Rajan, V., and Moret, B.M.E., "Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator," J. Computational Biology 18(9): 1131-1139 (2011). (special issue on RECOMB-CG'10).
• Lin, Y., Rajan, V., and Moret, B.M.E., "A metric for phylogenetic trees based on matching," Proc. 7th Int'l Symp. Bioinformatics Research & Appls. ISBRA'11, Lecture Notes in Computer Science 6674, 197-208, Springer Verlag (2011).
• Lin, Y., and Moret, B.M.E., "A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes," Proc. 8th RECOMB Workshop on Comparative Genomics RECOMB-CG'10, in Lecture Notes in Computer Science 6398, 228-239, Springer Verlag (2010).
• Lin, Y., Rajan, V., and Moret, B.M.E., "Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator," Proc. 8th RECOMB Workshop on Comparative Genomics RECOMB-CG'10, in Lecture Notes in Computer Science 6398, 137-148, Springer Verlag (2010).
• Lin, Y., Rajan, V., Swenson, K.M., and Moret, B.M.E., "Estimating true evolutionary distances under rearrangements, duplications, and losses," Proc. 8th Asia-Pacific Bioinformatics Conf. APBC'10, in BMC Bioinformatics 2010, 11 (Suppl. 1):S54.
• Rajan, V., Xu, A.W., Lin, Y., Swenson, K.M., and Moret, B.M.E., "Heuristics for the inversion median problem," Proc. 8th Asia-Pacific Bioinformatics Conf. APBC'10, in BMC Bioinformatics 2010, 11 (Suppl. 1):S30.
• Swenson, K.M., Rajan, V., Lin, Y., and Moret, B.M.E., "Sorting signed permutations by inversions in O(nlogn) time," J. Computational Biology, 17(3): 489-501 (2010) (special issue on RECOMB'09).
• Swenson, K.M., Lin, Y., Rajan, V., and Moret, B.M.E., "Hurdles and sorting by inversions: Combinatorial, statistical, and experimental results," J. Computational Biology, 16(10):1339-1351 (2009) (special issue on RECOMB-CG'08).
• Swenson, K.M., Rajan, V., Lin, Y., and Moret, B.M.E., "Sorting signed permutations by inversions in O(nlogn) time," Proc. 13th Int'l Conf. on Research in Comput. Molecular Biol. RECOMB'09, in Lecture Notes in Computer Science 5541, 386-399, Springer Verlag (2009).
• Lin, Y., and Moret, B.M.E., "Estimating true evolutionary distances under the DCJ model", Proc. 16th Conf. on Intelligent Systems for Molecular Biology ISMB'08, in Bioinformatics 24(13):i114-i122 (2008).
• Lin, Y., Qiao, Y., Sun, S., Yu, C, Dong G., and Bu, D. "A fragmentation event model for peptide identification by mass spectrometry," Proc. 12th Int'l Conf. on Research in Comput. Molecular Biol. RECOMB'08, in Lecture Notes in Computer Science 4955, 154-166, Springer Verlag (2008).
• Swenson, K.M., Lin, Y., Rajan, V., and Moret, B.M.E., "Hurdles hardly have to be heeded," Proc. 6th RECOMB Workshop on Comparative Genomics RECOMB-CG'08, in Lecture Notes in Computer Science5267, 239-249, Springer Verlag (2008).
• Wang, L., Lin, Y., and Liu, X., "Approximation algorithms for Biclustering problems," SIAM J. Comput. 38(4): 1504-1518 (2008).
• Sun, S., Yu, C., Qiao, Y., Lin, Y., Dong, G., Liu, C., Zhang, J., Zhang, Z., Cai, J., Zhang, H., and Bu, D., "Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra," J. Proteome Res., 7(01): 202-208 (2008).
• Yu, C., Lin, Y., Sun, S., Cai, J., Zhang, J., Bu, D., Zhang, Z., and Chen, R., "An iterative algorithm to quantify factors influencing peptide fragmentation during tandem mass spectrometry,"J Bioinform Comput Biol., 5(2a):297-311 (2007) (special issue on CSB'06).
• Wang, L., Lin, Y., andn Liu, X., "Approximation algorithms for Bi-clustering problems," Proc. 6th Workshop on Algorithms in Bioinformatics WABI'06, in Lecture Notes in Computer Science 4175, 310-320, Springer Verlag (2006).
• Yu, C., Lin, Y., Sun, S., Cai, J., Zhang, J., Bu, D., Zhang, Z., and Chen, R., "An iterative algorithm to quantify the factors influencing peptide fragmentation for MS/MS spectrum", Proc. 2006 LSS Computational Systems Bioinformatics Conference CSB'06, 353-360, Imperial College Press (2006)