Approximation Algorithms for Bi-clustering Problems. - Lusheng Wang 001; Yu Lin 001; Xiaowen Liu (WABI, 2006)

An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry. - Chungong Yu; Yu Lin 001; Shiwei Sun; Jinjin Cai; Jingfen Zhang; Dongbo Bu; Zhuo Zhang; Runsheng Chen (J. Bioinform. Comput. Biol., 2007)

Estimating true evolutionary distances under the DCJ model. - Yu Lin 001; Bernard M. E. Moret (ISMB, 2008)

A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. - Yu Lin 001; Yantao Qiao; Shiwei Sun; Chungong Yu; Gongjin Dong; Dongbo Bu (RECOMB, 2008)

Hurdles Hardly Have to Be Heeded. - Krister M. Swenson; Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (RECOMB-CG, 2008)

Approximation Algorithms for Biclustering Problems. - Lusheng Wang 001; Yu Lin 001; Xiaowen Liu (SIAM J. Comput., 2008)

Sorting Signed Permutations by Inversions in O(nlogn) Time. - Krister M. Swenson; Vaibhav Rajan; Yu Lin 001; Bernard M. E. Moret (RECOMB, 2009)

Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results. - Krister M. Swenson; Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (J. Comput. Biol., 2009)

Estimating true evolutionary distances under rearrangements, duplications, and losses. - Yu Lin 001; Vaibhav Rajan; Krister M. Swenson; Bernard M. E. Moret (BMC Bioinform., 2010)

Heuristics for the inversion median problem. - Vaibhav Rajan; Andrew Wei Xu; Yu Lin 001; Krister M. Swenson; Bernard M. E. Moret (BMC Bioinform., 2010)

Sorting Signed Permutations by Inversions in O(nlogn) Time. - Krister M. Swenson; Vaibhav Rajan; Yu Lin 001; Bernard M. E. Moret (J. Comput. Biol., 2010)

A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes. - Yu Lin 001; Bernard M. E. Moret (J. Comput. Biol., 2011)

Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator. - Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (J. Comput. Biol., 2011)

Bootstrapping phylogenies inferred from rearrangement data. - Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (Algorithms Mol. Biol., 2012)

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis. - Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (Bioinform., 2012)

Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion. - Mingfu Shao; Yu Lin 001 (BMC Bioinform., 2012)

A Metric for Phylogenetic Trees Based on Matching. - Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Models and Algorithms for Whole-Genome Evolution and their Use in Phylogenetic Inference. - Yu Lin 001 (2012)

Rearrangements in Phylogenetic Inference: Compare, Model, or Encode? - Bernard M. E. Moret; Yu Lin 001; Jijun Tang (Models and Algorithms for Genome Evolution, 2013)

Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 Eukaryotes. - Yu Lin 001; Fei Hu; Jijun Tang; Bernard M. E. Moret (Pacific Symposium on Biocomputing, 2013)

Phylogenetic Analysis of Cell Types Using Histone Modifications. - Nishanth Ulhas Nair; Yu Lin 001; Philipp Bucher; Bernard M. E. Moret (WABI, 2013)

Sorting genomes with rearrangements and segmental duplications through trajectory graphs. - Mingfu Shao; Yu Lin 001; Bernard M. E. Moret (BMC Bioinform., 2013)

An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes. - Mingfu Shao; Yu Lin 001; Bernard M. E. Moret (RECOMB, 2014)

Manifold de Bruijn Graphs. - Yu Lin 001; Pavel A. Pevzner (WABI, 2014)

MLGO: phylogeny reconstruction and ancestral inference from gene-order data. - Fei Hu; Yu Lin 001; Jijun Tang (BMC Bioinform., 2014)

Study of cell differentiation by phylogenetic analysis using histone modification data. - Nishanth Ulhas Nair; Yu Lin 001; Ana Manasovska; Jelena Antic; Paulina Grnarova; Avinash Das Sahu; Philipp Bucher; Bernard M. E. Moret (BMC Bioinform., 2014)

An Iterative Approach for Phylogenetic Analysis of Tumor Progression Using FISH Copy Number. - Jun Zhou; Yu Lin 001; William Hoskins; Jijun Tang (ISBRA, 2015)

Maximum Parsimony Analysis of Gene Copy Number Changes. - Jun Zhou; Yu Lin 001; Vaibhav Rajan; William Hoskins; Jijun Tang (WABI, 2015)

An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes. - Mingfu Shao; Yu Lin 001; Bernard M. E. Moret (J. Comput. Biol., 2015)

Assembly of Long Error-Prone Reads Using de Bruijn Graphs. - Yu Lin 001; Max W. Shen; Jeffrey Yuan; Mark Chaisson; Pavel A. Pevzner (RECOMB, 2016)

Analysis of gene copy number changes in tumor phylogenetics. - Jun Zhou; Yu Lin 001; Vaibhav Rajan; William Hoskins; Bing Feng; Jijun Tang (Algorithms Mol. Biol., 2016)

A maximum-likelihood approach for building cell-type trees by lifting. - Nishanth Ulhas Nair; Laura Hunter; Mingfu Shao; Paulina Grnarova; Yu Lin 001; Philipp Bucher; Bernard M. E. Moret (BMC Genom., 2016)

Assembly of long error-prone reads using de Bruijn graphs. - Yu Lin 001; Jeffrey Yuan; Mikhail Kolmogorov; Max W. Shen; Mark Chaisson; Pavel A. Pevzner (Proc. Natl. Acad. Sci. USA, 2016)

Assembly of Long Error-Prone Reads Using Repeat Graphs. - Mikhail Kolmogorov; Jeffrey Yuan; Yu Lin 001; Pavel A. Pevzner (RECOMB, 2018)

HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations. - Thomas K. F. Wong; Louis Ranjard; Yu Lin 001; Allen G. Rodrigo (BMC Bioinform., 2018)

Skyblocking: Learning Blocking Schemes on the Skyline. - Jingyu Shao; Qing Wang 002; Yu Lin 001 (CoRR, 2018)

A Median Solver and Phylogenetic Inference Based on Double-Cut-and-Join Sorting. - Ruofan Xia; Yu Lin 001; Jun Zhou; Bing Feng; Jijun Tang (J. Comput. Biol., 2018)

Can a breakpoint graph be decomposed into none other than 2-cycles? - Lianrong Pu; Yu Lin 001; Daming Zhu; Haitao Jiang (Theor. Comput. Sci., 2018)

A Highly Scalable Labelling Approach for Exact Distance Queries in Complex Networks. - Muhammad Farhan; Qing Wang 002; Yu Lin 001; Brendan D. McKay (EDBT, 2019)

Publishing Differentially Private Datasets via Stable Microaggregation. - Masooma Iftikhar; Qing Wang 002; Yu Lin 001 (EDBT, 2019)

Large-scale 3D chromatin reconstruction from chromosomal contacts. - Yanlin Zhang; Weiwei Liu 008; Yu Lin 001; Yen Kaow Ng; Shuaicheng Li 001 (BMC Genom., 2019)

Skyblocking for entity resolution. - Jingyu Shao; Qing Wang 002; Yu Lin 001 (Inf. Syst., 2019)

Phylogenetic Reconstruction for Copy-Number Evolution Problems. - Ruofan Xia; Yu Lin 001; Jun Zhou; Tieming Geng; Bing Feng; Jijun Tang (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Kmer2SNP: reference-free SNP calling from raw reads based on matching. - Yanbo Li; Hardip Patel; Yu Lin 001 (BIBM, 2020)

dK-Microaggregation: Anonymizing Graphs with Differential Privacy Guarantees. - Masooma Iftikhar; Qing Wang 002; Yu Lin 001 (PAKDD (2), 2020)

Modeling Dynamic Heterogeneous Network for Link Prediction Using Hierarchical Attention with Temporal RNN. - Hansheng Xue; Luwei Yang; Wen Jiang; Yi Wei; Yi Hu; Yu Lin 001 (ECML/PKDD (1), 2020)

GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs. - Vijini Mallawaarachchi; Anuradha Wickramarachchi; Yu Lin 001 (WABI, 2020)

GraphBin: refined binning of metagenomic contigs using assembly graphs. - Vijini Mallawaarachchi; Anuradha Wickramarachchi; Yu Lin 001 (Bioinform., 2020)

MetaBCC-LR: metagenomics binning by coverage and composition for long reads. - Anuradha Wickramarachchi; Vijini Mallawaarachchi; Vaibhav Rajan; Yu Lin 001 (Bioinform., 2020)

Query-by-Sketch: Scaling Shortest Path Graph Queries on Very Large Networks. - Ye Wang; Qing Wang 002; Henning Koehler; Yu Lin 001 (SIGMOD Conference, 2021)

LRBinner: Binning Long Reads in Metagenomics Datasets. - Anuradha Wickramarachchi; Yu Lin 001 (WABI, 2021)

Multiplex Bipartite Network Embedding using Dual Hypergraph Convolutional Networks. - Hansheng Xue; Luwei Yang; Vaibhav Rajan; Wen Jiang; Yi Wei; Yu Lin 001 (WWW, 2021)

SSNE: Effective Node Representation for Link Prediction in Sparse Networks. - Ming-Ren Chen; Ping Huang; Yu Lin 001; Shi-Min Cai (IEEE Access, 2021)

Improving metagenomic binning results with overlapped bins using assembly graphs. - Vijini Mallawaarachchi; Anuradha Wickramarachchi; Yu Lin 001 (Algorithms Mol. Biol., 2021)

RepBin: Constraint-Based Graph Representation Learning for Metagenomic Binning. - Hansheng Xue; Vijini Mallawaarachchi; Yujia Zhang; Vaibhav Rajan; Yu Lin 001 (AAAI, 2022)

Graph Coloring via Neural Networks for Haplotype Assembly and Viral Quasispecies Reconstruction. - Hansheng Xue; Vaibhav Rajan; Yu Lin 001 (NeurIPS, 2022)

MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs. - Vijini Mallawaarachchi; Yu Lin 001 (RECOMB, 2022)

Metagenomics Binning of Long Reads Using Read-Overlap Graphs. - Anuradha Wickramarachchi; Yu Lin 001 (RECOMB-CG, 2022)

Binning long reads in metagenomics datasets using composition and coverage information. - Anuradha Wickramarachchi; Yu Lin 001 (Algorithms Mol. Biol., 2022)

DBE-KT22: A Knowledge Tracing Dataset Based on Online Student Evaluation. - Ghodai Abdelrahman; Sherif Abdelfattah; Qing Wang 002; Yu Lin 001 (CoRR, 2022)

Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs. - Vijini Mallawaarachchi; Yu Lin 001 (J. Comput. Biol., 2022)

DCHap: A Divide-and-Conquer Haplotype Phasing Algorithm for Third-Generation Sequences. - Yanbo Li; Yu Lin 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs. - Anuradha Wickramarachchi; Yu Lin 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

MultiTrans: An Algorithm for Path Extraction Through Mixed Integer Linear Programming for Transcriptome Assembly. - Jin Zhao 005; Haodi Feng; Daming Zhu; Yu Lin 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

An Algorithm to Mine Therapeutic Motifs for Cancer From Networks of Genetic Interactions. - Herty Liany; Yu Lin 001; Anand Jeyasekharan; Vaibhav Rajan (IEEE J. Biomed. Health Informatics, 2022)

Fast fully dynamic labelling for distance queries. - Muhammad Farhan; Qing Wang 002; Yu Lin 001; Brendan D. McKay (VLDB J., 2022)

VStrains: De Novo Reconstruction of Viral Strains via Iterative Path Extraction from Assembly Graphs. - Runpeng Luo; Yu Lin 001 (RECOMB, 2023)