Yu Lin

Publication Activity (10 Years)

Years Active: 2006-2023
Publications (10 Years): 40

Top Topics

Entity Resolution

Phylogenetic Analysis

Graph Representation

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Runpeng Luo, Yu Lin
VStrains: De Novo Reconstruction of Viral Strains via Iterative Path Extraction from Assembly Graphs. RECOMB (2023)
Anuradha Wickramarachchi, Yu Lin
GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
Muhammad Farhan, Qing Wang, Yu Lin, Brendan D. McKay
Fast fully dynamic labelling for distance queries. VLDB J. 31 (3) (2022)
Anuradha Wickramarachchi, Yu Lin
Binning long reads in metagenomics datasets using composition and coverage information. Algorithms Mol. Biol. 17 (1) (2022)
Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, Yu Lin
RepBin: Constraint-Based Graph Representation Learning for Metagenomic Binning. AAAI (2022)
Vijini Mallawaarachchi, Yu Lin
Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs. J. Comput. Biol. 29 (12) (2022)
Yanbo Li, Yu Lin
DCHap: A Divide-and-Conquer Haplotype Phasing Algorithm for Third-Generation Sequences. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (3) (2022)
Vijini Mallawaarachchi, Yu Lin
MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs. RECOMB (2022)
Jin Zhao, Haodi Feng, Daming Zhu, Yu Lin
MultiTrans: An Algorithm for Path Extraction Through Mixed Integer Linear Programming for Transcriptome Assembly. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
Anuradha Wickramarachchi, Yu Lin
Metagenomics Binning of Long Reads Using Read-Overlap Graphs. RECOMB-CG (2022)
Hansheng Xue, Vaibhav Rajan, Yu Lin
Graph Coloring via Neural Networks for Haplotype Assembly and Viral Quasispecies Reconstruction. CoRR (2022)
Hansheng Xue, Vaibhav Rajan, Yu Lin
Graph Coloring via Neural Networks for Haplotype Assembly and Viral Quasispecies Reconstruction. NeurIPS (2022)
Herty Liany, Yu Lin, Anand Jeyasekharan, Vaibhav Rajan
An Algorithm to Mine Therapeutic Motifs for Cancer From Networks of Genetic Interactions. IEEE J. Biomed. Health Informatics 26 (6) (2022)
Hansheng Xue, Luwei Yang, Vaibhav Rajan, Wen Jiang, Yi Wei, Yu Lin
Multiplex Bipartite Network Embedding using Dual Hypergraph Convolutional Networks. CoRR (2021)
Hansheng Xue, Luwei Yang, Vaibhav Rajan, Wen Jiang, Yi Wei, Yu Lin
Multiplex Bipartite Network Embedding using Dual Hypergraph Convolutional Networks. WWW (2021)
Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, Yu Lin
RepBin: Constraint-based Graph Representation Learning for Metagenomic Binning. CoRR (2021)
Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin
Improving metagenomic binning results with overlapped bins using assembly graphs. Algorithms Mol. Biol. 16 (1) (2021)
Anuradha Wickramarachchi, Vijini Mallawaarachchi, Vaibhav Rajan, Yu Lin
MetaBCC-LR: metagenomics binning by coverage and composition for long reads. Bioinform. 36 (Supplement-1) (2020)
Hansheng Xue, Luwei Yang, Wen Jiang, Yi Wei, Yi Hu, Yu Lin
Modeling Dynamic Heterogeneous Network for Link Prediction Using Hierarchical Attention with Temporal RNN. ECML/PKDD (1) (2020)
Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs. WABI (2020)
Masooma Iftikhar, Qing Wang, Yu Lin
dK-Microaggregation: Anonymizing Graphs with Differential Privacy Guarantees. PAKDD (2) (2020)
Hansheng Xue, Luwei Yang, Wen Jiang, Yi Wei, Yi Hu, Yu Lin
Modeling Dynamic Heterogeneous Network for Link Prediction using Hierarchical Attention with Temporal RNN. CoRR (2020)
Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin
GraphBin: refined binning of metagenomic contigs using assembly graphs. Bioinform. 36 (11) (2020)
Yanlin Zhang, Weiwei Liu, Yu Lin, Yen Kaow Ng, Shuaicheng Li
Large-scale 3D chromatin reconstruction from chromosomal contacts. BMC Genom. 20 (S2) (2019)
Muhammad Farhan, Qing Wang, Yu Lin, Brendan D. McKay
A Highly Scalable Labelling Approach for Exact Distance Queries in Complex Networks. EDBT (2019)
Masooma Iftikhar, Qing Wang, Yu Lin
Publishing Differentially Private Datasets via Stable Microaggregation. EDBT (2019)
Jingyu Shao, Qing Wang, Yu Lin
Skyblocking for entity resolution. Inf. Syst. 85 (2019)
Ruofan Xia, Yu Lin, Jun Zhou, Tieming Geng, Bing Feng, Jijun Tang
Phylogenetic Reconstruction for Copy-Number Evolution Problems. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (2) (2019)
Ruofan Xia, Yu Lin, Jun Zhou, Bing Feng, Jijun Tang
A Median Solver and Phylogenetic Inference Based on Double-Cut-and-Join Sorting. J. Comput. Biol. 25 (3) (2018)
Thomas K. F. Wong, Louis Ranjard, Yu Lin, Allen G. Rodrigo
HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations. BMC Bioinform. 19 (1) (2018)
Muhammad Farhan, Qing Wang, Yu Lin, Brendan D. McKay
A Highly Scalable Labelling Approach for Exact Distance Queries in Complex Networks. CoRR (2018)
Lianrong Pu, Yu Lin, Daming Zhu, Haitao Jiang
Can a breakpoint graph be decomposed into none other than 2-cycles? Theor. Comput. Sci. 734 (2018)
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A. Pevzner
Assembly of Long Error-Prone Reads Using Repeat Graphs. RECOMB (2018)
Jun Zhou, Yu Lin, Vaibhav Rajan, William Hoskins, Bing Feng, Jijun Tang
Analysis of gene copy number changes in tumor phylogenetics. Algorithms Mol. Biol. 11 (2016)
Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Mark Chaisson, Pavel A. Pevzner
Assembly of long error-prone reads using de Bruijn graphs. Proc. Natl. Acad. Sci. USA 113 (52) (2016)
Yu Lin, Max W. Shen, Jeffrey Yuan, Mark Chaisson, Pavel A. Pevzner
Assembly of Long Error-Prone Reads Using de Bruijn Graphs. RECOMB (2016)
Nishanth Ulhas Nair, Laura Hunter, Mingfu Shao, Paulina Grnarova, Yu Lin, Philipp Bucher, Bernard M. E. Moret
A maximum-likelihood approach for building cell-type trees by lifting. BMC Genom. 17 (S-1) (2016)
Jun Zhou, Yu Lin, William Hoskins, Jijun Tang
An Iterative Approach for Phylogenetic Analysis of Tumor Progression Using FISH Copy Number. ISBRA (2015)
Mingfu Shao, Yu Lin, Bernard M. E. Moret
An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes. J. Comput. Biol. 22 (5) (2015)
Jun Zhou, Yu Lin, Vaibhav Rajan, William Hoskins, Jijun Tang
Maximum Parsimony Analysis of Gene Copy Number Changes. WABI (2015)
Yu Lin, Pavel A. Pevzner
Manifold de Bruijn Graphs. WABI (2014)
Fei Hu, Yu Lin, Jijun Tang
MLGO: phylogeny reconstruction and ancestral inference from gene-order data. BMC Bioinform. 15 (2014)
Nishanth Ulhas Nair, Yu Lin, Ana Manasovska, Jelena Antic, Paulina Grnarova, Avinash Das Sahu, Philipp Bucher, Bernard M. E. Moret
Study of cell differentiation by phylogenetic analysis using histone modification data. BMC Bioinform. 15 (2014)
Mingfu Shao, Yu Lin, Bernard M. E. Moret
An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes. RECOMB (2014)
Yu Lin, Fei Hu, Jijun Tang, Bernard M. E. Moret
Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 Eukaryotes. Pacific Symposium on Biocomputing (2013)
Nishanth Ulhas Nair, Yu Lin, Philipp Bucher, Bernard M. E. Moret
Phylogenetic Analysis of Cell Types Using Histone Modifications. WABI (2013)
Mingfu Shao, Yu Lin, Bernard M. E. Moret
Sorting genomes with rearrangements and segmental duplications through trajectory graphs. BMC Bioinform. 14 (S-15) (2013)
Mingfu Shao, Yu Lin
Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion. BMC Bioinform. 13 (S-19) (2012)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Bootstrapping phylogenies inferred from rearrangement data. Algorithms Mol. Biol. 7 (2012)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis. Bioinform. 28 (24) (2012)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
A Metric for Phylogenetic Trees Based on Matching. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (4) (2012)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Bootstrapping Phylogenies Inferred from Rearrangement Data. WABI (2011)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator. J. Comput. Biol. 18 (9) (2011)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
A Metric for Phylogenetic Trees Based on Matching. ISBRA (2011)
Yu Lin, Bernard M. E. Moret
A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes. J. Comput. Biol. 18 (9) (2011)
Yu Lin, Bernard M. E. Moret
A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses That Applies across Eukaryotes and Prokaryotes. RECOMB-CG (2010)
Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M. Swenson, Bernard M. E. Moret
Heuristics for the inversion median problem. BMC Bioinform. 11 (S-1) (2010)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator. RECOMB-CG (2010)
Yu Lin, Vaibhav Rajan, Krister M. Swenson, Bernard M. E. Moret
Estimating true evolutionary distances under rearrangements, duplications, and losses. BMC Bioinform. 11 (S-1) (2010)
Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret
) Time. J. Comput. Biol. 17 (3) (2010)
Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results. J. Comput. Biol. 16 (10) (2009)
Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret
Sorting Signed Permutations by Inversions in O(nlogn) Time. RECOMB (2009)
Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Hurdles Hardly Have to Be Heeded. RECOMB-CG (2008)
Yu Lin, Bernard M. E. Moret
Estimating true evolutionary distances under the DCJ model. ISMB (2008)
Lusheng Wang, Yu Lin, Xiaowen Liu
Approximation Algorithms for Biclustering Problems. SIAM J. Comput. 38 (4) (2008)
Yu Lin, Yantao Qiao, Shiwei Sun, Chungong Yu, Gongjin Dong, Dongbo Bu
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. RECOMB (2008)
Chungong Yu, Yu Lin, Shiwei Sun, Jinjin Cai, Jingfen Zhang, Dongbo Bu, Zhuo Zhang, Runsheng Chen
An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry. J. Bioinform. Comput. Biol. 5 (2a) (2007)
Lusheng Wang, Yu Lin, Xiaowen Liu
Approximation Algorithms for Bi-clustering Problems. WABI (2006)