Yu Lin

According to our database, Yu Lin authored at least 66 papers between 2006 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

VStrains: De Novo Reconstruction of Viral Strains via Iterative Path Extraction from Assembly Graphs.

Runpeng Luo, Yu Lin

Proceedings of the Research in Computational Molecular Biology, 2023

2022

Fast fully dynamic labelling for distance queries.

Muhammad Farhan, Qing Wang, Yu Lin, Brendan D. McKay

VLDB J., 2022

An Algorithm to Mine Therapeutic Motifs for Cancer From Networks of Genetic Interactions.

Herty Liany, Yu Lin, Anand Jeyasekharan, Vaibhav Rajan

IEEE J. Biomed. Health Informatics, 2022

MultiTrans: An Algorithm for Path Extraction Through Mixed Integer Linear Programming for Transcriptome Assembly.

Jin Zhao, Haodi Feng, Daming Zhu, Yu Lin

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs.

Anuradha Wickramarachchi, Yu Lin

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

DCHap: A Divide-and-Conquer Haplotype Phasing Algorithm for Third-Generation Sequences.

Yanbo Li, Yu Lin

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs.

Vijini Mallawaarachchi, Yu Lin

J. Comput. Biol., 2022

Binning long reads in metagenomics datasets using composition and coverage information.

Anuradha Wickramarachchi, Yu Lin

Algorithms Mol. Biol., 2022

Metagenomics Binning of Long Reads Using Read-Overlap Graphs.

Anuradha Wickramarachchi, Yu Lin

Proceedings of the Comparative Genomics - 19th International Conference, 2022

MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs.

Vijini Mallawaarachchi, Yu Lin

Proceedings of the Research in Computational Molecular Biology, 2022

Graph Coloring via Neural Networks for Haplotype Assembly and Viral Quasispecies Reconstruction.

Hansheng Xue, Vaibhav Rajan, Yu Lin

Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022

RepBin: Constraint-Based Graph Representation Learning for Metagenomic Binning.

Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, Yu Lin

Proceedings of the Thirty-Sixth AAAI Conference on Artificial Intelligence, 2022

2021

Improving metagenomic binning results with overlapped bins using assembly graphs.

Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin

Algorithms Mol. Biol., 2021

SSNE: Effective Node Representation for Link Prediction in Sparse Networks.

Ming-Ren Chen, Ping Huang, Yu Lin, Shi-Min Cai

IEEE Access, 2021

Multiplex Bipartite Network Embedding using Dual Hypergraph Convolutional Networks.

Hansheng Xue, Luwei Yang, Vaibhav Rajan, Wen Jiang, Yi Wei, Yu Lin

Proceedings of the WWW '21: The Web Conference 2021, 2021

LRBinner: Binning Long Reads in Metagenomics Datasets.

Anuradha Wickramarachchi, Yu Lin

Proceedings of the 21st International Workshop on Algorithms in Bioinformatics, 2021

Query-by-Sketch: Scaling Shortest Path Graph Queries on Very Large Networks.

Ye Wang, Qing Wang, Henning Koehler, Yu Lin

Proceedings of the SIGMOD '21: International Conference on Management of Data, 2021

2020

MetaBCC-LR: metagenomics binning by coverage and composition for long reads.

Anuradha Wickramarachchi, Vijini Mallawaarachchi, Vaibhav Rajan, Yu Lin

Bioinform., 2020

GraphBin: refined binning of metagenomic contigs using assembly graphs.

Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin

Bioinform., 2020

GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs.

Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin

Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 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

Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2020

dK-Microaggregation: Anonymizing Graphs with Differential Privacy Guarantees.

Masooma Iftikhar, Qing Wang, Yu Lin

Proceedings of the Advances in Knowledge Discovery and Data Mining, 2020

Kmer2SNP: reference-free SNP calling from raw reads based on matching.

Yanbo Li, Hardip Patel, Yu Lin

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

2019

Phylogenetic Reconstruction for Copy-Number Evolution Problems.

Ruofan Xia, Yu Lin, Jun Zhou, Tieming Geng, Bing Feng, Jijun Tang

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Skyblocking for entity resolution.

Jingyu Shao, Qing Wang, Yu Lin

Inf. Syst., 2019

Large-scale 3D chromatin reconstruction from chromosomal contacts.

Yanlin Zhang, Weiwei Liu, Yu Lin, Yen Kaow Ng, Shuaicheng Li

BMC Genom., 2019

Publishing Differentially Private Datasets via Stable Microaggregation.

Masooma Iftikhar, Qing Wang, Yu Lin

Proceedings of the Advances in Database Technology, 2019

A Highly Scalable Labelling Approach for Exact Distance Queries in Complex Networks.

Muhammad Farhan, Qing Wang, Yu Lin, Brendan D. McKay

Proceedings of the Advances in Database Technology, 2019

2018

Can a breakpoint graph be decomposed into none other than 2-cycles?

Lianrong Pu, Yu Lin, Daming Zhu, Haitao Jiang

Theor. Comput. Sci., 2018

A Median Solver and Phylogenetic Inference Based on Double-Cut-and-Join Sorting.

Ruofan Xia, Yu Lin, Jun Zhou, Bing Feng, Jijun Tang

J. Comput. Biol., 2018

Skyblocking: Learning Blocking Schemes on the Skyline.

Jingyu Shao, Qing Wang, Yu Lin

CoRR, 2018

HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations.

Thomas K. F. Wong, Louis Ranjard, Yu Lin, Allen G. Rodrigo

BMC Bioinform., 2018

Assembly of Long Error-Prone Reads Using Repeat Graphs.

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A. Pevzner

Proceedings of the Research in Computational Molecular Biology, 2018

2016

Assembly of long error-prone reads using de Bruijn graphs.

Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Mark Chaisson, Pavel A. Pevzner

Proc. Natl. Acad. Sci. USA, 2016

A maximum-likelihood approach for building cell-type trees by lifting.

Nishanth Ulhas Nair, Laura Hunter, Mingfu Shao, Paulina Grnarova, Yu Lin, Philipp Bucher, Bernard M. E. Moret

BMC Genom., 2016

Analysis of gene copy number changes in tumor phylogenetics.

Jun Zhou, Yu Lin, Vaibhav Rajan, William Hoskins, Bing Feng, Jijun Tang

Algorithms Mol. Biol., 2016

Assembly of Long Error-Prone Reads Using de Bruijn Graphs.

Yu Lin, Max W. Shen, Jeffrey Yuan, Mark Chaisson, Pavel A. Pevzner

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015

An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes.

Mingfu Shao, Yu Lin, Bernard M. E. Moret

J. Comput. Biol., 2015

Maximum Parsimony Analysis of Gene Copy Number Changes.

Jun Zhou, Yu Lin, Vaibhav Rajan, William Hoskins, Jijun Tang

Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

An Iterative Approach for Phylogenetic Analysis of Tumor Progression Using FISH Copy Number.

Jun Zhou, Yu Lin, William Hoskins, Jijun Tang

Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

2014

Study of cell differentiation by phylogenetic analysis using histone modification data.

Nishanth Ulhas Nair, Yu Lin, Ana Manasovska, Jelena Antic, Paulina Grnarova, Avinash Das Sahu, Philipp Bucher, Bernard M. E. Moret

BMC Bioinform., 2014

MLGO: phylogeny reconstruction and ancestral inference from gene-order data.

Fei Hu, Yu Lin, Jijun Tang

BMC Bioinform., 2014

Manifold de Bruijn Graphs.

Yu Lin, Pavel A. Pevzner

Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes.

Mingfu Shao, Yu Lin, Bernard M. E. Moret

Proceedings of the Research in Computational Molecular Biology, 2014

2013

Sorting genomes with rearrangements and segmental duplications through trajectory graphs.

Mingfu Shao, Yu Lin, Bernard M. E. Moret

BMC Bioinform., 2013

Phylogenetic Analysis of Cell Types Using Histone Modifications.

Nishanth Ulhas Nair, Yu Lin, Philipp Bucher, Bernard M. E. Moret

Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 Eukaryotes.

Yu Lin, Fei Hu, Jijun Tang, Bernard M. E. Moret

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Rearrangements in Phylogenetic Inference: Compare, Model, or Encode?

Bernard M. E. Moret, Yu Lin, Jijun Tang

Proceedings of the Models and Algorithms for Genome Evolution, 2013

2012

Models and Algorithms for Whole-Genome Evolution and their Use in Phylogenetic Inference.

Yu Lin

PhD thesis, 2012

A Metric for Phylogenetic Trees Based on Matching.

Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion.

Mingfu Shao, Yu Lin

BMC Bioinform., 2012

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis.

Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

Bioinform., 2012

Bootstrapping phylogenies inferred from rearrangement data.

Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

Algorithms Mol. Biol., 2012

2011

Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator.

Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

J. Comput. Biol., 2011

A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes.

Yu Lin, Bernard M. E. Moret

J. Comput. Biol., 2011

2010

Sorting Signed Permutations by Inversions in <i>O</i>(<i>n</i>log<i>n</i>) Time.

Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret

J. Comput. Biol., 2010

Heuristics for the inversion median problem.

Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M. Swenson, Bernard M. E. Moret

BMC Bioinform., 2010

Estimating true evolutionary distances under rearrangements, duplications, and losses.

Yu Lin, Vaibhav Rajan, Krister M. Swenson, Bernard M. E. Moret

BMC Bioinform., 2010

2009

Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results.

Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

J. Comput. Biol., 2009

Sorting Signed Permutations by Inversions in O(nlogn) Time.

Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret

Proceedings of the Research in Computational Molecular Biology, 2009

2008

Approximation Algorithms for Biclustering Problems.

Lusheng Wang, Yu Lin, Xiaowen Liu

SIAM J. Comput., 2008

Hurdles Hardly Have to Be Heeded.

Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

Proceedings of the Comparative Genomics, International Workshop, 2008

A Fragmentation Event Model for Peptide Identification by Mass Spectrometry.

Yu Lin, Yantao Qiao, Shiwei Sun, Chungong Yu, Gongjin Dong, Dongbo Bu

Proceedings of the Research in Computational Molecular Biology, 2008

Estimating true evolutionary distances under the DCJ model.

Yu Lin, Bernard M. E. Moret

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

2007

An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry.

Chungong Yu, Yu Lin, Shiwei Sun, Jinjin Cai, Jingfen Zhang, Dongbo Bu, Zhuo Zhang, Runsheng Chen

J. Bioinform. Comput. Biol., 2007

2006

Approximation Algorithms for Bi-clustering Problems.

Lusheng Wang, Yu Lin, Xiaowen Liu

Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006