Yu Lin

78 papers A* 3A 1B 9C 7Misc 1Journal 45Unranked 10
YearRankTypeTitle / Venue / Authors
2023 B conf
VStrains: De Novo Reconstruction of Viral Strains via Iterative Path Extraction from Assembly Graphs.
RECOMB
Runpeng Luo, Yu Lin
2022 J jnl
Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs.
J. Comput. Biol.
Vijini Mallawaarachchi, Yu Lin
2022 J jnl
An Algorithm to Mine Therapeutic Motifs for Cancer From Networks of Genetic Interactions.
IEEE J. Biomed. Health Informatics
Herty Liany, Yu Lin, Anand Jeyasekharan, Vaibhav Rajan
2022 J jnl
Binning long reads in metagenomics datasets using composition and coverage information.
Algorithms Mol. Biol.
Anuradha Wickramarachchi, Yu Lin
2022 J jnl
DBE-KT22: A Knowledge Tracing Dataset Based on Online Student Evaluation.
CoRR
Ghodai Abdelrahman, Sherif Abdelfattah, Qing Wang, Yu Lin
2022 J jnl
DCHap: A Divide-and-Conquer Haplotype Phasing Algorithm for Third-Generation Sequences.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yanbo Li, Yu Lin
2022 J jnl
Fast fully dynamic labelling for distance queries.
VLDB J.
Muhammad Farhan, Qing Wang, Yu Lin, Brendan D. McKay
2022 A* conf
Graph Coloring via Neural Networks for Haplotype Assembly and Viral Quasispecies Reconstruction.
NeurIPS
Hansheng Xue, Vaibhav Rajan, Yu Lin
2022 J jnl
Graph Coloring via Neural Networks for Haplotype Assembly and Viral Quasispecies Reconstruction.
CoRR
Hansheng Xue, Vaibhav Rajan, Yu Lin
2022 J jnl
GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs.
IEEE ACM Trans. Comput. Biol. Bioinform.
Anuradha Wickramarachchi, Yu Lin
2022 B conf
MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs.
RECOMB
Vijini Mallawaarachchi, Yu Lin
2022 — conf
Metagenomics Binning of Long Reads Using Read-Overlap Graphs.
RECOMB-CG
Anuradha Wickramarachchi, Yu Lin
2022 J jnl
MultiTrans: An Algorithm for Path Extraction Through Mixed Integer Linear Programming for Transcriptome Assembly.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jin Zhao, Haodi Feng, Daming Zhu, Yu Lin
2022 A* conf
RepBin: Constraint-Based Graph Representation Learning for Metagenomic Binning.
AAAI
Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, Yu Lin
2021 J jnl
Improving metagenomic binning results with overlapped bins using assembly graphs.
Algorithms Mol. Biol.
Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin
2021 C conf
LRBinner: Binning Long Reads in Metagenomics Datasets.
WABI
Anuradha Wickramarachchi, Yu Lin
2021 A* conf
Multiplex Bipartite Network Embedding using Dual Hypergraph Convolutional Networks.
WWW
Hansheng Xue, Luwei Yang, Vaibhav Rajan, Wen Jiang, Yi Wei, Yu Lin
2021 J jnl
Multiplex Bipartite Network Embedding using Dual Hypergraph Convolutional Networks.
CoRR
Hansheng Xue, Luwei Yang, Vaibhav Rajan, Wen Jiang, Yi Wei, Yu Lin
2021 — conf
Query-by-Sketch: Scaling Shortest Path Graph Queries on Very Large Networks.
SIGMOD Conference
Ye Wang, Qing Wang, Henning Koehler, Yu Lin
2021 J jnl
Query-by-Sketch: Scaling Shortest Path Graph Queries on Very Large Networks.
CoRR
Ye Wang, Qing Wang, Henning Koehler, Yu Lin
2021 J jnl
RepBin: Constraint-based Graph Representation Learning for Metagenomic Binning.
CoRR
Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, Yu Lin
2021 J jnl
SSNE: Effective Node Representation for Link Prediction in Sparse Networks.
IEEE Access
Ming-Ren Chen, Ping Huang, Yu Lin, Shi-Min Cai
2020 C conf
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs.
WABI
Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin
2020 J jnl
GraphBin: refined binning of metagenomic contigs using assembly graphs.
Bioinform.
Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin
2020 — conf
Kmer2SNP: reference-free SNP calling from raw reads based on matching.
BIBM
Yanbo Li, Hardip Patel, Yu Lin
2020 J jnl
MetaBCC-LR: metagenomics binning by coverage and composition for long reads.
Bioinform.
Anuradha Wickramarachchi, Vijini Mallawaarachchi, Vaibhav Rajan, Yu Lin
2020 — conf
Modeling Dynamic Heterogeneous Network for Link Prediction Using Hierarchical Attention with Temporal RNN.
ECML/PKDD (1)
Hansheng Xue, Luwei Yang, Wen Jiang, Yi Wei, Yi Hu, Yu Lin
2020 J jnl
Modeling Dynamic Heterogeneous Network for Link Prediction using Hierarchical Attention with Temporal RNN.
CoRR
Hansheng Xue, Luwei Yang, Wen Jiang, Yi Wei, Yi Hu, Yu Lin
2020 J jnl
SSNE: Effective Node Representation for Link Prediction in Sparse Networks.
CoRR
Ming-Ren Chen, Ping Huang, Yu Lin, Shi-Min Cai
2020 — conf
dK-Microaggregation: Anonymizing Graphs with Differential Privacy Guarantees.
PAKDD (2)
Masooma Iftikhar, Qing Wang, Yu Lin
2019 B conf
A Highly Scalable Labelling Approach for Exact Distance Queries in Complex Networks.
EDBT
Muhammad Farhan, Qing Wang, Yu Lin, Brendan D. McKay
2019 J jnl
Large-scale 3D chromatin reconstruction from chromosomal contacts.
BMC Genom.
Yanlin Zhang, Weiwei Liu, Yu Lin, Yen Kaow Ng, Shuaicheng Li
2019 J jnl
Phylogenetic Reconstruction for Copy-Number Evolution Problems.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ruofan Xia, Yu Lin, Jun Zhou, Tieming Geng, Bing Feng, Jijun Tang
2019 B conf
Publishing Differentially Private Datasets via Stable Microaggregation.
EDBT
Masooma Iftikhar, Qing Wang, Yu Lin
2019 J jnl
Skyblocking for entity resolution.
Inf. Syst.
Jingyu Shao, Qing Wang, Yu Lin
2018 J jnl
A Highly Scalable Labelling Approach for Exact Distance Queries in Complex Networks.
CoRR
Muhammad Farhan, Qing Wang, Yu Lin, Brendan D. McKay
2018 J jnl
A Median Solver and Phylogenetic Inference Based on Double-Cut-and-Join Sorting.
J. Comput. Biol.
Ruofan Xia, Yu Lin, Jun Zhou, Bing Feng, Jijun Tang
2018 B conf
Assembly of Long Error-Prone Reads Using Repeat Graphs.
RECOMB
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A. Pevzner
2018 J jnl
Can a breakpoint graph be decomposed into none other than 2-cycles?
Theor. Comput. Sci.
Lianrong Pu, Yu Lin, Daming Zhu, Haitao Jiang
2018 J jnl
HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations.
BMC Bioinform.
Thomas K. F. Wong, Louis Ranjard, Yu Lin, Allen G. Rodrigo
2018 J jnl
Skyblocking: Learning Blocking Schemes on the Skyline.
CoRR
Jingyu Shao, Qing Wang, Yu Lin
2016 J jnl
A maximum-likelihood approach for building cell-type trees by lifting.
BMC Genom.
Nishanth Ulhas Nair, Laura Hunter, Mingfu Shao, Paulina Grnarova, Yu Lin, Philipp Bucher, Bernard M. E. Moret
2016 J jnl
Analysis of gene copy number changes in tumor phylogenetics.
Algorithms Mol. Biol.
Jun Zhou, Yu Lin, Vaibhav Rajan, William Hoskins, Bing Feng, Jijun Tang
2016 B conf
Assembly of Long Error-Prone Reads Using de Bruijn Graphs.
RECOMB
Yu Lin, Max W. Shen, Jeffrey Yuan, Mark Chaisson, Pavel A. Pevzner
2016 J jnl
Assembly of long error-prone reads using de Bruijn graphs.
Proc. Natl. Acad. Sci. USA
Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Mark Chaisson, Pavel A. Pevzner
2015 J jnl
An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes.
J. Comput. Biol.
Mingfu Shao, Yu Lin, Bernard M. E. Moret
2015 — conf
An Iterative Approach for Phylogenetic Analysis of Tumor Progression Using FISH Copy Number.
ISBRA
Jun Zhou, Yu Lin, William Hoskins, Jijun Tang
2015 C conf
Maximum Parsimony Analysis of Gene Copy Number Changes.
WABI
Jun Zhou, Yu Lin, Vaibhav Rajan, William Hoskins, Jijun Tang
2014 B conf
An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes.
RECOMB
Mingfu Shao, Yu Lin, Bernard M. E. Moret
2014 J jnl
MLGO: phylogeny reconstruction and ancestral inference from gene-order data.
BMC Bioinform.
Fei Hu, Yu Lin, Jijun Tang
2014 C conf
Manifold de Bruijn Graphs.
WABI
Yu Lin, Pavel A. Pevzner
2014 J jnl
Study of cell differentiation by phylogenetic analysis using histone modification data.
BMC Bioinform.
Nishanth Ulhas Nair, Yu Lin, Ana Manasovska, Jelena Antic, Paulina Grnarova, Avinash Das Sahu, Philipp Bucher, Bernard M. E. Moret
2013 Misc conf
Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 Eukaryotes.
Pacific Symposium on Biocomputing
Yu Lin, Fei Hu, Jijun Tang, Bernard M. E. Moret
2013 C conf
Phylogenetic Analysis of Cell Types Using Histone Modifications.
WABI
Nishanth Ulhas Nair, Yu Lin, Philipp Bucher, Bernard M. E. Moret
2013 — ch.
Rearrangements in Phylogenetic Inference: Compare, Model, or Encode?
Models and Algorithms for Genome Evolution
Bernard M. E. Moret, Yu Lin, Jijun Tang
2013 J jnl
Sorting genomes with rearrangements and segmental duplications through trajectory graphs.
BMC Bioinform.
Mingfu Shao, Yu Lin, Bernard M. E. Moret
2012 J jnl
A Metric for Phylogenetic Trees Based on Matching.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
2012 J jnl
Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion.
BMC Bioinform.
Mingfu Shao, Yu Lin
2012 J jnl
Bootstrapping phylogenies inferred from rearrangement data.
Algorithms Mol. Biol.
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
2012 — —
Models and Algorithms for Whole-Genome Evolution and their Use in Phylogenetic Inference.
Yu Lin
2012 J jnl
TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis.
Bioinform.
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
2011 — conf
A Metric for Phylogenetic Trees Based on Matching.
ISBRA
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
2011 J jnl
A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes.
J. Comput. Biol.
Yu Lin, Bernard M. E. Moret
2011 C conf
Bootstrapping Phylogenies Inferred from Rearrangement Data.
WABI
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
2011 J jnl
Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator.
J. Comput. Biol.
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
2010 — conf
A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses That Applies across Eukaryotes and Prokaryotes.
RECOMB-CG
Yu Lin, Bernard M. E. Moret
2010 J jnl
Estimating true evolutionary distances under rearrangements, duplications, and losses.
BMC Bioinform.
Yu Lin, Vaibhav Rajan, Krister M. Swenson, Bernard M. E. Moret
2010 — conf
Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator.
RECOMB-CG
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
2010 J jnl
Heuristics for the inversion median problem.
BMC Bioinform.
Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M. Swenson, Bernard M. E. Moret
2010 J jnl
Sorting Signed Permutations by Inversions in
J. Comput. Biol.
Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret
2009 J jnl
Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results.
J. Comput. Biol.
Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
2009 B conf
Sorting Signed Permutations by Inversions in O(nlogn) Time.
RECOMB
Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret
2008 B conf
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry.
RECOMB
Yu Lin, Yantao Qiao, Shiwei Sun, Chungong Yu, Gongjin Dong, Dongbo Bu
2008 J jnl
Approximation Algorithms for Biclustering Problems.
SIAM J. Comput.
Lusheng Wang, Yu Lin, Xiaowen Liu
2008 A conf
Estimating true evolutionary distances under the DCJ model.
ISMB
Yu Lin, Bernard M. E. Moret
2008 — conf
Hurdles Hardly Have to Be Heeded.
RECOMB-CG
Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
2007 J jnl
An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry.
J. Bioinform. Comput. Biol.
Chungong Yu, Yu Lin, Shiwei Sun, Jinjin Cai, Jingfen Zhang, Dongbo Bu, Zhuo Zhang, Runsheng Chen
2006 C conf
Approximation Algorithms for Bi-clustering Problems.
WABI
Lusheng Wang, Yu Lin, Xiaowen Liu