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ORCIDYu Lin 0001
Person information
- affiliation: Australian National University, Canberra, ACT, Australia
- affiliation (former): University of California, San Diego, CA, USA
- affiliation (former): École Polytechnique Fédérale de Lausanne, Switzerland
Other persons with the same name
- Yu Lin — disambiguation page
- Yu Lin 0002 — University of Texas at Dallas. TX, USA
- Yu Lin 0003 — Eindhoven University of Technology, The Netherlands
- Yu Lin 0004 — Harbin Engineering University, China
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Books and Theses
- 2012
[b1]Yu Lin:
Models and Algorithms for Whole-Genome Evolution and their Use in Phylogenetic Inference. EPFL, Switzerland, 2012
Journal Articles
- 2022
- [j36]Anuradha Wickramarachchi
, Yu Lin:
Binning long reads in metagenomics datasets using composition and coverage information. Algorithms Mol. Biol. 17(1): 14 (2022) - [j35]Vijini Mallawaarachchi, Yu Lin:
Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs. J. Comput. Biol. 29(12): 1357-1376 (2022) - [j34]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): 48-56 (2022) - [j33]Anuradha Wickramarachchi, Yu Lin:
GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 57-67 (2022) - [j32]Yanbo Li, Yu Lin:
DCHap: A Divide-and-Conquer Haplotype Phasing Algorithm for Third-Generation Sequences. IEEE ACM Trans. Comput. Biol. Bioinform. 19(3): 1277-1284 (2022) - [j31]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): 2830-2838 (2022) - [j30]Muhammad Farhan, Qing Wang, Yu Lin, Brendan D. McKay:
Fast fully dynamic labelling for distance queries. VLDB J. 31(3): 483-506 (2022) - 2021
- [j29]Ming-Ren Chen, Ping Huang, Yu Lin, Shi-Min Cai:
SSNE: Effective Node Representation for Link Prediction in Sparse Networks. IEEE Access 9: 57874-57885 (2021) - [j28]Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin:
Improving metagenomic binning results with overlapped bins using assembly graphs. Algorithms Mol. Biol. 16(1): 3 (2021) - 2020
- [j27]Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin:
GraphBin: refined binning of metagenomic contigs using assembly graphs. Bioinform. 36(11): 3307-3313 (2020) - [j26]Anuradha Wickramarachchi, Vijini Mallawaarachchi, Vaibhav Rajan, Yu Lin:
MetaBCC-LR: metagenomics binning by coverage and composition for long reads. Bioinform. 36(Supplement-1): i3-i11 (2020) - 2019
- [j25]Yanlin Zhang, Weiwei Liu, Yu Lin, Yen Kaow Ng, Shuaicheng Li:
Large-scale 3D chromatin reconstruction from chromosomal contacts. BMC Genom. 20(S2) (2019) - [j24]Jingyu Shao, Qing Wang, Yu Lin:
Skyblocking for entity resolution. Inf. Syst. 85: 30-43 (2019) - [j23]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): 694-699 (2019) - 2018
- [j22]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): 389:1-389:11 (2018) - [j21]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): 302-312 (2018) - [j20]Lianrong Pu, Yu Lin, Daming Zhu, Haitao Jiang:
Can a breakpoint graph be decomposed into none other than 2-cycles? Theor. Comput. Sci. 734: 38-45 (2018) - 2016
- [j19]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: 26 (2016) - [j18]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): 14 (2016) - [j17]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): E8396-E8405 (2016) - 2015
- [j16]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): 425-435 (2015) - 2014
- [j15]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: 269 (2014) - [j14]Fei Hu, Yu Lin, Jijun Tang:
MLGO: phylogeny reconstruction and ancestral inference from gene-order data. BMC Bioinform. 15: 354 (2014) - 2013
- [j13]Mingfu Shao, Yu Lin, Bernard M. E. Moret:
Sorting genomes with rearrangements and segmental duplications through trajectory graphs. BMC Bioinform. 14(S-15): S9 (2013) - 2012
- [j12]Yu Lin, Vaibhav Rajan, Bernard M. E. Moret:
Bootstrapping phylogenies inferred from rearrangement data. Algorithms Mol. Biol. 7: 21 (2012) - [j11]Yu Lin, Vaibhav Rajan, Bernard M. E. Moret:
TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis. Bioinform. 28(24): 3324-3325 (2012) - [j10]Mingfu Shao, Yu Lin:
Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion. BMC Bioinform. 13(S-19): S13 (2012) - [j9]Yu Lin, Vaibhav Rajan, Bernard M. E. Moret:
A Metric for Phylogenetic Trees Based on Matching. IEEE ACM Trans. Comput. Biol. Bioinform. 9(4): 1014-1022 (2012) - 2011
- [j8]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): 1055-1064 (2011) - [j7]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): 1131-1139 (2011) - 2010
- [j6]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): 30 (2010) - [j5]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): 54 (2010) - [j4]Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret:
Sorting Signed Permutations by Inversions in O(nlogn) Time. J. Comput. Biol. 17(3): 489-501 (2010) - 2009
- [j3]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): 1339-1351 (2009) - 2008
- [j2]Lusheng Wang, Yu Lin, Xiaowen Liu:
Approximation Algorithms for Biclustering Problems. SIAM J. Comput. 38(4): 1504-1518 (2008) - 2007
- [j1]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): 297-311 (2007)
Conference and Workshop Papers
- 2023
- [c31]Runpeng Luo, Yu Lin:
VStrains: De Novo Reconstruction of Viral Strains via Iterative Path Extraction from Assembly Graphs. RECOMB 2023: 3-20 - 2022
- [c30]Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, Yu Lin:
RepBin: Constraint-Based Graph Representation Learning for Metagenomic Binning. AAAI 2022: 4637-4645 - [c29]Hansheng Xue, Vaibhav Rajan, Yu Lin:
Graph Coloring via Neural Networks for Haplotype Assembly and Viral Quasispecies Reconstruction. NeurIPS 2022 - [c28]Vijini Mallawaarachchi, Yu Lin:
MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs. RECOMB 2022: 70-85 - [c27]Anuradha Wickramarachchi, Yu Lin:
Metagenomics Binning of Long Reads Using Read-Overlap Graphs. RECOMB-CG 2022: 260-278 - 2021
- [c26]Ye Wang, Qing Wang, Henning Koehler, Yu Lin:
Query-by-Sketch: Scaling Shortest Path Graph Queries on Very Large Networks. SIGMOD Conference 2021: 1946-1958 - [c25]Anuradha Wickramarachchi, Yu Lin:
LRBinner: Binning Long Reads in Metagenomics Datasets. WABI 2021: 11:1-11:18 - [c24]Hansheng Xue, Luwei Yang, Vaibhav Rajan, Wen Jiang, Yi Wei, Yu Lin:
Multiplex Bipartite Network Embedding using Dual Hypergraph Convolutional Networks. WWW 2021: 1649-1660 - 2020
- [c23]Yanbo Li, Hardip Patel, Yu Lin:
Kmer2SNP: reference-free SNP calling from raw reads based on matching. BIBM 2020: 208-212 - [c22]Masooma Iftikhar, Qing Wang, Yu Lin:
dK-Microaggregation: Anonymizing Graphs with Differential Privacy Guarantees. PAKDD (2) 2020: 191-203 - [c21]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: 282-298 - [c20]Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin:
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs. WABI 2020: 8:1-8:21 - 2019
- [c19]Muhammad Farhan, Qing Wang, Yu Lin, Brendan D. McKay:
A Highly Scalable Labelling Approach for Exact Distance Queries in Complex Networks. EDBT 2019: 13-24 - [c18]Masooma Iftikhar, Qing Wang, Yu Lin:
Publishing Differentially Private Datasets via Stable Microaggregation. EDBT 2019: 662-665 - 2018
- [c17]Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A. Pevzner:
Assembly of Long Error-Prone Reads Using Repeat Graphs. RECOMB 2018: 261-262 - 2016
- [c16]Yu Lin, Max W. Shen, Jeffrey Yuan, Mark Chaisson, Pavel A. Pevzner:
Assembly of Long Error-Prone Reads Using de Bruijn Graphs. RECOMB 2016: 265 - 2015
- [c15]Jun Zhou, Yu Lin, William Hoskins, Jijun Tang:
An Iterative Approach for Phylogenetic Analysis of Tumor Progression Using FISH Copy Number. ISBRA 2015: 402-412 - [c14]Jun Zhou, Yu Lin, Vaibhav Rajan, William Hoskins, Jijun Tang:
Maximum Parsimony Analysis of Gene Copy Number Changes. WABI 2015: 108-120 - 2014
- [c13]Mingfu Shao, Yu Lin, Bernard M. E. Moret:
An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes. RECOMB 2014: 280-292 - [c12]Yu Lin, Pavel A. Pevzner:
Manifold de Bruijn Graphs. WABI 2014: 296-310 - 2013
- [c11]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: 285-296 - [c10]Nishanth Ulhas Nair, Yu Lin, Philipp Bucher, Bernard M. E. Moret:
Phylogenetic Analysis of Cell Types Using Histone Modifications. WABI 2013: 326-337 - 2011
- [c9]Yu Lin, Vaibhav Rajan, Bernard M. E. Moret:
A Metric for Phylogenetic Trees Based on Matching. ISBRA 2011: 197-208 - [c8]Yu Lin, Vaibhav Rajan, Bernard M. E. Moret:
Bootstrapping Phylogenies Inferred from Rearrangement Data. WABI 2011: 175-187 - 2010
- [c7]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: 137-148 - [c6]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: 228-239 - 2009
- [c5]Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret:
Sorting Signed Permutations by Inversions in O(nlogn) Time. RECOMB 2009: 386-399 - 2008
- [c4]Yu Lin, Bernard M. E. Moret:
Estimating true evolutionary distances under the DCJ model. ISMB 2008: 114-122 - [c3]Yu Lin, Yantao Qiao, Shiwei Sun, Chungong Yu, Gongjin Dong, Dongbo Bu:
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. RECOMB 2008: 154-166 - [c2]Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret:
Hurdles Hardly Have to Be Heeded. RECOMB-CG 2008: 241-251 - 2006
- [c1]Lusheng Wang, Yu Lin, Xiaowen Liu:
Approximation Algorithms for Bi-clustering Problems. WABI 2006: 310-320
Parts in Books or Collections
- 2013
- [p1]Bernard M. E. Moret, Yu Lin, Jijun Tang:
Rearrangements in Phylogenetic Inference: Compare, Model, or Encode? Models and Algorithms for Genome Evolution 2013: 147-171
Informal and Other Publications
- 2022
- [i8]Hansheng Xue, Vaibhav Rajan, Yu Lin:
Graph Coloring via Neural Networks for Haplotype Assembly and Viral Quasispecies Reconstruction. CoRR abs/2210.12158 (2022) - 2021
- [i7]Hansheng Xue, Luwei Yang, Vaibhav Rajan, Wen Jiang, Yi Wei, Yu Lin:
Multiplex Bipartite Network Embedding using Dual Hypergraph Convolutional Networks. CoRR abs/2102.06371 (2021) - [i6]Ye Wang, Qing Wang, Henning Koehler, Yu Lin:
Query-by-Sketch: Scaling Shortest Path Graph Queries on Very Large Networks. CoRR abs/2104.09733 (2021) - [i5]Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, Yu Lin:
RepBin: Constraint-based Graph Representation Learning for Metagenomic Binning. CoRR abs/2112.11696 (2021) - 2020
- [i4]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 abs/2004.01024 (2020) - [i3]Ming-Ren Chen, Ping Huang, Yu Lin, Shi-Min Cai:
SSNE: Effective Node Representation for Link Prediction in Sparse Networks. CoRR abs/2011.07788 (2020) - 2018
- [i2]Jingyu Shao, Qing Wang, Yu Lin:
Skyblocking: Learning Blocking Schemes on the Skyline. CoRR abs/1805.12319 (2018) - [i1]Muhammad Farhan, Qing Wang, Yu Lin, Brendan D. McKay:
A Highly Scalable Labelling Approach for Exact Distance Queries in Complex Networks. CoRR abs/1812.02363 (2018)
Coauthor Index
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