Yu Lin Yu Lin

Senior Lecturer
School of Computing
College of Engineering and Computer Science
Australian National University

E-Mail: yu.lin AT anu.edu.au

Address: R4,25, HN Building 145, Acton ACT 2601

Group Website: https://cgg-anu.github.io

I am currently a Senior Lecturer at the School of Computing, the Australian National University. Prior to this, I was a postdoctoral scholar, hosted by Prof. Pavel A. Pevzner, at the Department of Computer Science and Engineering, the University of California, San Diego, and I received my Ph.D. in computer science from EPFL, and my advisor was Prof. Bernard M.E. Moret.

Education
  • Ph.D. in Computer Science, EPFL, Lausanne, Switzerland.
  • M.S. in Computer Science, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
  • B.S. in Computer Science, University of Science and Technology of China, Hefei, China.
    •  Research Interests
  • Genome Assembly and Metagenomics
  • Comparative Genomics and Phylogeny Reconstruction
  • Computational Proteomics and Analytical Chemistry
  • Network Analysis and Data Management
    •  PhD Students
  • Yanbo Li, ANU School of Computng (primary supervisor, 08/2017-02/2022)
  • Anuradha Wickramarachchi, ANU School of Computing (primary supervisor, 08/2018-02/2022)
  • Vijini Mallawaarachchi, ANU School of Computing (primary supervisor, 08/2018-02/2022)
  • Hansheng Xue, ANU School of Computing (primary supervisor, 09/2019-)
  • Jin Zhao, School of Computer Science, Shandong University (visiting PhD student, 09/2019-09/2020)
  • Yujia Zhang, ANU School of Computing (primary supervisor, 06/2021-)
    •  Publications
     For a complete list of my publications, please see my publications, (or Google Scholar page). My Erdös number is 2.
    Program Committee
  • RECOMB-CG (Annual RECOMB Comparative Genomics Satellite Conference) 2021
  • WABI (Workshop on Algorithms in Bioinformatics) 2021
  • RECOMB-CG (Annual RECOMB Comparative Genomics Satellite Conference) 2020
  • APBC (Asia-Pacific Bioinformatics Conference) 2020
  • RECOMB-CG (Annual RECOMB Comparative Genomics Satellite Conference) 2019
  • WABI (Workshop on Algorithms in Bioinformatics) 2019
  • APBC (Asia-Pacific Bioinformatics Conference) 2019
  • WABI (Workshop on Algorithms in Bioinformatics) 2018
  • ACM BCB (ACM Conference on Bioinformatics, Computational Biology, and Health Informatics) 2018
  • APBC (Asia-Pacific Bioinformatics Conference) 2018
  • WABI (Workshop on Algorithms in Bioinformatics) 2017
  • APBC (Asia-Pacific Bioinformatics Conference) 2017
  • ISMB (International Conference on Intelligent Systems for Molecular Biology) 2016
  • ECCB (European Conference on Computational Biology) 2016
  • APBC (Asia-Pacific Bioinformatics Conference) 2016
  • ISMB/ECCB (International Conference on Intelligent Systems for Molecular Biology & European Conference on Computational Biology) 2015
  • ISMB (International Conference on Intelligent Systems for Molecular Biology) 2014
    •
    Software
  • GraphBin: A binning tool for metagenomic contigs using assembly graphs. Source code is at Github.
  • GraphBin2: A new generation of GraphBin that supports overlapped binning of metagenomic contigs. Source code is at Github.
  • MetaBCC-LR: Metagenomics binning by coverage and composition for long reads. Source code is at Github.
  • PlasLR: Adaptation of contig based plasmid classification for error prone long reads to improved genome assembly. Source code is at Github.
  • MultiTrans: Reconstruct transcripts through a mixed integer linear programming on assembly or splicing graphs. Source code is at Github.
  • Kmer2SNP: A reference-free and alignment-free variants calling tool for next-generation sequencing data. Source code is at Github.
  • DCHap: A divide-and-conquer haplotype phasing algorithm for third-generation sequencing data. Source code is at Github.
  • BacteriaMS-mixture: Bacterial mixture identification using MALDI-TOF mass spectrometry. Source code is at Github.
  • BaterialMS: Bacterial whole cell typing by mass spectra with bootstrapping assessment. Source code is at Github.
  • FLYE: A de novo assembler of long error-prone reads using repeat graphs. Source code is at Github.
  • ABruijn: A de novo assembler for PacBio and Oxford Nanopore Technologies reads. Source code is at Github.
  • MLGO: A web server designed for genome rearrangement and gene order analysis. The MLGO web server is available.
  • Matching distance: A distance measure for phylogenetic trees based on matching. The source code and instrustion are downloadable.
  • TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis. The source code and instrustion are downloadable.
    •