Weihua Pan

Ph.D. Candidate
Advisor: Dr. Stefano Lonardi
Department of Computer Science and Engineering
Bourns College of Engineering
University of California, Riverside

Contact:
University of California, Riverside
Winston Chung Hall, Room 362 (Algorithms and Computational Biology Lab)
Riverside, CA 92521
        
Phone:
Email:

 
(951)323-3581                      
wpan005 AT ucr DOT edu                       



I'm currently a fifth year Ph.D student in computer science with a special focus on computatioanl biology at University of California, Riverside. Here is my CV.

Education
  • Ph.D. Computer Science (2014.9 to present)
    University of California, Riverside

  • M.S. Statistics (2016.9 to present)
    University of California, Riverside

  • M.E. Computer Software and Theory (2011.9 to 2014.6)
    University of Science and Technology of China

  • B.E. Computer Science and Technology (2007.9 to 2011.7)
    Nanjing Normal University
Publications
  • OMGS: Optical Map-based Genome Scalding.
    Weihua Pan, Tao Jiang, Stefano Lonardi.
    RECOMB 2019.

  • Accurate detection of chimeric contigs via Bionano optical maps.
    Weihua Pan, Stefano Lonardi.
    Bioinformatics, vol. 34, to appear.

  • Novo&Stitch: Accurate Reconciliation of Multiple de novo Genome Assemblies via Optical Maps.
    Weihua Pan, Steve I. Wanamaker, Audrey M.V. Ah-Fong, Howard Judelson, and Stefano Lonardi.
    ISMB 2018. Bioinformatics, vol. 34, no. 13, pp. i43-i51, 2018.

  • ThIEF:Finding Genome-wide Trajectories of Epigenetics Marks.
    Anton Polishko, Md. Abid Hasan, Weihua Pan, Evelien M. Bunnik, Karine Le Roch and Stefano Lonardi.
    WABI 2017, 19:1-19:16.

  • MetaObtainer: a tool for obtaining specified species from metagenomic reads of next-generation sequencing
    Weihua Pan, Bo Chen and Yun Xu.
    Interdisciplinary Sciences: Computational Life Sciences, vol 7, no. 4, pp.405-413, 2015.

  • WinHAP2: an extremely fast haplotype phasing program for long genotype sequences
    Weihua Pan, Yanan Zhao, Yun Xu and Fengfeng Zhou.
    BMC Bioinformatics, 15:164, 2014.

  • Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization
    Xiaoquan Su $, Weihua Pan $, Baoxing Song, Jian Xu and Kang Ning.
    PLOS One, 9(3): e89323, 2014. (co-first author)

    • Softwares
    • OMGS
      • OMGS is an optical map based de novo genome scaffolding tool

    • Chimericognizer
      • Chimericognizer is an optical map based chimeric contigs correction tool

    • Novo&Stitch
      • Novo&Stitch is an optical map based de novo genome assemblies reconciliation tool

    • WinHAP
      • WinHAP is an extremely fast tool for large-scale haplotyping: inferring haplotype sequences from genotype sequences.

    • Parallel-MATA
      • Parallel-META is a GPGPU and Multi-Core CPU based software which can parallelly analyze massive metagenomic data structures, report the classification, construction and distribution on phylogenetic & taxonomic and functional level.

    • MetaObtainer
      • MetaObtainer is a tool for obtaining the specified species from next-generation sequencing short reads.
    Reviewing Activities

    • Scientific Reports

    • Research in Computational Biology (RECOMB) (2015)

    • International Conference on Intelligent Systems for Molecular Biology (ISMB) (2018, 2019)

    • ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) (2015, 2016, 2018)

    • RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-Seq) (2015)

    • Workshop on Algorithms in Bioinformatics (WABI) (2015, 2017)

    Teaching Assistant

    • Software Construction (CS100), University of Californina Riverside, Spring quarter, 2016.

    • Software Construction (CS100), University of Californina Riverside, Winter quarter, 2016.

    • Design and Analysis of Algorithm (CS218), University of Californina Riverside, Fall quarter, 2015.

    • Design and Analysis of Algorithm, University of Science and Technology of China, 2012.

    Links
    ACM Digital Library      IEEE Xplore     

    National Center for Biotechnology Information      HapMap Project      International Society for Computational Biology

    ISMB Conference      RECOMB Conference      BIOINFORMATCS Journal

    Weihua Pan
    Last modified: Monday March 18, 2019