林勇欣 副教授 國立交通大學 生物資訊及系統生物研究所

Yeong-Shin Lin, Associate Professor
Institute of Bioinformatics and Systems Biology
National Chiao Tung University
Hsinchu, Taiwan
Main Page Lab Members Lectures Resources Bioinformatics Center

Research Interests

Our major interest is in the processes and mechanisms of Evolution. We also use evolutionary concepts to study Genomics, Structural Biology, Systems Biology, Phylogenetics and Biogeography.



We use a wide range of research techniques, from the molecular to the organismal level, from DNA sequences to protein structures, from genomics to proteomics, and from experimental to computational studies, including developing Bioinformatic methods and tools, to study these problems.


Publications


  • Bioinformatics Tools and Applications

  • Computational Genomics
      Yi-Hsueh Lee, Chia-Pei Chang, Yu-Ju Cheng, Yi-Yi Kuo, Yeong-Shin Lin, and Chien-Chia Wang*. (2017). Evolutionary gain of highly divergent tRNA specificities by two isoforms of human histidyl-tRNA synthetase. Cellular and Molecular Life Sciences.
      [e-journal] [PubMed] [IF] [Cited by]

      Min-Kung Hsu, I-Ching Wu, Ching-Chia Cheng, Jen-Liang Su, Chang-Huain Hsieh, Yeong-Shin Lin, and Feng-Chi Chen*. (2015). Triple-layer dissection of the lung adenocarcinoma transcriptome: regulation at the gene, transcript, and exon levels. Oncotarget. 6: 28755-28773.
      [e-journal] [PubMed] [IF] [Cited by]

      Chia-Pei Chang, Chih-Yao Chang, Yi-Hsueh Lee, Yeong-Shin Lin, and Chien-Chia Wang*. (2015). Divergent alanyl-tRNA synthetase genes of Vanderwaltozyma polyspora descended from a common ancestor through whole-genome duplication followed by asymmetric evolution. Molecular and Cellular Biology. 35: 2242-2253.
      [e-journal] [PubMed] [IF] [Cited by]

      Han Liang, Yeong-Shin Lin, and Wen-Hsiung Li*. (2008). Fast evolution of core promoters in primate genomes. Molecular Biology and Evolution. 25: 1239-1244.
      [e-journal] [PubMed] [IF] [Cited by]

      Yeong-Shin Lin, Wei-Lun Hsu, Jenn-Kang Hwang*, and Wen-Hsiung Li*. (2007). Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. Molecular Biology and Evolution. 24: 1005-1011.
      [e-journal] [PubMed] [IF] [Cited by]

      Yeong-Shin Lin, Jenn-Kang Hwang, and Wen-Hsiung Li*. (2007). Protein complexity, gene duplicability and gene dispensability in the yeast genome. Gene. 387: 109-117.
      [e-journal] [PubMed] [IF] [Cited by]

      Yeong-Shin Lin, Jake K. Byrnes, Jenn-Kang Hwang, and Wen-Hsiung Li*. (2006). Codon usage bias versus gene conversion in the evolution of yeast duplicate genes. Proc. Natl. Acad. Sci. USA. 103: 14412-14416.
      [e-journal] [PubMed] [IF] [Cited by]

  • Computational Structural Biology
      Chien-Hua Shih, Chih-Min Chang, Yeong-Shin Lin, Wei-Cheng Lo, and Jenn-Kang Hwang*. (2012). Evolutionary information hidden in a single protein structure. Proteins: structure, function, and bioinformatics. 80: 1647-1657.
      [e-journal] [PubMed] [IF] [Cited by]

      Yeong-Shin Lin*. (2008). Using a strategy based on the concept of convergent evolution to identify residue substitutions responsible for thermal adaptation. Proteins: structure, function, and bioinformatics. 73: 53-62.
      [e-journal] [PubMed] [IF] [Cited by] [Data]

      Chih-Hao Lu, Yeong-Shin Lin, Yu-Ching Chen, Chin-Sheng Yu, Shi-Yu Chang, and Jenn-Kang Hwang*. (2006). The fragment transformation method to detect the protein structural motifs. Proteins: structure, function, and bioinformatics. 63: 636-643.
      [e-journal] [PubMed] [IF] [Cited by]

      Yu-Ching Chen, Yeong-Shin Lin, Chih-Jen Lin, and Jenn-Kang Hwang*. (2004). Prediction of the bonding states of cysteines using the Support Vector Machines based on multiple feature vectors and Cysteine State Sequences. Proteins: structure, function, and bioinformatics. 55: 1036-1042.
      [e-journal] [PubMed] [IF] [Cited by]

  • Phylogenetics, Systematics, and Biogeography
      Chia-Hao Chang, Yi Ta Shao, Wen-Chung Fu, Kazuhiko Anraku, Yeong-Shin Lin, and Hong Young Yan*. (2015). Differentiation of visual spectra and nuptial colorations of two Paratanakia himantegus subspecies (Cyprinoidea: Acheilognathidae) in response to the distinct photic conditions of their habitats. Zoological Studies. 54: 43.
      [e-journal] [PubMed] [IF] [Cited by]

      Chia-Hao Chang, Fan Li, Kwang-Tsao Shao, Yeong-Shin Lin, Takahiro Morosawa, Sungmin Kim, Hyeyoung Koo, Won Kim, Jae-Seong Lee, Shunping He, Carl Smith, Martin Reichard, Masaki Miya, Tetsuya Sado, Kazuhiko Uehara, Sbastien Lavoué, Wei-Jen Chen*, and Richard L. Mayden. (2014). Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: Evidence for necessary taxonomic revision in the family and the identification of cryptic species. Molecular Phylogenetics and Evolution. 81: 182-194.
      [e-journal] [PubMed] [IF] [Cited by]

      Hui-Yu Teng, Yeong-Shin Lin, and Chyng-Shyan Tzeng*. (2009). A new Anguilla species and a reanalysis of the phylogeny of freshwater eels. Zoological Studies. 48: 808-822.
      [e-journal] [PubMed] [IF] [Cited by]

      Chyng-Shyan Tzeng*, Yeong-Shin Lin, Si-Min Lin, Tzi-Yuan Wang, and Feng-Yung Wang. (2006). The phylogeography and population demographics of selected freshwater fishes in Taiwan. Zoological Studies. 45: 285-297.
      [e-journal] [PubMed] [IF] [Cited by]

      Yeong-Shin Lin*, Chyng-Shyan Tzeng, and Jenn-Kang Hwang*. (2005). Reassessment of morphological characteristics in freshwater eels (genus Anguilla, Anguillidae) shows congruence with molecular phylogeny estimates. Zoologica Scripta. 34: 225-234.
      [e-journal] [PubMed] [IF] [Cited by]

      Yeong-Shin Lin, Yu-Ping Poh, Si-Min Lin, and Chyng-Shyan Tzeng*. (2002). Molecular techniques to identify freshwater eels: RFLP analyses of PCR-amplified DNA fragments and allele-specific PCR from mitochondrial DNA. Zoological Studies. 41: 421-430.
      [e-journal] [PubMed] [IF] [Cited by]

      Yeong-Shin Lin, Yu-Ping Poh, and Chyng-Shyan Tzeng*. (2001). Which is the dispersal route of the ancient Atlantic eels: Reanalysis of the phylogeny of freshwater eels. Journal of Taiwan Fisheries Research. 9: 161-173.
      [e-journal] [PubMed] [IF] [Cited by]

      Yeong-Shin Lin, Yu-Ping Poh, and Chyng-Shyan Tzeng*. (2001). A phylogeny of freshwater eels inferred from mitochondrial genes. Molecular Phylogenetics and Evolution. 20: 252-261.
      [e-journal] [PubMed] [IF] [Cited by] [Cited by The Eel ]

  • DNA Barcode and Mitochondrial Genome
      Chia-Hao Chang, Han-Yang Lin, Qiu Ren, Yeong-Shin Lin, and Kwang-Tsao Shao*. (2016). DNA barcode identification of fish products in Taiwan: Government commissioned authentication cases. Food Control. 66: 38-43.
      [e-journal] [PubMed] [IF] [Cited by]

      Chia-Hao Chang, Wei-Chuan Chiang, Yeong-Shin Lin, Nian-Hong Jang-Liaw, and Kwang-Tsao Shao*. (2016). Complete mitochondrial genome of the longfin mako shark, Isuru spaucus (Chondrichthyes, Lamnidae). Mitochondrial DNA. 27: 690-691.
      [e-journal] [PubMed] [IF] [Cited by]

      Chia-Hao Chang, Nian-Hong Jang-Liaw, Yeong-Shin Lin, Aaron Carlisle, Hua Hsun Hsu, Yun-Chih Liao, and Kwang-Tsao Shao*. (2016). The complete mitochondrial genome of the salmon shark, Lamna ditropis (Chondrichthyes, Lamnidae). Mitochondrial DNA. 27: 316-317.
      [e-journal] [PubMed] [IF] [Cited by]

      Chia-Hao Chang, Rima W. Jabado, Yeong-Shin Lin, and Kwang-Tsao Shao*. (2015). The complete mitochondrial genome of the sand tiger shark, Carcharias taurus (Chondrichthyes, Odontaspididae). Mitochondrial DNA. 26: 728-729.
      [e-journal] [PubMed] [IF] [Cited by]

      Chia-Hao Chang, Kwang-Tsao Shao, Yeong-Shin Lin, An-Yi Tsai, Pin-Xuan Su, and Hsuan-Ching Ho*. (2015). The complete mitochondrial genome of the shortfin mako, Isurus oxyrinchus (Chondrichthyes, Lamnidae). Mitochondrial DNA. 26: 475-476.
      [e-journal] [PubMed] [IF] [Cited by]

      Fan Li, Kwang-Tsao Shao, Yeong-Shin Lin, and Chia-Hao Chang*. (2015). The complete mitochondrial genome of the Rhodeus shitaiensis (Teleostei, Cypriniformes, Acheilognathidae). Mitochondrial DNA. 26: 301-302.
      [e-journal] [PubMed] [IF] [Cited by]

      Chia-Hao Chang, Kwang-Tsao Shao, Yeong-Shin Lin, Yi-Chiao Fang, and Hsuan-Ching Ho*. (2014). The complete mitochondrial genome of the great white shark, Carcharodon carcharias (Chondrichthyes, Lamnidae). Mitochondrial DNA. 25: 357-358.
      [e-journal] [PubMed] [IF] [Cited by]

      Chia-Hao Chang, Kwang-Tsao Shao, Yeong-Shin Lin, Hsuan-Ching Ho, and Yun-Chih Liao*. (2014). The complete mitochondrial genome of the big-eye thresher shark, Alopias superciliosus (Chondrichthyes, Alopiidae). Mitochondrial DNA. 25: 290-292.
      [e-journal] [PubMed] [IF] [Cited by]

      Chia-Hao Chang, Kwang-Tsao Shao, Yeong-Shin Lin, Wei-Chuan Chiang, and Nian-Hong Jang-Liaw*. (2014). Complete mitochondrial genome of the megamouth shark Megachasma pelagios (Chondrichthyes, Megachasmidae). Mitochondrial DNA. 25: 185-187.
      [e-journal] [PubMed] [IF] [Cited by]

      Chia-Hao Chang, Kwang-Tsao Shao, Yeong-Shin Lin, Yun-Chih Liao*. (2013). The complete mitochondrial genome of the three-spot seahorse, Hippocampus trimaculatus (Teleostei, Syngnathidae). Mitochondrial DNA. 24: 665-667.
      [e-journal] [PubMed] [IF] [Cited by]

      Chia-Hao Chang, Han-Yang Lin, Nian-Hong Jang-Liaw, Kwang-Tsao Shao, Yeong-Shin Lin, Hsuan-Ching Ho*. (2013). The complete mitochondrial genome of the tiger tail seahorse, Hippocampus comes (Teleostei, Syngnathidae). Mitochondrial DNA. 24: 199-201.
      [e-journal] [PubMed] [IF] [Cited by]

      Chia-Hao Chang, Nian-Hong Jang-Liaw, Yeong-Shin Lin, Yi-Chiao Fang, and Kwang-Tsao Shao*. (2013). Authenticating the use of dried seahorses in the traditional Chinese medicine market in Taiwan using molecular forensics. Journal of Food and Drug Analysis. 21: 310-316.
      [e-journal] [PubMed] [IF] [Cited by]
  • Contact

    Office:+886-3-5712121 # 56960
    Fax:+886-3-5729288
    +886-3-5712121 # 56960
    Email:yslinfaculty.nctu.edu.tw
    Address:新竹市博愛街75號
    生科實驗二館 103室
    R103, BioLab-II, 75 Po-Ai Street, Hsinchu, Taiwan 30068


    Lab:+886-3-5712121 # 56961

    Lectures

    普通生物學(一)
    General Biology (I)


    計算生物實驗
    Computational Biology Lab.

    遺傳學
    Genetics

    演化生物學
    Evolutionary Biology


    分子演化
    Molecular Evolution

    Links

    NCBI
    EnsEMBL
    Genome OnLine Database
    Approved Sequencing Targets
    UCSC Genome Bioinformatics
    Stanford Genomic Resources
    TGI - The Gene Index
    J. Craig Venter Institute
    Broad Institute
    HapMap
    SGD
    SMD
    MIPS
    RCSB PDB
    SCOP
    ExPASy - SwissProt - PROSITE
    CE - Combinatorial Extension
    RepeatMasker

    MEGA
    PAUP
    PAML
    PhyML
    CONSEL
    MacClade
    MrBayes
    DAMBE
    LiKaKs
    Structure (population)
    DnaSP
    Arlequin
    MCL - a cluster algorithm for graphs
    The R Manuals
    SimpleR
    Chi-square Test
    Fisher's Exact Test
    Kolmogorov-Smirnov Test

    Nature
    Science
    PNAS
    PLoS Biology
    Current Biology
    Cell
    EMBO
    Nature Ecology & Evolution
    Nature Genetics
    Nature Biotechnology
    Trends in Genetics
    Genome Research
    Genome Biology
    Molecular Biology & Evolution
    Nucleic Acids Research
    Genetics
    Evolution
    Bioinformatics
    Journal of Molecular Biology
    Journal of Molecular Evolution
    MPE
    Proteins
    Gene

    科技部
    ISI Web of Knowledge
    集中採購共同供應契約一覽表
    政府電子採購網
    交大購運組
    學網網路電話
    Main Page Lab Members Lectures Resources Bioinformatics Center