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台灣鳥類誌 讀者回饋

學術演講

2017-03-28
3/28 15:30 Dr. Shin-Yi Lin 演講_ Genetic Dissection of TRA-1 Function and Regulation in the Sex Determination Pathways of Caenorhabditis Nematodes

中心消息

徵人

2017-03-31
李文雄院士-新世代高速定序中心誠徵資訊研究助理1名

2017-03-31
李文雄院士中研院新世代基因體定序核心實驗室誠徵實驗助理1名Positions Open in High Throughput Genomics Core Facility

2017-03-31
端木茂甯助研究員研究室誠徵專任研究助理1名

2017-03-31
野澤洋耕副研究員研究室誠徵研究助理1名

2017-04-07
綠島海洋研究站誠徵研究助理1名

2017-04-30
王忠信助研究員研究室誠徵約聘研究助理1名(進行Bioinformatics相關實驗)

2017-04-30
王忠信助研究員研究室誠徵約聘研究助理1名(操作基礎分生及genomics相關實驗)

2017-05-31
趙淑妙特聘研究員研究室誠徵研究助理1名

2017-05-31
陳國勤研究員研究室(潮間帶生態研究室)誠徵約聘助理1名

2017-05-31
台灣生物多樣性資訊機構(TaiBIF)誠徵生物多樣性資訊技術員 (研發替代役可) 1名

活動公告

2017-03-28
3/28 3月份「知識饗宴」- 臺灣史研究所謝國興研究員兼所長主講「後殖民?臺灣民間信仰中的日本記憶」

2017-03-31
「第六屆中央研究院人文及社會科學學術性專書獎」自本(106)年3月1日起至3月31日止受理申請

2017-03-31
3/31 3月份藝文活動「不可能的相聲」

2017-07-14
第24屆東元獎即日起至7月14日止受理申請

李文雄 特聘研究員

回研究人員

Dr. Wen-Hsiung Li

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tel: +886-2-2787-2256

Distinguished Research Fellow
Brown University, Providence, RI, USA Ph.D.
Research Fields
Evolutionary Genomics, Molecular Evolution, Bioinformatics and Computational Biology, Population Genetics, Human Genetics
Major Research Achievements (2013-2017)
Research Interests
  • Evolution of gene regulation: The importance of regulatory evolution has been proposed long ago (for instance, in the conspicuous morphological differences between human and chimp), but it has not been well studied due to experimental limitations. Making use of recent advances we are pursuing the following studies:
  • (1) Evolution of gene regulation in yeast strains and species. Our major question is whether evolution of gene regulation is mainly due to changes in cis elements or in trans factors. We are using microarrays and real time PCR to study expression differences, computational analysis of genomic data to identify sites of interest, and site-directed mutagenesis and fitness assays to test effects of regulatory changes.
  • (2) Evolution of gene expression patterns in mammals. Using data in the public domain, and in collaboration with other labs, we are investigating changes in tissue expression patterns between species or duplicate genes.
  • (3) Evolution of cis-regulatory modules and gene networks. Using statistical and experimental approaches we are identifying cis elements and gene networks, and studying how they have evolved.
  • Evolution of duplicate genes. :Gene duplication is a major source of raw material during genome evolution, and the analysis of duplicate genes provides insight into many evolutionary processes. We study patterns of duplicate gene survival across diverse genomes and what factors, such as gene structure, expression, or protein interaction, influence these patterns. We also study rates and mechanisms of structural and functional divergence in duplicate genes.
  • III. Development of statistical methods and computational analysis of genomic data.
  • The huge amount of genomic data currently available is a tremendous resource for understanding the organization and evolution of genomes. We are currently developing tools for analysis of segmental duplications, protein interaction data, and genomic
    Ongoing projects
    Publications (2013-2017)
    1. Ke HM, Prachumwat A, Yu CP, Yang YT, Promsri S, Liu KF, Lo CF, Lu MJ, Lai MC, Tsai IJ, Li WH, 2017, “Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade.”, Scientific reports, 7, 41394. (SCI) (IF: 5.228; SCI ranking: 11.1%)
    2. Chen CK, Yu CP, Li SC, Wu SM, Lu MJ, Chen YH, Chen DR, Ng CS, Ting CT, Li WH, 2017, “Identification and evolutionary analysis of long non-coding RNAs in zebra finch.”, BMC genomics, 18(1), 117. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    3. Li H, Xiang-Yu J, Dai G, Gu Z, Ming C, Yang Z, Ryder OA, Li WH*, Fu YX, Zhang YP, 2016, “Large numbers of vertebrates began rapid population decline in the late 19th century.”, Proceedings of the National Academy of Sciences of the United States of America, 113(49), 14079-14084. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    4. Tsai KJ, Lu MJ, Yang KJ, Li M, Teng Y, Chen S, Ku MS, Li WH*, 2016, “Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance.”, Scientific reports, 6, 35076. (SCI) (IF: 5.228; SCI ranking: 11.1%)
    5. Bhattacharjee MJ, Yu CP, Lin JJ, Ng CS, Wang TY, Lin HH, Li WH*, 2016, “Regulatory Divergence among Beta-Keratin Genes during Bird Evolution.”, Molecular biology and evolution, 33(11), 2769-2780. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    6. Chen CK, Ng CS, Wu SM, Chen JJ, Cheng PL, Wu P, Lu MY, Chen DR, Chuong CM, Cheng HC, Ting CT, Li WH*, 2016, “Regulatory Differences in Natal Down Development between Altricial Zebra Finch and Precocial Chicken.”, Molecular biology and evolution, 33(8), 2030-2043. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    7. Mei-Ju May Chen, Li-Kai Chen, Yu-Shing Lai, Yu-Yu Lin, Dung-Chi Wu, Yi-An Tung, Kwei-Yan Liu, Hsueh-Tzu Shih, Yi-Jyun Chen, Yan-Liang Lin, Li-Ting Ma, Jian-Long Huang, Po-Chun Wu, Ming-Yi Hong, Fang-Hua Chu, June-Tai Wu, Wen-Hsiung Li* and Chien-Yu Chen*, 2016, “Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster”, BMC Genomics, 17, 220. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    8. Huang CF, Chang YM, Lin JJ, Yu CP, Lin HH, Liu WY, Yeh S, Tu SL, Wu SH, Ku MS, Li WH*, 2016, “Insights into the regulation of C leaf development from comparative transcriptomic analysis.”, Current opinion in plant biology, 30, 1-10. (SCI) (IF: 6.78; SCI ranking: 3.3%)
    9. Yu CP, Lin JJ, Li WH*, 2016, “Positional distribution of transcription factor binding sites in Arabidopsis thaliana.”, Scientific reports, 6, 25164. (SCI) (IF: 5.228; SCI ranking: 11.1%)
    10. Su-Ying Yeh, Hau-Wen Chen, Chun-Yeung Ng, Chu-Yin Lin, Tung-Hai Tseng, Wen-Hsiung Li, Maurice S. B. Ku, 2015, “Down-Regulation of Cytokinin Oxidase 2 Expression Increases Tiller Number and Improves Rice Yield”, Rice, 8(1), 36. (SCI) (IF: 3.417; SCI ranking: 8.4%)
    11. Chen Siang Ng, Chih-Kuan Chen, Wen-Lang Fan, Ping Wu, Siao-Man Wu, Jiun-Jie Chen, Yu-Ting Lai, Chi-Tang Mao, Mei-Yeh Jade Lu, Di-Rong Chen, Ze-Shiang Lin, Kai-Jung Yang, Yuan-An Sha, Tsung-Che Tu, Chih-Feng Chen, Cheng-Ming Chuong and Wen-Hsiung Li*, 2015, “Transcriptomic analyses of regenerating adult feathers in chicken”, BMC Genomics, 16, 756. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    12. Jui-Jen Chang, Caroline Thia, Hao-Yeh Lin, Hsien-Lin Liu, Feng-Ju Ho, Jiunn-Tzong Wu, Ming-Che Shih, Wen-Hsiung Li, Chieh-Chen Huang, 2015, “Integrating an algal β-carotene hydroxylase gene into a designed carotenoid-biosynthesis pathway increases carotenoid production in yeast”, Bioresource Technology, 184, 2-8. (SCI) (IF: 4.917; SCI ranking: 10.6%,7.1%,12.5%)
    13. Lin YL, Ma LT, Lee YR, Lin SS, Wang SY, Chang TT, Shaw JF, Li WH, Chu FH, 2015, “MicroRNA-Like Small RNAs Prediction in the Development of Antrodia cinnamomea”, PLoS One, 10(4), e0123245. (SCI) (IF: 3.057; SCI ranking: 17.5%)
    14. Cheng F, Liu C, Lin CC, Zhao J, Jia P, Li WH, Zhao Z, 2015, “A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types.”, PLoS computational biology, 11(9), e1004497. (SCI) (IF: 4.587; SCI ranking: 11.7%,8.9%)
    15. Chen SC, Tsai TH, Chung CH, Li WH, 2015, “Dynamic association rules for gene expression data analysis.”, BMC genomics, 16, 786. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    16. Shiao MS, Chang JM, Fan WL, Lu MY, Notredame C, Fang S, Kondo R, Li WH*, 2015, “Expression Divergence of Chemosensory Genes between Drosophila sechellia and Its Sibling Species and Its Implications for Host Shift.”, Genome biology and evolution, 7(10), 2843-58. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    17. Shiao MS, Chang JM, Fan WL, Lu MY, Notredame C, Fang S, Kondo R, Li WH*, 2015, “Expression Divergence of Chemosensory Genes between Drosophila sechellia and Its Sibling Species and Its Implications for Host Shift.”, Genome biology and evolution, 7(10), 2843-58. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    18. Ling S, Hu Z, Yang Z, Yang F, Li Y, Lin P, Chen K, Dong L, Cao L, Tao Y, Hao L, Chen Q, Gong Q, Wu D, Li W, Zhao W, Tian X, Hao C, Hungate EA, Catenacci DV, Hudson RR, Li WH*, Lu X, Wu CI, 2015, “Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution.”, Proceedings of the National Academy of Sciences of the United States of America, 112(47), E6496-505. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    19. Ling S, Hu Z, Yang Z, Yang F, Li Y, Lin P, Chen K, Dong L, Cao L, Tao Y, Hao L, Chen Q, Gong Q, Wu D, Li W, Zhao W, Tian X, Hao C, Hungate EA, Catenacci DV, Hudson RR, Li WH*, Lu X, Wu CI, 2015, “Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution.”, Proceedings of the National Academy of Sciences of the United States of America, 112(47), E6496-E6505. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    20. Schaefke B, Wang TY, Wang CY, Li WH*, 2015, “Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus.”, Genome biology and evolution, 7(8), 2245-2257. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    21. Wu P, Ng CS, Yan J, Lai YC, Chen CK, Lai YT, Wu SM, Chen JJ, Luo W, Widelitz RB, Li WH*, Chuong CM, 2015, “Topographical mapping of alpha- and beta-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives.”, Proceedings of the National Academy of Sciences of the United States of America, 112(49), E6770-E6779. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    22. Yu CP, Chen SC, Chang YM, Liu WY, Lin HH, Lin JJ, Chen HJ, Lu YJ, Wu YH, Lu MY, Lu CH, Shih AC, Ku MS, Shiu SH, Wu SH, Li WH*, 2015, “Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors.”, Proceedings of the National Academy of Sciences of the United States of America, 112(19), E2477-86. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    23. Tsai DY, Hung KH, Lin IY, Su ST, Wu SY, Chung CH, Wang TC, Li WH, Shih AC, Lin KI, 2015, “Uncovering MicroRNA Regulatory Hubs that Modulate Plasma Cell Differentiation.”, Scientific reports, 5, 17957. (SCI) (IF: 5.228; SCI ranking: 11.1%)
    24. Lin CC, Chang YM, Pan CT, Chen CC, Ling L, Tsao KC, Yang RB, Li WH*, 2014, “Functional Evolution of cardiac microRNAs in heart development and functions.”, Mol Biol Evol., 31(10), 2722-2734. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    25. Chang JJ, C. Y. Ho, C. T. Mao, N. Barham, Y. R. Huang, F. J. Ho, Y. C. Wu, Y. H. Hou, M. C. Shih, W. H. Li, C. C. Huang, 2014, “A thermo- and toxin-tolerant kefir yeast for biorefinery and biofuel production”, Applied Energy, 132, 465-474. (SCI) (IF: 5.746; SCI ranking: 4.4%,11.4%)
    26. Lu MY, Fan WL, Wang WF, Chen T, Tang YC, Chu FH, Chang TT, Wang SY, Li MY, Chen YH, Lin ZS, Yang KJ, Chen SM, Teng YC, Lin YL, Shaw JF, Wang TF, Li WH*, 2014, “Genomic and transcriptomic analyses of the medicinal fungus Antrodia cinnamomea for its metabolite biosynthesis and sexual development.”, Proceedings of the National Academy of Sciences of the United States of America, 111(44), E4743-E4752. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    27. Ng CS, Wu P, Fan WL, Yan J, Chen CK, Lai YT, Wu SM, Mao CT, Chen JJ, Lu MY, Ho MR, Widelitz RB, Chen CF, Chuong CM, Li WH*, 2014, “Genomic Organization, Transcriptomic Analysis, and Functional Characterization of Avian alpha- and beta-Keratins in Diverse Feather Forms.”, Genome biology and evolution, 6(9), 2258-73. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    28. Lin JJ, Yu CP, Chang YM, Chen SC, Li WH*, 2014, “Maize and millet transcription factors annotated using comparative genomic and transcriptomic data.”, BMC genomics, 15, 818. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    29. Cheng F, Jia P, Wang Q, Lin CC, Li WH, Zhao Z., 2014, “Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome.”, Mol Biol Evol., 31, 2156-2169. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    30. Yang YT, Lee DY, Wang Y, Hu JM, Li WH, Leu JH, Chang GD, Ke HM, Kang ST, Lin SS, Kou GH, Lo CF, 2014, “The genome and occlusion bodies of marine Penaeus monodon nudivirus (PmNV, also known as MBV and PemoNPV) suggest that it should be assigned to a new nudivirus genus that is distinct from the terrestrial nudiviruses.”, BMC genomics, 15, 628. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
    31. Chang CH, Fan TC, Yu JC, Liao GS, Lin YC, Shih A, Li WH* and Yu A.*, 2014, “The prognostic significance of RUNX2 and miR-10a/10b and their inter-relationship in breast cancer”, Journal of Translational Medicine, 12, 257. (SCI) (IF: 3.694; SCI ranking: 24.2%)
    32. Wang TY, Huang CJ, Chen HL, Ho PC, Ke HM, Cho HY, Ruan SK, Hung KY, Wang IL, Cai YW, Sung HM, Li WH*, Shih MC*, 2013, “Systematic screening of glycosylation- and trafficking-associated gene knockouts in Saccharomyces cerevisiae identifies mutants with improved heterologous exocellulase activity and host secretion”, BMC Biotechnology, 13(1), 71. (SCI) (IF: 2.452; SCI ranking: 39.1%)
    33. Liu WY, Chang YM, Chen SC, Lu CH, Wu YH, Lu MY, Chen DR, Shih AC, Sheue CR, Huang HC, Yu CP, Lin HH, Shiu SH, Sun-Ben Ku M, Li WH*, 2013, “Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination.”, Proceedings of the National Academy of Sciences of the United States of America, 110(10), 3979-3984. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    34. Chu TC, Lu CH, Liu T, Lee GC, Li WH, Shih AC*, 2013, “Assembler for de novo assembly of large genomes”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, E3417-E3424. (SCI) (IF: 9.423; SCI ranking: 6.3%)
    35. Chang JJ, Ho FJ, Ho CY, Wu YC, Hou YH, Huang CC, Shih MC, Li WH*, 2013, “Assembling a cellulase cocktail and a cellodextrin transporter into a yeast host for CBP ethanol production.”, Biotechnology for biofuels, 6(1), 19. (SCI) (IF: 6.444; SCI ranking: 7.5%,8%)
    36. Wang HC, Chu FH, Chien SC, Liao JW, Hsieh HW, Li WH, Lin CC, Shaw JF, Kuo YH, Wang SY, 2013, “Establishment of the metabolite profile for an Antrodia cinnamomea health food product and investigation of its chemoprevention activity.”, Journal of agricultural and food chemistry, 61(36), 8556-64. (SCI) (IF: 2.857; SCI ranking: 5.3%,19.4%,16%)
    37. Fan WL, Ng CS, Chen CF, Lu MY, Chen YH, Liu CJ, Wu SM, Chen CK, Chen JJ, Mao CT, Lai YT, Lo WS, Chang WH, Li WH*, 2013, “Genome-wide patterns of genetic variation in two domestic chickens”, Genome Biol Evol., 5, 1376-1392. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    38. Chang YM, Chang CL, Li WH, Shih AC, 2013, “Historical profiling of maize duplicate genes sheds light on the evolution of C4 photosynthesis in grasses.”, Molecular phylogenetics and evolution, 66(2), 453-462. (SCI) (IF: 3.792; SCI ranking: 27.7%,28.3%,29.1%)
    39. Lin Z, Wang TY, Tsai BS, Wu FT, Yu FJ, Tseng YJ, Sung HM, Li WH*, 2013, “Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts”, Genome Biol Evol, 6, 1065-1078. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
    40. Schaefke B, Emerson JJ, Wang TY, Lu MY, Hsieh LC, Li WH*, 2013, “Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast”, Mol Biol Evol., 30, 2121-2133. (SCI) (IF: 13.649; SCI ranking: 1.7%,2.4%,4.3%)
    41. Ha M, Hong S, Li WH* , 2013, “Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context”, Bioinformatics, 29, 1199-11205. (SCI) (IF: 5.766; SCI ranking: 9.1%,5.4%,9.3%)
    42. Shiao MS, Fan WL, Fang S, Lu MYJ, Kondo R, Li WH*, 2013, “Transcriptional profiling of chemosensory genes in adult Drosophila antennae by High Throughput Sequencing”, ZOOLOGICAL STUDIES, 52, 42. (SCI) (IF: 0.885; SCI ranking: 56.5%)