人員 研究人員 李文雄 特聘研究員

李文雄 特聘研究員

實驗室主持人

Dr.李文雄

特聘研究員

Brown University, Providence, RI, USA Ph.D.

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辦公室: 跨領域 A203

電話: +886-2-2787-2256
研究領域
  • 演化基因體學
  • 分子演化
  • 生物資訊與計算生物學

研究方向

  • 1.鳥類羽毛的發育演化
    解釋我們周遭無窮盡的多樣性是如何及為何演化的，是生物學最重要的中心問題之一。我們研究的其中一個主題模式是鳥類的羽毛：羽毛有著高度次序和階層分支結構。羽毛也是演化創新產物的好例子：它們近期才在鳥類的譜系中演化出來，而且還經歷了快速及高度的多樣化。發育遺傳及基因體學能夠用來取得控制羽毛發育的分子機制之進一步瞭解。並且在家雞中現有的遺傳及分子工具，能夠讓我們用來檢驗及操控產生這類多樣性的分子及細胞路徑。而比較生物學的方法則能夠協助我們瞭解這些路徑究竟是如何演化的，以及這些路徑中的哪些變化負責產生新結構和程序的起源與多樣性。
  • 2.合成生物學：一種嶄新的生物科技策略
    合成生物學被視為人類歷史上繼農業革命、工業革命之後，另一次重要的產業革命。 我們研究團隊發展了一個合成生物學技術平台，命名為PGASO（Promoter-based Gene Assembly and Simultaneous Overexpression），其目標是透過創造可設計或修改基因體的技術，配合利用生物資訊得到的背景知識，去了解一個生物物質的製造及代謝過程。並藉由構建新的基因迴路來賦予一個微生物新的功能，以製造該微生物本來無法製造的產物。PGASO不僅適用於對生命現象的學術探索，未來人類所需求的能源燃料、昂貴藥物、稀少的天然物，甚至是分解廢棄物，都有機會透過經設計並完成基因體改造之微生物來進行量產。研究團隊期許如同畢卡索的創作精神一般，可以將抽象的生物資訊轉變為具體的作品。
  • 3.C4植物葉片發育演化
    與C3植物(如水稻)比起來，C4植物(如玉米)在二氧化碳的壓縮效能、水中氮原子的使用率上的優勢皆讓其更能適應炎熱與乾旱的環境。將玉米C4光合作用的反應路徑移植到水稻中將可增加水道的產量、提高其運用水的效能與降低肥料的使用。要達到這個目的最重要的是瞭解C4植物中如何調控kranz anatomy的發育。因此我們利用基因體學、分子生物學及生物資訊學的技術，來研究從C3到C4 光合作用的演化來找出調控kranz anatomy發育的關鍵基因。

 

最新發表

期刊論文 ( 2015 - 2020 )

  1. Lee MH, Hsu TL, Lin JJ, Lin YJ, Kao YY, Chang JJ, Li WH*, 2020, “Constructing a human complex type N-linked glycosylation pathway in Kluyveromyces marxianus.”, PloS one, 15(5), e0233492. (SCIE) (IF: 2.766; SCIE ranking: 23.4%) Link
  2. Anandharaj M, Lin YJ, Rani RP, Nadendla EK, Ho MC, Huang CC, Cheng JF, Chang JJ, Li WH*, 2020, “Constructing a yeast to express the largest cellulosome complex on the cell surface.”, Proceedings of the National Academy of Sciences of the United States of America, 117(5), 2385-2394. (SCIE) (IF: 9.504; SCIE ranking: 7.8%) Link
  3. Wang WF, Lu MJ, Cheng TR, Tang YC, Teng YC, Hwa TY, Chen YH, Li MY, Wu MH, Chuang PC, Jou R, Wong CH, Li WH*, 2020, “Genomic Analysis of Mycobacterium tuberculosis Isolates and Construction of a Beijing Lineage Reference Genome.”, Genome biology and evolution, 12(2), 3890-3905. (SCIE) (IF: 3.94; SCIE ranking: 28.6%,24.6%) Link
  4. Liu HL, Chang JJ, Thia C, Lin YJ, Lo SC, Huang CC, Li WH*, 2019, “Characterizing an engineered carotenoid-producing yeast as an anti-stress chassis for building cell factories.”, Microbial cell factories, 18(1), 155. (SCIE) (IF: 3.831; SCIE ranking: 22.4%) Link
  5. Wang L, Zhao L, Zhang X, Zhang Q, Jia Y, Wang G, Li S, Tian D, Li WH*, Yang S, 2019, “Large-scale identification and functional analysis of NLR genes in blast resistance in the Tetep rice genome sequence.”, Proceedings of the National Academy of Sciences of the United States of America, 116(37), 18479-18487. (SCIE) (IF: 9.504; SCIE ranking: 7.8%) Link
  6. Gomez Luciano LB, Jason Tsai I, Chuma I, Tosa Y, Chen YH, Li JY, Li MY, Jade Lu MY, Nakayashiki H, Li WH*, 2019, “Blast fungal genomes show frequent chromosomal changes, gene gains and losses, and effector gene turnover.”, Molecular biology and evolution, 36(6),1148-1161. (SCIE) (IF: 6.202; SCIE ranking: 12.8%,9%,10.4%) Link
  7. Chang YM, Lin HH, Liu WY, Yu CP, Chen HJ, Wartini PP, Kao YY, Wu YH, Lin JJ, Lu MJ, Tu SL, Wu SH, Shiu SH, Ku MSB, Li WH*, 2019, “Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes.”, Proceedings of the National Academy of Sciences of the United States of America, 116(8), 3091-3099. (SCIE) (IF: 9.504; SCIE ranking: 7.8%) Link
  8. Lin JJ, Bhattacharjee MJ, Yu CP, Tseng YY, Li WH*, 2019, “Many human RNA viruses show extraordinarily stringent selective constraints on protein evolution.”, Proceedings of the National Academy of Sciences of the United States of America, 116(38), 19009-19018. (SCIE) (IF: 9.504; SCIE ranking: 7.8%) Link
  9. Huang CJ, Lu MY, Chang YW, Li WH*, 2018, “Experimental Evolution of Yeast for High Temperature Tolerance.”, Molecular biology and evolution, 35(8), 1823-1839. (SCIE) (IF: 6.202; SCIE ranking: 12.8%,9%,10.4%) Link
  10. Huang J, Li J, Zhou J, Wang L, Yang S, Hurst LD, Li WH, Tian D, 2018, “Identifying a large number of high-yield genes in rice by pedigree analysis, whole-genome sequencing, and CRISPR-Cas9 gene knockout.”, Proceedings of the National Academy of Sciences of the United States of America, 115(32), E7559-E7567. (SCIE) (IF: 9.661; SCIE ranking: 6.3%) Link
  11. Pi HW, Anandharaj M, Kao YY, Lin YJ, Chang JJ, Li WH, 2018, “Engineering the oleaginous red yeast Rhodotorula glutinis for simultaneous beta-carotene and cellulase production.”, Scientific reports, 8(1), 10850. (SCIE) (IF: 4.259; SCIE ranking: 15.6%) Link
  12. Chang JJ, Anandharaj M, Ho CY, Tsuge K, Tsai TY, Ke HM, Lin YJ, Ha Tran MD, Li WH*, Huang CC, 2018, “Biomimetic strategy for constructing Clostridium thermocellum cellulosomal operons in Bacillus subtilis.”, Biotechnology for biofuels, 11, 157. (SCIE) (IF: 5.203; SCIE ranking: 12%,11.9%) Link
  13. Lee MH, Lin JJ, Lin YJ, Chang JJ, Ke HM, Fan WL, Wang TY, Li WH*, 2018, “Genome-wide prediction of CRISPR/Cas9 targets in Kluyveromyces marxianus and its application to obtain a stable haploid strain.”, Scientific reports, 8(1), 7305. (SCIE) (IF: 4.259; SCIE ranking: 15.6%) Link
  14. Chang JJ, Lin YJ, Lay CH, Thia C, Wu YC, Hou YH, Huang CC, Li WH, 2018, “Constructing a cellulosic yeast host with an efficient cellulase cocktail.”, Biotechnology and bioengineering, 115(3), 751-761. (SCIE) (IF: 4.481; SCIE ranking: 14.4%) Link
  15. Wu P, Yan J, Lai YC, Ng CS, Li A, Jiang X, Elsey RM, Widelitz R, Bajpai R, Li WH, Chuong CM, 2018, “Multiple Regulatory Modules Are Required for Scale-to-Feather Conversion.”, Molecular biology and evolution, 35(2), 417-430. (SCIE) (IF: 6.202; SCIE ranking: 12.8%,9%,10.4%) Link
  16. Ke HM, Prachumwat A, Yu CP, Yang YT, Promsri V, Liu KF, Lo CF, Lu MYJ, 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. (SCIE) (IF: 4.259; SCIE ranking: 15.6%) Link
  17. Su SC, Lin CW, Liu YF, Fan WL, Chen MK, Yu CP, Yang WE, Su CW, Chuang CY, Li WH, Chung WH, Yang SF, 2017, “Exome Sequencing of Oral Squamous Cell Carcinoma Reveals Molecular Subgroups and Novel Therapeutic Opportunities.”, Theranostics, 7(5), 1088-1099. (SCIE) (IF: 8.766; SCIE ranking: 6.3%) Link
  18. Chang JJ, Lin YJ, Lay CH, Thia C, Wu YC, Hou YH, Li WH*, 2017, “Constructing a Cellulosic Yeast Host with an Efficient Cellulase Cocktail”, BIOTECHNOLOGY AND BIOENGINEERING, 115(3), 751-761. (SCIE) (IF: 4.481; SCIE ranking: 14.4%) Link
  19. Huang CF, Yu CP, Wu YH, Lu MJ, Tu SL, Wu SH, Shiu SH, Ku MSB, Li WH*, 2017, “Elevated auxin biosynthesis and transport underlie high vein density in C4 leaves.”, Proceedings of the National Academy of Sciences of the United States of America, 114(33), E6884-E6891. (SCIE) (IF: 9.661; SCIE ranking: 6.3%) Link
  20. 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. (SCIE) (IF: 3.729; SCIE ranking: 21.9%,29.9%) Link
  21. Lin YJ, Chang JJ, Lin HY, Thia C, Kao YY, Huang CC, Li WH*, 2017, “Metabolic engineering a yeast to produce astaxanthin.”, Bioresource technology, 245(Pt A), 899-905. (SCIE) (IF: 5.651; SCIE ranking: 8.8%,7.1%,9.8%) Link
  22. Wu P, Yan J, Lai YC, Ng CS, Li A, Jiang X, Lin JJ, Elsey R, Widelitz R, Bajpai R, Li WH, Chuong CM, 2017, “Multiple regulatory modules are required for scale-to-feather conversion”, MOLECULAR BIOLOGY AND EVOLUTION, 35(2), 417-430. (SCIE) (IF: 6.202; SCIE ranking: 12.8%,9%,10.4%) Link
  23. Lin JJ, Wang FY, Li WH*, Wang TY, 2017, “The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation.”, Scientific reports, 7(1), 15568. (SCIE) (IF: 4.259; SCIE ranking: 15.6%) Link
  24. 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. (SCIE) (IF: 9.661; SCIE ranking: 6.3%) Link
  25. 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. (SCIE) (IF: 4.259; SCIE ranking: 15.6%) Link
  26. 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. (SCIE) (IF: 6.202; SCIE ranking: 12.8%,9%,10.4%) Link
  27. 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. (SCIE) (IF: 6.202; SCIE ranking: 12.8%,9%,10.4%) Link
  28. 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. (SCIE) (IF: 3.729; SCIE ranking: 21.9%,29.9%) Link
  29. 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. (SCIE) (IF: 7.357; SCIE ranking: 3.8%) Link
  30. Yu CP, Lin JJ, Li WH*, 2016, “Positional distribution of transcription factor binding sites in Arabidopsis thaliana.”, Scientific reports, 6, 25164. (SCIE) (IF: 4.259; SCIE ranking: 15.6%) Link
  31. 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. (SCIE) (IF: 3.739; SCIE ranking: 8.4%) Link
  32. 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. (SCIE) (IF: 3.73; SCIE ranking: 31%,24.8%) Link
  33. 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. (SCIE) (IF: 5.807; SCIE ranking: 7.1%,8.1%,13.4%) Link
  34. 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. (SCIE) (IF: 2.766; SCIE ranking: 23.4%) Link
  35. 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. (SCIE) (IF: 3.955; SCIE ranking: 16.5%,8.5%) Link
  36. Chen SC, Tsai TH, Chung CH, Li WH, 2015, “Dynamic association rules for gene expression data analysis.”, BMC genomics, 16, 786. (SCIE) (IF: 3.729; SCIE ranking: 21.9%,29.9%) Link
  37. 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. (SCIE) (IF: 3.979; SCIE ranking: 25.1%,29.2%) Link
  38. 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. (SCIE) (IF: 9.661; SCIE ranking: 6.3%) Link
  39. 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. (SCIE) (IF: 3.94; SCIE ranking: 28.6%,24.6%) Link
  40. 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. (SCIE) (IF: 9.661; SCIE ranking: 6.3%) Link
  41. 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. (SCIE) (IF: 9.504; SCIE ranking: 7.8%) Link
  42. 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. (SCIE) (IF: 4.259; SCIE ranking: 15.6%) Link