研究領域

• 功能基因組學
• 光合作用轉錄體
• 細菌比較基因組學

研究方向

• 次世代高通量定序技術為近年來在基因組研究的一個重大突破。它利用大量的DNA片段平行測序，將所需的時間和成本大大降低。目前的機型可在一天之內產生30 Giga 的鹼基，相當於10倍的人類基因組資料量，而人類基因組歷時10年的研究才完成了第一組序。
• 近幾年來有很多NGS平台陸續的開發出來。自我們的定序核心設施自2008年成立以來，已陸續建置了二定序平台 - 羅氏454 和 Illumina公司，已及三代的PacBio定序儀，並逐年升級到最新的讀取長度與產能。
• 羅氏的 454 XLR+能夠讀取1KB測序，為全新組裝的一大利器。Illumina HiSeq2500的高通量（每次運行產出600 GB）和快速模式（90GB在60小時），其高產值提供了定量分析所需的深度和廣度；小型Illumina MiSeq 定序儀則提供更靈活的長度和通量選擇，最長雙端PE2*300nt的定序為metagenomics amplicon-sequencing (例如16S 和ITS)的利器。隨著定序技術的快速發展和多樣性，我們於2017年建置了第三代的PacBio Sequel System，利用及時螢光偵測進行單分子的定序，可長達20-40kb的讀長，有利解決repeat sequencing 在基因體組裝上的困擾，也能提供16S 全長amplicon的定序和metagenome中物種分類的精細度。
• 為因應大量定序數據的計算分析，許多相關的生物資訊算法快度發展，以滿足數據處理的需求，及幫助解決各種高通量定序相關的研究課題，包括基因組解序，轉錄組表現分析，染色質修飾和基因表達調控。許多計算流程皆已提供開放源碼。
• 藉由進行各種研發，我們在NGS研究的不同方面都獲得了很多的經驗。我們提供高品質的樣品庫備製和定序資料，並適應中央研究院以及對外合作計畫對NGS研究的不同需求。我們將繼續利用現有的技術和能力，發掘和擴展到新的高通量定序研究領域。

期刊論文

1. Lin Ming-Der, Chuang Chia-Hsien, Kao Chih-Hsin, Chen Shu-Hwa, Wang Szu-Chieh, Hsieh Ping-Heng, Chen Guan-Yu, Mao Chun-Chia, Li Jeng-Yi, Jade Lu Mei-Yeh, Lin Chung-Yen, 2024, “Decoding the genome of bloodsucking midge Forcipomyia taiwana (Diptera: Ceratopogonidae): Insights into odorant receptor expansion”, Insect Biochemistry and Molecular Biology, 168, 104115. (SCIE) (IF: 3.8; SCI ranking: 47%,12%)
2. Hung Yu-Ling, Hong Syuan-Fei, Wei Wei-Lun, Cheng Shiuan, Yu Jia-Zhen, Tjita Veny, Yong Qian-Yuan, Nishihama Ryuichi, Kohchi Takayuki, Bowman John L, Chien Yuan-Chi, Chiu Yen-Hsin, Yang Ho-Chun, Lu Mei-Yeh Jade, Pan Zhao-Jun, Wang Chun-Neng, Lin Shih-Shun, 2024, “Dual Regulation of Cytochrome P450 Gene Expression by Two Distinct Small RNAs, a Novel tasiRNA and miRNA, in <i>Marchantia polymorpha</i>”, Plant And Cell Physiology, pcae029, pcae029. (SCIE) (IF: 4.9; SCI ranking: 41.9%,15.5%)
3. Kao Hsiao-Jung, Lin Ting-Yi, Hsieh Feng-Jen, Chien Jia-Ying, Yeh Erh-Chan, Lin Wan-Jia, Chen Yi-Hua, Ding Kai-Hsuan, Yang Yu, Chi Sheng-Chu, Tsai Ping-Hsing, Hsu Chih-Chien, Hwang De-Kuang, Tsai Hsien-Yang, Peng Mei-Ling, Lee Shi-Huang, Chau Siu-Fung, Chen Chen Yu, Cheang Wai-Man, Chen Shih-Jen, Kwok Pui-Yan*, Chiou Shih-Hwa*, Lu Mei-Yeh Jade*, Huang Shun-Ping*, 2024, “Highly efficient capture approach for the identification of diverse inherited retinal disorders”, npj Genomic Medicine, 9(1), 9:4. (SCIE) (IF: 6.083; SCI ranking: 14.7%)
4. Le My‐Hanh, Morgan Brett, Lu Mei‐Yeh, Moctezuma Victor, Burgos Oscar, Huang Jen‐Pan, 2024, “The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests”, Molecular Ecology Resources, 24(2), e13908. (SCIE) (IF: 8.678; SCI ranking: 14.5%,5.2%,11.5%)
5. Yeh Hsiao-hui, Chang Yao-Ming, Chang Yu-Wang, Lu Mei-Yeh Jade, Chen Yi-Hua, Lee Chia-Che, Chen Chien-Chang*, 2022, “Multiomic analyses reveal enriched glycolytic processes in β-myosin heavy chain-expressed cardiomyocytes in early cardiac hypertrophy”, Journal of Molecular and Cellular Cardiology Plus, 1, 100011.
6. Liu Wen-Yu, Yu Chun-Ping, Chang Chao-Kang, Chen Hsiang-June, Li Meng-Yun, Chen Yi-Hua, Shiu Shin-Han, Ku Maurice S. B., Tu Shih-Long*, Lu Mei-Yeh Jade*, Li Wen-Hsiung*, 2022, “Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(35), e2208795119. (SCIE) (IF: 12.779; SCI ranking: 12.2%)
7. Lee Tracy J, Liu Yuching, Liu Wei-An, Lin Yu-Fei, Lee Hsin-Han, Ke Huei-Mien, Huang Jen-Pen, Lu Mei-Yeh Jade, Hsieh Chia-Lun, Chung Kuo-Fang, Liti Gianni, Tsai Isheng J., 2022, “Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages.”, Genome research, 32(5), 864-877. (SCIE) (IF: 9.438; SCI ranking: 11.1%,8.1%,6.2%)
8. Yang Fang-Jung, Chen Chiao-Nung, Chang Tiffany, Cheng Ting-Wei, Chang Ni-Chen, Kao Chia-Yi, Lee Chih-Chi, Huang Yu-Ching, Hsu Jung-Chen, Li Jengyi, Lu Meiyeh J, Chan Shih-Peng, Wang John, 2022, “phiC31 integrase for recombination-mediated single-copy insertion and genome manipulation in Caenorhabditis elegans”, Genetics, 220(2), iyab206. (SCIE) (IF: 4.402; SCI ranking: 31.6%)
9. Ng Chen Siang, Lai Cheng-Kuo, Ke Huei-Mien, Lee Hsin-Han, Chen Chih-Feng, Tang Pin-Chi, Cheng Hsu-Chen, Lu Meiyeh J., Li Wen-Hsiung, Tsai Isheng Jason, 2022, “Genome assembly and evolutionary analysis of the mandarin duck <i>Aix galericulata</i> reveal strong genome conservation among ducks”, Genome Biology and Evolution, 14(6), evac083. (SCIE) (IF: 4.065; SCI ranking: 32.7%,41.2%)
10. Yeh Su-Ying, Lin Hsin-Hung, Chang Yao-Ming, Chang Yu-Lun, Chang Chao-Kang, Huang Yi-Cin, Ho Yi-Wen, Lin Chu-Yin, Zheng Jun-Ze, Jane Wann-Neng, Ng Chun-Yeung, Lu Mei-Yeh, Lai I-Ling, To Kin-Ying, Li Wen-Hsiung, Ku Maurice S B, 2022, “Maize Golden2-like transcription factors boost rice chloroplast development, photosynthesis, and grain yield”, Plant Physiology, 118(1), 442-459. (SCIE) (IF: 8.005; SCI ranking: 5%)
11. Lin Yu-Fei, Sung Chang Mu, Ke Huei-Mien, Kuo Chia-Jung, Liu Wei-an, Tsai Wen-Sy, Lin Cheng-Yu, Cheng Hao-Tsai, Lu Meiyeh J, Tsai Isheng. J., Hsieh Sen-Yung, 2021, “The rectal mucosal but not fecal microbiota detects subclinical ulcerative colitis”, Gut Microbes, 13(1), 1-10. (SCIE) (IF: 9.434; SCI ranking: 16.1%,13.8%)
12. Liu Hsien-Hao, Wang Jie, Wu Ping-Hu, Lu Mei-Yeh Jade, Li Jeng-Yi, Shen Yuan-Min, Tzeng Min-Nan, Kuo Chang-Hsin, Lin Ying-Hong, Chang Hao-Xun, 2021, “The Whole Genome Sequence Resource of Calonectria ilicicola, the Casual Pathogen of Soybean Red Crown Rot”, Molecular Plant-Microbe Interactions®, 34(7), 848-851.
13. Huang Chi-Fa, Liu Wen-Yu, Jade Lu Mei-Yeh, Chen Yi-Hua, Ku Maurice S B, Li Wen-Hsiung, 2021, “Whole genome duplication facilitated the evolution of C4 photosynthesis in Gynandropsis gynandra”, Molecular Biology and Evolution, 38 (11), 4715-4731. (SCIE) (IF: 8.8; SCI ranking: 13.1%,9.6%,8.5%)
14. Panibe Jerome P., Wang Long, Li Jengyi, Li Meng-Yun, Lee Yi-Chen, Wang Chang-Sheng, Ku Maurice S.B., Lu Mei-Yeh Jade, Li Wen-Hsiung, 2021, “Chromosomal-level genome assembly of the semi-dwarf rice Taichung Native 1, an initiator of Green Revolution”, Genomics, 113(4), 2656-2674. (SCIE) (IF: 4.31; SCI ranking: 36.6%,33.9%)
15. Fan Wen-Lang, Yang Lan-Yan, Hsieh Jason Chia-Hsun, Lin Tsung-Chieh, Lu Mei-Yeh Jade, Liao Chun-Ta, 2021, “Prognostic Genetic Biomarkers Based on Oncogenic Signaling Pathways for Outcome Prediction in Patients with Oral Cavity Squamous Cell Carcinoma”, Cancers, 13(11), 2709. (SCIE) (IF: 6.575; SCI ranking: 24.4%)
16. Lin Che-Yi, Lu Mei-Yeh Jade, Yue Jia-Xing, Li Kun-Lung, Le Pétillon Yann, Yong Luok Wen, Chen Yi-Hua, Tsai Fu-Yu, Lyu Yu-Feng, Chen Cheng-Yi, Hwang Sheng-Ping L., Su Yi-Hsien, Yu Jr-Kai, 2020, “Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling”, PLOS Genetics, 16(12), e1009294. (SCIE) (IF: 6.02; SCI ranking: 15.3%)
17. Ke Huei-Mien, Lee Hsin-Han, Lin Chan-Yi Ivy, Liu Yu-Ching, Lu Min R., Hsieh Jo-Wei Allison, Chang Chiung-Chih, Wu Pei-Hsuan, Lu Meiyeh Jade, Li Jeng-Yi, Shang Gaus, Lu Rita Jui-Hsien, Nagy László G., Chen Pao-Yang, Kao Hsiao-Wei, Tsai Isheng Jason, 2020, “Mycenagenomes resolve the evolution of fungal bioluminescence”, Proceedings of the National Academy of Sciences, 117(49), 31267-31277.
18. Yang Hsin-Chou, Chen Chun-houh, Wang Jen-Hung, Liao Hsiao-Chi, Yang Chih-Ting, Chen Chia-Wei, Lin Yin-Chun, Kao Chiun-How, Lu Mei-Yeh Jade, Liao James C., 2020, “Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations”, Proceedings of the National Academy of Sciences, 117(48), 30679-30686.
19. Lin Kun-Yang, Wang Wen-Der, Lin Chi-Hung, Rastegari Elham, Su Yu-Han, Chang Yu-Tzu, Liao Yung-Feng, Chang Yi-Chieh, Pi Haiwei, Yu Bo-Yi, Chen Shu-Hwa, Lin Chung-Yen, Lu Mei-Yeh, Su Tsu-Yi, Tzou Fei-Yang, Chan Chih-Chiang, Hsu Hwei-Jan, 2020, “Piwi reduction in the aged niche eliminates germline stem cells via Toll-GSK3 signaling”, Nature Communications, 11(1). (SCIE) (IF: 17.694; SCI ranking: 8.1%)
20. Vu TD, Iwasaki Y, Shigenobu S, Maruko A, Oshima K, Iioka E, Huang CL, Abe T, Tamaki S, Lin YW, Chen CK, Lu MY, Hojo M, Wang HV, Tzeng SF, Huang HJ, Kanai A, Gojobori T, Chiang TY, Sun HS, Li WH, Okada N, 2020, “Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens.”, PLoS genetics, 16(6), e1008831. (SCIE) (IF: 6.02; SCI ranking: 15.3%)
21. 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 Biol Evol., 12(2):3890-3905. (SCIE) (IF: 4.065; SCI ranking: 32.7%,41.2%)
22. Liu Wen-Yu, Lin Hsin-Hung, Yu Chun-Ping, Chang Chao-Kang, Chen Hsiang-June, Lin Jinn-Jy, Lu Mei-Yeh Jade, Tu Shih-Long, Shiu Shin-Han, Wu Shu-Hsing, Ku Maurice S. B., Li Wen-Hsiung, 2020, “Maize ANT1 modulates vascular development, chloroplast development, photosynthesis, and plant growth”, Proceedings of the National Academy of Sciences, 117(35), 21747-21756.
23. Luis B. Gómez Luciano, Isheng Jason Tsai, Izumi Chuma, Yukio Tosa, Yi-Hua Chen, Jeng-Yi Li, Meng-Yun Li, Mei-Yeh Jade Lu*, Hitoshi Nakayashiki*, Wen-Hsiung Li*, 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: 8.8; SCI ranking: 13.1%,9.6%,8.5%)
24. 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: 12.779; SCI ranking: 12.2%)
25. Sung Chang Mu, Lin Yu-fei, Chen Kuan-Fu, Ke Huei-mien, Huang Hao-Yi, Gong Yu-Nong, Tsai Wen-Sy, Lu Meiyeh J., Cheng Hao-Tsai, Lin Cheng-Yu, Kuo Chia-Jung, Tsai Isheng J., Hsieh Sen-Yung, 2019, “Predicting clinical outcomes of cirrhosis patients with hepatic encephalopathy from the fecal microbiome”, Cellular and Molecular Gastroenterology and Hepatology, 8(2),301-318.e2. (SCIE) (IF: 8.797; SCI ranking: 18.3%)
26. Cho HY, Lu MJ, Shih MC, 2019, “The SnRK1-eIFiso4G1 signaling relay regulates the translation of specific mRNAs in Arabidopsis under submergence.”, The New phytologist, 222(1), 366-381. (SCIE) (IF: 10.323; SCI ranking: 3.3%)

專書、論文集

1. Shih-Shun Lin*, Yihua Chen, Mei-Yeh Jade Lu*, 2019, Plant MicroRNAs, 1932:197-213 (DOI: 10.1007/978-1-4939-9042-9_15) pages, USA: Methods in molecular biology (Clifton, N.J.), MiMB Springer, Humana Press.

專書(論文集)之一章

1. Shih-Shun Lin*, Yihua Chen, Mei-Yeh Jade Lu, 2019, “Degradome Sequencing in Plants”, editor(s): Stefan de Folter, Plant MicroRNAs - Methods and Protocols, pp. 1932, USA: MiMB Springer, Humana Press..