Research Interest

• Functional genomics
• Photosynthetic transcriptomics
• Bacterial comparative genomics

Research Directions

• Next Generation Sequencing is a major breakthrough technology in genomic research. It enables sequencing of massive amounts of DNA fragments in parallel, greatly reduces the time and cost required for sequencing. The current platform can generate throughput of 30 Gb in one day, equivalent to 10 times of a human genome, which took 10 years to achieve the first assembly draft. Many NGS platforms have been developed, but the second generation models are the most mature and popular nowadays. Since the establishment of our NGS Core Facility in 2008, we have acquired several models of Roche 454 and Illumina, and annually upgraded them to the newest capacity. Currently we have the Roche 454 XLR+ capable of 1kb sequencing and very powerful in de novo assembly, as well as the Illumina HiSeq 2500 for high throughput (600 Gb per run) and rapid run (90Gb in 60 hrs), whose high output provides depth and width for quantitative analyses. In response to the computational analyses required for the big data, many bioinfomatic algorithms have been developed rapidly to meet the demand of data processing as well as to help investigate the diverse biological questions, including genome unraveling, transcriptome profiling, chromatin modification, and regulation of expression. Many computational pipelines are also developed in- house or are available as open source. We perform various R&D and have gained much experience in various aspects of NGS research. We provide high-quality library construction and sequencing data, and adapt to the different NGS research needs in Academia Sinica as well as external collaborative projects. We will continue to use our existing techniques and capacity to explore and extend to new sequencing research areas.

期刊論文

1. Chang Yi-Hsuan, Hsu Min-Feng, Chen Wei-Nan, Wu Min-Hao, Kong Wye-Lup, Lu Mei-Yeh Jade, Huang Chih-Heng, Chang Fang-Ju, Chang Lan-Yi, Tsai Ho-Yang, Tung Chao-Ping, Yu Jou-Hui, Kuo Yali, Chou Yu-Chi, Bai Li-Yang, Chang Yuan-Chih, Chen An-Yu, Chen Cheng-Cheung, Chen Yi-Hua, Liao Chun-Che, Chang Chih-Shin, Liang Jian-Jong, Lin Yi-Ling, Angata Takashi, Hsu Shang-Te Danny, Lin Kuo-I, 2024, “Functional and structural investigation of a broadly neutralizing SARS-CoV-2 antibody”, JCI Insight, 9(10), e179726. (SCIE) (IF: 8; SCI ranking: 16.2%)
2. 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%)
3. 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%)
4. 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%)
5. Hong SF, Wei WL, Pan ZJ, Yu JZ, Cheng S, Hung YL, Tjita V, Wang HC, Komatsu A, Nishihama R, Kohchi T, Chen HM, Chen WC, Lo JC, Chiu YH, Yang HC, Lu MY, Liu LD, Lin SS, 2024, “Molecular insights into MpAGO1 and its regulatory miRNA, miR11707, in the high-temperature acclimation of Marchantia polymorpha.”, Plant & cell physiology, pcae080, Online ahead of print. (SCIE) (IF: 4.9; SCI ranking: 41.9%,15.5%)
6. 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%)
7. 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.
8. 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%)
9. 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%)
10. 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%)
11. 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%)
12. 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%)
13. 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%)
14. 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.
15. 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%)
16. 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%)
17. 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%)
18. 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%)
19. 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.
20. 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.
21. 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%)
22. 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%)
23. 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%)
24. 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.
25. 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%)
26. 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%)
27. 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%)
28. 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..