- Functional genomics
- Photosynthetic transcriptomics
- Bacterial comparative genomics
- 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.
- 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: 7.74; SCI ranking: 12.5%,9.6%)
- 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.
- 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: 11.062; SCI ranking: 6.1%,7.8%,3.9%)
- 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: 6.205; SCI ranking: 10.1%,10.3%)
- 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: 6.126; SCI ranking: 15.2%)
- 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, 2021, “phiC31 integrase for recombination-mediated single-copy insertion and genome manipulation in Caenorhabditis elegans”, Genetics, iyab206, doi: 10.1093/genetics/iyab206. (SCIE) (IF: 4.015; SCI ranking: 27.5%)
- 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, 2021, “Maize Golden2-like transcription factors boost rice chloroplast development, photosynthesis, and grain yield”, Plant Physiology, 118, kiab511. (SCIE) (IF: 6.902; SCI ranking: 4.3%)
- 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: 5.175; SCI ranking: 14.6%)
- 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.
- 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.
- 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: 12.121; SCI ranking: 8.5%)
- 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: 5.175; SCI ranking: 14.6%)
- 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: 3.462; SCI ranking: 35.3%,34.8%)
- 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.
- 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: 11.062; SCI ranking: 6.1%,7.8%,3.9%)
- 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: 9.412; SCI ranking: 11.3%)
- 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: 7.076; SCI ranking: 17%)
- 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: 8.512; SCI ranking: 3%)
- Huang Chih-Jen, Lu Mei-Yeh, Chang Ya-Wen, Li Wen-Hsiung, 2018, “Experimental Evolution of Yeast for High-Temperature Tolerance”, Molecular Biology and Evolution, 35(8), 1823-1839. (SCIE) (IF: 11.062; SCI ranking: 6.1%,7.8%,3.9%)
- Chuang TJ, Chen YJ, Chen CY, Mai TL, Wang YD, Yeh CS, Yang MY, Hsiao YT, Chang TH, Kuo TC, Cho HH, Shen CN, Kuo HC, Lu MY, Chen YH, Hsieh SC, Chiang TW, 2018, “Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells.”, Nucleic acids research, 46(7), 3671-3691.. (SCIE) (IF: 11.502; SCI ranking: 5.1%)
- Chung CL, Lee TJ, Akiba M, Lee HH, Kuo TH, Liu D, Ke HM, Yokoi T, Roa MB, Lu MJ, Chang YY, Ann PJ, Tsai JN, Chen CY, Tzean SS, Ota Y, Hattori T, Sahashi N, Liou RF, Kikuchi T, Tsai IJ, 2017, “Comparative and population genomic landscape of Phellinus noxius: A hypervariable fungus causing root rot in trees.”, Molecular ecology, 26(22), 6301-6316. (SCIE) (IF: 5.163; SCI ranking: 16.8%,11.2%,13.7%)
- 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: 9.412; SCI ranking: 11.3%)
- Ke Huei-Mien, Prachumwat Anuphap, Yu Chun-Ping, Yang Yi-Ting, Promsri Sutitcha, Liu Kuan-Fu, Lo Chu-Fang, Lu Mei-Yeh Jade, Lai Mei-Chin, Tsai Isheng J., Li Wen-Hsiung, 2017, “Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade”, Scientific Reports, 7, 41394. (SCIE) (IF: 3.998; SCI ranking: 23.9%)
- 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: 3.594; SCI ranking: 27.6%,32%)
- 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.
- 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..
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