台灣大學漁業科學研究所

研究重點:
ㄧ、以網路生物學角度，解析在病原感染過程中的調控機制與所被控制的宿主蛋白複合體，及其扮演關鍵角色的蛋白質
二、解析不同環境與動物腸胃道之微生物菌相類別、數量與基因表現及交互作用
 三、轉化我們的研究成果與衍生的分析工具使之成為可供研究社群使用的線上資料庫與線上分析工具，提昇我們研究結果的可見度與影響力

1.網路生物及系統生物學研究

利用大規模蛋白質交互實驗資料，以統計模型預測新的交互作用，並將兩者與相關生物註解資料庫加以整合，以web為基礎，建置多種模式生物的全蛋白質體交互網路如幽門桿菌(http://dpi.nhri.org.tw/hp, Bioinformatics 2005)，果蠅(http://flydpi.nhri.org.tw, BMC Bioinformatics 2006)，以及較為複雜的人類蛋白質交互關係推演法(BMC Bioinformatics, 2007, highly accessed)。研究團隊亦進行網路的拓樸分析，可將複雜生物網路中的關鍵蛋白與脆弱模組加以辨識，可做為網路醫學(Network medicine)研究重要工具(hubba, http://hub.iis.sinica.edu.tw, Nucleic Acids Research, 2008, spotlight, http://hub.iis.sinica.edu.tw/spotlight/, Gene 2014, cytohubba, http://hub.iis.sinica.edu.tw/cytohubba, BMC Genomics, 2014)。另外，目前本團隊正進行建置生物網路比對系統，以找出其中隱含的重要保守調控模組(http://hub.iis.sinica.edu.tw/Hunter, BMC Bioinformatics, 2009)，並以幹細胞分化機制與轉錄因子調節，及病原體感染宿主細胞交互調控機制為研究標的。

2.生物資訊加值資料庫與應用系統之建置

近幾年已發表多個生物資訊系統與分析工具於國際知名生物醫學期刊，譬如Primer Design Assistant (PDA) (http://dbb.nhri.org.tw/primer/, Nucleic Acids Research, 2003), 大規模PCR 核酸引子設計線上輔助系統，截自2014年九月，共有來自全球各地超過二十一萬人次上線使用，共已處理一百三十萬餘條序列，除了於2004年協助衛生署疾病管制局發展SARS快速診斷試劑之外，相關的研究也取得多項專利。

結合熱力學與實驗室經驗，研究團隊也發展出一套可作為基因晶片與雜合探針設計的自動化流程，Unique Probe Selector (UPS, http://array.iis.sinica.edu.tw/ups, BMC Bioinformatics 2008, BMC Genomics, 2010)，可提昇實驗精準度與減低雜訊，設計快速病原體偵測晶片與探針(Sensor, 2012)。

本研究室亦於2005年七月在Nucleic Acid Research，發表一個生物巨分子序列親源關係的分析架構自動化平台，POWER: PhylOgenetic WEb Repeater - An integrated and user-optimized framework for bio-molecular phylogenetic analysis (http://power.nhri.org.tw)，獲多個生物資訊網站推薦使用，如歐洲重要生物資訊網站Expasy將POWER列入Life Science Directory中。目前研究團隊已完成新一代系統的開發，解決親源樹建置過程裏重要的關鍵核心，也就是最佳親緣演化統計模型選取的問題，並協助多個國際研究團隊，以簡明的方式建構複雜的親緣分析關係(PALM, http://palm.iis.sinica.edu.tw/, PLoS ONE, 2009)，自2009年十二月發表以來，已有近4,100使用人次及22萬條處理序列。

3. 實驗室電子記錄本（實驗室多人版與USB版本,相關資訊請參閱 http://eln.iis.sinica.edu.tw）

將實驗室中所產生的各種紀錄，以電子化方式儲存於網路伺服器/一般桌上型電腦/筆記型電腦/USB隨身碟，並經由瀏覽器方便管理、分享、搜尋、備份、列印，及與研究伙伴線上討論相關問題。

 
1. 大型實驗室群組版本: 相容於 Linux平台環境
2. 中小型實驗室與個人單機版本: 可相容於微軟視窗/麥金塔 作業環境。

近年重要著作 (2017- ):

*責任作者

Yi-Jie Li, Chia-Hsien Chuang, Wen-Chih Cheng, Shu-Hwa Chen, Wen-Ling Chen, Yu-Jie Lin, Chung-Yen Lin, Yang-hsin Shih, "A metagenomics study of hexabromocyclododecane degradation with a soil microbial community," Journal of Hazardous Materials, volume 430, pages 128465, May 2022, IF=10.588

Chen, Che-Chun, Chang-Wen Huang, Chung-Yen Lin, Chia-Hui Ho, Hong N. Pham, Te-Hua Hsu, Tzu-Tang Lin, Rong-Hwa Chen, Shuenn-Der Yang, Chin-I. Chang, and Hong-Yi Gong., "Development of Disease-Resistance-Associated Microsatellite DNA Markers for Selective Breeding of Tilapia (Oreochromis spp.) Farmed in Taiwan," Genes, volume 13, number 1, pages 99, January 2022, Selected as Feature Paper

Yi-Jie Li, Reuben Wang, Chung-Yen Lin, Shu-Hwa Chen, Chia-Hsien Chuang, Tzu-Ho Chou, Chi-Fang Ko, Pei-Hsin Chou, Chi-Te Liu, Yang-hsin Shih, "The degradation mechanisms of Rhodopseudomonas palustris toward hexabromocyclododecane by time-course transcriptome analysis," Chemical Engineering Journal, volume 425, pages 130489, December 2021. 

Tzu-Tang Lin, Li-Yen Yang, I-Hsuan Lu, Wen-Chih Cheng, Zhe-Ren Hsu, Shu-Hwa Chen, Chung-Yen Lin, "AI4AMP: An Antimicrobial Peptide Predictor Using Physicochemical Property-Based Encoding Method and Deep Learning," mSystems, volume 6, number 6, pages x, December 2021, website: http://symbiosis.iis.sinica.edu.tw/PC_6/, IF=6.49

Chu, Pei-Yun, Jia-Xian Li, Te-Hua Hsu, Hong-Yi Gong, Chung-Yen Lin, Jung-Hua Wang, and Chang-Wen Huang., "Identification of Genes Related to Cold Tolerance and Novel Genetic Markers for Molecular Breeding in Taiwan Tilapia (Oreochromis spp.) via Transcriptome Analysis," Animals, volume 11, number 12, pages 3538, December 2021.

Yung-Sen Huang, Chung-Yen Lin, Wen-Chih Cheng, "Investigating the Transcriptomic and Expression Presence-Absence Variation Exist in Japanese Eel (Anguilla japonica), a Primitive Teleost," Marine Biotechnology, volume x, number x, pages x, October 2021, Online ahead of print 

Mai-Huong T. Ngo, Sue-Wei Peng, Yung-Che Kuo, Chun-Yen Lin, Ming-Heng Wu, Chia-Hsien Chuang, Cheng-Xiang Kao, Han-Yin Jeng, Gee-Way Lin, Thai-Yen Ling, Te-Sheng Chang *, Yen-Hua Huang *, "A Yes-Associated Protein (YAP) and Insulin-like Growth Factor 1 Receptor (IGF-1R) Signaling Loop Is Involved in Sorafenib Resistance in Hepatocellular Carcinoma," Cancers, volume 13, number 15, pages 3812, July 2021.

Yung-Sen Huang, Wen-Chih Cheng, Chung-Yen Lin, "Androgenic sensitivities and ovarian gene expression profiles prior to treatment in Japanese eel (Anguilla japonica)," Marine Biotechnology, volume 23, pages 430-444, June 2021.

Rita Jui-Hsein Lu, Yen-Ting Liu, Chih Wei Huang, Ming-Ren Yen, Chung-Yen Lin and Pao-Yang Chen, "ATACgraph: profiling genome wide chromatin accessibility from ATAC-seq," Frontiers in Genetics, volume 11, pages 1749, January 2021.

Tzu-Tang Lin, Li-Yen Yang, I-Hsuan Lu, Wen-Chih Cheng, Zhe-Ren Hsu, Shu-Hwa Chen, Chung-Yen Lin, "AI4AMP: Sequence-based antimicrobial peptides predictor using physicochemical properties-based encoding method and deep learning," BioRxiv, volume -, number -, pages -, December 2020.

Shu-Hwa Chen , Bo-Yi Yu , Wen-Yu Kuo , Ya-Bo Lin , Sheng-Yao Su , I-Hsuan Lu , Chung-Yen Lin, "mySORT: A Web Framework by using Deconvolution Approach to Estimating Immune Cell Composition from Complex Tissues," Preprint, volume -, number -, pages -, November 2020, doi: 10.20944/preprints202011.0385.v1

Chen Yen-Cheng, Miao Zhi-Feng, Yip Kwan-Ling, Cheng Yi-An, Liu Chung-Jung, Li Ling-Hui, Lin Chung-Yen, Wang Jiunn-Wei, Wu Deng-Chyang, Cheng Tian-Lu, Wang Jaw-Yuan, "Gut Fecal Microbiota Transplant in a Mouse Model of Orthotopic Rectal Cancer," Frontier in Oncology, volume 10, pages 2369, October 2020.

Ying-Chieh Ko, Ting-Yu Lai, Shu-Ching Hsu,Fu-Hui Wang, Sheng-Yao Su, Yu-Lian Chen, Min-Lung Tsai, Chung-Chun Wu, Jenn-Ren Hsiao, Jang-Yang Chang, Yi-Mi Wu, Dan R Robinson, Chung-Yen Lin, Su-Fang Lin, "Index of Cancer-Associated Fibroblasts Is Superior to the Epithelial-Mesenchymal Transition Score in Prognosis Prediction," Cancers, volume 12, number 7, pages E1718, July 2020, IF=6.37

Kun-Yang Lin, Wen-Der Wang, Chi-Hung Lin, Elham Rastegari, Yu-Han Su, Yi-Chieh Chang, Yu-Tzu Chang, Yung-Feng Liao, Haiwei Pi, Bo-Yi Yu, Shu-Hwa Chen, Chung-Yen Lin, Mei-Yeh Lu, Tsu-Yi Su, Fei-Yang Tzou, Chih-Chiang Chan, and Hwei-jan Hsu, "Piwi Reduction in the Aged Niche Eliminates Germline Stem Cells via Toll-GSK3 Signaling," Nature Communications, volume 11, pages 3147, June 2020, IF=11.88

Sheng-Yao Su, I-Hsuan Lu, Wen-Chih Cheng, Wei-Chun Chung, Pao-Yang Chen, Jan-Ming Ho, Shu-Hwa Chen, Chung-Yen Lin, "EpiMOLAS: An Intuitive Web-based Framework for Genome-wide DNA Methylation Analysis," BMC Genomics, volume 21(Suppl 3), pages 163, April 2020.

Wen-Chun Huang, Chung-Yen Lin, Masayuki Hashimoto, Jiunn-Jong Wu, Ming-Cheng Wang, Wei-Hung Lin, Chang-Shi Chen & Ching-Hao Teng, "The role of the bacterial protease Prc in the uropathogenesis of extraintestinal pathogenic Escherichia coli," Journal of Biomedical Science, volume 27, number 14, pages 1-22, January 2020, (IF= 5.2)

Reuben Wang, Chung-Yen Lin, Shu-Hwa Chen, Kai-Jiun Lo, Chi-Te Liu, Tzu-Ho Chou, Yang-hsin Shih, "Using high-throughput transcriptome sequencing to investigate the biotransformation mechanism of hexabromocyclododecane with Rhodopseudomonas palustris in water," Science of the Total Environment, volume 692, pages 249-258, November 2019, IF=5.6

Li-An Yang, Yu-Jung Chang, Shu-Hwa Chen, Chung-Yen Lin and Jan-Ming Ho, "SQUAT: A Sequencing Quality Assessment Tool for Data Quality Assessments before and after Genome Assemblies," BMC Genomics, volume 19, number Suppl 9, pages 238, April 2019.

Tsung-Chieh Yao, Ren-Hua Chung, Chung-Yen Lin, et al.,, "Genetic Loci Determining Total Immunoglobulin E from Birth through Adulthood Identified from Genome-wide Association Study of Asians," Allergy, volume 1, number 4, pages 1-4, November 2018, (IF:6.08)

Hsiang-Yi Hsu, Fang-Chi Chang, Yu-Bin Wang, Shu-Hwa Chen, Ya-Bo Lin, Chung-Yen Lin, Yu-San Han*, "Revealing the compositions of the intestinal microbiota of three Anguillid eel species by using 16S rDNA sequencing," Aquaculture Research, volume 1, pages 1-12, May 2018. 

Shu-Hwa Chen, Wen-Yu Kuo, Sheng-Yao Su, Wei-Chun Chung, Jen-Ming Ho, Henry Horng-Shing Lu, Chung-Yen Lin, "A Gene Profiling Deconvolution Approach to Estimate Immune Cell Composition from Complex Tissues," BMC Bioinformatics, volume 19, number (Suppl 4), pages 154, May 2018, https://doi.org/10.1186/s12859-018-2069-6 

Hsiao-Pei Lu, Po-Yu Liu, Yu-bin Wang, Ji-Fan Hsieh, Han-Chen Ho, Shiao-Wei Huang, Chung-Yen Lin, Chih-hao Hsieh, Hon-Tsen Yu, "Functional Characteristics of the Flying Squirrels Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling," Frontiers in Microbiology, volume 8, pages 2622, January 2018.

Hangfei Qi, Virginia Chu, Nicholas C. Wu, Zugen Chen, Shawna Truong, Gurpreet Brar, Sheng-Yao Su, Yushen Du, Vaithilingaraja Arumugaswami, C. Anders Olson, Shu-Hua Chen, Chung-Yen Lin, Ting-Ting Wu, and Ren Sun, "Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein," Proceedings of the National Academy of Sciences of the United States of America (PNAS), volume 114, number 8, pages 2018–2023, February 2017, Collaboration with team in UCLA, doi: 10.1073/pnas.1614623114