Institute of Fisheries Science, NTU

Research Interests:
(1) Network comparison: Identification of biological machineries from Host-pathogen interations for the mechanism of infection.
(2) Analysis of Transcriptomics and metagenomics on environmental samples and inside animal's gastrointestinal tracts.
(3) Converting the outputs and tools derived from our research projects into databases and web applications for research community.

(1) Network analysis of human protein interactions for Tumorigenesis and infectious diseases in the approach of systems biology
We have implemented a statistical model into our protein interaction database for validation of two-hybrid assays ofHelicobacter pylori, and prediction of putative protein interactions not yet discovered experimentally. By this approach, we can compare the interacting network of various strains with different virulence to decipher the secret between hosts and pathogens (http://dpi.nhri.org.tw/hp/, Bioinformatics  2005). Using the more sophisticated statistical method with expression profile, we integrated a database named as flydpi for the interactome of Drosophila Melanogaster(http://flydpi.nhri.org.tw, BMC Bioinfo, 2006). And we also constructed a topological analyzer for complex network named as Hubba (NAR, 2008, http://hubba.iis.sinica.edu.tw). Objectives of our work are to improve our understanding of the puzzle during development stage, carcinogenesis and infectious mechanism, and to furthermore introduce a new paradigm for the diagnosis and treatment of human disease to revolutionize current medical services delivered.
 
(2) Developing value-added databases and web applications for biomedical research communities
We have published several web applications and databases related with bioinformatics for biomedical research community. For example, the web application, Primer Design Assistant (PDA) (NAR, 2003, ,http://dbb.nhri.org.tw/primer/), can be helpful to large scale PCR for high throughput experiments like microarray experiments. From July 2003 to Mar 2008, the accumulated visits and processed sequences go beyond 100,000 and 620,000, respectively. PDA is not only served for research groups, but also was used to develop the rapid diagnostic kit for SARS for Central of Disease Control (CDC), Taiwan in 2004. Until now, there are several diagnostic kits developed by PDA.  Based on similar idea, we have implemented a platform for unique probe design for various uses in hybridization, like microarray and blots named as "Unique Probe Selector, UPS" (http://array.iis.sinica.edu.tw/ups , BMC Bioinfo 2008).
In 2005, we have implemented a phylogenetic platform for topology construction and visualization named as POWER (http://power.nhri.org.tw, NAR, 2005). We are working on the best model selection in automatic way and try to integrate two systems for biomedical research groups.
 
(3) Metagenomics
According to the advance in sequencing technology, time for sequencing large genome like human genome would not take several months/years but weeks/days. Several shotgun sequencing projects of various communities have been completed and started. Following the flood of massive sequence data, there are several interesting computational problems that arise from WGS sequencing of communities. Those issues related with how to compare communities, how to separate sequence from different organisms in silico, and how to model population structures using WGS assembly statistics, will be new challenges in the field of bioinformatics. Our approach here is to integrate various databases, gene expression analysis, proteomic results and phylogenetic reconstruction to achieve a comprehensive view of microbial communities.

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