Research Fellow/Professor  |  Lin, Chung-Yen  
lab (New window)
1. Ming-Der Lin, Chia-Hsien Chuang, Chih-Hsin Kao, Shu-Hwa Chen, Szu-Chieh Wang, Ping-Heng Hsieh, Guan-Yu Chen, Chun-Chia Mao, Jeng-Yi Li, Mei-Yeh Jade Lu, Chung-Yen Lin, "Decoding the genome of bloodsucking midge Forcipomyia taiwana (diptera: Ceratopogonidae): Insights into odorant receptor expansion," Insect Biochemistry and Molecular Biology, volume 168, pages 104115, 2024, :::icon
2. Tzu-Tang Lin, Li-Yen Yang, Chung-Yen Lin, Ching-Tien Wang, Chia-Wen Lai, Chi-Fong Ko, Yang-Hsin Shih, Shu-Hwa Chen, "Intelligent De Novo Design of Novel Antimicrobial Peptides Against Antibiotic-Resistant Bacteria Strains," International Journal of Molecular Sciences, volume 24, number 7, pages 6788, April 2023, (IF=6.208, 69/297, BIOCHEMISTRY & MOLECULAR BIOLOGY ) :::icon
3. Hsiang-Yi Hsu, Chia-Hsien Chuang, I-Hsuan Lu, Chung-Yen Lin, and Yu-San Han, "Identification of Sexually Dimorphic Genes in Pectoral Fin as Molecular Markers for Assessing the Sex of Japanese Silver Eels (Anguilla japonica)," Zoological Studies, volume 62, number 02, pages 1-16, March 2023. :::icon
4. Tzu-Tang Lin, Yih-Yun Sun, Ching-Tien Wang, Wen-Chih Cheng, I-Hsuan Lu, Chung-Yen Lin*, Shu-Hwa Chen*, "AI4AVP: An Antiviral Peptides Predictor in Deep Learning Approach with Generative Adversarial Network Data Augmentation," Bioinformatics Advances, volume 2, number 1, pages vbac080, October 2022, Online first :::icon
5. Chia-Hui Lo, Deng-Chyang Wu, Shu-Wen Jao, Chang-Chieh Wu, Chung-Yen Lin, Chia-Hsien Chuang, Ya-Bo Lin, Chien-Hsiun Chen, Ying-Ting Chen, Jiann-Hwa Chen, Koung-Hung Hsiao, Ying-Ju Chen, Yuan-Tsong Chen, Jaw-Yuan Wang, Ling-Hui Li, "Enrichment of Prevotella intermedia in human colorectal cancer and its additive effects with Fusobacterium nucleatum on the malignant transformation of colorectal adenomas," Journal of Biomedical Science, volume 29, pages 88, October 2022, (IF=8.41) :::icon
6. Chen, SL, Lundy, DJ, Ruan, SC, Chen, HC, Chao, YK, Cheng, YY, Prajnamitra, PR, Liao, CC, Lin, CY, Lai, JJ, Hsieh, PC, "The gut microbiota regulates acute foreign body reaction and tissue repair after biomaterial implantation," Biomaterials, volume 19, number 289, pages 121807, October 2022, IF=15.30 (1/53, Materials Science, Biomaterials) :::icon
7. Yen-Cheng Chen, Chia-Hsien Chuang, Zhi-Feng Miao, Kwan-Ling Yip, Chung-Jung Liu, Ling-Hui Li, Deng-Chyang Wu, Tian-Lu Cheng, Chung-Yen Lin* and Jaw-Yuan Wang*, "Gut Microbiota Composition in Chemotherapy and Targeted Therapy of Patients with Metastatic Colorectal Cancer," Frontiers in Oncology, volume 12, pages 955313, September 2022, (IF=5.738, 78/245, ONCOLOGY) :::icon
8. Chih-Wei Huang, Wei-Hsuan Chuang, Chung-Yen Lin, Shu-Hwa Chen, "Elegancy: Digitizing the Wisdom from Laboratories to the Cloud with Free No-Code Platform," iScience, volume 25, number 8, pages 104710, July 2022, (IF= 6.107, 20/134, MULTIDISCIPLINARY SCIENCES), Availability: :::icon
9. Tsai, Chia-Fen, Chuang, Chia-Hsien, Wang, Yen-Po, Lin, Ya-Bo, Tu, Pei-Chi, Liu Pei-Yi, Wu, Po-Shan, Lin, Chung-Yen, Lu, Ching-Liang, "Differences in gut microbiota correlate with symptoms and regional brain volumes in patients with late-life depression," Frontiers in Aging Neuroscience, volume 14, pages 885393, July 2022, IF= 5.7 (16/54, GERIATRICS & GERONTOLOGY) :::icon
10. 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=14.24, 3/54, ENGINEERING, ENVIRONMENTAL) :::icon
11. Yao-Tsung Tsai, Chih-Yi Li, Yen-Hua Huang, Te-Sheng Chang, Chung-Yen Lin, Chia-Hsien Chuang, Chih-Yang Wang, Gangga Anuraga, Tzu-Hao Chang, Tsung-Chieh Shih, Zu-Yau Lin, Yuh-Ling Chen, Ivy Chung, Kuen-Haur Lee, Che-Chang Chang, Shian-Ying Sung, Kai-Huei Yang, Wan-Lin Tsui, Chee-Voon Yap, Ming-Heng Wu, "Galectin-1 orchestrates an inflammatory tumor-stroma crosstalk in hepatoma by enhancing TNFR1 protein stability and signaling in carcinoma-associated fibroblasts," Oncogene, volume 41, number -, pages 3011–3023, April 2022, (IF=8.756, 25/321, BIOCHEMISTRY & MOLECULAR BIOLOGY) :::icon
12. Yih-Yun Sun†, Tzu-Tang Lin†, Wen-Chih Cheng, I-Hsuan Lu, Chung-Yen Lin,* and Shu-Hwa Chen *, "Peptide-Based Drug Predictions for Cancer Therapy Using Deep Learning," Pharmaceuticals, volume 15, number 4, pages 422, March 2022, IF=5.863 :::icon
13. Chun-Chieh Liao, Po-Ying Fu, Chih-Wei Huang, Chia-Hsien Chuang, Yun Yen, Chung-Yen Lin*, Shu-Hwa Chen*, "An integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification," Bioinformatics, volume btac184, pages -, March 2022, IF=6.937, Q1, 3/239, Statistics and Probability :::icon
14. 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 :::icon
15. 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 e0029921, December 2021, website:, IF=7.331 :::icon
16. 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. :::icon
17. 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, (IF-16.774) :::icon
18. 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 :::icon
19. 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. :::icon
20. 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. :::icon
21. 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. :::icon
22. 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. :::icon
23. 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 :::icon
24. 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 :::icon
25. 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. :::icon
26. 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) :::icon
27. 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 :::icon
28. 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. :::icon
29. 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) :::icon
30. 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. :::icon
31. 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, :::icon
32. 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. :::icon
33. 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 :::icon
34. Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang, Yu-Bin Wang, Pao-Yang Chen, Chung-Yen Lin*, "TEA: The Epigenome platform for Arabidopsis methylome study," BMC Genomics, volume 17(S13), pages 1027, December 2016, Tea website: :::icon
35. Jen-Chieh Lee, Sheng-Yao Su, Chun A, Changou, Rong-Sen Yang, Keh-Sung Tsai, Michael T. Collins, Eric S. Orwoll, Chung-Yen Lin, Shu-Hwa Chen, Shyang-Rong Shih, Chen-Han Lee, Yoshinao Oda, Steven D. Billings, Chien-Feng Li, G. Petur Nielsen, Eiichi Konishi, Fredrik Petersson, Thomas O. Carpenter, Hsuan-Ying Huang, and Andrew L. Folpe, "Characterization of FN1-FGFR1 and Novel FN1-FGF1 Fusion Genes in a Large Series of Phosphaturic Mesenchymal Tumors," Modern Pathology, volume 29, pages 1335-1346, November 2016, (IF: 6.4), collaboration with NTUH, doi:10.1038/modpathol.2016.137 :::icon
36. Anderson B. Mayfield, Yu-Bin Wang, Chii-Shiarng Chen, Shu-Hwa Chen, and Chung-Yen Lin*, "Dual-compartmental transcriptomic + proteomic analysis of a marine endosymbiosis exposed to environmental change," Molecular Ecology, volume 25, number 23, pages 5944-5958, November 2016, The web database can be found at (IF: 5.98) :::icon
37. Tzu-Po Chuang, Jaw-Yuan Wang, Shu-Wen Jao, Chang-Chieh Wu, Jiann-Hwa Chen, Koung-Hung Hsiao, Chung-Yen Lin, Shu-Hwa Chen, Sheng-Yao Su, Ying-Ju Chen, Yuan-Tsong Chen, Deng-Chyang Wu, Ling-Hui Li, "Over-expression of AURKA, SKA3 and DSN1 contributes to colorectal adenoma to carcinoma progression," Oncotarget, volume 7, number 29, pages 45803-45818, June 2016, DOI: 10.18632/oncotarget.9960 (IF: 6.4 ) :::icon
38. Chih-Hao Fang, Yu-Jung Chang, Wei-Chun Chung, Ping-Heng Hsieh, Chung-Yen Lin and Jan-Ming Ho, "Subset selection of high-depth next generation sequencing reads for de novo genome assembly using MapReduce framework," BMC Genomics, volume 16, number Suppl 12, pages S9, December 2015. :::icon
39. Lin CH, Chen SH,Wang YB, Hsiung CA, Lin CY*, "Precise Genotyping and Recombination Detection in Enterovirus," BMC Genomics, volume 16, number Suppl 12, pages S8, December 2015, Cooperation with Team in NHRI. *:Corresponding Author. (SCI/4.4, BIOTECHNOLOGY & APPLIED MICROBIOLOGY/ Q1) :::icon
40. Hsu HY, Chen SH, Cha YR, Aoyama J, Miller M, Watanabe S, Tsukamoto K, Lin CY*, Han YS*., "Deciphering the Digestive and Absorptive Capacities of Embryo, Pre-leptocephalus, Leptocephalus, and Glass eel stages of the Japanese Eel (Anguilla japonica) Using Next-Generation Sequencing," PLoS One, volume 10, number 9, pages e0139105, September 2015, Cooperation with Team in NTU. *:Corresponding author.(IF: 3.730,Journal ranking: Multidisciplinary Sciences/Q1: 7/56, 12.5%) :::icon
41. Kuo, C. Y., Chen, C. H., Chen, S. H., Lu, I. H., Lu, Huang, L. C., Lin, C. Y., Lin, Chen, C. Y., Lo, H. F., Jeng, S. T., Chen, L. F. O., "The Effect of Red Light and Far-Red Light Conditions on Secondary Metabolism in Agarwood," BMC Plant Biology, volume 15, pages 139, June 2015, The website for whole results can be found at (IF: 3.94, Journal ranking: PLANT SCIENCES: 22/199, 11%) :::icon
42. Jiann-Horng Leu, Kuan-Fu Liu, Kuan-Yu Chen, Shu-Hwa Chen, Yu-Bin Wang, Chung-Yen Lin, Chu-Fang Lo., "The novel white spot syndrome virus-induced gene, PmERP15, encodes an ER stress- responsive protein in black tiger shrimp, Penaeus monodon," Developmental & Comparative Immunology, volume 49, number 2, pages 239-248, April 2015, (IF: 3.70,Journal ranking: Zoology/Q1: 4/153, 2.6%) :::icon
43. Jen-Chieh Lee,Yung-Ming Jeng, Sheng-Yao Su, Chen-Tu Wu, Keh-Sung Tsai, Cheng-Han Lee, Chung-Yen Lin, Jodi M. Carter, Jeng-Wen Huang, Shu-Hwa Chen, Shyang-Rong Shih, Adrián Mariño-Enríquez, Chih-Chih Chen, Andrew L. Folpe, Yih-Leong Chang and Cher-Wei Liang, "Identification of a Novel FN1-FGFR1 Genetic Fusion as a Frequent Event in Phosphaturic Mesenchymal Tumour," The Journal of Pathology, volume 235, number 4, pages 539-45, March 2015, Collaboration with team in NTU hospital for rare disease (IF: 7.33, Journal ranking: Pathology/Q1: 3/76, 3.9%) :::icon
44. Chia-Hao Chin, Shu-Hwa Chen, Hsin-Hung Wu, Chin-Wen Ho, Ming-Tat Ko *, and Chung-Yen Lin, "cytoHubba: a Cytoscape Plug-in for Hub Object Analysis in Network Biology," BMC Systems Biology, volume 8, number Suppl 4, pages S11, December 2014, Plug-in for cytoscape, accumulated download over 7,500 times (IF: 2.85, Journal ranking: MATHEMATICAL & COMPUTATIONAL BIOLOGY/Q1: 7/52, 13.5%) :::icon
45. Mayfield, Anderson; Wang, Yu-Bin; Chen, Chii-Shiarng; Lin, Chung-Yen; Chen, Shu-Hwa, "Compartment-specific transcriptomics in a reef-building coral exposed to elevated temperatures," Molecular Ecology, volume 23, number 23, pages 5816-5830, December 2014, Collaboration with Living Oceans Foundation (IF: 5.84,Journal ranking: Ecology/Q1: 11/141, 7.8%) :::icon
46. Roland Gilbert Remenyi , Hangfei Qi , Sheng-Yao Su , Zugen Chen , Nicholas C. Wu , Vaithilingaraja Arumugaswami , Shawna Truong , Virginia Chu , Tamar Stokelman , Hung-Hao Lo , C. Anders Olson ,Ting-Ting Wu , Shu-Hwa Chen , Chung-Yen Lin, Ren Sun, "A Comprehensive Functional Map of the Hepatitis C Virus Genome Provides a Resource for Probing Viral Proteins)," mBio, volume 5, number 5, pages e01469-14, September 2014, Collaboration with team in UCLA (IF: 6.85,Journal ranking: MICROBIOLOGY/Q1: 12/119, 10%) :::icon
47. Wei-Chun Chung, Chien-Chih Chen, Jan-Ming Ho, Chung-Yen Lin, Wen-Lian Hsu, Yu-Chun Wang, Der-Tsai Lee, Feipei Lai, Chih-Wei Huang and Yu-Jung Chang, "CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce," PLoS One, volume 9, number 6, pages 10.1371/journal.pone.0098146, June 2014, (IF: 3.730,Journal ranking: Multidisciplinary Sciences/Q1: 7/56, 12.5%) :::icon
48. Shu-Hwa Chen, Kun-Lin Li, I-Hsuan Lu, Yu-Bin Wang,Che-Huang Tung, Hsiu-Chi Ting, Ching-Yi Lin, Chung-Yen Lin*, Yi-Hsien Su*, Jr-Kai Sky Yu, "Sequencing and analysis of the transcriptome of the acorn worm Ptychodera flava, an indirect developing hemichordate," Marine Genomics, volume (14)00049-X, pages S1874-7787, May 2014, Web database: (IF: 1.97, Journal ranking: GENETICS & HEREDITY/Q3: 110/165, 67%) :::icon
49. Nicholas C Wu, Arthur P Young, Laith Q Al-Mawsawi, C Anders Olson, Jun Feng, Hangfei Qi, Shu-Hwa Chen, I-Hsuan Lu, Chung-Yen Lin, Robert G Chin, Harding H Luan, Nguyen Nguyen, Stanley F Nelson, Xinmin Li, Ting-Ting Wu, Ren Sun, "High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution," Scientific Reports, volume 4, pages 4942, May 2014, Collaboration with scientists in UCLA (IF: 5.06,Journal ranking: MULTIDISCIPLINARY SCIENCES/Q1: 5/55, 9%) :::icon
50. Qi H, Olson CA, Wu NC, Ke R, Loverdo C, Chu V, Truong S, Remenyi R, Chen Z, Du Y, Su SY, Al-Mawsawi LQ, Wu TT, Chen SH, Lin CY, Zhong W, Lloyd-Smith JO, Sun R., "A quantitative high-resolution genetic profile rapidly identifies sequence determinants of viral fitness and drug sensitivity," PLoS Pathogens, volume 10, number 4, pages e1004064, April 2014, Collaboration with Team in UCLA (IF: 8.06,Journal ranking: PARASITOLOGY/Q1: 2/37, 5.4%) :::icon
51. Chia-Hao Chin, Shu-Hwa Chen, Chun-Yu Chen, Chao. A Hsiung, Chin-Wen Ho, Ming-Tat Ko and Chung-Yen Lin, "Spotlight: Assembly of Protein Complexes by Integrating Graph Clustering Methods," Gene, volume 518, number 1, pages 42-51, April 2013, Collaboration with scientists in NHRI and NCU (IF: 2.08,,) :::icon
52. Lei-Chin Chen, Jung-Chi Chen, Jwu-Ching Shu, Chien-Yen Chen, Ssu-Ching Chen, Shu-Hwa Chen, Chun-Yen-Lin, Chi-Yu Lu, and Chien-Cheng Chen, "Interplay of RsbM and RsbK controls the theta B activity of Bacillus cereus," Environmental Microbiology, volume 14, number 10, pages 2788–2799, October 2012, Collaborated with team in NKNU (SCI/ 5.54, , MICROBIOLOGY/Q1) :::icon
53. Hsiao-Pei Lu, Yu-bin Wang, Shiao-Wei Huang, Chung-Yen Lin, Martin Wu, Chih-hao Hsieh and Hon-Tsen Yu, "Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena)," BMC Genomics, volume 13, pages 466, September 2012, Collaborated with team in Dept. Life Sci, NTU (SCI/4.4, BIOTECHNOLOGY & APPLIED MICROBIOLOGY/ Q1) :::icon
54. Yu-BinWang, Shu-Hwa Chen, Chun-Yen Lin and Jr-Kai Yu, "EST and transcriptome analysis of cephalochordate amphioxus - past, present, and future," Brief in Functional Genomics, volume 11, number 2, pages 96-106, March 2012, (SCI/4.13, MICROBIOLOGY/Q1) :::icon :::icon
55. Chin-I Chang, Pei-Hsin Hung, Chia-Che Wu, Ta Chih Cheng, Jyh-Ming Tsai, King-Jung Lin and Chung-Yen Lin, "Simultaneous Detection of Multiple Fish Pathogens Using a Naked-Eye Readable DNA Microarray," Sensors, volume 12, number 3, pages 2710-2728, February 2012, Collaborated with team in Fisheries Research Institute (SCI/2.05, INSTRUMENTS & INSTRUMENTATION/Q1) :::icon
56. Jiann-Horng Leu, Shu-Hwa Chen, Yu-Bin Wang, Yen-Chen Chen, Sheng-Yao Su, Chung-Yen Lin*, Jan-Ming Ho, Chu-Fang Lo*, "A Review of the Major Penaeid Shrimp EST Studies and the Construction of a Shrimp Transcriptome Database Based on the ESTs from Four Penaeid Shrimp," Marine Biotechnology, volume 13, number 4, pages 608-21, August 2011, (SCI/2.74, MARINE & FRESHWATER BIOLOGY/ Q1) :::icon
57. Chen, S. H., Lo, C. Z., Su, S. Y., Kuo, B. H., Hsiung, A. C., Lin, C. Y.*, "UPS 2.0: Unique Probe Selector for Probe Design and Oligonucleotide Microarrays in Pangenomic/ Genomic Level," BMC Genomics, volume 11, number 8, pages S6, December 2010, (SCI/4.4, BIOTECHNOLOGY & APPLIED MICROBIOLOGY/ Q1) :::icon :::icon
58. Shiao, Y.M., Lee, C. C., Hsu, Y. H., Huang, S. F., Lin, C. Y., Li, L. H., Fann, C. S. J., Tsai, C. Y., Tsai, S. F., Chiu, H. C., "Ectopic and High CXCL13 Chemokine Expression in Myasthenia Gravis with Thymic Lymphoid Hyperplasia," Journal of Neuroimmunology, volume 165, number 10, pages 62-, April 2010, Collaborated works with wet lab teams in NHRI and YM University, Available online 11 March 2010 (SCI/2.84, IMMUNOLOGY/Q2 ) :::icon :::icon
59. Chin, C. H., Chen, S. H., Ho, C. W., Ko, M. T. Lin, C. Y., "A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles," BMC Bioinformatics, volume 11, number S1, pages S25, January 2010, (SCI/3.02, MATHEMATICAL & COMPUTATIONAL BIOLOGY/Q1) :::icon
60. Chen, S.H., Su,S. Y., Lo, C. Z., Huang, T. J., Kuo, B. H., Lin, C. Y.*, "Phylogenetic reconstruction by Automatic Likelihood Model Selector (PALM) : A Framework for Phylogenetic Analysis with the Best Substitution Model," PLoS ONE, volume 4, number 12, pages e8116, December 2009, (SCI/ 3.73, MULTIDISCIPLINARY SCIENCES/Q1) :::icon
61. Lin, C. Y.*, Chin, C. H., Wu, H. H., Chen, S. H., Ho, C. W.,* Ko, M. T.*, "Hubba: Hub Objects Analyzer : A Framework of Interactome Hubs Identification for Network Biology," Nucleic Acids Research, volume 36, number 2008 Web application Issue, pages W438-W443, July 2008, (SCI/ 8.026) :::icon :::icon
62. Chen, S.H., Lo, C.Z., Tsai, M. C., Hsiung C.A., Lin, C.Y.*, "Unique Probe Selector (UPS): A Comprehensive Web Service for Probe Design and Oligo Nucleotide Arrays," BMC Bioinformatics, volume 8, number 10, pages S8, January 2008, (URL: :::icon
63. Tao-Wei Huang, Chung-Yen Lin* and Cheng-Yan Kao*, "Reconstruction of human protein interolog network using evolutionary conserved network," BMC Bioinformatics, volume 8, number 152, pages 1-14, May 2007, (SCI/4.96)(*: Corresponding Authors) :::icon
64. Tom Strachan and Andrew P. Read (Translated in Chinese by Chung-Yen Lin et al,), "Human Molecular Genetics 3," Garland Science, January 2007, ISBN: 957-616-895-3
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66. Jiang S. S., Chang I. S., Huang L. W., Chen P. C., Wen C. C., Liu S. C., Chien L. C., Lin C. Y., Hsiung C. A., Juang J. L., "Temporal Transcription Program of Recombinant Autographa californica Multiple Nucleopolyhedrosis Virus.," Journal of Virology, volume 80, pages 8989-8999, July 2006, (SCI/ 5.178) :::icon
67. Wen, C. C., Wu, Y. J., Huang, Y. H., Chen, W. C., Liu, S. C., Jiang, S. S., Juang, J. L., Lin, C. Y., Fang, W. T., Hsiung, C. A., Chang, I. S., "A Bayes Regression Approach to Array-CGH Data," Statistical Applications in Genetics and Molecular Biology, volume 5, number 1, May 2006, (SCI/1.77) :::icon
68. Chang, C. C., Lin, H. C., Lin, I. P., Chang, T. Y., Chen, H. H., Chen, W. H. Cheng, C. H., Lin, C. Y. Liu, S. M. Chang, C. C. Chaw, S. M., "The Chloroplast Genome of Phalaenopsis aphrodite (Orchidaceae): Comparative Analysis of Evolutionary Rate with That of Grasses and Its Phylogenetic Implications.," Molecular Biology and Evolution, volume 23, pages 279 - 291, April 2006, (SCI/ 6.355) :::icon
69. Pan W. H., Lynn K. S., Chen C. H., Wu Y. L., Lin C. Y., Chang H.Y., "Using endophenotypes for pathway clusters to map complex disease genes.," Genetic Epidemiology, volume 30, number 2, pages 143-154, March 2006, (SCI/5.42) :::icon
70. Lin, C. Y., Lin, F.K., Lin, C.H., Lai, L.W., Hsu, S.J., Chen, S.H., Hsiung, C. A., "POWER: PhylOgenetic WEb Repeater - An integrated and user-optimized framework for bio-molecular phylogenetic analysis.," Nucleic Acids Research, volume 33, pages 553-556, July 2005, (SCI/ 7.62) (Access URL : :::icon
71. Chen, S. H., Lin, C. Y. and Kuo, C. M., "In silico Analysis of the Crustacean Hyperglycemic Hormone Family," Marine Biotechnology, volume 7, number 3, pages 193-206, June 2005, (SCI/ 2.54) :::icon
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73. Chen, S. H., Lin, C. Y., Huang, F. L. and Kuo, C. M., "Cloning of Two Crustacean Hyperglycemic Hormone Isoforms from the Freshwater Giant Prawn, Macrobrachium rosenbergii: Evidence of Alternative Splicing," Marine Biotechnology, volume 6, number 1, pages 83-94, October 2004, (SCI/2.54) :::icon
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