Associate Research Fellow  |  Lin, Chung-Yen  
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Journal Articles
1. 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
2. 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
3. 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
4. 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
5. 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
6. 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
7. 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
8. 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
9. 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
10. 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
11. 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
12. 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
13. 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
14. 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
15. 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
16. 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
17. 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
18. 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
19. 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
20. 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
21. 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
22. 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
23. 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
24. 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
25. 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
26. 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
27. 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
28. 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
29. 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
30. 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
31. 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
32. 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
33. 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
34. 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
35. Lin C.Y. , Chen S. H., Cho C. S., Chen C. L., Lin F. K., Lin C. H., Chen P. Y., Lo C. Z., and Hsiung C.A., "Fly-DPI: Database of Protein Interactomes for D. melanogaster in the Approach of Systems Biology.," BMC Bioinformatics, volume 7, number 5, pages S18, December 2006, (SCI/4.96) (URL: :::icon :::icon
36. 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
37. 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
38. 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
39. 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
40. 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
41. 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
42. Lin, C. Y., Chen C.L., Cho, C.S., Wang L.M., Chang C. M., Chen P. Y., Lo, C.Z., Hsiung, C. A., "hp-DPI: Helicobacter pylori Database of Protein Interactomes, A Combined Experimental and Inferring Interactions," Bioinformatics, volume 21, pages 1288-1290, April 2005, (SCI/ 6.701)( :::icon
43. 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
44. Li, L.H., Li, J. C., Lin, Y. F., Lin, C. Y., Chen, C.Y., Tsai, S. F., "Genomic Shotgun Array: A Procedure Linking Large-Scale DNA Sequencing with Regional Transcript Mapping.," Nucleic Acids Research, volume 32, number 3, pages 27-35, February 2004, (SCI/ 7.62) :::icon
45. Lin, C. Y., Chen, S. H, Lo, C.Z., Cho, C.S., Hsiung, C. A., "Primer Design Assistant (PDA): a Web-based Primer Design Tool.," Nucleic Acids Research, volume 31, pages 3751-3754, July 2003, (SCI/ 7.62) (Access URL : :::icon
Book & Book Chapters
1. 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
2. Cynthia Gibas, Per Jambeck (Translated in Chinese by Chung-Yen Lin et al.,), "Developing Bioinformatics Computer Skills," O’REILLY, 2002, ISBN: 986-7794-05-2