| Issue Date | Title | Author(s) | Relation | scopus | WOS | Fulltext/Archive link |
| 2014 | A Comprehensive Functional Map of the Hepatitis C Virus Genome Provides a Resource for Probing Viral Proteins) | 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 | mBio 5, e01469-14 | | | |
| - | A Deconvolution Approach to Unveiling the Immune Microenvironment of Complex Tissues and Tumors in Transcriptomics | Shu-Hwa Chen; Bo-Yi Yu; Wen-Yu Kuo; Ya-Bo Lin; Sheng-Yao Su; Wei-Hsuan Chuang; I-Hsuan Lu; Chung-Yen Lin | BMC Bioinformatics | | | |
| 2018 | A gene profiling deconvolution approach to estimating immune cell composition from complex tissues | Shu-Hwa Chen; Wen-Yu Kuo; Sheng-Yao Su; Wei-Chun Chung; Jen-Ming Ho; Henry Horng-Shing Lu; Chung-Yen Lin | BMC Bioinformatics 19, 154 | | | |
| 2010 | A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles | Chia-Hao Chin; Shu-Hwa Chen; Chin-Wen Ho; Ming-Tat Ko; Chung-Yen Lin | BMC Bioinformatics 11(Suppl 1):S25 | | | |
| 2022 | A metagenomics study of hexabromocyclododecane degradation with a soil microbial community | Yi-Jie Li; Chia-Hsien Chuang; Wen-Chih Cheng; Shu-Hwa Chen; Wen-Ling Chen; Yu-Jie Lin; Chung-Yen Lin ; Yang-hsin Shih | Journal of Hazardous Materials 430, 128465 | | | |
| 2021 | AI4AMP: An Antimicrobial Peptide Predictor Using Physicochemical Property-Based Encoding Method and Deep Learning | Tzu-Tang Lin; Li-Yen Yang; I-Hsuan Lu; Wen-Chih Cheng; Zhe-Ren Hsu; Shu-Hwa Chen; Chung-Yen Lin | mSystems 6(6), e0029921 | | | |
| 2022 | AI4AVP: An Antiviral Peptides Predictor in Deep Learning Approach with Generative Adversarial Network Data Augmentation | Tzu-Tang Lin; Yih-Yun Sun; Ching-Tien Wang; Wen-Chih Cheng; I-Hsuan Lu; Chung-Yen Lin ; Shu-Hwa Chen | Bioinformatics Advances 2(1), vbac080 | | | |
| 2017 | An machine-learning approach based on quality-score and K-mer landscape for NGS de novo genome assembly | Li-An Yang; Wei-Chun Chung; Yu-Jung Chang; Shu-Hwa Chen; Jan-Ming Ho ; Ho, Jan-Ming | | | | |
| 2016 | Characterization of FN1-FGFR1 and Novel FN1-FGF1 Fusion Genes in a Large Series of Phosphaturic Mesenchymal Tumors | 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; Andrew L. Folpe | Modern Pathology 29(11), 1335-1346 | | | |
| 2014 | cytoHubba: identifying hub objects and sub-networks from complex interactome | Chia-Hao Chin; Shu-Hwa Chen; Hsin-Hung Wu; Chin-Wen Ho; Ming-Tat Ko; Chung-Yen Lin | BMC Systems Biology 8(Suppl 4), S11 | | | |
| 2024 | Decoding the genome of bloodsucking midge Forcipomyia taiwana (diptera: Ceratopogonidae): Insights into odorant receptor expansion | 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 | Insect Biochemistry and Molecular Biology 168, 104115 | | | |
| 2016 | Dual-compartmental transcriptomic proteomic analysis of a marine endosymbiosis exposed to environmental change | Anderson B. Mayfield; Yu-Bin Wang; Chii-Shiarng Chen; Shu-Hwa Chen; Chung-Yen Lin | Molecular Ecology 25(23), 5944-5958 | | | |
| 2022 | Elegancy: Digitizing the Wisdom from Laboratories to the Cloud with Free No-Code Platform | Chih-Wei Huang; Wei-Hsuan Chuang; Chung-Yen Lin ; Shu-Hwa Chen | iScience 25(8), 104710 | | | |
| 2020 | EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis | Sheng-Yao Su; I-Hsuan Lu; Wen-Chih Cheng; Wei-Chun Chung; Pao-Yang Chen ; Jan-Ming Ho ; Shu-Hwa Chen; Chung-Yen Lin | BMC Genomics 21, 163 | | | |
| 2012 | EST and transcriptome analysis of cephalochordate amphioxus - past, present, and future | Yu-Bin Wang; Shu-Hwa Chen; Chun-Yen Lin; Jr-Kai Yu | Brief in Functional Genomics 11(2), 96-106 | | | |
| 2014 | High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution | 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 | Scientific Reports 4, 4942 | | | |
| 2008 | Hubba: Hub Objects Analyzer : A Framework of Interactome Hubs Identification for Network Biology | Chung-Yen Lin; Chia-Hao Chin; Hsin-Hung Wu; Shu-Hwa Chen; Chin-Wen Ho; Ming-Tat Ko | Nucleic Acids Research volume 36(Web Server issue), W438-W443 | | | |
| 2015 | Identification of a Novel FN1-FGFR1 Genetic Fusion as a Frequent Event in Phosphaturic Mesenchymal Tumour | 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; Cher-Wei Liang | The Journal of Pathology 235(4), 539-545 | | | |
| 2012 | Interplay of RsbM and RsbK controls the theta B activity of Bacillus cereus | Lei-Chin Chen; Jung-Chi Chen; Jwu-Ching Shu; Chien-Yen Chen; Ssu-Ching Chen; Shu-Hwa Chen; Chun-Yen Lin; Chi-Yu Lu; Chien-Cheng Chen | Environmental Microbiology 14(10), 2788-2799 | | | |
| 2022 | MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification | Chun-Chieh Liao; Po-Ying Fu; Chih-Wei Huang; Chia-Hsien Chuang; Yun Yen; Chung-Yen Lin ; Shu-Hwa Chen | Bioinformatics 38(10), 2930-2931 | | | |
