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Journal Paper
Journal Paper
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Ching-Tai Chen, Rui-Ru Wang, Yin-Yin Hsu, Ya-Sin Li, Jing-Chen Yang, Cheng-Sheng Chen, Yi-Chun Yeh*, Hong-Jie Dai*. 2026. Explainable machine learning on linked electronic health records to predict suicide reattempts and short-term risk . Under review.
Ching-Tai Chen, Ya-Sin Li, Ruei-Ru Wang, Benjamin K. T’souc, Hin-Tat Cheung*. 2026. Machine Learning Optimization of Language Assessments Through Clinical Feature Reduction. Under review.
Sih-Han Chen, Jen-Chieh Yu, Yi-Hsiang Lin, Shao-Chun Kuo, Kuan Ni, Ching-Tai Chen*. 2025. "HEPAD: enhancing hemolytic peptide prediction with adaptive feature engineering and diverse sequence descriptors." BMC Bioinformatics 26: 234 (2025). (*corresponding author, IF = 4.4, rank = 15/67 (IF) in the category of Mathematical & Computational Biology, rank = 34/680 (CIteScore) in the category of Applied Mathematics).
Yi-Yun Chou, Jing-Chen Yang, Tun-Chu Tsai, Ching-Tai Chen*. 2025. "IQUP identifies quantitatively unreliable spectra with machine learning for isobaric labeling-based proteomics." Scientific Reports 15:31900. (*corresponding author, IF = 4.9, rank = 25/135 (IF), 29/223 (CiteScore) in the category of Multidisciplinary Sciences)
Hong-Jie Dai, Tatheer Hussain Mir, Ching-Tai Chen, Chien-Chang Chen, Hao-Ping Yang, Chung-Hong Lee, Yi-Yun Chou, Yu-Chin Teng, Shalini Gupta, Omkar Panchal, Divyabharathy Ramesh Nadar, Wei-Hsiang Liao, Yu-Chuan Lin, Zi-Rui Zhao, Richard Tzong-Han Tsai, Yung-Chun Chang & Jitendra Jonnagaddala. 2025. "Leveraging large language models for the deidentification and temporal normalization of sensitive health information in electronic health records." npj Digital Medicine 8: 517. (IF = 18, rank = 1/101 (IF) in the category of Health Care Sciences & Services, 2/138 (CiteScore) in the category of Health Information Management)
Saptashwa Datta, Jen-Chieh Yu, Yi-Hsiang Lin, Yun-Chen Cheng and Ching-Tai Chen*. 2025. "AAGP integrates physicochemical and compositional features for machine learning-based prediction of anti-aging peptides." Scientific Reports 15: 29036. (*corresponding author, IF = 4.9, rank = 25/135 (IF), 29/223 (CiteScore) in the category of multidisciplinary sciences)
Yu, Jen-Chieh, Kuan Ni, and Ching-Tai Chen*. 2024. "ENCAP: Computational Prediction of Tumor T Cell Antigens with Ensemble Classifiers and Diverse Sequence Features." PLOS ONE 19 (7): e0307176. (*corresponding author, IF=3.7, rank = 15/120 in the category of multidisciplinary sciences)
Lee, Yun-Chen, Jen-Chieh Yu, Kuan Ni, Yu-Chuan Lin, and Ching-Tai Chen*. 2024. "Improved Prediction of Anti-Angiogenic Peptides Based on Machine Learning Models and Comprehensive Features from Peptide Sequences." Scientific Reports 14 (1): 14387. (*corresponding author, IF=4.6, rank = 11/120 (CiteScore) in the category of multidisciplinary sciences)
You-Qian Lee*, Ching-Tai Chen*, Chien-Chang Chen, Chung-Hong Lee, Peitsz Chen, Chi-Shin Wu, Hong-Jie Dai. 2024. "Unlocking the Secrets Behind Advanced Artificial Intelligence Language Models in De-Identifying Chinese-English Mixed Clinical Text," Journal of Medical Internet Research 26 (1): e48443. (*co-first authors, SCI, IF = 7.4, rank = 3/105 in the category of Health Care Sciences and Services)
Tzu-Yun Kuo, Jen-Hung Wang, Yung-Wen Huang, Ting-Yi Sung*, Ching-Tai Chen*. 2023. "Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter." Scientific Reports 13 14119 (2023). (*corresponding authors, IF = 4.996, rank = 8/110 (CiteScore) in the category of Multidisciplinary Sciences).
Jen-Hung Wang, Wai-Kok Choong, Ching-Tai Chen*, Ting-Yi Sung*. 2022. "Calibr improves spectral library search for spectrum-centric analysis of data independent acquisition proteomics." Scientific Reports 12 (1), 1-13 (*corresponding authors, IF = 4.996, rank = 8/110 (CiteScore) in the category of multidisciplinary sciences).
Ching-Tai Chen*, Jen-Hung Wang, Cheng-Wei Cheng, Wei-Che Hsu, Chu-Ling Ko, Wai-Kok Choong, Ting-Yi Sung*. 2021. "Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage." Scientific Reports 11 (1), 1-12. (*corresponding authors, IF = 4.996, rank = 8/110 (CiteScore) in the category of multidisciplinary sciences)
Chen, Yi-Ju#, Theodoros I. Roumeliotis#, Ya-Hsuan Chang#, Ching-Tai Chen*, Chia-Li Han*, Miao-Hsia Lin*, Huei-Wen Chen, Gee-Chen Chang, Yih-Leong Chang, Chen-Tu Wu, Mong-Wei Lin, Min-Shu Hsieh, Yu-Tai Wang, Yet-Ran Chen, Inge Jonassen, Fatemeh Zamanzad Ghavidel, Ze-Shiang Lin, Kuen-Tyng Lin, Ching-Wen Chen, Pei-Yuan Sheu, Chen-Ting Hung, Ke-Chieh Huang, Hao-Chin Yang, Pei-Yi Lin, Ta-Chi Yen, Yi-Wei Lin, Jen-Hung Wang, Lovely Raghav, Chien-Yu Lin, Yan-Si Chen, Pei-Shan Wu, Chi-Ting Lai, Shao-Hsing Weng, Kang-Yi Su, Wei-Hung Chang, Pang-Yan Tsai, Ana I. Robles, Henry Rodriguez, Yi-Jing Hsiao, Wen-Hsin Chang, Ting-Yi Sung, Jin-Shing Chen, Sung-Liang Yu, Jyoti S. Choudhary, Hsuan-Yu Chen, Pan-Chyr Yang, and Yu-Ju Chen. 2020. "Proteogenomics of Non-Smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression." Cell 182(1):226-244.e17. (#equal contribution, *equal contribution, IF = 66.85, rank = 1/299 in the category of biochemistry and molecular biology)
Lin, Yang-Ming.*, Ching-Tai Chen*, and Jia-Ming Chang. 2019. "MS2CNN: Predicting MS/MS Spectrum Based on Protein Sequence Using Deep Convolutional Neural Networks." BMC Genomics 20 (9): 906. (*co-first authors, IF=3.969, rank = 66/282 in the category of biotechnology and applied microbiology)
Choong, Wai-Kok, Ching-Tai Chen, Jen-Hung Wang, and Ting-Yi Sung. 2019. "iHPDM: In Silico Human Proteome Digestion Map with Proteolytic Peptide Analysis and Graphical Visualizations." Journal of Proteome Research 18 (12): 4124–32. (IF = 5.37, rank = 61/398 in the category of chemistry)
Pitti, Thejkiran, Ching-Tai Chen*, Hsin-Nan Lin, Wai-Kok Choong, Wen-Lian Hsu, and Ting-Yi Sung*. 2019. "N-GlyDE: A Two-Stage N-Linked Glycosylation Site Prediction Incorporating Gapped Dipeptides and Pattern-Based Encoding." Scientific Reports 9 (1): 1–11. (*corresponding authors, IF = 4.996, rank = 8/110 (CiteScore) in the category of multidisciplinary sciences)
Chen, Ching-Tai*+, Chu-Ling Ko*, Wai-Kok Choong*, Jen-Hung Wang, Wen-Lian Hsu, and Ting-Yi Sung+. 2019. "WinProphet: A User-Friendly Pipeline Management System for Proteomics Data Analysis Based on Trans-Proteomic Pipeline." Analytical Chemistry 91 (15): 9403–6. (*co-first authors; +corresponding authors, IF = 8.008, rank = 7/122 in the category of chemistry, analytical)
Chang, Hui-Yin*, Ching-Tai Chen*, Chu-Ling Ko, Yi-Ju Chen, Yu-Ju Chen, Wen-Lian Hsu, Chiun-Gung Juo, and Ting-Yi Sung. 2017. "iTop-Q: An Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm." Analytical Chemistry, 89 (24): 13128-13136. (*co-first authors, IF = 8.008, rank = 7/122 in the category of chemistry, analytical)
Lih, T. Mamie, Wai-Kok Choong, Chen-Chun Chen, Cheng-Wei Cheng, Hsin-Nan Lin, Ching-Tai Chen, Hui-Yin Chang, Wen-Lian Hsu, and Ting-Yi Sung. 2016. "MAGIC-Web: A Platform for Untargeted and Targeted N-Linked Glycoprotein Identification." Nucleic Acids Research 44 (W1): W575–80. (IF = 19.16, rank = 5/325 in the category of biochemistry and molecular biology)
Jiang, Yuxiang, Tal Ronnen Oron, Wyatt T. Clark, Asma R. Bankapur, Daniel D’Andrea, Rosalba Lepore, Christopher S. Funk, et al. 2016. "An Expanded Evaluation of Protein Function Prediction Methods Shows an Improvement in Accuracy." Genome Biology 17: 184. (IF = 17.906, rank = 11/647 in the category of biotechnology and applied microbiology)
Chang, Hui-Yin, Ching-Tai Chen, T. Mamie Lih, Ke-Shiuan Lynn, Chiun-Gung Juo, Wen-Lian Hsu, and Ting-Yi Sung. 2016. "iMet-Q: A User-Friendly Tool for Label-Free Metabolomics Quantitation Using Dynamic Peak-Width Determination." PLOS ONE 11 (1): e0146112. (IF = 3.24, rank = 9/110 in the category of Multidisciplinary Sciences)
Choong, Wai-Kok*, Hui-Yin Chang*, Ching-Tai Chen*, Chia-Feng Tsai, Wen-Lian Hsu, Yu-Ju Chen, and Ting-Yi Sung. 2015. "Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics." Journal of Proteome Research 14 (12): 5396–5407. (*co-first authors, IF = 5.37, rank = 61/398 in the category of Biochemical Research Methods)
Yu, Chung-Ming, Hung-Pin Peng, Ing-Chien Chen, Yu-Ching Lee, Jun-Bo Chen, Keng-Chang Tsai, Ching-Tai Chen, et al. 2012. "Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface." PloS One 7 (3): e33340. (IF = 3.24, rank = 9/110 in the category of Multidisciplinary Sciences)
Tsai, Keng-Chang, Jhih-Wei Jian, Ei-Wen Yang, Po-Chiang Hsu, Hung-Pin Peng, Ching-Tai Chen, Jun-Bo Chen, Jeng-Yih Chang, Wen-Lian Hsu, and An-Suei Yang. 2012. "Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms." PloS One 7 (7): e40846. (IF = 3.24, rank = 9/110 in the category of Multidisciplinary Sciences)
Chen, Ching-Tai, Hung-Pin Peng, Jhih-Wei Jian, Keng-Chang Tsai, Jeng-Yih Chang, Ei-Wen Yang, Jun-Bo Chen, Shinn-Ying Ho, Wen-Lian Hsu, and An-Suei Yang. 2012. "Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces." PloS One 7 (6): e37706. (IF = 3.24, rank = 9/110 in the category of Multidisciplinary Sciences)
Lin, Hsin-Nan, Ching-Tai Chen, Ting-Yi Sung, Shinn-Ying Ho, and Wen-Lian Hsu. 2009. "Protein Subcellular Localization Prediction of Eukaryotes Using a Knowledge-Based Approach." BMC Bioinformatics 10 Suppl 15: S8. (IF = 3.328, rank = 44/548 in the category of mathematical and computational biology)
Chen, Ching-Tai*, Ei-Wen Yang*, Hung-Ju Hsu, Yi-Kun Sun, Wen-Lian Hsu, and An-Suei Yang. 2008. "Protease Substrate Site Predictors Derived from Machine Learning on Multilevel Substrate Phage Display Data." Bioinformatics (Oxford, England) 24 (23): 2691–97. (*co-first authors, IF = 6.931, rank = 5/57 in the category of Mathematical and Computational Biology)
Chen, Ching-Tai, Hsin-Nan Lin, Ting-Yi Sung, and Wen-Lian Hsu. 2006. "HYPLOSP: A Knowledge-Based Approach to Protein Local Structure Prediction." Journal of Bioinformatics and Computational Biology 4 (6): 1287–1307. (IF = 1.122, rank = 371/693 in the category of Computer Science Applications)
Su, Jun-Ming, Shian-Shyong Tseng, Ching-Tai Chen, and Wen-Nung Tsai. 2004. "Adaptive Learning Environments to Meet Pedagogical Needs." Journal of Information Science and Engineering 20: 1057–1077.
Jitendra Jonnagaddala, Hong-Jie Dai, Ching-Tai Chen. Large Language Models for Automatic Deidentification of Electronic Health Record Notes. (ISBN: 9789819779666). New York, NY 10004-1562, USA: Springer Nature. Jan, 2024.
Mir, Tatheer Hussain, Hao-Ping Yang, Yi-Yun Chou, Yu-Chin Teng, Wei-Hsiang Liao, Yu-Chuan Lin, Shalini Gupta, Omkar Panchal, Jitendra Jonnagaddala*, Ching-Tai Chen* & Hong-Jie Dai*. "Deidentification and Temporal Normalization of the Electronic Health Record Notes Using Large Language Models: The 2023 SREDH/AI-Cup Competition for Deidentification of Sensitive Health Information." In Large Language Models for Automatic Deidentification of Electronic Health Record Notes, edited by Jitendra Jonnagaddala, Hong-Jie Dai, and Ching-Tai Chen, 1–16. Singapore: Springer Nature, 2025. https://doi.org/10.1007/978-981-97-7966-6_1. (*corresponding authors)
Ru, Zhu-Jian, Omkar Panchal, Ching-Tai Chen, Jitendra Jonnagaddala, Hong-Jie Dai, and Sheng-Chun Hsueh. Utilizing Large Language Models for Privacy Protection and Advancing Medical Digitization." In Large Language Models for Automatic Deidentification of Electronic Health Record Notes, edited by Jitendra Jonnagaddala, Hong-Jie Dai, and Ching-Tai Chen, 177–88. Singapore: Springer Nature, 2025. https://doi.org/10.1007/978-981-97-7966-6_13.
Min-Yuh Day, Wei-Chen Huang, Hsin-Ting Lu, Wen-Ze Chen, Yu-Han Huang, Ching-Tai Chen, Yohei Seki and Chung-Chi Chen. VeriPromiseESG4K: A Traditional Chinese ESG Promise Verification Dataset for AI CUP 2026. 15th IEEE International Workshop on Empirical Methods for Recognizing Inference in Text (IEEE EM-RITE 2026).
Ruei-Ru Wang, Ya-Sin Li, Yi-Shuo Yin, Tao-Yu Chen, Hint-Tat Cheung, Ching-Tai Chen*. MINAS: Mandarin Intelligent Narrative Assessment of Syntax for Children. The 37th Conference on Computational Linguistics and Speech Processing (ROCLING 2025), Taipei, Taiwan. (*corresponding author)
Yun-Cheng Cheng, Ting-Hsuan Wang, Ching-Tai Chen*. Computational Method for IL-6-inducing Peptide Prediction. Intelligent Computing Symposium 2025, Taipei, Taiwan. (*corresponding author)
Yi-Yun Chou, Li-Kai Chen, Wei-Ren Liu, Hong-Jie Dai*, Ching-Tai Chen*. Enhancing Protein-Protein Interaction Recognition Accuracy in Large Language Models through Sentence Reduction and Few-Shot Learning. The 36th Conference on Computational Linguistics and Speech Processing (ROCLING 2024), Taipei, Taiwan. (*corresponding authors)
Jen-Chieh Yu, Kuan Ni, Ching-Tai Chen*. Sequence-based Prediction of Antimicrobial Peptides with CatBoost Classifier. The 22nd IEEE International Conference on BioInformatics and BioEngineering (IEEE BIBE 2022), Taichung, Taiwan. (*corresponding authors)
Lin, Y.-M.*, Chen, C.-T.*, Chang, J.-M. "Predicting MS/MS spectrum based on protein sequence by deep convolutional neural networks." International Conference on Bioinformatics 2019, Jakarta, Indonesia (Oral presentation) (*co-first authors).
Lin, H.-N., Chen, C.-T., Sung, T.-Y., Ho, S.-Y., and Hsu, W.-L. Protein subcellular localization prediction of eukaryotes using a knowledge-based approach. Eighth International Conference on Bioinformatics (InCoB 2009), Singapore, 2009 (Oral presentation).
Chen, C.-T., Lin, H.-N., Sung, T.-Y., and Hsu, W.-L. A knowledge-based approach to protein local structure prediction. Proceedings of the 4th Asia-Pacific Bioinformatics Conference (APBC), 2006, 3:257-266 (Oral presentation, acceptance rate 30%, 35/118), Taipei, Taiwan.
Ching-Tai Chen*, Sih-Han Chen, Jen-Chieh Yu. Improving Hemolytic Peptide Prediction with Adaptive Feature Engineering. 16th International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2026). Kobe University, Kobe, Japan.
Saptashwa Datta, Jen-Chieh Yu, Yi-Hsiang Lin, Yun-Chen Cheng, Ching-Tai Chen*. Machine Learning Framework For Prediction of Anti-aging Peptides Using Diverse Physicochemical And Compositional Features. 1st Asia-Pacific Bioinformatics Joint Conference (APBJC 2024), Okinawa, Japan.
Ching-Tai Chen, Chu-Ling Ko*, Wai-Kok Choong*, Jen-Hung Wang, Wen-Lian Hsu, and Ting-Yi Sung. WinProphet: A User-Friendly Pipeline Management System for Proteomics Data Analysis Based on Trans-Proteomic Pipeline. 18th Human Proteome Organization World Congress, Adelaide, Australia, 2019.
Chen, C.-T., Wang, J.-H., Chen, Y.-J., Chen, Y.-J., Sung, T.-Y. Impact of Different Quantitation and Normalization Algorithms on Proteomics-based Biomarker Discovery – A Case Study on Lung Cancer Tissue Data. 17th Human Proteome Organization World Congress, Orlando, Florida, United States, 2018.
Chen, C.-T., Ko, C.-L., Choong, W.-K., Wang, J.-H., Hsu, W.-L., Sung T.-Y. WinProphet: a user-friendly pipeline management system to automatically perform protein and peptide identifications based on Trans-Proteomic Pipeline. 66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego, United States, 2018.
Chen, C.-T., Cheng, C.-W, Hsu W.-J, Chang H.-Y., Lin T. M., Chen Y.-J., Chen Y.-J., Hsu W.-L., Sung T.-Y. Multi-Q 2: automated and robust isobaric labeling quantitation analysis with enhanced graphical visualization of protein ratio clustering. 65th ASMS Conference on Mass Spectrometry and Allied Topics, Indianapolis, United States, 2017.
Chen, C.-T., Peng, H.-P., Jian, J.-W., Tsai, K.-C., Chang, J.-Y., Yang, E.-W., Chen, J.-B., Ho, S.-Y., Hsu, W.-L., and Yang, A.-S. Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces. The 11th International Conference on Bioinformatics (InCoB), Bangkok, Thailand, 2012.
Chen, C.-T., Yang, E.-W., Hsu, H.-J., Sun, Y.-K., Hsu, W.-L., and Yang, A.-S. Protease substrate site predictors derived from machine learning on multilevel substrate phage display data. The 7th Asia-Pacific Bioinformatics Conference (APBC), Beijing, China, 2009.