Journal Papers
- You-Qian Lee*, Ching-Tai Chen*, Chien-Chang Chen, Chung-Hong Lee, Peitsz Chen, Chi-Shin Wu, Hong-Jie Dai. 2023. “Unlocking the Secrets Behind Advanced Artificial Intelligence Language Models in De-Identifying Chinese-English Mixed Clinical Text,” Journal of Medical Internet Research. (accepted for publication) (*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 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 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 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. https://doi.org/10.1186/s12864-019-6297-6. (*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. https://doi.org/10.1021/acs.jproteome.9b00350. (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. https://doi.org/10.1038/s41598-019-52341-z. (*corresponding authors, IF = 4.996, rank = 8/110 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. https://doi.org/10.1021/acs.analchem.9b01556. (*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. https://doi.org/10.1021/acs.analchem.7b02343. (*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. https://doi.org/10.1093/nar/gkw254. (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. https://doi.org/10.1186/s13059-016-1037-6. (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. https://doi.org/10.1371/journal.pone.0146112. (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. https://doi.org/10.1021/acs.jproteome.5b00482. (*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. https://doi.org/10.1371/journal.pone.0033340. (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. https://doi.org/10.1371/journal.pone.0040846. (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. https://doi.org/10.1371/journal.pone.0037706. (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. https://doi.org/10.1186/1471-2105-10-S15-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. https://doi.org/10.1093/bioinformatics/btn538. (*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.
Conference Papers
- 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).
- 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.
Conference Posters
- Chen, C.-T., 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.