Publications by authors named "Ching-Tai Chen"

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HEPAD: enhancing hemolytic peptide prediction with adaptive feature engineering and diverse sequence descriptors.
Sih-Han Chen, Jen-Chieh Yu, Yi-Hsiang Lin, Shao-Chun Kuo, Kuan Ni, Ching-Tai Chen

BMC Bioinformatics· October 2025

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AAGP integrates physicochemical and compositional features for machine learning-based prediction of anti-aging peptides.
Saptashwa Datta, Jen-Chieh Yu, Yi-Hsiang Lin, Yun-Chen Cheng, Ching-Tai Chen

Sci Rep· August 2025

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Leveraging large language models for the deidentification and temporal normalization of sensitive health information in electronic health records.
Hong-Jie Dai, Tatheer Hussain Mir, Ching-Tai Chen, Chien-Chang Chen, Hao-Ping Yang

NPJ Digit Med· August 2025

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IQUP identifies quantitatively unreliable spectra with machine learning for isobaric labeling-based proteomics.
Yi-Yun Chou, Jing-Chen Yang, Tun-Chu Tsai, Ching-Tai Chen

Sci Rep· August 2025

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ENCAP: Computational prediction of tumor T cell antigens with ensemble classifiers and diverse sequence features.
Jen-Chieh Yu, Kuan Ni, Ching-Tai Chen

PLoS One· July 2024

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Improved prediction of anti-angiogenic peptides based on machine learning models and comprehensive features from peptide sequences.
Yun-Chen Lee, Jen-Chieh Yu, Kuan Ni, Yu-Chuan Lin, Ching-Tai Chen

Sci Rep· June 2024

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Unlocking the Secrets Behind Advanced Artificial Intelligence Language Models in Deidentifying Chinese-English Mixed Clinical Text: Development and Validation Study.
You-Qian Lee, Ching-Tai Chen, Chien-Chang Chen, Chung-Hong Lee, Peitsz Chen

J Med Internet Res· January 2024

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A wandering Ozurdex in the anterior chamber.
Ching-Tai Chen, Shih-Chun Chao, Hung-Yu Lin

Taiwan J Ophthalmol· September 2023

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Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter.
Tzu-Yun Kuo, Jen-Hung Wang, Yung-Wen Huang, Ting-Yi Sung, Ching-Tai Chen

Sci Rep· August 2023

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Nasopharyngeal Carcinoma and Its Effect on Dry Eye Disease: A Nationwide Cohort Study.
Ching-Tai Chen, Shun-Fa Yang, Shih-Chun Chao, Chia-Yi Lee, Jing-Yang Huang

Int J Environ Res Public Health· December 2022

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Calibr improves spectral library search for spectrum-centric analysis of data independent acquisition proteomics.
Jen-Hung Wang, Wai-Kok Choong, Ching-Tai Chen, Ting-Yi Sung

Sci Rep· February 2022

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Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage.
Ching-Tai Chen, Jen-Hung Wang, Cheng-Wei Cheng, Wei-Che Hsu, Chu-Ling Ko

Sci Rep· January 2021

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Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression.
Yi-Ju Chen, Theodoros I Roumeliotis, Ya-Hsuan Chang, Ching-Tai Chen, Chia-Li Han, Huei-Wen Chen, Gee-Chen Chang, Chen-Tu Wu, Yet-Ran Chen, Ching-Wen Chen, Chen-Ting Hung, Yan-Si Chen, Jin-Shing Chen, Hsuan-Yu Chen, Yu-Ju Chen

Cell· July 2020

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HPDM: In Silico Human Proteome Digestion Map with Proteolytic Peptide Analysis and Graphical Visualizations.
Wai-Kok Choong, Ching-Tai Chen, Jen-Hung Wang, Ting-Yi Sung

J Proteome Res· December 2019

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MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks.
Yang-Ming Lin, Ching-Tai Chen, Jia-Ming Chang

BMC Genomics· December 2019

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N-GlyDE: a two-stage N-linked glycosylation site prediction incorporating gapped dipeptides and pattern-based encoding.
Thejkiran Pitti, Ching-Tai Chen, Hsin-Nan Lin, Wai-Kok Choong, Wen-Lian Hsu

Sci Rep· November 2019

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WinProphet: A User-Friendly Pipeline Management System for Proteomics Data Analysis Based on Trans-Proteomic Pipeline.
Ching-Tai Chen, Chu-Ling Ko, Wai-Kok Choong, Jen-Hung Wang, Wen-Lian Hsu

Anal Chem· August 2019

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iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm.
Hui-Yin Chang, Ching-Tai Chen, Chu-Ling Ko, Yi-Ju Chen, Yu-Ju Chen

Anal Chem· December 2017

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An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Yuxiang Jiang, Tal Ronnen Oron, Wyatt T Clark, Asma R Bankapur, Daniel D'Andrea, Da Chen Emily Koo, Jianlin Cheng, Ching-Tai Chen

Genome Biol· September 2016

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iMet-Q: A User-Friendly Tool for Label-Free Metabolomics Quantitation Using Dynamic Peak-Width Determination.
Hui-Yin Chang, Ching-Tai Chen, T Mamie Lih, Ke-Shiuan Lynn, Chiun-Gung Juo

PLoS One· July 2016

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MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification.
T Mamie Lih, Wai-Kok Choong, Chen-Chun Chen, Cheng-Wei Cheng, Hsin-Nan Lin, Ching-Tai Chen

Nucleic Acids Res· July 2016

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Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics.
Wai-Kok Choong, Hui-Yin Chang, Ching-Tai Chen, Chia-Feng Tsai, Wen-Lian Hsu, Yu-Ju Chen

J Proteome Res· December 2015

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Prediction of carbohydrate binding sites on protein surfaces with 3-dimensional probability density distributions of interacting atoms.
Keng-Chang Tsai, Jhih-Wei Jian, Ei-Wen Yang, Po-Chiang Hsu, Hung-Pin Peng, Ching-Tai Chen, Jun-Bo Chen

PLoS One· April 2013

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Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.
Ching-Tai Chen, Hung-Pin Peng, Jhih-Wei Jian, Keng-Chang Tsai, Jeng-Yih Chang, Jun-Bo Chen

PLoS One· November 2012

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Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface.
Chung-Ming Yu, Hung-Pin Peng, Ing-Chien Chen, Yu-Ching Lee, Jun-Bo Chen, Ching-Tai Chen

PLoS One· August 2012

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