| An expanded evaluation of protein function prediction methods shows an improvement in accuracy Y Jiang, TR Oron, WT Clark, AR Bankapur, DD Andrea, R Lepore, ... Genome Biology 17 (184), 2016 | 438 | 2016 |
| Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression YJ Chen, TI Roumeliotis, YH Chang, CT Chen, CL Han, MH Lin, ... Cell 182 (1), 226-244. e17, 2020 | 263 | 2020 |
| N-GlyDE: a two-stage N-linked glycosylation site prediction incorporating gapped dipeptides and pattern-based encoding T Pitti, CT Chen, HN Lin, WK Choong, WL Hsu, TY Sung Scientific reports 9 (1), 15975, 2019 | 72 | 2019 |
| Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface CM Yu, HP Peng, C Chen, YC Lee, JB Chen, KC Tsai, CT Chen, ... PLoS One 7 (3), e33340, 2012 | 63 | 2012 |
| Protein subcellular localization prediction of eukaryotes using a knowledge-based approach HN Lin, CT Chen, TY Sung, SY Ho, WL Hsu BMC bioinformatics 10, 1-13, 2009 | 56 | 2009 |
| Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces CT Chen, HP Peng, JW Jian, KC Tsai, JY Chang, EW Yang, JB Chen, ... PloS one 7 (6), e37706, 2012 | 37 | 2012 |
| MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks YM Lin, CT Chen, JM Chang BMC genomics 20, 1-10, 2019 | 36 | 2019 |
| Prediction of carbohydrate binding sites on protein surfaces with 3-dimensional probability density distributions of interacting atoms KC Tsai, JW Jian, EW Yang, PC Hsu, HP Peng, CT Chen, JB Chen, ... PloS one 7 (7), e40846, 2012 | 32 | 2012 |
| iMet-Q: a user-friendly tool for label-free metabolomics quantitation using dynamic peak-width determination HY Chang, CT Chen, TM Lih, KS Lynn, CG Juo, WL Hsu, TY Sung PloS one 11 (1), e0146112, 2016 | 27 | 2016 |
| Protease substrate site predictors derived from machine learning on multilevel substrate phage display data CT Chen, EW Yang, HJ Hsu, YK Sun, WL Hsu, AS Yang Bioinformatics 24 (23), 2691-2697, 2008 | 21 | 2008 |
| MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification TM Lih, WK Choong, CC Chen, CW Cheng, HN Lin, CT Chen, HY Chang, ... Nucleic acids research 44 (W1), W575-W580, 2016 | 15 | 2016 |
| Informatics view on the challenges of identifying missing proteins from shotgun proteomics WK Choong, HY Chang, CT Chen, CF Tsai, WL Hsu, YJ Chen, TY Sung Journal of proteome research 14 (12), 5396-5407, 2015 | 15 | 2015 |
| Adaptive learning environment to meet pedagogical needs JM Su, SS Tseng, CT Chen, WN Tsai Journal of information science and engineering 20 (6), 1057-1077, 2004 | 10 | 2004 |
| Calibr improves spectral library search for spectrum-centric analysis of data independent acquisition proteomics JH Wang, WK Choong, CT Chen, TY Sung Scientific Reports 12 (1), 2045, 2022 | 8 | 2022 |
| WinProphet: a user-friendly pipeline management system for proteomics data analysis based on Trans-Proteomic Pipeline CT Chen, CL Ko, WK Choong, JH Wang, WL Hsu, TY Sung Analytical chemistry 91 (15), 9403-9406, 2019 | 8 | 2019 |
| HYPLOSP: a knowledge-based approach to protein local structure prediction CT Chen, HN Lin, TY Sung, WL Hsu Journal of bioinformatics and computational biology 4 (06), 1287-1307, 2006 | 8 | 2006 |
| Unlocking the secrets behind advanced artificial intelligence language models in deidentifying Chinese-English mixed clinical text: Development and validation study YQ Lee, CT Chen, CC Chen, CH Lee, P Chen, CS Wu, HJ Dai Journal of Medical Internet Research 26, e48443, 2024 | 7 | 2024 |
| N-GlyDE: a two-stage N-linked glycosylation site prediction incorporating gapped dipeptides and pattern-based encoding. Sci Rep 9: 15975 TP Itti, CT Chen, HN Lin, WK Choong, WL Hsu, TY Sung | 5 | 2019 |
| Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage CT Chen, JH Wang, CW Cheng, WC Hsu, CL Ko, WK Choong, TY Sung Scientific reports 11 (1), 2233, 2021 | 4 | 2021 |
| iHPDM: In Silico Human Proteome Digestion Map with Proteolytic Peptide Analysis and Graphical Visualizations WK Choong, CT Chen, JH Wang, TY Sung Journal of proteome research 18 (12), 4124-4132, 2019 | 4 | 2019 |
