| Issue Date | Title | Author(s) | Relation | scopus | WOS | Fulltext/Archive link |
| 2010 | An Informatics-assisted Label-free Quantitation Strategy that Depicts Phosphoproteomic Profiles in Lung Cancer Cell Invasion | Wang, Yi-Ting; Tsai, Chia-Feng; Hong, Tzu-Chan; Tsou, Chih-Chiang; Lin, Pei-Yi; Pan, Szu-Hua; Hong, Tse-Ming; Yang, Pan-Chyr; Sung, Ting-Yi ; Hsu, Wen-Lian ; Chen, Yu-Ju | JOURNAL OF PROTEOME RESEARCH 9(11), 5582-5597 | | | |
| 2021 | Comparison of different variant sequence types coupled with decoy generation methods used in concatenated target-decoy database searches for proteogenomic research | Wai-Kok Choong; Ting-Yi Sung | Journal of Proteomics 231, 104021 | | | |
| 2017 | Decoding the effect of isobaric substitutions on identifying missing proteins and variant peptides in human proteome | Wai-Kok Choong; T. Mamie Lih; Yu-Ju Chen; Ting-Yi Sung | Journal of Proteome Research 16(12), 4415-4424 | | | |
| 2007 | Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online) | Hsu, Chun-Nan ; Lai, Jin-Mei; Liu, Chia-Hung; Tseng, Huei-Hun; Lin, Chih-Yun; Lin, Kuan-Ting; Yeh, Hsu-Hua; Sung, Ting-Yi ; Hsu, Wen-Lian ; Su, Li-Jen; Lee, Sheng-An; Chen, Chan-Han; Lee, Gen-Cher; Lee, D. T. ; Shiue, Yow-Ling; Yeh, Chang-Wei; Chang, Chao-Hui; Kao, Cheng-Yan; Huang, Chi-Ying F. | BMC Bioinformatics 8, 1471-2105 | | | |
| 2018 | Evaluating the Possibility of Detecting Variants in Shotgun Proteomics via LeTE-Fusion Analysis Pipeline | Tung-Shing Mamie Lih; Wai-Kok Choong; Yu-Ju Chen ; Ting-Yi Sung | Journal of Proteome Research 17(9), 2937-2952 | | | |
| 2010 | IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation | Tsou, Chih-Chiang; Tsai, Chia-Feng; Tsui, Ying-Hao; Sudhir, Putty-Reddy; Wang, Yi-Ting; Chen, Yu-Ju ; Chen, Jeou-Yuan ; Sung, Ting-Yi ; Hsu, Wen-Lian | Molecular and Cellular Proteomics 9(1), 131-144 | | | |
| 2016 | iMet-Q: a user-friendly tool for metabolomics quantitation using dynamic peak-width determination | Hui-Yin Chang; Ching-Tai Chen; T. Mamie Lih; Ke-Shiuan Lynn; Chiun-Gung Juo; Wen-Lian Hsu ; Ting-Yi Sung | PLoS ONE 11(1), e0146112 | | | |
| 2015 | 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 ; Ting-Yi Sung ; Yu-Ju Chen | Journal of Proteome Research 14(12), 5396-5407 | | | |
| 2017 | 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 ; Wen-Lian Hsu ; Chiun-Gung Juo; Ting-Yi Sung | Analytical Chemistry 89(24), 13128-13136 | | | |
| 2016 | 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; Hui-Yin Chang; Wen-Lian Hsu ; Ting-Yi Sung | Nucleic Acids Research 44(W1), W575-580 | | | |
| 2015 | MAGIC: An Automated N-Linked Glycoprotein Identification Tool Using a Y1-Ion Pattern Matching Algorithm and in Silico MS2 Approach | Ke-Shiuan Lynn; Chen-Chun Chen; T. Mamie Lih; Cheng-Wei Cheng; Wan-Chih Su; Chun-Hao Chang; Chia-Ying Cheng; Wen-Lian Hsu ; Yu-Ju Chen ; Ting-Yi Sung | Analytical Chemistry 87(4), 2466-2473 | | | |
| 2009 | MaXIC-Q Web: A Fully Automated Web Service Using Statistical and Computational Methods for Protein Quantitation Based on Stable Isotope Labeling and LC-MS | Tsou, Chih-Chiang; Tsui, Yin-Hao; Yian, Yi-Hwa; Chen, Yi-Ju; Yang, Han-Yin; Yu, Chuan-Yih; Lynn, Ke-Shiuan; Chen, Yu-Ju ; Sung, Ting-Yi ; Hsu, Wen-Lian | Nucleic Acids Research 37(suppl_2), W661-W669 | | | |
| 2015 | Metabolite identification for mass spectrometry-based metabolomics using multiple types of correlated ion information. | Lynn, KS; Cheng, ML; Chen, YR ; Hsu, C; Chen, A; Lih, TM; Chang, HY; Huang, CJ; Shiao, MS; Pan, WH ; Sung, TY ; Hsu, WL | Analytical chemistry 87(4), 2143-2151 | | | |
| 2015 | Mining Missing Membrane Proteins by High-pH Reverse Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry | Kitata, Reta Birhanu; Dimayacyac-Esleta, Baby Rorielyn; Choong, Wai-Kok; Chia-Feng Tsai; Tai-Du Lin; Chih-Chiang Tsou; Shao-Hsing Weng; Yi-Ju Chen; Pan-Chyr Yang; Arco, Susan; Nesvizhskii, Alexey; Ting-Yi Sung ; Yu-Ju Chen | Journal of Proteome Research 14(9), 3658-3669 | | | |
| 2020 | MinProtMaxVP: Generating a minimized number of protein variant sequences containing all possible variant peptides for proteogenomic analysis | Wai-Kok Choong; Jen-Hung Wang; Ting-Yi Sung | Journal of Proteomics 223, 103819 | | | |
| 2021 | 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; Wai-Kok Choong; Ting-Yi Sung | Scientific Reports 11, 2233 | | | |
| 2022 | Multiaspect Examinations of Possible Alternative Mappings of Identified Variant Peptides: A Case Study on the HEK293 Cell Line | Wai-Kok Choong; Ting-Yi Sung | ACS Omega 7(19), 16454-16467 | | | |
| 2019 | 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 ; Ting-Yi Sung | Scientific Reports 9, 15975 | | | |
| 2011 | Phosphoproteomics identifies oncogenic Ras signaling targets and their involvement in lung adenocarcinomas. | Sudhir, P. -R.; Hsu, C. -L.; Wang, Y. -T.; Chen, Y. -J. ; Sung, T. -Y. ; Hsu, W. -L. ; Yang, U. -C.; Chen, J. -Y. | PLoS One 6(5), e20199 | | | |
| 2020 | 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; 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; Yu-Ju Chen | Cell 182(1), 226-244.e17 | | | |
