Publications

Results 1-25 of 25 (Search time: 0.005 seconds).

Issue DateTitleAuthor(s)RelationscopusWOSFulltext/Archive link
12022Multiaspect Examinations of Possible Alternative Mappings of Identified Variant Peptides: A Case Study on the HEK293 Cell LineWai-Kok Choong; Ting-Yi Sung ACS Omega 7(19), 16454-16467
22021Somatic mutation subtypes of lung adenocarcinoma in East Asian reveal divergent biological characteristics and therapeutic vulnerabilitiesWai-Kok Choong; Ting-Yi Sung iScience 24(6), 102522
32021Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverageChing-Tai Chen; Jen-Hung Wang; Cheng-Wei Cheng; Wei-Che Hsu; Chu-Ling Ko; Wai-Kok Choong; Ting-Yi Sung Scientific Reports 11, 2233
42021Comparison of different variant sequence types coupled with decoy generation methods used in concatenated target-decoy database searches for proteogenomic researchWai-Kok Choong; Ting-Yi Sung Journal of Proteomics 231, 104021
52020Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and ProgressionYi-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
62020MinProtMaxVP: Generating a minimized number of protein variant sequences containing all possible variant peptides for proteogenomic analysisWai-Kok Choong; Jen-Hung Wang; Ting-Yi Sung Journal of Proteomics 223, 103819
72019N-GlyDE: a two-stage N-linked glycosylation site prediction incorporating gapped dipeptides and pattern-based encodingThejkiran Pitti; Ching-Tai Chen; Hsin-Nan Lin; Wai-Kok Choong; Wen-Lian Hsu ; Ting-Yi Sung Scientific Reports 9, 15975
82019WinProphet: A User-Friendly Pipeline Management System for Proteomics Data Analysis Based on Trans-Proteomic PipelineChing-Tai Chen; Chu-Ling Ko; Wai-Kok Choong; Jen-Hung Wang; Wen-Lian Hsu; Ting-Yi Sung Analytical Chemistry 91(15), 9403-9406
92018Evaluating the Possibility of Detecting Variants in Shotgun Proteomics via LeTE-Fusion Analysis PipelineTung-Shing Mamie Lih; Wai-Kok Choong; Yu-Ju Chen ; Ting-Yi Sung Journal of Proteome Research 17(9), 2937-2952
102018Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane ProteinsWeldemariam, Mehari Muuz; Han, Chia-Li; Shekari, Faezeh; Kitata, Reta Birhanu; Chuang, Ching-Yu; Hsu, Wei-Ting; Kuo, Hung-Chih; Choong, Wai-Kok; Sung, Ting-Yi ; He, Fu-Chu; Chung, Maxey, Ching Ming; Salekdeh, Ghasem Hosseini; Chen, Yu-Ju Journal of Proteome Research 17(12), 4138-4151
112017Decoding the effect of isobaric substitutions on identifying missing proteins and variant peptides in human proteomeWai-Kok Choong; T. Mamie Lih; Yu-Ju Chen; Ting-Yi Sung Journal of Proteome Research 16(12), 4415-4424
122017iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND AlgorithmHui-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
132016MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identificationT. 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
142016iMet-Q: a user-friendly tool for metabolomics quantitation using dynamic peak-width determinationHui-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
152015Informatics View on the Challenges of Identifying Missing Proteins From Shotgun ProteomicsWai-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
162015Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic ProfilingBaby Rorielyn Dimayacyac-Esleta; Chia-Feng Tsai; Reta Birhanu Kitata; Pei-Yi Lin; Wai Kok Choong; Tai-Du Lin; Yi-Ting Wang; Shao-Hsing Weng; Pan-Chyr Yang; Susan Arco; Ting-Yi Sung ; Yu-Ju Chen Analytical Chemistry 87(24), 12016-12023
172015Mining Missing Membrane Proteins by High-pH Reverse Phase StageTip Fractionation and Multiple Reaction Monitoring Mass SpectrometryKitata, 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
182015Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome ProjectHorvatovich, Péter; Lundberg, Emma; Yu-Ju Chen ; Ting-Yi Sung ; Fuchu He; Edouard Nice; Robert Goode; Simon Yu; Shoba Ranganathan; Mark Baker; Gilberto Domont; Erika Velasquez; Dong Li; Siqi Liu; Quanhui Wang; Qing-Yu He; Rajasree Menon; Yuanfang Guan; Fernando Corrales; Victor Segura; José Ignacio Casal; Alberto Pascual-Montano; Juan Albar; Manuel Fuentes; Maria Gonzalez-Gonzalez; Paula Diez; Nieves Ibarrola; Rosa Degano; Yassene Mohammed; Christoph Borchers; Andrea Urbani; Alessio Soggiu; Tadashi Yamamoto; Alexander Archakov; Elena Ponomarenko; Andrey Lisitsa; Cheryl Lichti; Ekaterina Mostovenko; Roger Kroes; Melinda Rezeli; Akos Vegvari; Thomas Fehniger; Rainer Bischoff; Juan Antonio Vizcaíno; Eric Deutsch; Lydie Lane; Carol Nilsson; György Marko-Varga; Gilbert Omenn; Seul-Ki Jeong; Jin-Young Cho; Young-Ki Paik; William HancockJOURNAL OF PROTEOME RESEARCH 14(9), 3415-3431
192015MAGIC: An Automated N-Linked Glycoprotein Identification Tool Using a Y1-Ion Pattern Matching Algorithm and in Silico MS2 ApproachKe-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
202011Phosphoproteomics 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
212010An Informatics-assisted Label-free Quantitation Strategy that Depicts Phosphoproteomic Profiles in Lung Cancer Cell InvasionWang, 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
222010IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validationTsou, 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
232009MaXIC-Q Web: A Fully Automated Web Service Using Statistical and Computational Methods for Protein Quantitation Based on Stable Isotope Labeling and LC-MSTsou, 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
242007Detection 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
252006RIBRA—An Error-Tolerant Algorithm for the NMR Backbone Assignment ProblemWu, K. P; Chang, J. M.; Chen, J. B.; Chang, C. F.; Wu, W. J. ; Huang, T. H. ; Sung, T. Y. ; Hsu, W. L. Journal of computational biology : a journal of computational molecular cell biology 13(2), 229-244