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Research Fellow/Professor  |  Sung, Ting-Yi  
 
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Publications
 
Journal Articles
 
1. Tzu-Yun Kuo, Jen-Hung Wang, Yung-Wen Huang, Ting-Yi Sung* and Ching-Tai Chen*, "Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter," Scientific Reports, volume 13, pages 14119, August 2023.
2. Wai-Kok Choong and Ting-Yi Sung*, "Multi-aspect examinations of possible alternative mappings of identified variant peptides: a case study on the HEK293 cell line," ACS Omega, volume 7, number 19, pages 16454-16467, May 2022.
3. Jen‑Hung Wang, Wai‑Kok Choong, Ching‑Tai Chen*, and Ting‑Yi Sung*, "Calibr improves spectral library search for spectrum‑centric analysis of data independent acquisition proteomics," Scientific Reports, volume 12, pages 2045, February 2022.
4. Wai-Kok Choong and Ting-Yi Sung*, "Somatic mutation subtypes of lung adenocarcinoma in East Asian reveal divergent biological characteristics and therapeutic vulnerabilities," iScience, volume 24, number 6, pages 102522, June 2021. :::icon
5. Reta Birhanu Kitata, Wai-Kok Choong, Chia-Feng Tsai, Pei-Yi Lin, Bo-Shiun Chen, Yun-Chien Chang, Alexey I. Nesvizhskii, Ting-Yi Sung and Yu-Ju Chen, "A data-independent acquisition-based global phosphoproteomics system enables deep profiling," Nature Communications, volume 12, pages 2539, May 2021.
6. Wai-Kok Choong and Ting-Yi Sung*, "Comparison of different variant sequence types coupled with decoy generation methods used in concatenated target-decoy database searches for proteogenomic research," Journal of Proteomics, volume 231, pages 104021, January 2021.
7. Ching-Tai Chen*, Jen-Hung Wang, Cheng-Wei Cheng, Wei-Che Hsu, Chu-Ling Ko, Wai-Kok Choong, and Ting-Yi Sung*, "Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage," Scientific Reports, volume 11, pages 2233, January 2021.
8. 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*, and Yu-Ju Chen*, "Proteogenomics of non-smoking lung cancer in East Asia delineates molecular signatures of pathogenesis and progression," Cell, volume 182, number 1, pages 226-244, July 2020.
9. Wai-Kok Choong, Jen-Hung Wang, Ting-Yi Sung*, "MinProtMaxVP: Generating a minimized number of protein variant sequences containing all possible variant peptides for proteogenomic analysis," Journal of Proteomics, volume 223, pages 103819, July 2020.
10. Wai-Kok Choong, Ching-Tai Chen, Jen-Hung Wang, and Ting-Yi Sung*, "iHPDM: in silico human proteome digestion map with proteolytic peptide analysis and graphical visualizations," Journal of Proteome Research, volume 18, number 12, pages 4124-4132, December 2019. :::icon
11. Thejkiran Pitti, Ching-Tai Chen*, Hsin-Nan Lin, Wai-Kok Choong, Wen-Lian Hsu, and Ting-Yi Sung*, "N-GlyDE: a two-stage N-linked glycosylation site prediction incorporating gapped dipeptides and pattern-based encoding," Scientific Reports, volume 9, pages 15975, November 2019.
12. Ching-Tai Chen*, Chu-Ling Ko, Wai-Kok Choong, Jen-Hung Wang, Wen-Lian Hsu, and Ting-Yi Sung*, "WinProphet: a user-friendly pipeline management system for prote-omics data analysis based on Trans-Proteomic Pipeline," Analytical Chemistry, volume 91, number 15, pages 9403-9406, August 2019. :::icon
13. Mehari Muuz Weldemariam, Chia-Li Han , Faezeh Shekari, Reta Birhanu Kitata, Ching-Yu Chuang, Wei-Ting Hsu, Hung-Chih Kuo, Wai-Kok Choong, Ting-Yi Sung, Fu-Chu He, Maxey Ching Ming Chung, Ghasem Hosseini Salekdeh, and Yu-Ju Chen, "Subcellular proteome landscape of human embryonic stem cells revealed missing membrane proteins," Journal of Proteome Research, volume 17, number 12, pages 4138–4151, December 2018.
14. Tung-Shing Mamie Lih, Wai-Kok Choong, Yu-Ju Chen, Ting-Yi Sung*, "Evaluating the possibility of detecting variants in shotgun proteomics via LeTE-fusion analysis pipeline," Journal of Proteome Research, volume 17, number 9, pages 2937-2952, September 2018. :::icon
15. Hui-Yin Chang, Ching-Tai Chen, Chu-Ling Ko, Yi-Ju Chen, Yu-Ju Chen, Wen-Lian Hsu, Chiun-Gung Juo*, Ting-Yi Sung*, "iTop-Q: an intelligent tool for top-down proteomics quantita-tion using DYAMOND algorithm," Analytical Chemistry, volume 89, number 24, pages 13128–13136, December 2017, DOI: 10.1021/acs.analchem.7b02343 :::icon
16. Wai-Kok Choong, T. Mamie Lih, Yu-Ju Chen, Ting-Yi Sung*, "Decoding the effect of isobaric substitutions on identifying missing proteins and variant peptides in human proteome," Journal of Proteome Research, volume 16, number 12, pages 4415-4424, December 2017. :::icon
17. Yi-Ting Wang, Szu-Hua Pan, Chia-Feng Tsai, Ting-Chun Kuo, Yuan-Ling Hsu, Hsin-Yung Yen, Wai-Kok Choong, Hsin-Yi Wu, Yen-Chen Liao, Tse-Ming Hong, Ting-Yi Sung, Pan-Chyr Yang, and Yu-Ju Chen, "Phosphoproteomics reveals HMGA1, a CK2 substrate, as a drug-resistant target in non-small cell lung cancer," Scientific Reports, volume 7, pages 44021, March 2017.
18. T. Mamie Lih, 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*, "MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification," Nucleic Acids Research, volume 44, number Web Server Issue, pages W575-580, July 2016.
19. Hui-Yin Chang, Ching-Tai Chen, T. Mamie Lih, Ke-Shiuan Lynn, Chiun-Gung Juo, Wen-Lian Hsu, and Ting-Yi Sung*, "iMet-Q: a user-friendly tool for metabolomics quantitation using dynamic peak-width determination," PLoS ONE, volume 11, number 1, pages e0146112, January 2016.
20. Baby Rorielyn T. 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 D. Arco, Ting-Yi Sung, and Yu-Ju Chen, "Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling," Analytical Chemistry, volume 87, number 24, pages 12016–12023, December 2015.
21. Wai-Kok Choong, Hui-Yin Chang, Ching-Tai Chen, Chia-Feng Tsai, Wen-Lian Hsu, Yu-Ju Chen, and Ting-Yi Sung*, "Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics," Journal of Proteome Research, volume 14, number 12, pages 5396-5407, December 2015.
22. P. Horvatovich, EK Lunberg, Yu-Ju Chen, Ting-Yi Sung, F. He, et al., "Quest for missing proteins: Update 2015 on Chromosome-Centric Human Proteome Project," Journal of Proteome Research, volume 14, number 9, pages 3415–3431, September 2015.
23. Reta Birhanu Kitata, Baby Rorielyn T. Dimayacyac-Esleta, Wai-Kok Choong, Chia-Feng Tsai, Tai-Du Lin, Chih-Chiang Tsou, Shao-Hsing Weng, Yi-Ju Chen, Pan-Chyr Yang, Susan D. Arco, Alexey I. Nesvizhskii, Ting-Yi Sung, and Yu-Ju Chen, "Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry," Journal of Proteome Research, volume 14, number 9, pages 3658–3669, September 2015.
24. Ke-Shiuan Lynn, Mei-Ling Cheng, Yet-Ran Chen, Chin Hsu, Ann Chen, T. Mamie Lih, Hui-Yin Chang, Ching-jang Huang, Ming-Shi Shiao, Wen-Harn Pan*, Ting-Yi Sung*, and Wen-Lian Hsu*, "Metabolite Identification for Mass Spectrometry-Based Metabolomics Using Multiple Types of Correlated Ion Information," Analytical Chemistry, volume 87, number 4, pages 2143–2151, February 2015.
25. 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*, and Ting-Yi Sung*, "MAGIC: An Automated N-Linked Glycoprotein Identification Tool Using a Y1-Ion Pattern Matching Algorithm and in Silico MS2 Approach," Analytical Chemistry, volume 87, number 4, pages 2466-2473, February 2015. :::icon
26. Sakdithep Chaiyarit, Nilubon Singhto, Yi-Ju Chen, Chia-Ying Cheng, Wararat Chiangjong , Rattiyaporn Kanlaya, Henry H. N. Lam, Paleerath Peerapen, Ting-Yi Sung, Phornpimon Tipthara, Akhilesh Pandey, Terence C. W. Poon, Yu-Ju Chen, Ravi Sirdeshmukh, Maxey C. M. Chung, and Visith Thongboonkerd, "Chromosome-centric Human Proteome Project (C-HPP): Chromosome 12," Journal of Proteome Research, volume 13, number 7, pages 3160-3165, July 2014.
27. Chia-Feng Tsai, Chuan-Chih Hsu, Jo-Nan Hung, Yi-Ting Wang, Wai-Kok Choong, Ming-Yao Zeng, Pei-Yi Lin, Ruo-Wei Hong, Ting-Yi Sung, and Yu-Ju Chen, "Sequential phosphoproteomic enrichment through complementary metal-directed immobilized metal ion affinity chromatography," Analytical Chemistry, volume 86, number 1, pages 685–693, January 2014. :::icon
28. Jhih-Siang Lai, Cheng-Wei Cheng, Allan Lo*, Ting-Yi Sung*, and Wen-Lian Hsu, "Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices," BMC Bioinformatics, volume 14, pages 304, October 2013.
29. Jia-Ming Chang, Jean-Francois Taly, Ionas Erb, Ting-Yi Sung, Wen-Lian Hsu, Chuan Yi Tang, Cedric Notredame, Emily Chia-Yu Su, "Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations," PLoS ONE, volume 8, number 10, pages e75542, October 2013. :::icon
30. Chia-Ying Cheng, Chia-Feng Tsai, Yu-Ju Chen, Ting-Yi Sung* and Wen-Lian Hsu, "Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications," Journal of Proteome Research, volume 12, number 5, pages 2305-2310, May 2013.
31. Lien-Chin Chen, Mei-Ying Liu, Yung-Chin Hsiao, Wai-Kok Chong, Hsin-Yi Wu, Wen-Lian Hsu, Pao-Chi Liao*, Ting-Yi Sung*, Shih-Feng Tsai*, Jau-Song Yu*, Yu-Ju Chen*, "Decoding the disease-associated proteins encoded in the human chromosome 4," Journal of Proteome Research, volume 12, number 1, pages 33-44, January 2013. :::icon
32. Emily CY Su, Jia-Ming Chang, Cheng-Wei Cheng, Ting-Yi Sung, Wen-Lian Hsu, "Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing," BMC Bioinformatics, volume 13, number Suppl 17, pages S13, October 2012.
33. Putty-Reddy Sudhir, Chein-Hung Chen, Madireddy Pavana Kumari, Mei-Jung Wang, Chih-Chiang Tsou, Ting-Yi Sung, Jeou-Yuan Chen, and Chung-Hsuan Chen, "Label-free quantitative proteomics and N-glycoproteomics analysis of KRAS-activated human bronchial epithelial cells," Molecular and Cellular Proteomics, volume 11, number 10, pages 901-915, October 2012.
34. Jhih-Siang Lai, Cheng-Wei Cheng, Ting-Yi Sung*, Wen-Lian Hsu*, "Computational comparative study of tuberculosis proteomes using a modellLearned from signal peptide structures," PLoS ONE, volume 7, number 4, pages e35018, April 2012.
35. Ting Lo, Chia-Feng Tsai, Yu-Ru V. Shih, Yi-Ting Wang, Sheng-Chieh Lu, Ting-Yi Sung, Wen-Lian Hsu, Yu-Ju Chen, and Oscar K. Lee, "Phosphoproteomic analysis of human mesenchymal stromal cells during osteogenic differentiation," Journal of Proteome Research, volume 11, number 2, pages 586-598, February 2012.
36. Hsin-Nan Lin, Cedric Notredame, Jia-Ming Chang, Ting-Yi Sung*, and Wen-Lian Hsu*, "Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words," PLoS ONE, volume 6, number 12, pages e27872, December 2011.
37. Putty-Reddy Sudhir, Chia-Lang Hsu, Mei-Jung Wang, Yi-Ting Wang, Yu-Ju Chen, Ting-Yi Sung, Wen-Lian Hsu, Ueng-Cheng Yang, Jeou-Yuan Chen, "Phosphoproteomics identifies oncogenic Ras signaling targets and their involvement in lung adenocarcinomas," PLoS ONE, volume 6, number 5, pages e20199, May 2011.
38. Allan Lo, Cheng-Wei Cheng, Yi-Yuan Chiu, Ting-Yi Sung*, Wen-Lian Hsu*, "TMPad: an integrated structural database for helix-packing folds in transmembrane proteins," Nucleic Acids Research, volume 39, number Database issue (Suppl. 1 ), pages D347--355, January 2011.
39. Hsin-Nan Lin, Ting-Yi Sung, Shinn-Ying Ho, and Wen-Lian Hsu, "Improving protein secondary structure prediction based on short subsequences with local structure similarity," BMC Genomics, volume 11, number S4, December 2010.
40. Chih-Chiang Tsou, Chia-Feng Tsai, Ying-Hao Tsui, Putty-Reddy Sudhir, Yi-Ting Wang, Yu-Ju Chen, Jeou-Yuan Chen, Ting-Yi Sung*, Wen-Lian Hsu*, "IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation," Molecular and Cellular Proteomics, volume 9, pages 131-144, January 2010.
41. Yi-Ting Wang, Chia-Feng Tsai, Tzu-Chan Hong, Chih-Chiang Tsou, Pei-Yi Lin, Szu-Hua Pan, Tse-Ming Hong, Pan-Chyr Yang, Ting-Yi Sung, Wen-Lian Hsu, and Yu-Ju Chen, "An Informatics-assisted Label-free Quantitation Strategy that Depicts Phosphoproteomic Profiles in Lung Cancer Cell Invasion," Journal of Proteome Research, volume 9, pages 5582--5597, 2010.
42. Hsin-Nan Lin, Ching-Tai Chen, Ting-Yi Sung, Shinn-Ying Ho and Wen-Lian Hsu, "Protein subcellular localization prediction of eukaryotes using a knowledge-based approach," BMC Bioinformatics, volume 10, number Suppl 15, pages S8, December 2009.
43. Chih-Chiang Tsou, Yin-Hao Tsui, Yi-Hwa Yian, Yi-Ju Chen, Han-Yin Yang, Chuan-Yih Yu, Ke-Shiuan Lynn, Yu-Ju Chen, Ting-Yi Sung*, and Wen-Lian Hsu*, "MaXIC-Q Web: A Fully Automated Web Service Using Statistical and Computational Methods for Protein Quantitation Based on Stable Isotope Labeling and LC-MS," Nucleic Acids Research, volume 37, number suppl_2 (Web Server Issue), pages W661-W669, July 2009.
44. Allan Lo, Yi-Yuan Chiu, Einar Andreas Rødland, Ping-Chiang Lyu, Ting-Yi Sung*, and Wen-Lian Hsu*, "Predicting helix-helix interactions from residue contacts in membrane proteins," Bioinformatics, volume 25, number 8, pages 996-1003, April 2009.
45. Cheng-Wei Cheng, Emily Chia-Yu Su, Jenn-Kang Hwang, Ting-Yi Sung and Wen-Lian Hsu, "Predicting RNA-binding sites of proteins using support vector machines and evolutionary information," BMC Bioinformatics, volume 9, number (Suppl 12), pages S6, December 2008.
46. Jeng-Jung Wang, Tung-Yang Ho, Daniela Ferrero, Ting-Yi Sung, "Diameter variability of cycles and tori," Information Sciences, volume 178, number 14, pages 2960-2967, July 2008.
47. Jia-Ming Chang, Emily Chia-Yu Su, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung*, and Wen-Lian Hsu*, "PSLDoc: protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis," PROTEINS: Structure, Function, and Bioinformatics, volume 72, number 2, pages 693-710, February 2008. :::icon
48. Allan Lo,Hua-Sheng Chiu, Ting-Yi Sung, Ping-Chiang Lyu, and Wen-Lian Hsu, "Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function," Journal of Proteome Research, volume 7, number 2, pages 487–496, January 2008. :::icon
49. Richard Tzong-Han Tsai, Wen-Chi Chou, Ying-Shan Su, Yu-Chun Lin, Cheng-Lung Sung, Hong-Jie Dai, Irene Tzu-Hsuan Yeh, Wei Ku, Ting-Yi Sung*, and Wen-Lian Hsu*, "BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features," BMC Bioinformatics, volume 8, pages 325-339, September 2007.
50. Chuan-Yih Yu, Yin-Hao Tsui, Yi-Hwa Yian, Ting-Yi Sung* and Wen-Lian Hsu*, "The Multi-Q web server for multiplexed protein quantitation," Nucleic Acids Research, volume 35, number Web Server Issue (No. suppl_2), pages W707-W712, June 2007. :::icon
51. Chun-Nan Hsu, Jin-Mei Lai, Chia-Hung Liu,Huei-Hun Tseng, Chih-Yun Lin, Kuan-Ting Lin, Hsu-Hua Yeh, Ting-Yi Sung, Wen-Lian Hsu, Li-Jen Su, Sheng-An Lee, Chan-Han Chen, Gen-Cher Lee, D.T. Lee, Yow-Ling Shiue, Chang-Wei Yeh, Chao-Hui Chang, Cheng-Yan Kao, Chi-Ying F. Huang, "Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)," BMC Bioinformatics, volume 8, number 66, pages 1471-2105, February 2007.
52. Emily Chia-Yu Su, Hua-Sheng Chiu, Allan Lo, Jenn-Kang Hwang, Ting-Yi Sung, and Wen-Lian Hsu, "Protein subcellular localization prediction based on compartment-specific features and structure conservation," BMC Bioinformatics, volume 8, number 330, 2007. :::icon
53. Richard Tzong-Han Tsai, Cheng-Lung Sung, Hong-Jie Dai, Hsieh-Chuan Hung, Ting-Yi Sung* and Wen-Lian Hsu*, "NERBio: using selected word conjunction, term normalization, and global patterns to improve biomedical named entity recognition," BMC Bioinformatics, volume 7, number Suppl 5, pages S11, December 2006.
54. Wen-Ting Lin, Wei-Neng Hung, Yi-Hwa Yian, Kun-Pin Wu*, Chia-Li Han, Yet-Ran Chen, Yu-Ju Chen, Ting-Yi Sung*, and Wen-Lian Hsu,, "Multi-Q: A Fully Automated Tool for Multiplexed Protein Quantitation," Journal of Proteome Research, volume 5, number 9, pages 2328--2338, September 2006.
55. Kuen-Pin Wu, Jia-Ming Chang, Jun-Bo Chen, Chi-Fon Chang, Wen-Jin Wu, Tai-Huang Huang, Ting-Yi Sung and Wen-Lian Hsu, "RIBRA-an Error-Tolerant Algorithm for the NMR Backbone Assignment Problem," Journal of Computational Biology, volume 13, number 2, pages 229-244, March 2006.
56. Tzong-Han Tsai, Shih-Hung Wu, Wen-Chi Chou, Yu-Chun Lin, Ding He, Ting-Yi Sung*, Wen-Lian Hsu*, "Various Criteria in the Evaluation of Biomedical Named Entity Recognition," BMC Bioinformatics, volume 7, pages 92, February 2006.
57. Richard Tzong-Han Tsai, Wen-Chi Chou, Shih-Hung Wu, Ting-Yi Sung, Jieh Hsiang, Wen-Lian Hsu, "Integrating Linguistic Knowledge into a Conditional Random Field Framework to Identify Biomedical Named Entities," Expert Systems with Applications, volume 30, number 1, pages 117-128, 2006. :::icon
58. Hsin-Nan Lin, Jia-Ming Chang, Kuen-Pin Wu, Ting-Yi Sung and Wen-Lian Hsu, "HYPROSP II - A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence," Bioinformatics, volume 21, pages 3227--3233, August 2005.
59. Hsin-Nan Lin, Kuen-Pin Wu, Jia-Ming Chang, Ting-Yi Sung and Wen-Lian Hsu, "GANA – A Genetic Algorithm for NMR Backbone Resonance Assignment," Nucleic Acids Research, volume 33, number 14, pages 4593-4601, August 2005.
60. Tung-Yang Ho, Ting-Yi Sung and Lih-Hsing Hsu, "A note on edge fault tolerance with respect to hypercubes," Applied Mathematics Letters, volume 18, pages 1125--1128, 2005. :::icon
61. Kuen-Pin Wu, Hsin-Nan Lin, Jia-Ming Chang, Ting-Yi Sung and Wen-Lian Hsu, "HYPROSP: A Hybrid Protein Secondary Structure Prediction Algorithm—A Knowledge-Based Approach," Nucleic Acids Research, volume 32, number 17, pages 5059-5065, September 2004. :::icon
62. Tseng-Kuei Li, Jimmy J.M. Tan, Lih-Hsing Hsu and Ting-Yi Sung, "The shuffle-cubes and their generalization," Information Processing Letters, volume 77, number 1, pages 35-41, 2001.
63. Chun-Nan Hung, Lih-Hsing Hsu and Ting-Yi Sung, "On the construction of combined k-fault-tolerant hamiltonian graphs," Networks, volume 37, pages 165--170, 2001. :::icon
64. Jeng-Jung Wang, Ting-Yi Sung and Lih-Hsing Hsu, "A family of optimal 1-Hamiltonian graphs with diameter O(log n)," Journal of Information Science and Engineering, volume 17, pages 435--448, 2001. :::icon
65. Ting-Yi Sung, Tung-Yang Ho, Chien-Ping Chang and Lih-Hsing Hsu, "Optimal k-fault-tolerant networks for token rings," Journal of Information Science and Engineering, volume 16, pages 381--390, 2000, also in Proceedings of National Computer Symposium, 1995, 382-388.
66. Jeng-Jung Wang, Chun-Nan Hung, Jimmy J.M. Tan, Lih-Hsing Hsu and Ting-Yi Sung, "Construction schemes for fault tolerant Hamiltonian graphs," Networks, volume 35, pages 233--245, 2000. :::icon
67. Chien-Ping Chang, Ting-Yi Sung and Lih-Hsing Hsu, "Edge congestion and topological properties of crossed cubes," IEEE Transactions on Parallel and Distributed Systems, volume 11, pages 64--80, 2000. :::icon
68. Chun-Nan Hung, Jeng-Jung Wang, Ting-Yi Sung and Lih-Hsing Hsu, "On the isomorphism between cyclic-cubes and wrapped butterfly network," IEEE Transactions on Parallel and Distributed Systems, volume 11, pages 864, 2000. :::icon
69. Tseng-Kuei Li, Jimmy J.M. Tan, Ting-Yi Sung and Lih-Hsing Hsu, "Optimum congested routing strategy on twisted cubes," Journal of Interconnection Networks, volume 1, pages 115--134, 2000.
70. Chun-Nan Hung, Lih-Hsing Hsu and Ting-Yi Sung, "Christmas tree: a versatile 1-fault-tolerant design for token rings," Information Processing Letters, volume 72, pages 55--63, 1999, a preliminary version also in the Proceedings of 1998 International Conference on Parallel and Distributed Systems, 383--388 :::icon
71. Tung-Yang Ho, Ting-Yi Sung, Lih-Hsing Hsu, Chang-Hsiung Tsai and Jeng-Yan Hwang, "The recognition of double euler trails in series-parallel networks," Algorithms, volume 28, pages 216--257, 1998. :::icon
72. Ting-Yi Sung, Chun-Yuan Lin, Yen-Chu Chuang and Lih-Hsing Hsu, "Fault-tolerant token ring embedding in double loop networks," Information Processing Letters, volume 66, pages 201--207, 1998. :::icon
73. Lih-Hsing Hsu , Shih-Yih Wang and Ting-Yi Sung, "Faithful 1-edge fault tolerant graphs," Information Processing Letters, volume 61, pages 173-181, 1997, also presented at the Eighth SIAM Conference on Discrete Mathematics, Baltimore, Maryland, 1996 :::icon
74. Manfred Padberg and Ting-Yi Sung, "An analytic symmetrization of max flow-min cut," Discrete Mathematics, volume 165, number 166, pages 531-545, 1997.
75. Jenn-Jung Wang, Shih-Yih Wang, Lih-Hsing Hsu and Ting-Yi Sung, "Extended tree contraction for some parallel algorithms on series-parallel networks," Journal of Information Science and Engineering, volume 13, pages 665-680, 1997.
76. Ting-Yi Sung, Men-Yang Lin and Tung-Yang Ho, "Multiple-edge-fault tolerance with respect to hypercubes," IEEE Transactions on Parallel and Distributed Systems, volume 8, pages 187--192, 1997, also accepted by ISPAN '96 :::icon
77. Tung-Yang Ho, Lih-Hsing Hsu and Ting-Yi Sung, "Transmitting on various network topologies," Networks, volume 27, pages 145--157, 1996, also presented at ICCI'94 Sixth International Conference
78. Chun-nan Hung, Lih-Hsing Hsu and Ting-Yi Sung, "A response to Volgenant's addendum on the most vital edges," Networks, volume 27, pages 255, 1996.
79. Zhen Liu and Ting-Yi Sung, "Routing and transmitting problems in de Bruijn networks," IEEE Transactions on Computers, volume 45, pages 1056--1062, 1996.
80. Fu-Shang P. Tsen, Ting-Yi Sung, Men-Yang Lin and Lih-Hsing Hsu, "Finding the most vital edges with respect to the number of spanning trees," IEEE Trans. on Reliability, volume 43, pages 600--603, 1994. :::icon
81. Chun-Nan Hung, Lih-Hsing Hsu and Ting-Yi Sung, "The most vital edges of matching in bipartite graphs," Networks, volume 35, pages 309--313, 1993.
82. Manfred Padberg and Ting-Yi Sung, "An analytical comparison of different formulations of the travelling salesman problem," Mathematical Programming, volume 52, pages 315--357, 1991.
83. Ting-Yi Sung, Her-Jiun Sheu and Denis Naddef, "Heuristic approach to the Artificial Intelligence Design Challenge," Guidance, Control, and Dynamics, volume 11, pages 406--411, November 1988.
84. Manfred Padberg and Ting-Yi Sung, "A polynomial-time solution to Papadimitriou and Steiglitz's ``traps," Operations Research Letters, volume 7, pages 117-125, 1988.
 
 
Conference Papers
 
1. Jen-Hung Wang, Tung-Shing Mamie Lih, Wai-Kok Choong, Wen-Lian Hsu, Ting-Yi Sung, "Evaluating the possibility of misinterpreting MS/MS spectra caused by isobaric substitutions: a case study on human missing proteins," 66th ASMS Conference on Mass Spectrometry and Allied Topics, June 2018.
2. Ching-Tai Chen, Chu-Ling Ko, Wai-Kok Choong, Jen-Hung Wang, Wen-Lian Hsu, and Ting-Yi Sung, "WinProphet: a user-friendly pipeline management system based on Trans-Proteomic Pipeline," 66th ASMS Conference on Mass Spectrometry and Allied Topics, June 2018.
3. Cheng-Wei Cheng, Wen-Lian Hsu, Ting-Yi Sung, "Automated identification of intact N-linked glycoproteins with multiple protein search engines," 65th ASMS Conference on Mass Spectrometry and Allied Topics, June 2017.
4. Ching-Tai Chen, Cheng-Wei Cheng, Wei-Jhe Hsu, Hui-Yin Chang, Chu-Ling Ko, T. Mamie Lih, Yi-Ju Chen, Yu-Ju Chen, Wen-Lian Hsu, Ting-Yi Sung, "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, June 2017.
5. Hui-Yin Chang, Ching-Tai Chen, Chiun-Gung Juo, Wen-Lian Hsu, Ting-Yi Sung, "iTop-Q: an intelligent top-down proteomics quantification tool using the DYAMOND algorithm for charge state deconvolution," 15th HUPO World Congress, September 2016.
6. Chen-Chun Chen, Cheng-Wei Cheng, Ke-Shiuan Lynn, Wan-Chih Su, Chia-Ying Cheng, Wen-Lian Hsu, Chi-Huey Wong, Yu-Ju Chen and Ting-Yi Sung, "GlycoPepDecipher: Automated Identification of Intact N-linked Glycopeptides," 12th HUPO World Congress, September 2013.
7. T. Mamie Lih, Ke-Shiuan Lynn, Hui-Ying Chang, Mei-Ling Cheng, Ming-Shi Shiao, Wen-Harn Pan, Ting-Yi Sung and Wen-Lian Hsu, "Metab-ID: a software for metabolite identification from MS1 data," 61th ASMS Conference on Mass Spectrometry and Allied Topics, June 2013.
8. Hui-Yin Chang, Nai-Yuan Chiang, Chia-Feng Tsai, Ya-Wen Tsai, Yu-Ju Chen, Ting-Yi Sung and Wen-Lian Hsu, "ProtDIA-id: An automatic tool to extract MS/MS spectra for protein identification in proteomic experiments using data-independent acquisition," 61th ASMS Conference on Mass Spectrometry and Allied Topics, June 2013.
9. Hui-Yin Chang, Ke-Shiuan Lynn, T. Mamie Lih, Nai-Yuan Chiang, Mei-Ling Cheng, Wen-Harn Pan, Yet-Ran Chen, Ting-Yi Sung, Wen-Lian Hsu, "Metab-Q: An automatic tool for metabolic fingerprinting," 60th ASMS Conference on Mass Spectrometry and Allied Topics, ASMS, May 2012.
10. Chih-Chiang Tsou, Han-Yin Yang, Ying-Che Chang, Kay-Hooi Khoo, Yu-Ju Chen, Alexey Nesvizhskii, Ting-Yi Sung, Wen-Lian Hsu, "IDEAL-Q+: computational tool for labeling and label-free mass spectrometry-based proteomics," 60th ASMS Conference on Mass Spectrometry and Allied Topics, ASMS, May 2012.
11. Chia-Ying Cheng, Chia-Feng Tsai, Han-Yin Yang, Yu-Ju Chen, Ting-Yi Sung, Wen-Lian Hsu, "Improving peptide identification by integrating database searching and spectral library searching," 60th ASMS Conference on Mass Spectrometry and Allied Topics, ASMS, May 2012.
12. Sheng-Chieh Lu, Chia-Feng Tsai, Chih-Chiang Tsou, Han-Yin Yang, Lien-Chin Chen, Yu-Ju Chen, Ting-Yi Sung and Wen-Lian Hsu, "Improving phosphorylation site assignment by statistical analysis," the 8th Taiwan Society for Mass Spectrometry Anaual Conference (TSMS2011), Taipei, Taiwan, July 2011.
13. Han-Yin Yang, Chih-Chiang Tsou, Yi-Ju Chen, Yen-Yi Lin, Yu-Ju Chen, Ting-Yi Sung, and Wen-Lian Hsu, "An automated tool for detecting modification-specific marker ions to improve the sensitivity of modified peptide identification," 59th ASMS Conference on Mass Spectormetry, June 2011.
14. Chih-Chiang Tsou, Han-Yin Yang, Ting-Yi Sung, and Wen-Lian Hsu, "IDEAL-Q Plus: extended version for stable isotope labeling, label-free, and comparative quantitation analysis with assigning reliability to protein quantitation ratio," HUPO2010, September 2010.
15. Sheng-Shieh Lu, Chia-Feng Tsai, Chih-Chiang Tsou, Han-Ying Yang, Lien-Chin Chen, Yu-Ju Chen, Ting-Yi Sung, and Wen-Lian Hsu, "Improving phosphorylation site assignment by statistical analysis on CID fragmentation," 58th ASMS Conference on Mass Spectrometry, Salt Lake City, Utah, July 2010.
16. Yi-Ting Wang, Chia-Feng Tsai, Tzu-Chan Hong, Chih-Chiang Tsou, Pei-Yi Lin, Sih-Hua Pan, Tse-Ming Hong, Pan-Chyr Yang, Ting-Yi Sung, Wen-Lian Hsu, and Yu-Ju Chen, "An informatics-assisted label-free quantitation strategy that depicts phosphoproteomic profiles in lung cancer cell invasion," 58th ASMS Conference on Mass Spectrometry, May 2010.
17. Pei-Yi Lin, Chia-Feng Tsai, Chih-Chiang Tsou, Chia-Li Han, Yi-Ting Wang, Ting-Yi Sung, Wen-Lian Hsu, and Yu-Ju Chen, "High-speed proteomic signature by informatics-assisted label-free quantitation," 58th ASMS Conference on Mass Spectrometry, May 2010.
18. Yi-Ting Wang, Chia-feng Tsai, Tzu-Chan Hong, Chih-Chiang Tsou, Pei-Yi Lin, Tse-Ming Hong, Pan-Chyr Yang, Ting-Yi Sung, Wen-Lian Hsu, and Yu-Ju Chen, "A Simple Label-free LC-MS/MS Strategy Towards Comprehensive Phosphoproteomics View that Depict the Mechanisms of Cancer Cell Invasion," 57th ASMS Conference on Mass Spectrometry, June 2009.
19. Chih-Chiang Tsou, Ting-Yi Sung, and Wen-Lian Hsu, "MassComp-Q: A comprehensive quantitation software tool for stable isotope labeling and label-free quantitative proteomics," 57th ASMS Conference on Mass Spectrometry, June 2009.
20. Emily Chia-Yu Su, Jia-Ming Chang, Ting-Yi Sung, and Wen-Lian Hsu, "Prediction of Protein Nuclear Localization Based on Smoothed Evolutionary Information and Probabilistic Latent Semantic Indexing," The 7th Asia Pacific Bioinformatics Conference, Beijing, China, 2009.
21. Chien-Peng Wu, Pei-Yi Lin, Chih-Wei Chien, Chia-Li Han, Chih-Chiang Tsou, Ting-Yi Sung, Wen-Lian Hsu, and Yu-Ju Chen, "Altered Membrane Proteomic Signature in Human Colorectal Cancer Revealed by Label-free Quantitation Strategy," 56th ASMS Conference on Mass Spectrometry, June 2008.
22. Chih-Chiang Tsou, Chia-Feng Tsai, Ethan Yin-Hao Tsui, Paul Chuan-Yih Yu, Yi-Ting Wang, Pei-Yi Lin, Yu-Ju Chen, Ting-Yi Sung, and Wen-Lian Hsu, "IDEAL-Q: An automated tool for high-performance label-free quantitative analysis," 56th ASMS Conference on Mass Spectrometry, June 2008.
23. Pei-Yi Lin, Chia-feng Tsai, Chih-Chiang Tsou, Chien-Peng Wu, Yi-Ting Wang, Ting-Yi Sung, Wen-Lian Hsu, and Yu-Ju Chen, "High-speed Proteomic Signature by Swift LC-MS/MS and Label-free Quantitation," 56th ASMS Conference on Mass Spectrometry, June 2008.
24. Yi-Ting Wang, Chia-Feng Tsai, Pei-Yi Lin, Tzu-Chan Hong, Chih-Chiang Tsou, Wen-Lian Hsu, Ting-Yi Sung, Tze Min Hong, Pan-Chyr Yang, and Yu-Ju Chen, "SEMI-quantitation Strategy for Label-free Quantitative Profiling of Phosphoproteome in Lung Cancer of Different Invasive Potential," 56th ASMS Conference on Mass Spectrometry, June 2008.
25. Emily Chia-Yu Su, Jia-Ming Chang, Ting-Yi Sung, Wen-Lian Hsu, "Prediction of Protein Nuclear Localization Based on Smoothed Evolutionary Information and Probabilistic La-tent Semantic Indexing," The 19th International Conference on Genome Informatics, Gold Coast , Australia, 2008.
26. Ethan Y. H. Tsui, Yi-Hwa Yian, Chih-Chiang Tsou, Paul C. Y. Yu, Ke-Shiuan Lynn, Wen-Chi Chou, Yi-Ju Chen, Yu-Ju Chen, Ting-Yi Sung, Wen-Lian Hsu, "MaXIC-Q: A Fully Automated Generic Tool Using Statistical and Computational Methods for Protein Quantitation Based on Isotope Labeling and LC-MS," 56th ASMS Conference on Mass Spectrometry, Denver, Colorado, 2008.
27. Chih-Chiang. Tsou, Chuan-Yih Yu, Ethan Yin-Hao Tsui, Ting-Yi Sung, Wen-Lian Hsu, "LaFree-Q: A New Generic Tool for Label-free Quantitative Proteomics," Proteomics Society International Conference 2007, December 2007, Poster
28. Chuan-Yih Yu, Ethan Yin-Hao Tsui, Chih-Chiang Tsou, Ting-Yi Sung, and Wen-Lian Hsu, "MSMRI: A Comprehensive Visualization and Validation Tool for Mass Spectral Analysis," Taiwan Proteomics Society International Conference 2007, December 2007, Poster
29. Ching-Tai Chen, Hsin-Nan Lin, Kun-Pin Wu, Ting-Yi Sung, and Wen-Lian Hsu, "A Knowledge-based Approach to Protein Local Structure Prediction," Asia Pacific Bioinformatics Conference (APBC), 2006, (acceptance rate: 29%) :::icon
30. Emily Chia-Yu Su, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu, "Protein Subcellular Localization Prediction Based on Compartment-Specific Biological Features," Proceedings of IEEE Computational Systems Bioinformatics Conference (CSB'06), Stanford, CA, 2006. :::icon
31. Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu, "Transmembrane Helix and Topology Prediction Using Hierarchical SVM Classifiers and an Alternating Geometric Scoring Function," Proceedings of IEEE Computational Systems Bioinformatics Conference (CSB), Stanford, CA, 2006. :::icon
32. Hua-Sheng Chiu, Hsin-Nan Lin, Allan Lo, Ting-Yi Sung, Wen-Lian Hsu, "A two-stage classifier for protein beta-turn prediction using support vector machines," Proceedings of IEEE International Conference on Granular Computing (IEEE GrC), 2006. :::icon
33. Wen-Chi Chou, Richard Tzong-Han Tsai, Ying-Shan Su,Wei Ku, Ting-Yi Sung and Wen-Lian Hsu, "A Semi-Automatic Method for Annotating a Biomedical Proposition Bank," Proceedings of ACL Workshop on Frontiers in Linguistically Annotated Corpora, 2006. :::icon
34. Tzong-Han Tsai, Chia-Wei Wu, Chun-Nan Chi, Ding He, Ting-Yi Sung and Wen-Lian Hsu, "Biomedical Literature Mining: Technologies and IASL’s Experiences," The Workshop on the Sciences of the Artificial, National Dong Hwa University, Hualien, December 2005.
35. Tzong-Han Tsai, Chia-Wei Wu, Chun-Nan Chi, Ding He, Ting-Yi Sung, Wen-Lian Hsu, "Biomedical Literature Mining: Technologies and IASL's Experiences," Workshop on the Sciences of Artificial (WSA) 2005, invited paper, 2005.
36. Kuen-Pin Wu, Jia-Ming Chang, Jun-Bo Chen, Chi-Fon Chang, Wen-Jin Wu, Tai-Huang Huang, Ting-Yi Sung and Wen-Lian Hsu, "RIBRA—an Error-Tolerant Algorithm for the NMR Backbone Assignment Problem," RECOMB, 2005. :::icon
37. Yi-Feng Lin, Tzong-Han Tsai, Wen-Chi Chou, Kuen-Pin Wu, Ting-Yi Sung and Wen-Lian Hsu, "A Maximum Entropy Approach to Biomedical Named Entity Recognition," Proceedings of the 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD 2004), pages 56-61, August 2004. :::icon
38. Wen-Lian Hsu, Jia-Ming Chang, Wen-Chi Chou, Philip Chen, Kuen-Pin Wu, Ting-Yi Sung, Chi-Fang Chang, Wen-Jin Wu and Tai-Huang Huang, "An Iterative Relaxation Technique for the NMR Backbone Assignment Problem," IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE), 2004.
39. Yi-Feng Lin, Wen-Chi Chou, Kuen-Pin Wu, Ting-Yi Sung, and Wen-Lian Hsu, "InfoMap: A Framework for Integrated Proteomic Knowledge Base," Proceedings of 3rd International Proteomics Conference (IPC' 04), 2004, invited talk
40. Kuen-Pin Wu, Hsin-Nan Lin, Ting-Yi Sung and Wen-Lian Hsu, "A new similarity measure among protein sequences," 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference (CSB), 2003.
41. Ting-Yi Sung and Jeng-Jung Wang, "Changing diameter on graph products," Annual International Computing and Combinatorics Conference, Lecture Notes in Computer Science, pages 390--394, 2001.
42. Chien-Ping Chang, Ting-Yi Sung and Lih-Hsing Hsu, "A new shortest path routing algorithm and embedding cycles of crossed cubes," the 1997 International Symposium on Parallel Architectures, Algorithms, and Networks (I-SPAN'97), Feipei Lai, Bruce Maggs and and D. Frank Hsu, editors, IEEE Computer Society Press, pages 125-131, 1997. :::icon
43. Ting-Yi Sung, Tung-Yang Ho and Lih-Hsing Hsu, "Projevctive torus networks," Annual International Computing and Combinatorics Conference, Lecture Notes in Computer Science, 1276, Tao Jiang and D.T. Lee, editor, Springer-Verlag, pages 451-459, 1997.
44. Ting-Yi Sung, "The undirected de Bruijn graph: shortest paths and transmitting,," INFORMS Meeting, New Orleans, October 1995.
45. Ting-Yi Sung and Men-Yang Lin, "Edge fault tolerance in hypercubes," TIMS/ORSA Joint National Meeting, Boston, April 1994.
46. Lih-Hsing Hsu, Chang-Hsiung Tsai and Ting-Yi Sung, "On the compositions of networks having double Euler trails," The Seventh International Conference on Graph Theory, Combinatorics, Algorithms, and Applications, 1992.
47. Ting-Yi Sung, Lih-Hsing Hsu and Jeng-Yan Hwang, "Data structure for graph representations of a network having double Euler trails," Information Processing 92, Algorithms, Software, Architecture, volume I, J. van Leeuwen, editor, Elsevier Science Publishers B.V, pages 436--442, 1992.
48. Jan-Ming Ho, Ming-Tat Ko, Tze-Heng Ma and Ting-Yi Sung, "Algorithms for rectilinear optimal multicast tree problem," the 3rd Symposium on Algorithms and Computation, Nagoya, Japan, 1992.
 
 
Others
 
1. Wen-Lian Hsu and Ting-Yi Sung,, chapter "Automated generic analysis tools for protein quantitation using stable isotope labeling," "Proteome Bioinformatics," Simon J. Hubbard and Andrew R. Jones, editors, Methods in Molecular Biology, volume 604, pages 257-272, Humana Press, 2010.
2. Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu, TR-IIS-007-010, "On the accuracy of transmembrane helix prediction methods using an updated benchmark," Institute of Information Science, Academia Sinica, 2007. :::icon
 
 
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