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Publications
 
Journal Articles
 
1. 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
2. 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.
3. 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
4. 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, pages 2305-2310, April 2013.
5. 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
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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
21. 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
22. 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.
23. 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
24. 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
25. 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, 2007.
26. 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.
27. 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.
28. 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.
29. 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.
30. 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
31. 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.
32. 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.
33. 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
34. 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
35. 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
36. 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
37. 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.
38. 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.
39. 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
40. 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
41. 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.
42. 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
43. 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
44. 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
45. 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
46. 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.
47. Manfred Padberg and Ting-Yi Sung, "An analytic symmetrization of max flow-min cut," Discrete Mathematics, volume 165, number 166, pages 531-545, 1997.
48. 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
49. 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
50. 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
51. Zhen Liu and Ting-Yi Sung, "Routing and transmitting problems in de Bruijn networks," IEEE Transactions on Computers, volume 45, pages 1056--1062, 1996.
52. 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.
53. 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
54. 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.
55. 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.
56. 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.
57. 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. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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
23. 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
24. 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
25. 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
26. 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
27. 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
28. 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
29. 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.
30. 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.
31. 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
32. 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
33. 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
34. 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.
35. 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.
36. 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.
37. 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
38. 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.
39. Ting-Yi Sung, "The undirected de Bruijn graph: shortest paths and transmitting,," INFORMS Meeting, New Orleans, October 1995.
40. Ting-Yi Sung and Men-Yang Lin, "Edge fault tolerance in hypercubes," TIMS/ORSA Joint National Meeting, Boston, April 1994.
41. 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.
42. 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.
43. 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.
 
 
Technical Reports
 
1. Ethan Yin-Hao Tsui, Yi-Hwa Yian, Chih-Chiang Tsou, Paul Chuan-Yih Yu, Ke-Shiuan Lynn, Wen-Chi Chou, Yi-Ju Chen, Yu-Ju Chen, Ting-Yi Sung, and Wen-Lian Hsu, "MaXIC-Q: A Fully Automated Generic Tool Using Statistical and Computational Methods for Protein Quantitation Based on Stable Isotope Labeling and LC-MS," TR-IIS-08-004, Institute of Information Science, Academia Sinica 2008.
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
 
 
Book & Book Chapters
 
1. Hsin-Nan Lin, Ting-Yi Sung and Wen-Lian Hsu, "Sequence and Genome Analysis: Methods and Applications," Z. Zhao, editor, iConcept Press, 2010.
2. 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.
 
 
 
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