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Adjunct Research Fellow/Professor  |  Hsu, Wen-Lian  
 
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Publications
 
Journal Articles
 
1. Neha Warikoo, Yung-Chun Chang, and Wen-Lian Hsu, "LBERT: Lexically-aware Transformers based Bidirectional Encoder Representation model for learning Universal Bio-Entity Relations," to appear in Bioinformatics.
2. Ting-Hao Yang, Yu-Lun Hsieh, Shih-Hung Liu, Yung-Chun Chang, and Wen-Lian Hsu, "A Flexible Template Generation and Matching Method with Applications for Publication Reference Metadata Extraction," to appear in Journal of the Association for Information Science and Technology.
3. Chi-Jen Chen, Neha Warikoo, Yung-Chun Chang, Jin-Hua Chen, and Wen-Lian Hsu, "Medical Knowledge Infused Convolutional Neural Networks for Cohort Selection in Clinical Trials," to appear in JAMIA(Journal of the American Medical Informatics Association) ).
4. Ming-Siang Huang, Po-Ting Lai, Pei-Yen Lin, Yu-Ting You, Richard Tzong-Han Tsai and Wen-Lian Hsu, "Biomedical Named Entity Recognition and Linking Datasets: Survey and Our Recent Development," Briefings in Bioinformatics, July 2020.
5. Hsin-Nan Lin ,Wen-Lian Hsu, "GSAlign: an efficient sequence alignment tool for intra-species genomes," BMC Genomics, volume 21, number 182, pages 1-10, February 2020. :::icon
6. Hsi-Yuan Huang, Yang-Chi-Dung Lin, Jing Li, Kai-Yao Huang, Sirjana Shrestha, Hsiao-Chin Hong, Yun Tang, Yi-Gang Chen, Chen-Nan Jin, Yuan Yu, Jia-Tong Xu, Yue-Ming Li, Xiao-Xuan Cai, Zhen-Yu Zhou, Xiao-Hang Chen, Yuan-Yuan Pei, Liang Hu, Jin-Jiang Su, Shi-Dong Cui, Fei Wang, Yue-Yang Xie, Si-Yuan Ding, Meng-Fan Luo, Chih-Hung Chou, Nai-Wen Chang, Kai-Wen Chen, Yu-Hsiang Cheng, Xin-Hong Wan, Wen-Lian Hsu, Tzong-Yi Lee, Feng-Xiang Wei, Hsien-Da Huang, "miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database," Nucleic Acids Research (Oxford), volume 48, number D1, pages D148–D154, October 2019.
7. Hong-Jie Dai, Chen-Kai Wang, Nai-Wen Chang, Ming-Siang Huang, Jitendra Jonnagaddala, Feng-Duo Wang, Wen-Lian Hsu, "Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature," Database (Oxford), volume 2019, pages Appeared, February 2019.
8. Cheng-Wei Cheng, Yixuan Zhou, Wen-Harn Pan, Supriya Dey, Chung-Yi Wu, Wen-Lian Hsu and Chi-Huey Wong, "Hierarchical and programmable one-pot synthesis of oligosaccharides," Nature Communications, volume 9, number 5202, pages 1-9, December 2018.
9. Po-Ting Lai, Ming-Siang Huang, Ting-Hao Yang, Richard Tzong-Han Tsai, Wen-Lian Hsu, "Statistical Principle-based Approach for Gene and Protein Related Object Recognition," Journal of Cheminformatics, volume 10, pages 64, December 2018.
10. Neha Warikoo, Yung-Chun Chang, and Wen-Lian Hsu, "LPTK: A Linguistic Pattern-Aware Dependency Tree Kernel Approach for the BioCreative VI CHEMPROT Task," Database (Oxford), volume 2018, pages bay108, October 2018.
11. Yung-Chun Chang, Cheng-Wei Shih, and Wen-Lian Hsu, "Entailment-based Intelligent Agent for Software Project Monitoring and Control," IEEE Systems Journal, volume 12, number 1, pages 216-227, March 2018, 10.1109/JSYST.2016.2563463
12. Hsin-Nan Lin and Wen-Lian Hsu, "DART: a fast and accurate RNA-seq mapper with a partitioning strategy," Bioinformatics, volume 34, number 2, pages 190-197, January 2018.
13. 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
14. Shih-Hung Liu, Kuan-Yu Chen, Yu-Lun Hsieh, Berlin Chen, Hsin-Min Wang, Hsu-Chun Yen, and Wen-Lian Hsu, "A Position-Aware Language Modeling Framework for Extractive Broadcast News Speech Summarization," ACM Transactions on Asian and Low-Resource Language Information Processing, volume 16, number 4, pages 1-13, Article 27, August 2017.
15. Hsin-Nan Lin and Wen-Lian Hsu, "Kart: a divide-and-conquer algorithm for NGS read alignment," Bioinformatics, volume 1;33(15), pages 2281-2287, August 2017.
16. Yung-Chun Chang, Pi-Hua Chuang, Chien Chin Chen and Wen-Lian Hsu, "FISER: A Feature-based Detection System for Topic Person Interactions," Computational Intelligence, volume 2017, pages 5, May 2017.
17. Yung-Chun Chang, Cheng-Wei Shih, Wen-Lian Hsu, "Entailment-based Intelligent Agent for Software Project Monitoring and Control," IEEE Systems Journal, volume 12, pages 216-227, March 2017.
18. Nai-Wen Chang, Hong-Jie Dai, Yung-Yu Shih, Chi-Yang Wu, Mira Anne C Dela Rosa, Rofeamor P Obena, Yu-Ju Chen, Wen-Lian Hsu, Yen-Jen Oyang, "Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy," Database (Oxford), volume 2017, pages bax082, January 2017.
19. Yuxiang Jiang, ..., Caster Chen, Wen-Lian Hsu et al., "An expanded evaluation of protein function prediction methods shows an improvement in accuracy," Genome Biology, volume 7;17(1), pages 184, September 2016.
20. Yung-Chun Chang, Chun-Han Chu, Chien Chin Chen, and Wen-Lian Hsu, "Linguistic Template Extraction for Recognizing Reader-Emotion," International Journal of Computational Linguistics and Chinese Language Processing, volume 21, number 1, pages 29-50, September 2016.
21. Yung-Chun Chang, Chun-Han Chu, Yu-Chen Su, Chien Chin Chen, and Wen-Lian Hsu, "PIPE: A BioC Module for Protein-protein Interaction Passage Extraction," Database (Oxford), volume 2016, pages baw101, August 2016.
22. Yung-Chun Chang, Chien Chin Chen, and Wen-Lian Hsu, "SPIRIT: A Tree Kernel-based Method for Topic Person Interaction Detection," IEEE Transactions on Knowledge and Data Engineering (TKDE), volume 28, number 9, pages 2494-2507, August 2016.
23. 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.
24. Hong-Jie Dai, Chu-Hsien Su, Po-Ting Lai, Ming-Siang Huang, Jitendra Jonnagaddala, Toni Rose Jue, Shruti Rao, Hui-Jou Chou, Marija Milacic, Onkar Singh, Syed Abdul Shabbir, Wen-Lian Hsu, "MET network in PubMed: a text-mined network visualization and curation system," Database (Oxford), volume ., number ., pages ., May 2016.
25. Hui-Yin Chang, Ching-Tai Chen, T. Mamie Lih, Ke-Shiuan Lynn, Chiun-Gung Juo, Wen-Lian Hsu, 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.
26. 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.
27. Nai-Wen Chang, Hong-Jie Dai, Jitendra Jonnagaddala, Chih-Wei Chen, Richard Tzong-Han Tsai, Wen-Lian Hsu, "A Context-Aware Approach for Progression Tracking of Medical Concepts in Electronic Medical Records," Journal of Biomedical Informatics, volume S150-7, pages ., December 2015.
28. Yung-Chun Chang, Zhong-Yong Chen, Chien Chin Chen, and Wen-Lian Hsu, "Constructing Topic Person Interaction Networks Using a Tree Kernel-based Method," International Journal of Languages, Literature and Linguistics, volume 1, number 4, pages 238-245, December 2015.
29. Chih-Hung Chou, Nai-Wen Chang, Sirjana Shrestha, Sheng-Da Hsu, Yu-Ling Lin, Wei-Hsiang Lee, Chi-Dung Yang, Hsiao-Chin Hong, Ting-Yen Wei, Siang-Jyun Tu, Tzi-Ren Tsai, Shu-Yi Ho, Ting-Yan Jian, Hsin-Yi Wu, Pin-Rong Chen, Nai-Chieh Lin, Hsin-Tzu Huang, Tzu-Ling Yang, Chung-Yuan Pai, Chun-San Tai, Wen-Liang Chen, Chia-Yen Huang, Chun-Chi Liu, Shun-Long Weng, Kuang-Wen Liao, Wen-Lian Hsu,* and Hsien-Da Huang*, "miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database," Nucleic Acids Research, volume doi: 10.1093/nar/gkv1258, pages ., November 2015.
30. Kuan-Yu Chen, Shih-Hung Liu, Berlin Chen, Hsin-Min Wang, Ea-Ee Jan, Wen-Lian Hsu, Hsin-Hsi Chen, "Extractive broadcast news summarization leveraging recurrent neural network language modeling techniques," IEEE/ACM Transactions on Audio, Speech, and Language Processing, volume 23, number 8, pages 1322-1334, August 2015. :::icon
31. Yung-Chun Chang, Yu-Lun Hsieh, Cen-Chieh Chen, and Wen-Lian Hsu, "A Semantic Frame-based Intelligent Agent for Topic Detection," Soft Computing, volume 2015, pages 1-11, July 2015.
32. Shih-Hung Liu, Kuan-Yu Chen, Berlin Chen, Hsin-Min Wang, Hsu-Chun Yen, and Wen-Lian Hsu, "Combining Relevance Language Modeling and Clarity Measure for Extractive Speech Summarization," IEEE/ACM Transactions on Audio, Speech, and Language Processing, volume 23, number 6, pages 957 - 969, June 2015. :::icon
33. 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
34. 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.
35. Hong-Jie Dai, Johnny Chi-Yang Wu , Wei-San Lin, Aaron James F. Reyes, Mira Anne C. dela Rosa, Shabbir Syed-Abdul, Richard Tzong-Han Tsai and Wen-Lian Hsu, "LiverCancerMarkerRIF: a liver cancer biomarker interactive curation system combining text mining and expert annotations," Database-The Journal of Biological Databases and Curation, volume ., number ., pages pii: bau085, August 2014.
36. Yung-Chun Chang, Yu-Lun Hsieh, Cen-Chieh Chen, Wen-Lian Hsu, "Semantic Frame-based Natural Language Understanding for Intelligent Topic Detection Agent," Lecture Notes in Computer Science, volume 8481, pages 339-348, June 2014.
37. Wei-Chun Chung, Chien-Chih Chen, Jan-Ming Ho, Chung-Yen Lin, Wen-Lian Hsu, Yu-Chun Wang, Der-Tsai Lee, Feipei Lai, Chih-Wei Huang and Yu-Jung Chang, "CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce," PLoS One, volume 9, number 6, pages 10.1371/journal.pone.0098146, June 2014, http://clouddoe.iis.sinica.edu.tw/ (IF: 3.730，Journal ranking: Multidisciplinary Sciences/Q1: 7/56, 12.5%) :::icon
38. Yung-Chun Chang, Johnny Chi-Yang Wu, Jian-Ming Chen, Hong-Jie Dai, Wen-Lian Hsu, "TEMPTing System: A Hybrid Method of Rule and Machine Learning for Temporal Relation Extraction in Patient Discharge Summaries," Journal of Biomedical Informatics, volume 46, pages 54-62, November 2013.
39. 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
40. Ke-Shiuan Lynn, Chen-Hua Lu, Han-Ying Yang, Wen-Lian Hsu and Wen-Harn Pan, "Construction of Gene Clusters Resembling Genetic Causal Mechanisms for Common Complex Disease with an Application to Young-Onset Hypertension," BMC Genomics, volume 14, number 497, pages ., July 2013.
41. 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.
42. Chia-Ying Cheng, Chia-Feng Tsai, Yu-Ju Chen, Ting-Yi Sung, and Wen-Lian Hsu, "A spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications," Journal of Proteome Research, volume 3, number 12(5), pages 2305-10, April 2013.
43. MIKE TIAN-JIAN JIANG, TSUNG-HSIEN LEE, WEN-LIAN HSU, "The Left and Right Context of a Word: Overlapping Chinese Syllable Word Segmentation with Minimal Context," Transactions on Asian Language Information Processing (TALIP), volume 12, number Issue 1, pages 2:1-23, March 2013. :::icon
44. Hong-Jie Dai, Johnny Chi-Yang Wu, Richard Tzong-Han Tsai, Wen-Harn Pan,Wen-Lian Hsu, "T-HOD: A Literature-based Candidate Gene Database for Hypertension, Obesity, and Diabetes," Database-The Journal of Biological Databases and Curation, volume 2013, number 10.1093, pages bas061, February 2013.
45. 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
46. Cheng-Wei Shih, Cheng-Wei Lee, Richard Tzong-Han Tsai, Wen-Lian Hsu, "Validating Contradiction in Texts Using Online Co-Mention Pattern Checking," Transactions on Asian Language Information Processing (TALIP), volume 11, number Issue 4, pages 17:1-12:21, December 2012.
47. 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.
48. Ching-Tai Chen, Hung-Pin Peng, Jhih-Wei Jian, Keng-Chang Tsai, Jeng-Yih Chang, Ei-Wen Yang, Jun-Bo Chen, Wen-Lian Hsu*, An-Suei Yang*, "Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces," PLoS ONE, volume 7(6), pages e37706, June 2012.
49. Hong-Jie Dai, Chun-Yu Chen, Chi-Yang Wu, Po-Ting Lai, Richard Tzong-Han Tsai, Wen-Lian Hsu, "Coreference resolution of medical concepts in discharge summaries by exploiting," JAMIA(Journal of the American Medical Informatics Association) ), volume 19, number 5, pages 888-896, May 2012.
50. Jhih-Siang Lai, Cheng-Wei Cheng, Ting-Yi Sung*, Wen-Lian Hsu*, "Computational comparative study of tuberculosis proteomes using a model learned from signal peptide structures," PLoS ONE, volume 7, number 4, pages e35018, April 2012.
51. Chung-Ming Yu, Hung-Pin Peng, Ing-Chien Chen, Yu-Ching Lee, Jun-Bo Chen, Keng-Chang Tsai, Ching-Tai Chen, Jeng-Yih Chang, Ei-Wen Yang, Po-Chiang Hsu, Jhih-Wei Jian,Hung-Ju Hsu, Hung-Ju Chang, Wen-Lian Hsu, Kai-Fa Huang, Alex Che Ma and An-Suei Yang, "Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface," PLoS ONE, volume 7, number 3, pages e33340, March 2012. :::icon
52. 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.
53. Yu-Ching Fang, Po-Ting Lai, Hong-Jie Dai and Wen-Lian Hsu*, "MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature," BMC Bioinformatics, volume 12, pages 471, December 2011.
54. Hsin-Nan Lin, Cédric Notredame, Jia-Ming Chang, Ting-Yi Sung*, 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.
55. Hong-Jie Dai, Yen-Ching Chang, Richard Tzong-Han Tsai,and Wen-Lian Hsu, "Integration of Gene Normalization Stages and Co-reference Resolution Using a Markov-Logic Network," Bioinformatics, volume 27, number 18, pages 2586-2594, June 2011.
56. 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.
57. 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.
58. 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.
59. Wei-Chao Chang, Chuan-Kai Chou, Chih-Chiang Tsou, Sheng-Hsiang Li, Chein-Hung Chen, Yu-Xing Zhuo, Wen-Lian Hsu, and Chung-Hsuan Chen, "Comparative Proteomic Analysis of Proteins Involved in Tumorigenic Process of Seminal Vesicle Carcinoma in Transgenic Mice," International Journal of Proteomics, 2010.
60. Hong-Jie Dai, Yen-Ching Chang, Richard Tzong-Han Tsai, and Wen-Lian Hsu, "New challenges for biological text-mining in the next decade," Journal of Computer Science and Technology, volume 25, pages 169-179, 2010.
61. 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.
62. 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.
63. Richard Tsai, Po T. Lai, Hong J. Dai, Chi H. Huang, Yue Y. Bow, Yen C. Chang, Wen H. Pan, Wen L. Hsu, "HypertenGene: Extracting key hypertension genes from biomedical literature with position and automatically-generated template features," BMC Bioinformatics, volume 10, number Suppl 15., pages S9, December 2009.
64. Chorng-Shyong Ong, Min-Yuh Day and Wen-Lian Hsu, "The measurement of user satisfaction with question answering systems," Information & Management, volume Volume 46, number Issue 7, pages 397-403, October 2009.
65. Chih-Chiang Tsou, Yin-Hao Tsui, Yi-Hwa Yian, Yi-Ju Chen, Chuan-Yih Yu, Han-Yin Yang, 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, pages W661-W669, June 2009.
66. Cheng-Lung Sung, Cheng-Wei Lee, Hsu-Chun Yen, and Wen-Lian Hsu, "Alignment-based surface patterns for factoid question answering systems," Integrated Computer-Aided Engineering, volume 16, number 3, pages 259-269, June 2009.
67. 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.
68. Ke-Shiuan Lynn, Li-Lan Li, Yen-Ju Lin, Chiuen-Huei Wang, Shu-Hui Sheng, Ju-Hwa Lin, Wayne Liao, Wen-Lian Hsu and Wen-Harn Pan, "A Neural Network Model for Constructing Endophenotypes of Common Complex Diseases - An Application to Male Young-onset Hypertension Microarray Data," Bioinformatics, volume 25(8), pages 981-988, April 2009.
69. Yu-Chun Wang, Richard Tzong-Han Tsai & Wen-Lian Hsu, "Web-based pattern learning for named entity translation in Korean–Chinese cross-language information retrieval," Expert Systems with Applications, volume 36(2), number Part 2, pages 3990-3995, 2009.
70. Richard Tzong-Han Tsai, Hong-Jie Dai, Chi-Hsin Huang and Wen-Lian Hsu, "Semi-automatic conversion between biomedical predicate argument structure standards," BMC Bioinformatics, volume 9, number (Suppl 12):S18., December 2008.
71. 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.
72. Chia-Wei Wu, Cheng-Wei Lee, Wen-Lian Hsu, Richard Tzong-Han Tsai, "Web taxonomy integration with hierarchical shrinkage algorithm and fine-grained relations," Expert Systems with Applications, volume 35, number 4, pages 2123-2131, November 2008.
73. Chia-Wei Wu, Cheng-Wei Lee, Wen-Lian Hsu, Richard Tzong-Han Tsai, "Web Taxonomy Integration System with Hierarchical Shrinkage and Fine-Grained Relations," Expert Systems with Applications, volume 35(4),, pages 2123-2131, November 2008.
74. Hong-Jie Dai, Chi-Hsin Huang, Ryan T. K. Lin, Richard Tzong-Han Tsai, and Wen-Lian Hsu*, "BIOSMILE web search: a web application for annotating biomedical entities and relations," Nucleic Acids Research, volume 36, pages W390-W398, July 2008.
75. Richard Tzong-Han Tsai, Hsi-Chuan Hung, Hong-Jie Dai, Yi-Wen Lin, and Wen-Lian Hsu, "Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles," BMC Bioinformatics, number 9(Suppl 1), pages S3, February 2008.
76. 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
77. Ching-Tai Chen, Ei-Wen Yang, Wen-Lian Hsu*, and An-Suei Yang*, "Protease Substrate Site Predictors Derived from Machine Learning on Multilevel Substrate Phage Display Data," Bioinformatics, volume 24(23), pages 2691-2697, 2008.
78. Cheng-Wei Lee, Min-Yuh Day, Cheng-Lung Sung, Yi-Hsun Lee, Tian-Jian Jiang, Chia-Wei Wu, Cheng-Wei Shih, Yu-Ren Chen, Wen-Lian Hsu, "Boosting Chinese Question Answering with Two Lightweight Methods: ABSPs and SCO-QAT," ACM Transactions on Asian Language Information Processing, volume 7, number Issue 4, 2008.
79. Cheng-Wei Lee, Yi-Hsun Lee, and Wen-Lian Hsu, "Exploring Shallow Answer Ranking Features in Cross-Lingual and Monolingual Factoid Question Answering," International Journal of Computational Linguistics and Chinese Language Processing, volume 13,, number 1-26,, 2008.
80. Richard Tzong-Han Tsai, Wen-Chi Chou, Yu-Chun Lin, Ying-Shan Su, 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, number 325, pages ., September 2007.
81. 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 W707-712, pages 35, June 2007.
82. Wing-Kwong Wong, Sheng-Cheng Hsu, Shih-Hung Wu, Cheng-Wei Lee, and Wen-Lian Hsu, "LIM-G: Learner-initiating Instruction Model based on Cognitive Knowledge for Geometry Word Problem Comprehension," Computers and Education, volume 48, pages 582-601, May 2007.
83. Min-Yuh Day, Richard Tzong-Han Tsai, Cheng-Lung Sung, Chiu-Chen Hsieh, Cheng-Wei Lee, Shih-Hung Wu, Kun-Pin Wu, Chorng-Shyong Ong, Wen-Lian Hsu, "Reference Metadata Extraction Using a Hierarchical Knowledge Representation Framework," Decision Support Systems, volume 43, number Issue 1, pages 152-167, February 2007.
84. 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.
85. Chun-Hung Lu, Chorng-Shyong Ong, Wen-Lian Hsu*, "Using an ITS as an Arithmetic Assistant for Teachers-3-year Review," Journal of Internet Technology, volume ., pages ., January 2007.
86. 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
87. 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 S11, pages ., December 2006.
88. 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.
89. 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.
90. Ching-Tai Chen, Hsin-Nan Lin, Ting-Ying Sung, Wen-Lian Hsu, "HYPLOSP: A Knowledge-based Approach to Protein Local Structure Prediction," Journal of Bioinformatics and Computational Biology, volume 4, pages 1287-1307, February 2006.
91. Richard 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, number 92, pages ., February 2006.
92. 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
93. 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.
94. 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.
95. Chun-Hung Lu, Shih-Hung Wu, LiongYu Tu, Wen-Lian Hsu, "Ontological Support in Modeling Learners' Problem Solving Process," Journal of Educational Technology & Society, volume 8, number 4, pages 64-74, 2005.
96. 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.
97. Tsai, Jia-Lin, Gladys Hsieh and Wen-Lian Hsu, "Auto-Generation of NVEF Knowledge in Chinese," International Journal of Computational Linguistics and Chinese Language Processing, volume 9, number 1, pages 41-46, February 2004.
98. Richard Tzong-Han Tsai, Shih-Hung Wu, Cheng-Wei Lee, Cheng-Wei Shih and Wen-Lian Hsu, "Mencius: A Chinese Named Entity Recognizer Using Maximum Entropy-based Hybrid Model," International Journal of Computational Linguistics and Chinese Language Processing, volume 9, number 1, pages 65-82, February 2004.
99. W. L. Hsu and R. McConnell, "PC-trees and circular-ones arrangements," Theoretical Computer Science, volume 296, number 1, pages 99-116, 2003.
100. W. F. Lu and W. L. Hsu, "A Test for Interval Graphs on Noisy Data," Lecture Notes in Computer Science, volume 2647, pages 195-208, 2003.
101. W. F. Lu and W. L. Hsu, "A Test for the Consecutive Ones Property on Noisy Data - Application to Physical Mapping and Sequence Assembly," Journal of Computational Biology, volume 10, number 5, pages 709-735, 2003, also appeared in Lecture Notes in Computer Science 1276
102. W. L. Hsu, "A simple test for the consecutive ones property," J. Algorithms, volume 43, pages 1-16, January 2002.
103. Jia-Lin Tsai, Wen-Lian Hsu and Jeng-Woei Su, "Word Sense Disambiguation and Sense-Based NV Event Frame Identifier," International Journal of Computational Linguistics and Chinese Language Processing, number 29-46, 2002.
104. W. L. Hsu and Yi-Shiou Chen, "On Phoneme-to-Character Conversion Systems in Chinese Processing," Chinese Institute of Engineers, volume 5, pages 573-579, 1999.
105. W. K. Shih and W. L. Hsu, "A new planarity test," Theoretical Computer Science, volume 223, pages 179-191, 1999.
106. W. L. Hsu and T. H. Ma, "Fast and simple algorithms for recognizing chordal comparability graphs and interval gragh," SIAM J. Computing, volume 28, pages 1004-1020, 1999.
107. W. L. Hsu, "Perfect Graphs," Advances in the Theory of Computation and Computational Mathematics, volume 1, pages 81-122, January 1996.
108. W. L. Hsu and J. P. Spinrad, "Independent sets in circular-arc graphs," J. Algorithms, volume 19, pages 145-160, January 1995.
109. W. L. Hsu, "Chinese parsing in a phoneme-to-character conversion systembased on semantic pattern matching," International Journal on Computer Processing of Chinese and Oriental Languages, volume 40, pages 227-236, 1995.
110. W. L. Hsu, "O(mn) algorithms for the recognition and isomorphism problems on circular-arc graphs," volume 24, pages 411-439, 1995.
111. K. H. Tsai and W. L. Hsu, "Fast algorithms for the minimum dominating set problem on permutation graphs," Algorithmica, pages 601-614, 1993.
112. W. K. Shih, W. L. Hsu and T. C. Chen, "An O(n2logn) algorithm for the Hamiltonian cycle problem on circular-arc graphs," volume 21, pages 1026-1046, 1992.
113. W. L. Hsu and K. H. Tsai, "Linear time algorithms on circular-arc graphs," Information processing Letters, volume 40, pages 123-129, 1991.
114. C. Gabor, W. L. Hsu and K. Supowit, "Recognizing circle graphs in polynomial time," volume 36, number 3, pages 435-473, July 1989.
115. W. K. Shih and W. L. Hsu, "An O(n1.5) algorithm for coloring proper circular-arc graphs," Discrete Applied Mathematics, volume 25, pages 321-323, 1989.
116. W. K. Shih and W. L. Hsu, "An O(nlogn + mloglogn) algorithm for finding a maximum weight clique in circular-arc graphs," Infor. Process. Letters, pages 129-134, 1989.
117. W. L. Hsu, "The coloring and maximum independent set problems on planar perfect graphs," volume 35, number 3, pages 535-563, July 1988.
118. W. L. Hsu, "Recognizing planar perfect graphs," J. Assoc. Comput. Machin., volume 34, number 2, pages 255-288, April 1987.
119. W. L. Hsu, "Decomposition of perfect graphs," J. Combin. Theory, volume 43, pages 70-94, 1987.
120. W. L. Hsu, "Coloring planar perfect graphs by decomposition," Combinatorica, volume 6, number 4, pages 381-385, 1986.
121. W. L. Hsu, "Maximum weight clique algorithms for circle graphs and circular-arc graphs," SIAM J. Computing, volume 14, pages 224-231, 1985.
122. W. L. Hsu and G. L. Nemhauser, "Algorithms for maximum weight cliques, minimum weighted clique covers and cardinality colorings of claw-free perfect graphs," Annals of Discrete Mathematics, volume 21, pages 317-329, 1984.
123. W. L. Hsu, "Approximation algorithms for the assembly line crew scheduling problem," Math. of Operations Research, volume 9, pages 376-383, 1984.
124. A. Naamad, W. L. Hsu and D. T. Lee, "On the maximum empty rectangle problem," Discrete Applied Mathematics, volume 8, pages 267-277, 1984.
125. W. L. Hsu, "Berge's strong perfect graph conjecture on special graphs: A Survey," Annals of Discrete Mathematics, volume 21, pages 107-117, 1984.
126. W. L. Hsu, "On the general feasibility test of scheduling lot sizes for several products on one machine," Management Science, volume 29, pages 93-105, 1983.
127. W. L. Hsu, "The distance-domination numbers of trees," Operations Research Letters, volume 1, number 3, pages 96-100, 1982.
128. W. L. Hsu and G. L. Nemhauser, "A polynomial algorithm for the minimum weighted clique cover problem on claw-free perfect graphs," Discrete Mathematics, volume 38, pages 65-71, 1982.
129. W. L. Hsu, Y. Ikura and G. L. Nemhauser, "A polynomial algorithm for maximum weighted vertex packing on graphs without long odd cycles," Math., volume 20, pages 225-232, 1981.
130. W. L. Hsu and G. L. Nemhauser, "Algorithm for minimum covering by cliques and maximum cliques in claw-free perfect graphs," Discrete Mathematics, volume 37, pages 181-191, 1981.
131. W. L. Hsu, "How to color claw-free perfect graphs," Annals of Discrete Mathematics, volume 11, pages 189-197, 1981.
132. W. L. Hsu and G. L. Nemhauser, "Easy and hard bottleneck location problems," Discrete Applied Mathematics, volume 1, pages 209-215, 1979.
 
 
 
 
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