期刊論文

Journal papers

  • 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, Volume 2017, bax082, January 2017.
  • Hsin-Nan Lin and Wen-Lian Hsu, “ DART: a fast and accurate RNA-seq mapper with a partitioning strategy,” Bioinformatics, btx558, September 2017.
  • 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.
  • Hsin-Nan Lin and Wen-Lian Hsu, “Kart: a divide-and-conquer algorithm for NGS read alignment,” 1;33(15):2281-2287, Bioinformatics, August 2017.
  • 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.
  • 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.
  • 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 2016 (2016).
  • Yung-Chun Chang, Chen, Chien Chin, 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.
  • Yuxiang Jiang, …, Caster Chen, Wen-Lian Hsu et al., “An expanded evaluation of protein function prediction methods shows an improvement in accuracy,” 7;17(1):184, Genome Biology, 2016.
  • 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.
  • 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.
  • 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, (2016).
  • 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 Label-Free Metabolomics Quantitation Using Dynamic Peak-Width Determination”, PLoS One, 11(1):e0146112, (2016).
  • 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 S150-7, Journal of Biomedical Informatics, 2015.
  • 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, doi: 10.1093/nar/gkv1258, November 20, (2015).
  • 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, 14(12):5396-5407, (2015).
  • 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.
  • 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, Vol. 23, No. 8, pages 1322-1334, (2015).
  • 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, 87(4), 2466-2473,(2015).
  • Shih-Hung Liu, Kuan-Yu Chen, Berlin Chen, Hsin-Min Wang, Hsu-Chun Yen, Wen-Lian Hsu, “Combining Relevance Language Modeling and Clarity Measure for Extractive Speech Summarization,” IEEE/ACM Transactions on Audio, Speech, and Language Processing, Vol. 23, No. 6, (2015).
  • 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.
  • 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, 87 (4), pp 2143–2151, February 17, (2015).
  • 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, (2014).
  • Wei-Chun Chung, Chien-Chih Chen, Jan-Ming Ho, Chung-Yen Lin, Wen-Lian Hsu, Yu-Chun Wang, D. T. Lee, Feipei Lai, Chih-Wei Huang, Yu-Jung Chang, “CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce,” PLoS ONE, 9(6): e98146, (2014).
  • Hong-Jie Dai, Richard Tzong-Han Tsai, Wen-Lian Hsu,”Joint Learning of Entity Linking Constraints Using a Markov-Logic Network,” Computational Linguistics and Chinese Language Processing, vol. 19, No. 1, pp. 11-32, March 2014.
  • 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, 3;12(5):2305-10, (2013).
  • 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 14:497, (2013).
  • 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.
  • 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.
  • Yung-Chun Chang,Hong-Jie Dai,Johnny Chi-Yang Wu,Jian-Ming Chen,Richard Tzong-Han Tsai, 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, Supplement, Pages S54–S62, September 2013.
  • Hong-Jie Dai, Johnny Chi-Yang Wu, Richard Tzong-Han Tsai, Wen-Harn Pan,Wen-Lian Hsu1*, “T-HOD: A Literature-based Candidate Gene Database for Hypertension, Obesity, and Diabetes,” Database-The Journal of Biological Databases and Curation,2013.
  • 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.
  • 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.
  • 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,” Volume 12 Issue 1, pages 2:1-23, ACM Transactions on Asian Language Information Processing (TALIP), (2013).
  • Mike Tian-Jian Jiang, Cheng-Wei Shih, Ting-Hao Yang,Chan-Hung Kuo, Richard Tzong-Han Tsai and Wen-Lian Hsu, “Enhancement of Feature Engineering for Conditional Random Field Learning in Chinese Word Segmentation Using Unlabeled Data”, Computational Linguistics & Chinese Language Processing 9, 45-86, (2012)
  • 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.
  • 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 contextual information,” JAMIA, 19(5): 888-896, (2012)
  • Cheng-Wei Shih, Cheng-Wei Lee, Richard Tzong-Han Tsai, Wen-Lian Hsu, “Validating Contradiction in Texts Using Online Co-Mention Pattern CheckingACM Transactions on Asian Language Information Processing (TALIP), Volume 11 Issue 4, December 2012, pp. 17:1-12:21, (2012).
  • 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, 7(6): e37706, (2012).
  • 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, Issue 4, e35018, April (2012).
  • 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, Issue 3, e33340, March (2012).
  • 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.
  • 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, 6(5): e20199, (2011).
  • 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 12:471, (2011).
  • 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 6(12): e27872, (2011).
  • 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 first published online June 17, 2011 doi:10.1093/bioinformatics/btr358 (2011)
  • 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 Acid Research 39, D347-D355, (2011).
  • Hsin-Nan Lin, Ting-Yi Sung and Wen-Lian Hsu,”Identification of Essential Residues from Protein Secondary Structure Prediction and Applications,” in Sequence and Genome Analysis: Methods and Applications, Z. Zhao, Editor., iConcept Press.(2010)
  • Wei-Chao Chang, Chuan-Kai Chou, Chih-Chiang tsou, S.-H. Li, Chein-Hung Chen, Yu-Xing Zhuo, Wen-Lian Hsu and Chung-Hsuan Chen, “Comparative Proteomic Analysis of Proteins Involved in the Tumorigenic Process of Seminal Vesicle Carcinoma in Transgenic Mice,” International Journal of Proteomics 2010, Article ID 726968, (2010).
  • 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 9, 5582-5597, (2010).
  • Hsin-Nan Lin, Ting-Yi Sung, Shinn-Ying Ho, Wen-Lian Hsu, “Improving protein secondary structure prediction based on short subsequences with local structure similarity,” BMC Genomics 11(Suppl 4):S4, (2010).
  • Dai, H.-J., Chang, Y.-C., Tsai, R.T.-H. and Hsu, W.-L., “New challenges for biological text-mining in the next decade,” Journal of Computer Science and Technology, 25, 169-179, (2010).
  • Chih-Chiang Tsou, Chia-Feng Tsai, Ying-Hao Tsui, Putty-Reddy Sudhir, Yi-Ting Wang, Yu-Ju Chen, Jeou-Yuan Chen, Ting-Yi Sung*, and Wen-Lian Hsu*, “IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation,” Molecular & Cellular Proteomics,  9, 131-144, (2010)
  • Richard Tzong-Han Tsai, Po-Ting Lai, Hong-Jie Dai, Chi-Hsin Huang, Yue-Yang Bow, Yen-Ching Chang, Wen-Harn Pan, and Wen-Lian Hsu*, “HypertenGene: Extracting key hypertension genes from biomedical literature with position and automatically-generated template features,” BMC Bioinformatics, 10(Suppl 15):S9, 3 December (2009).
  • Hsin-Nan Lin, Ching-Tai Chen, Ting-Yi Sung, Shinn-Ying Ho and WenLian Hsu, “Protein subcellular localization prediction of eukaryotes using a knowledge-based approach,” BMC Bioinformatics, 10(Suppl 15):S8, December 3, (2009) .[slides]
  • Chorng-Shyong Ong, Min-Yuh Day and Wen-Lian Hsu, “The measurement of user satisfaction with question answering systems,” Information & Management , Volume 46, Issue 7, pp. 397-403, October, (2009).
  • 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 Vol. 37, No. suppl_2 W661-W669e, June 15, (2009).
  • 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 25(8), 996-1003, February 25, (2009).
  • Ke-Shiuan Lynn, Li-Lan Li, Yen-Ju Lin, Chiuen-Huei Wang, Shu-Hui Sheng, Ju-Hwa Lin, Wayne Liao, Wen-Lian Hsu*, Wen-Harn Pan*, “A Neural Network Model for Constructing Endophenotypes of Common Complex Diseases – An Application to Male Young-onset Hypertension Microarray Data.” Bioinformatics 25(8), 981-988, February 23, (2009).
  • Ryan T.K. Lin, Justin Liang-Te Chiu, Hong-Jie Dai, Richard Tzong-Han Tsai, Min-Yuh Day, and Wen-Lian Hsu, “A supervised learning approach to biological question answering,” Integrated Computer-Aided Engineering 16, 271–281, August, (2009).
  • 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 16, 259-269, August, (2009).
  • 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, 36(2), Part 2, 3990-3995, March, (2009).
  • 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 , 35:4, 2123-2131, (2008)
  • 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 24(23):2691-2697, (2008).
  • Cheng-Wei Cheng, Emily Chia-Yu Su, Ting-Yi Sung and Wen-Lian Hsu, “Predicting RNA-binding sites of proteins using support vector machines and evolutionary information,” BMC Bioinformatics 9(Suppl 12):S6, (2008).
  • Jia-Ming Chang, Emily Chia-Yu Su, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu, “PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis,” PROTEINS: Structure, Function, and Bioinformatics 72, 693-710, (2008).
  • 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 7, 487-496, (2008).
  • 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 9(Suppl 12):S18,  (2008).
  • 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 Acid Research 36, W390-W398, (2008).
  • 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, 9(Suppl 1):S3, (2008).
  • 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 , Issue 4, November 2008, pp. 12:1-12:29, (2008).
  • Cheng-Wei Lee, Yi-Hsun Lee, and Wen-Lian Hsu, “ Exploring Shallow Answer Ranking Features in Cross-Lingual and Monolingual Factoid Question Answering,” Computational Linguistics & Chinese Language Processing 13, 1-26, (2008).
  • Chia-Wei Wu, Richard Tzong-Han Tsai, Cheng-Wei Lee,Wen-Lian Hsu, “ Web Taxonomy Integration System with Hierarchical Shrinkage and Fine-Grained Relations,” Expert Systems With Applications , 35(4), 2123-2131, (2008).
  • 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.35, W707-712, (2007).
  • 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, Chang-Han Chen, Gen-Cher Lee, Der-Tsai Lee, Yow-Ling Shiue, Chang-Wei Yeh, Chao-Hui Chang, Cheng-Yan Kao and Chi-Ying Huang, “Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online),” BMC Bioinformatics 8:66, (2007).
  • 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, 8:330, (2007). [slides]
  • 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, Issue 1, February 2007, pp.152-167. (2007)
  • 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 8, 289-298, (2007).
  • 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 48, , 582-601, (2007).
  • 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 13, 229-244 (2006); also, in Proceedings of the International conference on Research in Computational Molecular Biology (RECOMB’05), acceptance rate: 18% (39/217).
  • 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, 8:325, (2007).
  • 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, 2006. 5(9): p.2328-2338
  • Ching-Tai Chen, Hsin-Nan Lin, Ting-Ying Sung and Wen-Lian Hsu, “A Knowledge-based Approach to Protein Local Structure Prediction,Journal of Bioinformatics and Computational Biology, Vol. 4, (2006), 1287-1307, also in Proceedings of Asia Pacific Bioinformatics Conference (APBC).
  • 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 7(Suppl 5) :S11, (2006).
  • 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. 7:92, (2006) (Impact Factor: 4.96).
  • 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 30 (1), 117-128, (2006).
  • Chun-Hung Lu, Guey-Fa Chiou, Min-Yuh Day, Chorng-Shyong Ong, Wen-Lian Hsu, “Using Instant Messaging to Provide an Intelligent Learning Environment.Intelligent Tutoring Systems, Lecture Notes in Computer Science 4053, 575-583, (2006).[slides]
  • 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 33(14), 4593-4601, (2005).
  • 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 21, 3227-3233, (2005).
  • Wu, C.-W., Tsai, T.-H. and Hsu, W.-L. , “Learning to Integrate Web Taxonomies with Fine-Grained Relations: A Case Study Using Maximum Entropy Model”, AIRS-2005. Springer, Jeju Island, Korea. (2005) acceptance rate: 23% (32/136) [slides]
  • Chun-Hung Lu, Shih-Hung Wu, LiongYu Tu, Wen-Lian Hsu, “Ontological Support in Modeling Learners’ Problem Solving Process,” Journal of Educational Technology & Society 8(4), 64-74, (2005).
  • 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 32(17):5059-5065, (2004).
  • Jia-Lin Tsai, Gladys Hsieh and Wen-Lian Hsu, “Auto-Generation of NVEF Knowledge in Chinese,” Computational Linguistics & Chinese Language Processing 9, 41-64, (2004)
  • Tzong-Han Tsai, Shih-Hung Wu, Cheng-Wei Lee, Cheng-Wei Shih and Wen-Lian Hsu, “Mencius: A Chinese Named Entity Recognizer Based on a Maximum Entropy Framework ,” Computational Linguistics & Chinese Language Processing 9, 65-82, (2004).
  • W. F. Lu and W. L. Hsu, “A Test for Interval Graphs on Noisy Data,Lecture Notes in Computer Science 2647, 195-208, (2003).
  • 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 10(5), (2003), 709-735; also appeared in Lecture Notes in Computer Science 1276
  • W. L. Hsu and R. McConnell, “PC-trees and circular-ones arrangementsTheoretical Computer Science 296(1), 99-116, (2003).
  • Jia-Lin Tsai, Wen-Lian Hsu and Jeng-Woei Su, “Word Sense Disambiguation and Sense-Based NV Event Frame Identifier”,  Computational Linguistics & Chinese Language Processing 7, (2002), 29-46.
  • W. L. Hsu, “A simple test for the consecutive ones property,” Journal of Algorithms 43, 1-16, (2002).
  • W. L. Hsu and Yi-Shiou Chen, “On Phoneme-to-Character Conversion Systems in Chinese Processing,” invited paper, Journal of Chinese Institute of Engineers 5, (1999), 573-579.
  • W. L. Hsu and T. H. Ma, “ Fast and simple algorithms for recognizing chordal comparability graphs and interval gragh,” SIAM J. Comput. 28, 1004-1020, (1999).
  • W. K. Shih and W. L. Hsu, “A new planarity test,Theoretical Computer Science 223, 179-191, (1999).
  • Y. K. Wang , Y. S. Chen and W. L. Hsu, “A knowledge-based approach for natural language processing,” Technical Report, (1998).
  • W. L. Hsu, “Perfect graphs,” Advances in the Theory of Computation and Computational Mathematics 1, 81-122, (1996).
  • W. L. Hsu, “O(mn) algorithms for the recognition and isomorphism problems on circular-arc graphs,” SIAM J. Comput24, 411-439, (1995).
  • W. L. Hsu and J. P. Spinrad, “Independent sets in circular-arc graphs,” J. Algorithms 19, 145-160, (1995).
  • W. L. Hsu, “Chinese parsing in a phoneme-to-character conversion system   based on semantic pattern matching,” International Journal on Computer Processing of Chinese and Oriental Languages 40, (1995), 227-236.
  • K. H. Tsai and W. L. Hsu, “Fast algorithms for the minimum dominating set problem on permutation graphs,” Algorithmica 9, (1993), 601-614.
  • W. L. Hsu, “A new test for interval graphs,” Lecture Notes in Computer Science 657, 11-16, (1992).
  • W. K. Shih, W. L. Hsu and T. C. Chen, “An O(n2 logn ) algorithm for the Hamiltonian cycle problem on circular-arc graphs,” SIAM J. Comput 21, 1026-1046, (1992).
  • W. L. Hsu and K. H. Tsai, “Linear time algorithms on circular-arc graphs,” Information processing Letters 40, 123-129, (1991).
  • 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, 129-134, (1989).
  • W. K. Shih and W. L. Hsu, “An O(n1.5) algorithm for coloring proper circular-arc graphs,” Discrete Applied Math 25, 321-323, (1989).
  • C. Gabor, W. L. Hsu and K. Supowit, “Recognizing circle graphs in polynomial time,” J. Assoc. Comput. Machin., 435-473, (1989).
  • W. L. Hsu, “The coloring and maximum independent set problems on planar perfect graphs,” J. Assoc. Comput. Machin., 535-563, (1988).
  • W. L. Hsu, “Recognizing planar perfect graphs,” J. Assoc. Comput. Machin. 34, 255-288, (1987).
  • W. L. Hsu, “Decomposition of perfect graphs,” J. Combin. Theory (B) 43, 70-94, (1987).
  • W. L. Hsu, “Coloring planar perfect graphs by decomposition,” Combinatorica 6 (4), 381-385, (1986).
  • W. L. Hsu, “Maximum weight clique algorithms for circle graphs and circular-arc graphs,” SIAM J. Computing 14, 224-231, (1985).
  • W. L. Hsu, “Berge’s strong perfect graph conjecture on special graphs: A Survey,” Annals of Discrete Math. 21, 107-117, (1984).
  • W. L. Hsu, “Approximation algorithms for the assembly line crew scheduling problem,” Math. of Operations Research 9, 376-383, (1984).
  • 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 Math. 21, 317-329, (1984).
  • Naamad, W. L. Hsu and D. T. Lee, “On the maximum empty rectangle problem,” Discrete Applied Math. 8, 267-277, (1984).
  • W. L. Hsu, “On the general feasibility test of scheduling lot sizes for several products on one machine,’ Management Science 29, 93-105, (1983).
  • W. L. Hsu, “The distance-domination numbers of trees,” Operations Research Letters 1, (3), 96-100, (1982).
  • W. L. Hsu and G. L. Nemhauser, “A polynomial algorithm for the minimum weighted clique cover problem on claw-free perfect graphs,” (with G. L. Nemhauser), Discrete Math. 38, 65-71, (1982).
  • W. L. Hsu, Y. Ikura and G. L. Nemhauser, “A polynomial algorithm for maximum weighted vertex packing on graphs without long odd cycles,” Math. Prog. 20, 225-232, (1981).
  • W. L. Hsu, “How to color claw-free perfect graphs,” Annals of Discrete Math. 11, 189-197, (1981).
  • W. L. Hsu and G. L. Nemhauser, “Algorithm for minimum covering by cliques and maximum cliques in claw-free perfect graphs,” Discrete Math. 37, 181-191, (1981).
  • W. L. Hsu and G. L. Nemhauser, “Easy and hard bottleneck location problems,” Discrete Applied Math.   1, 209-215, (1979).