期刊論文

Journal papers

  • Yung-Chun Chang, Siu Hin Ng, Jung-Peng Chen, Yu-Chi Liang, Wen-Lian Hsu, “Semantic Template-based Convolutional Neural Network for Text Classification”, ACM Transactions on Asian and Low-Resource Language Information Processing, Volume 22, Issue 11, pp 1–21, November 2023
  • Sheng-Jie Lin, Wen-Chao Yeh, Yu-Wen Chiu, Yung-Chun Chang*, Min-Huei Hsu, Yi-Shin Chen, and Wen-Lian Hsu, “A BERT-based Ensemble Learning Approach for the BioCreative VII Challenges: Full-text Chemical Identification and Multi-label Classification in PubMed Articles,” Database (Oxford) Volume 2022, baac056, July 2022
  • Singh, O., Hsu, W. L. & Su, E. C. Y., “Ileukin10pred: A computational approach for predicting il-10-inducing immunosuppressive peptides using combinations of amino acid global features,” Biology 5: 11:1, December 2021
  • Singh, O., Hsu, W. L. & Su, E. C. Y., “ Co-AMPpred for in silico-aided predictions of antimicrobial peptides by integrating composition-based features,” BMC Bioinformatics 22:389, July 2021
  • Hsin-Nan Lin, Wen-Lian Hsu, “MapCaller – An Integrated and Efficient Tool for Short-Read Mapping and Variant Calling Using High-Throughput Sequenced Data,” Journal of Bioinformatics and Comparative Genomics 4: 1-11, May 2021
  • Neha Warikoo, Yung-Chun Chang, and Wen-Lian Hsu, “LBERT: Lexically-aware Transformers based Bidirectional Encoder Representation model for learning Universal Bio-Entity Relations,” Bioinformatics, April 2021.
  • 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,” Journal of the Association for Information Science and Technology, Volume 72, Issue 1, August 2020.
  • 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 Issue D1, Pages D148–D154, January 2020.
  • Hsin-Nan Lin, Wen-Lian Hsu, “GSAlign: an efficient sequence alignment tool for intra-species genomes,” BMC Genomics 21, 182 , September 2020.
  • 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 (Oxford), Volume 21, Issue 6, Pages 2219–2238, November 2020.
  • CW Cheng, CY Wu, WL Hsu, CH Wong, ““Programmable One-pot Synthesis of Oligosaccharides,” Biochemistry, 2019.
  • 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.
  • Cheng-Wei Cheng, Yixuan Zhou, Wen-Harn Pan, Supriya Dey, Chung-Yi Wu, Wen-Lian Hsu, Chi-Huey Wong, “Hierarchical and Programmable One-Pot Oligosaccharide Synthesis,” J. Vis. Exp. (151), e59987, doi: 10.3791/59987, 2019.
  • 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), February 2019.
  • 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, JAMIA (Journal of American Medical Informatics Association), 26(11) : 1227-1236, June 2019.
  • Neha Warikoo, Yung-Chun Chang, and Wen-Lian Hsu, LPTK: A Linguistic Pattern-Aware Dependency Tree Kernel Approach for the Bio-Creative VI CHEMPROT Task, Database (Oxford), October 2018.
  • Cheng-Wei Cheng, Yixuan Zhou, Wen-Harn Pan, Supriya Dey, Chung-Yi Wu, Wen-Lian Hsu, Chi-Huey Wong, “Hierarchical and programmable one-pot synthesis of oligosaccharides,” Nature Communications, 9, Article number:5202, December 2018.
  • 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, 10:64, December 2018.
  • 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.
  • Hsin-Nan Lin and Wen-Lian Hsu, “DART: a fast and accurate RNA-seq mapper with a partitioning strategy,” Bioinformatics, volume 34, number 2, page 190–197, January 2018.
  • 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 quantitation using DYAMOND algorithm,” Analytical Chemistry, volume 89, number 24, pages 13128–13136, December 2017.
  • 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.
  • 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,” Bioinformatics 33, number 15, page 2281–2287, August 2017.
  • 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 33, Issue 4, Pages 656-679, February 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, Chun-Han Chu, Yu-Chen Su, Chien Chin Chen, and Wen-Lian Hsu, “PIPE: a protein–protein interaction passage extraction module for BioCreative challenge,” Database (Oxford), volume 2016, pages baw101, August 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, 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, vol. 21, Issue 2, pp. 391-401, 2017.
  • 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 (Journal of American Medical Informatics Association), 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 Checking” ACM 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 arrangements” Theoretical 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).