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	1.	Proceedings Prediction of B-cell epitopes using evolutionary information and propensity scales Scott Lin, Cheng-Wei Cheng, Emily Su BMC Bioinformatics 2013, 14(Suppl 2):S10 (21 January 2013) Abstract \| Full text \| PDF
	2.	Research article *Evolution of cis-regulatory elements in yeast de novo and duplicated new genes* Zing Tsung-Yeh Tsai, Huai-Kuang Tsai, Jen-Hao Cheng, Chih-Hsu Lin, Yuan-Fan Tsai, Daryi Wang BMC Genomics 2012, 13:717 (21 December 2012) Abstract \| Full text \| PDF \| PubMed
	3.	Proceedings A de novo next generation genomic sequence assembler based on string graph and MapReduce cloud computing framework Yu-Jung Chang, Chien-Chih Chen, Chuen-Liang Chen, Jan-Ming Ho BMC Genomics 2012, 13(Suppl 7):S28 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	4.	Proceedings A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on a pedigree En-Yu Lai, Wei-Bung Wang, Tao Jiang, Kun-Pin Wu BMC Bioinformatics 2012, 13(Suppl 17):S19 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	5.	Proceedings Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing Emily Su, Jia-Ming Chang, Cheng-Wei Cheng, Ting-Yi Sung, Wen-Lian Hsu BMC Bioinformatics 2012, 13(Suppl 17):S13 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	6.	Research Label-free quantitative proteomics of CD133-positive liver cancer stem cells Sheng-Ta Tsai, Chih-Chiang Tsou, Wan-Yu Mao, Wei-Chao Chang, Hsin-Ying Han, Wen-Lian Hsu, Chung-Leung Li, Chia-Ning Shen, Chung-Hsuan Chen Proteome Science 2012, 10:69 (21 November 2012) Abstract \| Full text \| PDF \| PubMed
	7.	Research Cancer classification: Mutual information, target network and strategies of therapy Wen-Chin Hsu, Chan-Cheng Liu, Fu Chang, Su-Shing Chen Journal of Clinical Bioinformatics 2012, 2:16 (2 October 2012) Abstract \| Full text \| PDF \| PubMed
	8.	Research article *Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena)* Hsiao-Pei Lu, Yu-bin Wang, Shiao-Wei Huang, Chung-Yen Lin, Martin Wu, Chih-hao Hsieh, Hon-Tsen Yu BMC Genomics 2012, 13:466 (10 September 2012) Abstract \| Full text \| PDF \| PubMed
	9.	Database MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature Yu-Ching Fang, Po-Ting Lai, Hong-Jie Dai, Wen-Lian Hsu BMC Bioinformatics 2011, 12:471 (14 December 2011) Abstract \| Full text \| PDF \| PubMed
	10.	Research Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization Cheng-Ju Kuo, Maurice HT Ling, Chun-Nan Hsu BMC Bioinformatics 2011, 12(Suppl 8):S6 (3 October 2011) Abstract \| Full text \| PDF \| PubMed
	11.	Research The gene normalization task in BioCreative III Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illes Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sergio Matos, David Campos, Karin Verspoor, Kevin M Livingston, W Wilbur BMC Bioinformatics 2011, 12(Suppl 8):S2 (3 October 2011) Abstract \| Full text \| PDF \| PubMed
	12.	Research Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses Tzi-Yuan Wang, Hsin-Liang Chen, Mei-Yeh J Lu, Yo-Chia Chen, Huang-Mo Sung, Chi-Tang Mao, Hsing-Yi Cho, Huei-Mien Ke, Teh-Yang Hwa, Sz-Kai Ruan, Kuo-Yen Hung, Chih-Kuan Chen, Jeng-Yi Li, Yueh-Chin Wu, Yu-Hsiang Chen, Shao-Pei Chou, Ya-Wen Tsai, Te-Chin Chu, Chun-Chieh A Shih, Wen-Hsiung Li, Ming-Che Shih Biotechnology for Biofuels 2011, 4:24 (17 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	13.	Research Concurrent image-guided intensity modulated radiotherapy and chemotherapy following neoadjuvant chemotherapy for locally advanced nasopharyngeal carcinoma Pei-Wei Shueng, Bing-Jie Shen, Le-Jung Wu, Li-Jen Liao, Chi-Huang Hsiao, Yu-Chin Lin, Po-Wen Cheng, Wu-Chia Lo, Yee-Min Jen, Chen-Hsi Hsieh Radiation Oncology 2011, 6:95 (13 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	14.	Research article Evidence of association between Nucleosome Occupancy and the Evolution of Transcription Factor Binding Sites in Yeast Krishna BS Swamy, Wen-Yi Chu, Chun-Yi Wang, Huai-Kuang Tsai, Daryi Wang BMC Evolutionary Biology 2011, 11:150 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	15.	Research article Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles Richard Tsai, Po-Ting Lai BMC Bioinformatics 2011, 12:60 (23 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	16.	Research UMARS: Un-MAppable Reads Solution Sung-Chou Li, Wen-Ching Chan, Chun-Hung Lai, Kuo-Wang Tsai, Chun-Nan Hsu, Yuh-Shan Jou, Hua-Chien Chen, Chun-Hong Chen, Wen-chang Lin BMC Bioinformatics 2011, 12(Suppl 1):S9 (15 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	17.	Proceedings Discovery and characterization of medaka miRNA genes by next generation sequencing platform Sung-Chou Li, Wen-Ching Chan, Meng-Ru Ho, Kuo-Wang Tsai, Ling-Yueh Hu, Chun-Hung Lai, Chun-Nan Hsu, Pung-Pung Hwang, Wen-chang Lin BMC Genomics 2010, 11(Suppl 4):S8 (2 December 2010) Abstract \| Full text \| PDF \| PubMed
	18.	Proceedings UPS 2.0: unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/ genomic level Shu-Hwa Chen, Chen-Zen Lo, Sheng-Yao Su, Bao-Han Kuo, Chao A Hsiung, Chung-Yen Lin BMC Genomics 2010, 11(Suppl 4):S6 (2 December 2010) Abstract \| Full text \| PDF \| PubMed
	19.	Proceedings Improving protein secondary structure prediction based on short subsequences with local structure similarity Hsin-Nan Lin, Ting-Yi Sung, Shinn-Ying Ho, Wen-Lian Hsu BMC Genomics 2010, 11(Suppl 4):S4 (2 December 2010) Abstract \| Full text \| PDF \| PubMed
	20.	Research article Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency Francis C Weng, Chien-Hao Su, Ming-Tsung Hsu, Tse-Yi Wang, Huai-Kuang Tsai, Daryi Wang BMC Bioinformatics 2010, 11:565 (18 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	21.	Research article Sequence features involved in the mechanism of 3' splice junction wobbling Kuo-Wang Tsai, Wen-Ching Chan, Chun-Nan Hsu, Wen-chang Lin BMC Molecular Biology 2010, 11:34 (7 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	22.	Research A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles Chia-Hao Chin, Shu-Hwa Chen, Chin-Wen Ho, Ming-Tat Ko, Chung-Yen Lin BMC Bioinformatics 2010, 11(Suppl 1):S25 (18 January 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	23.	Research Learning to predict expression efficacy of vectors in recombinant protein production Wen-Ching Chan, Po-Huang Liang, Yan-Ping Shih, Ueng-Cheng Yang, Wen-chang Lin, Chun-Nan Hsu BMC Bioinformatics 2010, 11(Suppl 1):S21 (18 January 2010) Abstract \| Full text \| PDF \| PubMed
	24.	Proceedings HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features Richard Tsai, Po-Ting Lai, Hong-Jie Dai, Chi-Hsin Huang, Yue-Yang Bow, Yen-Ching Chang, Wen-Harn Pan, Wen-Lian Hsu BMC Bioinformatics 2009, 10(Suppl 15):S9 (3 December 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	25.	Proceedings Protein subcellular localization prediction of eukaryotes using a knowledge-based approach Hsin-Nan Lin, Ching-Tai Chen, Ting-Yi Sung, Shinn-Ying Ho, Wen-Lian Hsu BMC Bioinformatics 2009, 10(Suppl 15):S8 (3 December 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central