Che-Wei Chang, Wen-Bin Lee, An Chen-Deng, Tsunglin Liu, Joseph T. Tseng and Darby Tien-Hao Chang*, “Light-RCV: a lightweight read coverage viewer for next generation sequencing data”, accepted by BMC Genomics. (SCI) (MOST 104-2628-E-006-004-MY3)

Wei-Sheng Wu, Ming-Liang Wei, Chia-Ming Yeh and Darby Tien-Hao Chang*, “A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae”, BMC Systems Biology, 8(Suppl 5):S9, 2014. (SCI) (NSC 102-2221-E-006-085-MY2)

Hao Wang, Wen-Hao Chiang, Chia-Wei Chou and Darby Tien-Hao Chang*, “Integrating Phosphorylation and Catalytic Sites Information into AH-DB”, The SIJ Transactions on Computer Science Engineering & its Applications, 2(3), 77-81, 2014. (NSC 102-2221-E-006-085-MY2)

Tzu-Wen Lin, Jian-Wei Wu and Darby Tien-Hao Chang*, “Combining Phylogenetic Profiling-Based and Machine Learning-Based Techniques to Predict Functional Related Proteins,” PLOS ONE, 8, e75940, 2013. (SCI) (NSC 102-2221-E-006-085-MY2)

Jung-Hsien Chiang*, Darby Tien-Hao Chang, Hung-Yu Kao, “Introduction to the 23rd International Conference on Genome Informatics (GIW2012),” Gene, 518(1), 1, 2013. (SCI) (NSC 101-2221-E-006-264-)

Chien-Yu Chen, Ting-Ying Chien, Chih-Kang Lin, Chih-Wei Lin, Yi-Zhong Weng and Darby Tien-Hao Chang*, “Predicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound Structures,” PLOS ONE, 7(2), e30446, 2012. (SCI) (NSC 98-2627-B-002-011)

Darby Tien-Hao Chang*, Chi-Yeh Wu and Chen-Yu Fan, “A study on promoter characteristics of head-to-head genes in Saccharomyces cerevisiae,” BMC Genomics, 13(Suppl 1):S11, 2012. (SCI) (NSC 99-2628-E-006-017-)

Yi-Zhong Weng, Darby Tien-Hao Chang*, Yu-Feng Huang and Chih-Wei Lin, “A study on the flexibility of enzyme active sites,” BMC Bioinformatics, 12(Suppl 1):S32, 2011. (SCI) (NSC 98-2221-E-006-180)

Darby Tien-Hao Chang, Jung-Hsin Lin, Chih-Hung Hsieh and Yen-Jen Oyang*, “On the design of optimization algorithms for prediction of molecular interactions,” International Journal on Artificial Intelligence Tools, 19, 3, 267-280, 2010. (SCI) (NSC 97-2627-P-001-002-, 98-2627-B-002-011- and 98-2221-E-006-180-)

Chi-Yuan Yu, Lih-Ching Chou and Darby Tien-Hao Chang*, “Predicting protein-protein interactions in unbalanced data using the primary structure of proteins,” BMC Bioinformatics, 11:167, 2010. (SCI) (NSC 98-2627-B-002-011 and 98-2221-E-006-180)

Chih-Hung Hsieh, Darby Tien-Hao Chang*, Cheng-Hao, Hsueh, Chi-Yeh Wu and Yen-Jen Oyang, “Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm,” BMC Bioinformatics, 11(Suppl 1):S52, 2010. (SCI) (NSC 97-2627-P-001-002, 96-2320-B-006-027-MY2 and 96-2221-E-006-232-MY2)

Darby Tien-Hao Chang*, Yu-Tang Syu and Po-Chang Lin, “Predicting the protein-protein interactions using primary structures with predicted protein surface,” BMC Bioinformatics, 11(Suppl 1):S3, 2010. (SCI) (NSC 97-2627-P-001-002, 96-2320-B-006-027-MY2 and 96-2221-E-006-232-MY2)

Darby Tien-Hao Chang*, Hsuan-Yu Huang, Yu-Tang Syu and Chih-Peng Wu, “Real value prediction of protein solvent accessibility using enhanced PSSM features,” BMC Bioinformatics, 9(Suppl 12):S12, 2008. (SCI) (NSC 97-2627-P-001-002, 96-2320-B-006-027-MY2 and 96-2221-E-006-232-MY2)

Darby Tien-Hao Chang*, Chih-Ching Wang and Jian-Wei Chen, “Using a kernel density estimation based classifier to predict species-specific microRNA precursors,” BMC Bioinformatics, 9(Suppl 12):S2, 2008. (SCI) (NSC 97-2627-P-001-002, 96-2320-B-006-027-MY2 and 96-2221-E-006-232-MY2)

Darby Tien-Hao Chang, Yu-Yen Ou, Hao-Geng Hung, Meng-Han Yang, Chien-Yu Chen and Yen-Jen Oyang*, “Prediction of protein secondary structures with a novel kernel density estimation based classifier,” BMC Research Notes, 1:51, 2008. (NSC 96-2320-B-006-027-MY2 and 96-2221-E-006-232-MY2)

Che-Wei Chang, Wen-Bin Lee, An Chen-Deng, Tsunglin Liu, Joseph T. Tseng and Darby Tien-Hao Chang, “Light-RCV: a lightweight read coverage viewer for next generation sequencing data”, in proceedings of the GIW/InCoB 2015, Tokyo, Japan, September 9-11, 2015. (GIW/InCoB 2015)

Chia-Pin Kang, Hung-Chi Tu, Tzu-Fun Fu and Darby Tien-Hao Chang, “An Automatic Method to Calculate Heartbeat from Zebrafish Embryo Videos ”, in poster proceedings of the GIW/InCoB 2015, Tokyo, Japan, September 9-11, 2015. (GIW/InCoB 2015)

Wei-Sheng Wu, Ming-Liang Wei, Chia-Ming Yeh and Darby Tien-Hao Chang, “A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae”, in proceedings of the 25th International Conference on Genome Informatics, Tokyo, Japan, December 15-17, 2014. (GIW / ISCB-Asia 2014)

Darby Tien-Hao Chang, Guan-Yu Shiu and Yu-Chieh Sun, “Predicting Cis-Regulatory Modules by Method Integration,” in proceedings of the 11th IEEE International Conference on Control & Automation, Taichung, Taiwan, June 18-20, 2014. (ICCA 2014)

Darby Tien-Hao Chang, Chia-Ming Yeh, Ming Liang Wei and Wei-Sheng Wu, “A Metric for Computing Regulatory Similarity of Two Genes,” in proceedings of the 11th IEEE International Conference on Control & Automation, Taichung, Taiwan, June 18-20, 2014. (ICCA 2014)

Darby Tien-Hao Chang, Wen-Hao Chiang and Hao Wang, “An enhanced database of protein structure pairs before and after binding,” in proceedings of the Annual Conference on Engineering & Information Technology, Tokyo, Japan, March 28-30, 2014. (ACEAIT 2014)

Tzu-Wen Lin and Darby Tien-Hao Chang, “Combining Phylogenetic Profiling-based and Machine Learning-based Techniques to Predict Functional Related Proteins,” in proceedings of the International Symposium on Evolutionary Genetic and Bioinformatics, Taichung, Taiwan, November 8-9, 2013. (ISEGB 2013)

Jhih-Jheng Zeng and Darby Tien-Hao Chang, “A mobile game for biomedical literature mining,” in poster proceedings of the International Symposium on Evolutionary Genetic and Bioinformatics, Taichung, Taiwan, November 8-9, 2013. (ISEGB 2013)

Shao-Ting Jang and Darby Tien-Hao Chang, “A systematic analysis on regulatory characteristics of genes with protein-protein interactions,” in poster proceedings of the International Symposium on Evolutionary Genetic and Bioinformatics, Taichung, Taiwan, November 8-9, 2013. (ISEGB 2013)

Darby Tien-Hao Chang, Wen-Hao Chiang and Chia-Wei Chou, “Identifying structure variation profiles corresponding to biological processes and functions,” in poster proceedings of the International Symposium on Evolutionary Genetic and Bioinformatics, Taichung, Taiwan, November 8-9, 2013. (ISEGB 2013)

Darby Tien-Hao Chang, Wen-Hao Chiang and Hao Wang, “An enhanced repository of protein structure pairs before and after binding,” in poster proceedings of the 2013 (35th) Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Osaka, Japan, July 3-7, 2013. (EMBC 2013)

Darby Tien-Hao Chang, Yu-Hsiu Hung, Shu-Chun Li, Hsaing-Hung Cheng, Hao Wang, Chia-Wei Chou and Yen-Cheng Tang, “An orange social platform for young people,” in proceedings of the 2013 International Conference on Orange Technologies, Tainan, Taiwan, March 12-16, 2013. (ICOT 2013)

Chen-Yu Fan, Yi-Han Bai, Cheng-Yi Huang, Tsung-Ju Yao and Darby Tien-Hao Chang, “PRASA: an integrated web server that analyzes protein interaction types,” in proceedings of the 23th International Conference on Genome Informatics, Tainan, Taiwan, December 12-14, 2012. (GIW 2012)

Darby Tien-Hao Chang, Wen-Si Li, Yi-Han Bai and Wei-Sheng Wu, “YGA: identifying distinct biological features between yeast gene sets,” in proceedings of the 23th International Conference on Genome Informatics, Tainan, Taiwan, December 12-14, 2012. (GIW 2012)

Jung-Hsien Chiang, Darby Tien-Hao Chang, Hung-Yu Kao, “Introduction to the 23rd International Conference on Genome Informatics (GIW2012),” in proceedings of the 23th International Conference on Genome Informatics, Tainan, Taiwan, December 12-14, 2012. (GIW 2012)

Guan-Yu Shiu and Darby Tien-Hao Chang, “Combining Multiple Cis-regulatory Module Predictors to Improve Prediction Accuracy,” in poster proceedings of the International Symposium on Evolutionary Genetic and Bioinformatics, Kaohsiung, Taiwan, October 19-21, 2012. (ISEGB 2012)

Hao Wang and Darby Tien-Hao Chang, “Molecule society: elucidating the complicated relations among biological molecules from literature and structural information,” in poster proceedings of the International Symposium on Evolutionary Genetic and Bioinformatics, Kaohsiung, Taiwan, October 19-21, 2012. (ISEGB 2012)

Jhih-Jheng Zeng and Darby Tien-Hao Chang, “Integrating an Android App and social network for mining biomedical literature,” in poster proceedings of the International Symposium on Evolutionary Genetic and Bioinformatics, Kaohsiung, Taiwan, October 19-21, 2012. (ISEGB 2012)

Shao-Ting Jang and Darby Tien-Hao Chang, “A systematic analysis on regulatory characteristics of genes with protein-protein interactions,” in poster proceedings of the International Symposium on Evolutionary Genetic and Bioinformatics, Kaohsiung, Taiwan, October 19-21, 2012. (ISEGB 2012)

Tzu-Wen Lin and Darby Tien-Hao Chang, “Predicting Protein-protein Interactions Based on Frequent Short Sequences in Proteome,” in poster proceedings of the International Symposium on Evolutionary Genetic and Bioinformatics, Kaohsiung, Taiwan, October 19-21, 2012. (ISEGB 2012)

You-Jie Sun and Darby Tien-Hao Chang, “Enhancing cis-regulatory model prediction by including interaction information between transcription factors,” in poster proceedings of the International Symposium on Evolutionary Genetic and Bioinformatics, Kaohsiung, Taiwan, October 19-21, 2012. (ISEGB 2012)

Chien-Ju Li, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu and Darby Tien-Hao Chang, “SIMGraph: Simplifying contig graph to improve de novo genome assembly using next-generation sequencing data,” in proceedings of the XXXII International Conference on Bioinformatics, Computational and Systems Biology, Tokyo, Japan, May 29-30, 2012. (ICBCSBB 2012)

Darby Tien-Hao Chang, Chih-Yun Chiang, Fung-Wei Lin and Chen-Yu Fan, “Studying Disorder-to-Order Transitions from Structural Analysis,” in proceedings of the 1st IEEE International Conference on Computational Advances in Bio and medical Sciences, Orlando, Florida, February 3-5, 2011. (ICCABS 2011)

Yi-Zhong Weng, Darby Tien-Hao Chang, Yu-Feng Huang and Chih-Wei Lin, “A study on the flexibility of enzyme active sites,” in proceedings of the 9th Asia Pacific Bioinformatics Conference, Incheon, Korea, January 11-14, 2011. (APBC 2011)

Chen-Hao Hsueh, Darby Tien-Hao Chang and Chih-Yun Chien, “Predicting DNA-binding Proteins using Disorder Information,” in poster proceedings of the 9th International Conference of Bioinformatics, Tokyo, Japan, Sepetmber 26-28, 2010. (InCoB 2010)

Ting-Ying Chien, Chien-Yu Chen, Chih-Kang Lin, Chih-Wei Lin, Cheng-Yi Huang and Darby Tien-Hao Chang, “Prediction of DNA-binding profiles by protein-DNA complexes,” in poster proceedings of the 9th International Conference of Bioinformatics, Tokyo, Japan, Sepetmber 26-28, 2010. (InCoB 2010)

Jian-Wei Wu, Darby Tien-Hao Chang and Chien-Ju Li, “Predicting Protein-protein Interactions using a Hybrid Approach,” in poster proceedings of the 9th International Conference of Bioinformatics, Tokyo, Japan, Sepetmber 26-28, 2010. (InCoB 2010)

Chih-Hung Hsieh, Darby Tien-Hao Chang, Cheng-Hao, Hsueh, Chi-Yeh Wu and Yen-Jen Oyang, “Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm,” in proceedings of the 8th Asia Pacific Bioinformatics Conference, Bangalore, India, January 18-21, 2010. (APBC 2010)

Darby Tien-Hao Chang, Yu-Tang Syu and Po-Chang Lin, “Predicting the protein-protein interactions using primary structures with predicted protein surface,” in proceedings of the 8th Asia Pacific Bioinformatics Conference, Bangalore, India, January 18-21, 2010. (APBC 2010)

Darby Tien-Hao Chang, Jung-Hsin Lin, Chih-Hung Hsieh and Yen-Jen Oyang, “On the Design of Optimization Algorithms for Prediction of Molecular Interactions,” in proceedings of the 9th International Conference on Bioinformatics and BioEngineering, Taichung, Taiwan, June 22-24, 2009. (BIBE 2009)

Chih-Hung Hsieh, Darby Tien-Hao Chang and Yen-Jen Oyang, “Data Classification with a Generalized Gaussian Components based Density Estimation Algorithm,” in poster Proceedings of the 2009 International Joint Conference on Neural Networks, Atlanta, Georgia, June 14-19, 2009. (IJCNN 2009)

Yi-Zhong Weng, Chien-Kang Huang, Yu-Feng Huang, Chi-Yuan Yu and Darby Tien-Hao Chang, “Introducing sequence-order constraint into prediction of protein binding sites with automatically extracted templates,” in proceedings of the 6th International Conference on Bioinformatics and Bioengineering, Tokyo, Japan, May 27-29, 2009. (ICBB 2009)

Darby Tien-Hao Chang, Hsuan-Yu Huang, Yu-Tang Syu and Chih-Peng Wu, “Real value prediction of protein solvent accessibility using enhanced PSSM features,” in proceedings of the 7th International Conference of Bioinformatics, Taipei, Taiwan, October 20-23, 2008. (InCoB 2008)

Darby Tien-Hao Chang, Chih-Ching Wang and Jian-Wei Chen, “Using a kernel density estimation based classifier to predict species-specific microRNA precursors,” in proceedings of the 7th International Conference of Bioinformatics, Taipei, Taiwan, October 20-23, 2008. (InCoB 2008)

Ting-Ying Chien, Darby Tien-Hao Chang and Chien-Yu Chen, “Catalytic Site Prediction Using E1DS Server,” in poster proceedings of the 7th Annual International Conference on Computational Systems Bioinformatics, Stanford, California, August 26-29, 2008. (CSB 2008)

Ting-Ying Chien, arby Tien-Hao Chang, Chien-Yu Chen, Yi-Zhong Weng, and Chen-Ming Hsu, “E1DS: catalytic site prediction based on 1-dimensional signatures of concurrent conservation,” in poster Proceedings of the 16th Annual International Conference Intelligent Systems for Molecular Biology, Toronto, Canada, July 19-23, 2008. (ISMB 2008)

Yen-Jen Oyang, Darby Tien-Hao Chang, Yu-Yen Ou, Hao-Geng Hung, and Chien-Yu Chen, “Prediction of Protein Secondary Structures with a Novel Kernel Density Estimator,” in proceedings of the 2007 International Conference on Machine Learning: Models, Technologies & Applications, Monte Carlo Resort, Las Vegas, Nevada, USA, June 25-28, 2007. (MLMTA 2007)

Ting-Ying Chien, Chien-Yu Chen, Darby Tien-Hao Chang, and Chen-Ming Hsu, “Deriving Functional Signatures from Protein Sequences by Iterative Pattern Mining,” in proceedings of the Eleventh Annual International Conference of Research in Computational Molecular Biology, San Francisco Bay Area, April 21-25, 2007. (RECOMB 2007)

Yen-Jen Oyang, Darby Tien-Hau Chang, Yu-Yien Ou, Shien-Ching Hwang, and Chien-Yu Chen, “On the Convergence Rates of the Locally Relaxed Kernel Density Estimator,” in proceedings of the 2006 Hawaii International Conference on Statistics, Mathematics and Related Fields, Honolulu, Hawaii, January 16-18, 2006.

Yen-Jen Oyang, Yu-Yien Ou, Shien-Ching Hwang, Chien-Yu Chen, and Darby Tien-Hau Chang, “The Locally Relaxed Model of Variable Kernel Density Estimation,” in proceedings of the 2006 Hawaii International Conference on Statistics, Mathematics and Related Fields, Honolulu, Hawaii, January 16-18, 2006.

Yen-Jen Oyang, Yu-Yien Ou, Shien-Ching Hwang, Chien-Yu Chen, and Darby Tien-Hau Chang, “Data Classification with a Relaxed Model of Kernel Density Estimation,” in proceedings of the 2005 International Joint Conference on Neural Networks, Montreal, Canada, July 31-August 4, 2005. (IJCNN 2005)

Darby Tien-Hau Chang, Chien-Yu Chen, Yen-Jen Oyang, Hsueh-Fen Juan, Hsuan-Cheng Huang, “An Efficient Mechanism for Prediction of Protein-Ligand Interactions Based on Analysis of Protein Tertiary Substructures,” in proceedings of IEEE Fourth Symposium on Bioinformatics and Bioengineering, Taichung, Taiwan, May 19-21, 2004. (BIBE 2004)

Yen-Jen Oyang, Darby Tien-Hau Chang, Chien-Yu Chen, and Shien-Ching Hwang, “Expediting Protein Structural Analysis with an Efficient Kernel Density Estimation Algorithm,” in proceedings of IEEE 5th International Symposium on Multimedia Software Engineering, Taichung, Taiwan, December 10-12, 2003. (MSE 2003)

Tien-Hao Chang (2012). Computational Approaches to Predict Protein Interaction, Protein-Protein Interactions - Computational and Experimental Tools, Dr. Weibo Cai (Ed.), ISBN: 978-953-51-0397-4, InTech, Available from: http://www.intechopen.com/books/protein-protein-interactions-computational-and-experimental-tools/computational-approaches-to-predict-protein-interaction