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Publications: (* Correspondence Author)

 Journals

  1. C Xie, J Tan, P Chen, J Zhang, L He, Collaborative object tracking model with local sparse representation, Journal of Visual Communication and Image Representation, 2014, 25 (2), 423–434.

  2. Li C.X., Wang R.J., Chen P.*, Huang H., Su Y.R., Interaction relation ontology learning. Journal of Computational Biology, 2014, 21(1):80-8.

  3. Chengjun Xie, Jieqing Tan, Peng Chen*, Jie Zhang, Lei He, “A Multiple Instance Learning Tracking Method with Local Sparse Representation”, IET Computer Vision, 2013, 7 (5), 320-334.

  4. Peng Chen, Jinyan Li, Limsoon Wong, Jianhua Huang, and Xin Gao, Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences, PROTEINS: Structure, Function, and Bioinformatics. 2013, 81(8):1351-62.

  5. B Wang, J Zhang, P Chen, Z Ji, S Deng, C Li, Prediction of peptide drift time in ion mobility mass spectrometry from sequence-based features, BMC bioinformatics 2013, 14 (Suppl 8), S9.

  6. B Wang, W Sun, J Zhang, P Chen, Current Status of Machine Learning-Based Methods for Identifying Protein-Protein Interaction Sites, Current Bioinformatics 2013, 8 (2), 177-182.

  7. 胡宜敏, 宋良图, 陈鹏*, 魏圆圆, 苏雅茹, 一种基于 Markov 逻辑网的中文地理名称实体解析方法, 模式识别与人工智能 26 (1), 114-122.

  8. Peng Chen, Limsoon Wong, Jinyan Li, "Outlier detection: a challenge to clean interface data in protein hetero-complexes and the application", IEEE Transactions on Computational Biology and Bioinformatics, 2012, 9(4):1155-65. [Website Availability Full Paper]

  9. Chuanxi Li, Peng Chen*, Rujing Wang, "PPI-IRO: A Two Stage Method for Protein-Protein Interaction Extraction Based on Interaction Relation Ontology". International Journal of Data Mining and Bioinformatics, 2012, Accepted.

  10. Yaru Su, Rujing Wang, Peng Chen*, "Agricultural ontology based feature optimization for agricultural text clustering", Journal of Integrative Agriculture 11 (5), 752-759.

  11. Peng Chen, Jinyan Li, "Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information", BMC Bioinformatics, 2010,11:402. [Website Availability Full Paper]

  12. Peng Chen*, Chunmei Liu, Legand Burge, Jinyan Li, Mahmood Mohanmad, Bill Southerland, and Clay Gloster, "DomSVR: Domain Boundary Prediction with Support Vector Regression from sequence information Alone", Amino Acids, 2010, 39(3), 713-726 . [Website Availability Full Paper]

  13. Peng Chen, Jinyan Li, "Prediction of Protein Long-Range Contacts Using an Ensemble of Genetic Algorithm Classifiers with Sequence Profile Centers", BMC Structural Biology, 2010, 10(Suppl 1):S2. [Website Availability Full Paper]

  14. Peng Chen, Chunmei Liu, Legand Burge, Mahmood Mohanmad, William Southerland, and Clay Gloster, "Prediction of Inter-residue Contact Clusters from Hydrophobic Cores", International Journal of Data Mining and Bioinformatics, 2010, 4(6), 720-732. (In press)

  15. B. Wang, P. Chen, J. Zhang, G. Zhao and X. Zhang, "Inferring Protein-Protein Interactions Using a Hybrid Genetic Algorithm/Support Vector Machine Method", Protein & Peptide Letters , 17(9), Pp. 1079-1084, 2010. [Full Paper]

  16. B. Wang , P. Chen, P. Wang, G. Zhao and X. Zhang, "Radial Basis Function Neural Network Ensemble for Predicting Protein-Protein Interaction Sites in Heterocomplexes", Protein & Peptide Letters , 17(9), Pp. 1111-1116, 2010. [Full Paper].

  17. Peng Chen, Chunmei Liu, Legand Burge, Mahmood Mohanmad, William Southerland, and Clay Gloster, "Protein Fold Classification with Genetic Algorithms and Feature Selection", Journal of Bioinformatics and Computational Biology, vol.7, no.5, pp. 773-788, 2009. [Website   Full Paper]

  18. Peng Chen, Kyungsook Han, Xueling Li, D.S. Huang, "Predicting Key Long-Range Interaction Sites by B-Factors". Protein & Peptide Letters. 15(5):478-483, 2008. [ Full Paper]

  19. Peng Chen, D.S. Huang, "Predicting Contact Map Using Radial Basis Function Neural Network with Conformational Energy Function", International Journal of Bioinformatics Research and Applications, vol. 4, no.2, pp. 123 - 136, 2008. [ Full Paper]

  20. Peng Chen, Bing Wang, Hau San Wong, D.S., Huang, "Prediction of Protein B-factors Using Multi-class Bounded SVM". Protein & Peptide Letters, vol.14, no.2, pp.185-190, 2007. [ Full Paper]

  21. Bing Wang, Peng Chen, D.S. Huang, Jing-Jing Li, Tat-Ming Lok, Michael R. Lyu, "Predicting protein interaction sites from residue spatial sequence profile and evolution rate," FEBS Letters, vol.580, no.2, pp. 380-384, 2006 (Co-first author). [ Full Paper]

  22. Jing-Jing Li, D.S.Huang, Bing Wang, Peng Chen, "Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores," International Journal of Biological Macromolecules, vol.38, nos.3-5, pp.241-247, 2006.

 Conferences

  1. Chuan-Xi Li, Peng Chen, Ru-Jing Wang and Ya-Ru Su, “Paper Title: A Web entity extraction method based on entity attribute classification”, In: 2011 International Conference on Software and Computing Technology (ICSCT 2011). (EI, ISTP) (Accepted)

  2. Yaru Su, Rujing Wang, Chuanxi Li, Peng Chen,  “A dynamic subspace learning method for tumor classification”, In: The 7th International Conference on Natural Computation(ICNC’11). (EI, ISTP) (Accepted)

  3. Peng Chen, Jinyan Li, "Prediction of Protein Long-Range Contacts Using GaMC Approach with Sequence Profile Centers", In: Bioinformatics and Biomedicine Workshop, 2009. BIBMW 2009. IEEE International Conference on, Washington DC, USA, 2009 128-135. (EI, ISTP)  [Website Availability  Full Paper]

  4. Peng Chen, Chunmei Liu, Legand Burge, Mahmood Mohanmad, William Southerland, and Clay Gloster, "DomSVR: Domain Boundary Prediction with Support Vector Regression and Evolutionary Information", In: The 3rd International Conference on Bioinformatics and Biomedical Engineering (ICBBE 2009), China, 2009, 1-5. (EI, ISTP)

  5. Peng Chen, Chunmei Liu, Legand Burge, Mahmood Mohammad, Bill Southerland, Clay Gloster, Bing Wang, "IRCDB: A Database of Inter-residues Contacts in Protein Chains", In: Advances in Databases, Knowledge, and Data Applications, 2009. DBKDA '09. First International Conference on, 1-6. (EI, ISTP)  [Website Availability  Abstract]

  6. Peng Chen, Chunmei Liu, Legand Burge, Mahmood Mohanmad, Bill Southerland, and Clay Gloster, "Prediction of Inter-residue Contact Clusters from Hydrophobic Cores". In: Machine Learning and Applications, 2008. ICMLA '08. Seventh International Conference on, San Diego, California, USA, 2008, 703-708. (EI, ISTP)

  7. Peng Chen, Bing Wang, Hau San Wong, D.S.Huang, "Prediction of Long-range Contacts from Sequence Profile", In: Neural Networks, 2007. IJCNN 2007. International Joint Conference on, Orlando, Florida, USA, 2007, 938-943. (EI, ISTP)  [ Full Paper]

  8. Peng Chen, Hau-San Wong, Bing Wang and De-Shuang Huang, "Long-range interaction analysis using principal component analysis", In: Neural Networks, 2006. IJCNN 2006. International Joint Conference on, Vancouver, British Columbia, Canada, 2006, 2331-2336. (EI, ISTP)

  9. Bing Wang, Hau San Wong, Peng Chen, Hong-Qiang Wang and De-Shuang Huang, "Predicting protein-protein interaction sites using radial basis function neural networks", In: Neural Networks, 2006. IJCNN 2006. International Joint Conference on, Vancouver, British Columbia, Canada, 2006, 2325- 2330. (EI, ISTP)

  10. Peng Chen, De-Shuang Huang, Bing Wang, "Prediction of contact map integrated PNN with conformational energy", In: Neural Networks, 2005. IJCNN 2005. International Joint Conference on, Montreal, Canada, 2005, 499- 502. (EI, ISTP)

  11. Bing Wang, De-Shuang Huang, Peng Chen, "Predicting protein-protein interactions based on protein-domain relationships", In: Neural Networks, 2005. IJCNN 2005. International Joint Conference on, Montreal, Canada, 2005, 316- 319. (EI, ISTP)

  Book Charpter

  1. P Chen, Consensus of Sample-Balanced Classifiers for Identifying Ligand-Binding Residue by Co-evolutionary Physicochemical Characteristics of Amino Acids, Emerging Intelligent Computing Technology and Applications, 2014, 206-212.

  2. B Wang, P Chen, J Zhang, "Protein Interface Residues Prediction Based on Amino Acid Properties Only", Bio-Inspired Computing and Applications, Lecture Notes in Computer Science, 2012, Volume 6840/2012, 448-452. 

 


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