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IIM

博士，教授/博导

物质科学与信息技术研究院，安徽大学

安徽省合肥市经开区九龙路111号，320601

邮箱：pchen.ustc10（at）yahoo.com

Google Citation, Researchgate, Office website

个人简介：

安徽肥东人。安徽大学物质科学与信息技术研究院教授/博士生导师。1997年毕业于国防科技大学（合肥）电气工业自动化专业，2003年毕业于昆明理工大学控制理论与控制工程专业，2007年获中国科学技术大学模式识别与智能系统博士学位。2006年-2014年期间曾在美国霍华德大学做博士后研究、新加坡南洋理工大学担任Research Fellow、沙特阿卜杜拉国王科技大学做博士后研究。2011年-2013年在中科院合肥智能机械研究所任副研究员，硕导/副博导。

 曾经在IEEE/ACM TCBB等国际重要刊物上发表了60多篇学术论文。主持了2项国家自然科学基金和数项省部级项目。入选2017年度安徽省人社厅留学归国人员创新创业扶持计划重点计划。另外，还授权了5篇关于农业信息化及农业传感器方面的专利成果。此外，还是数个国际杂志的编辑委员会委员以及数个国际会议的PC Member。同时，还兼任IEEE国际电子电工工程师协会会员、国际工程学会会员、中国计算机学会会员、安徽省计算机学会青工委委员。

重要活动:

 The 16th International Conference on Bioinformatics (InCoB 2017) will be held at Shenzhen from 20-22, September, 2017.

Research Interests:

  • Computational Biology: Protein structure prediction, protein-protein interaction, gene expression, ...

  • Algorithms: Machine Learning, Data mining, Machine Vision, ...

Funding:

Publications: (* Correspondence Author)

 Journals (Selected)：

  1. Quanya Liu, Peng Chen*, Chun-Hou Zheng, Bing Wang, dbMPIKT: A kinetic and thermodynamic database of mutant protein interaction. Submitted.(arXiv e-prints)

  2. ShanShan Hu, Peng Chen*, DeNan Xia, Bing Wang and Jinyan Li, A New Structure of Convolutional Neural Networks to Discriminate Drug-target Interactions. Submitted.

  3. Weilu Li, Peng Chen*, Chengjun Xie, Rui Li, Automatic Recognition and Counting of Wheat mites in Wheat Fields Based on Deep Learning. Submitted.

  4. ShanShan Hu, Peng Chen*, Bing Wang, and Jinyan Li, Protein binding hot spots prediction from sequence only by a new ensemble learning method. Amino Acids (2017) 49:1773–1785, Online paper.

  5. MuChun Zhu, Jinjian Jiang, Peng Chen*, Chunhou Zheng, Bing Wang and Jinyan Li, dbHDPLS: Database of Human Disease Protein-Ligand Structure. BMC System Biology 2017, Accepted.

  6. Jinjian Jiang, Nian Wang, Peng Chen*, Chun-Hou Zheng, Bing Wang, Prediction of protein hot spots from whole sequences by a random projection ensemble system. International Journal of Molecular Sciences 2017, 18(7), 1543. [Journal paper]

  7. Jinjian Jiang, Nian Wang, Peng Chen*, Jun Zhang, Bing Wang, DrugECs: ensemble system with feature subspaces to accurate drug-target interaction prediction. BioMed Research International 2017, Accepted. [Journal paper]

  8. Jinjian Jiang, Jun Zhang, Zhi Yang, Chun-Hou Zheng, Peng Chen*, Bing Wang, The Second Dimension Retention Index Calculation in Comprehensive Two-Dimensional Gas Chromatography Time-of-Flight Mass Spectrometry Based on Different Column Configurations. BioMed Research International 2017, Accepted. [Journal paper]

  9. Chengjun Xie, Rujing Wang, Jie Zhang, Peng Chen*, Wei Dong, Rui Li, Jian Yu, Deeply learned features for automatic classification of field crop insects. submitted.

  10. Jun Zhang, Chun-Hou Zheng, Yi Xia, Bing Wang, Peng Chen*, Optimization enhanced genetic algorithm-support vector regression for the prediction of compound retention indices in gas chromatography, NeuroComputing, 2017, 240: 183–190.

  11. Jun Zhang, Muchun Zhu, Peng Chen*, Bing Wang, DrugRPE: random projection ensemble approach to drug-target interaction prediction, Neurocomputing 2017, 228: 256–262.

  12. Di Zhang, Peng Chen*, Chun-Hou Zheng, and Junfeng Xia, Identification of ovarian cancer subtype specific network modules and candidate drivers through an integrative genomics approach, Oncotarget 2016, 7(4):4298-309. Co-first author

  13. P Chen, B Wang, J Zhang, X Gao, J Li, and J Xia, A sequence-based dynamic ensemble learning system for protein ligand-binding site prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2016, 13(5):901-912.

  14. Bing Wang, Hao Shen, Aiqin Fang, De-shuang Huang, Changjun Jiang, Jun Zhang, Peng Chen*, A regression model for calculating the second dimension retention index in comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry, Journal of Chromatography A, 2016, 1451(17): 127–134.  

  15. Chengjun Xie, Jie Zhang, Rui Li, Jinyan Li, Peilin Hong, Junfeng Xia, Peng Chen*, Automatic classification for field crop insects via multiple-task sparse representation and multiple-kernel learning, Computers and Electronics in Agriculture, 2015, 119:123-132.

  16. P Chen, J Huang, and X Gao, LigandRFs: Meta approach to identifying ligand-binding residues by co-evolutionary physicochemical characteristics of amino acids, BMC Bioinformatics, 2014, 15(S15): S4

  17. 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.

  18. 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.

  19. 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, 2014, 10 (1), 98-119.

  20. Yaru Su, Rujing Wang, Peng Chen, Chuan-Xi Li, Sparse Representation-Based Approach for Unsupervised Feature Selection, Int. J. Patt. Recogn. Artif. Intell., 2014, 28(3), 1450006.

  21. 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.

  22. 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.

  23. 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.

  24. 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.

  25. 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.

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

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

  28. 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]

  29. 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]

  30. 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]

  31. 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)

  32. 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]

  33. 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].

  34. 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]

  35. 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]

  36. 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]

  37. 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]

  38. 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]

  39. 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.

 

Main Collaborators:

Xin Gao (Postdoc advisor), Dept. Computer Engineering, KAUST, Saudi Arabia
Jinyan Li (Postdoc advisor), Dept. Computer Engineering, NTU, Singapore
Steven Chu-Hong HOI (Postdoc advisor), Dept. Computer Engineering, NTU, Singapore
Legand L. Burge, III (Postdoc advisor), Dept. Systems and Computer Science, Howard Univ.
Chunmei Liu (Postdoc advisor), Dept. Systems and Computer Science, Howard Univ.
Hau-San Wong Dept. Computer Science, City Univ. Hong Kong.

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