Peng Chen, Ph.D


Institute of Health Sciences, Anhui University
No. 111 Jiulong Road, Hefei, Anhui 230601, China
Email: pchen.ustc10(at)yahoo.com

Google Citation, Researchgate, Office website


Dr. Peng Chen is currently an Professor at the Institute of Health Sciences, Anhui University, and Adjunct Professor at the Hefei Institute of Intelligent Machine, Chinese Academy Sciences. Prior to Anhui University, he was Associate Professor at the Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei Anhui, P.R.China. He received his Ph.D degree in Pattern Recognition and Intelligent System from University of Science and Technology of China, and Bachelor and Master degrees in Control Science and Engineering from Electronic Engineering Institute and Kunming University of Science and Technology, respectively. From Jan. 2006 to Jun. 2006, he was a senior research associate in City University of HongKong.  During Apr. 2008 to Feb. 2014, he severed as a postdoc fellow or Research Fellow in foreign countries. From Aug. 2016 to Sep. 2016, he was a visiting professor in University of Technology, Sydney, Australia.

Dr. Chen's research interests include machine learning and data mining with applications to pattern recognition, bioinformatics, etc. He has published more than 50 high quality referred papers in top conferences and journals, including TCBB, BMC Bioinformatics, Amino Acids, and FEBS Letters, etc. Dr. Chen has been often invited as PC member and/or referee/reviewer for many premier international conferences and journals, including TNN, NN, IJDMB, DMIN2011~2014, BIFE2010, IJCNN2007, and others.

Selected Professional Services:

--Editorial Board Member:

                 JILSA (2012.11 - ), JCBBR (2013.5 - ), IJMIA (2011 – present).

--TPC Member:

                 GIW2018, InCoB2018, InCoB2017, DMIN2011~2014, BIFE2010, NCM2009, NISS2009, ICIC2008, etc.


                 NN, TNN, IJDMB, NCA...| ICIC2005-2007, WICB2007, IJCNN2007, ISNN2007, etc.

Call for paper:

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

 The 29th International Conference on Genome Informatics (GIW 2018) will be held at Kunming from 3-5, December, 2018.

Research Interests:

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

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


Publications: (* Correspondence Author)

 Journals (Selected):

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

  2. Qingxin Xiao, Peng Chen*, Bing Wang, Jun Zhang, Prediction of the Occurrence of Pests and Diseases in Cotton with Bidirectional Recurrent Neural Networks. Expert Systems With Applications. Submitted

  3. Weilu Li, Peng Chen*, Bing Wang, Chengjun Xie, Automatic Localization and Count of Agricultural Crop Pests Based on an Improved Deep Learning-Based Pipeline, Scientific Reports, in revision.

  4. Denan Xia, Peng Chen*, Bing Wang, Jun Zhang, Chengjun Xie, Insect detection and classification based on improved convolutional neural network. Sensors, 2018, 18: 4169.

  5. ShanShan Hu, DeNan Xia, Benyue Su, Peng Chen*, Bing Wang and Jinyan Li, A Convolutional Neural Network System to Discriminate Drug-Target Interactions. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2018. Accepted.

  6. Quanya Liu, Peng Chen*, Bing Wang, Jun Zhang, Jinyan Li, dbMPIKT: A kinetic and thermodynamic database of mutant protein interaction. BMC Bioinformatics 2018. Accept. (arXiv e-prints)

  7. Quanya Liu, Bing Wang, Jinyan Li, Hot Spot prediction in protein-protein interactions by an ensemble learning. BMC Systems  Biology 2018. Accepted.

  8. ShanShan Hu, Peng Chen*, Bing Wang and Jinyan Li, Drug-target Interaction predictions Based on A Convolutional Neural Network System. BMC Genomics 2018. Accepted

  9. Qingxin Xiao, Jun Zhang, Peng Chen*, Bing Wang, Prediction of the Occurrence of Pests and Diseases in Cotton on the basis of Weather by Long Short Term Memory Network. BMC Medical Informatics and Decision Making. Accepted

  10. Bing Wang, Kun Lu, Xiao Zheng, Benyue Su, Yuming Zhou, Peng Chen* and Jun Zhang, Early Stage Identification of Alzheimer’s Disease Using a Two-stage Ensemble Classifier. Current Bioinformatics (2018) 13(5): 529 - 535.

  11. Chengjun Xie, Rujing Wang, Jie Zhang, Peng Chen*, Wei Dong, Rui Li, Jian Yu, Multi-level learning features for automatic classification of field crop insects. Computers and Electronics in Agriculture, (2018) 152: 233–241.

  12. Yanhua Qiao, Yi Xiong, Hongyun Gao, Xiaolei Zhu and Peng Chen*, Protein-Protein Interface Hot Spots Prediction Based on a Hybrid Feature Selection Strategy. BMC Bioinformatics (2018) 19:14. Online paper

  13. 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.

  14. MuChun Zhu, Xiaoping Song, Peng Chen*, Wenyan Wang and Bing Wang, dbHDPLS: Database of Human Disease Protein-Ligand Structure. Computational Biology and Chemistry 2018, Accepted.

  15. 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]

  16. 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]

  17. 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]

  18. 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.

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

  20. 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

  21. 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.

  22. 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.  

  23. 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.

  24. 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

  25. 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.

  26. 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.

  27. 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.

  28. 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.

  29. 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.

  30. 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.

  31. 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.

  32. 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.

  33. 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.

  34. 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]

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

  36. 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]

  37. 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]

  38. 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]

  39. 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)

  40. 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]

  41. 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].

  42. 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]

  43. 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]

  44. 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]

  45. 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]

  46. 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]

  47. 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.

Copyright© Peng Chen 2004-2011

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