Biography:

Dr. Peng Chen is currently an Professor at theInstitutes of Physical Science and Information Technology, 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 100 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:

                 InCoB2019, GIW2018, InCoB2018, InCoB2017, DMIN2011~2014, BIFE2010, NCM2009, NISS2009, ICIC2008, etc.

--Reviewer:

                 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 Topic on Deep Learning in Crop Diseases and Insect Pests in Frontiers in Plant Science, with Manuscript Submission Deadline, 01 September, 2022.

Research Interests:

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

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

Funding:

• National Natural Science Foundation of China (No. 61300058): Predicting protein hot spot residues based on co-evolutionary encoding from amino acid sequence only（基于氨基酸序列协同进化编码的蛋白质热点残基预测）

• National Natural Science Foundation of China (No. 61300058): Predicting protein hot spot residues based on co-evolutionary encoding from amino acid sequence only（基于氨基酸序列协同进化编码的蛋白质热点残基预测）

• National Natural Science Foundation of China (No. 61672035): Research on protein-ligand interaction network by deep learning autoencoder and random projection（蛋白质-配体相互作用的深度学习自动编码和随机映射研究）

Publications: (* Correspondence Author)

 Journals (Selected)：

1. Peng Chen, Weilu Li, Sijie Yao, Chun Ma, Chunhou Zheng, Jun Zhang, Chengjun Xie, Bing Wang, Dong Liang, Recognition and Counting of Wheat Mites in Wheat Fields by A Three-Step Deep Learning Method. Neurocomputing 2021, 437: 21-30. (SCI, JCR二区）

2. Bing Wang, Changqing Mei, Yuanyuan Wan, Jun Zhang, Peng Chen*, Yan Xiong*, Imbalance Data Processing Strategy for Protein Interaction Sites Prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2021, 18(3): 985 - 994. in print. (SCI, JCR二区）

3. Wenyan Wang, Yuming Zhou, Mu-Tian Cheng, Yan Wang, Chun-Hou Zheng, Yan Xiong, Peng Chen*, Zhiwei Ji, Bing Wang, Potential Pathogenic Genes Prioritization Based on Protein Domain Interaction Network Analysis, IEEE/ACM Transactions on Computational Biology and Bioinformatics 2021, 18(3): 1026 - 1034. in print. (SCI, JCR二区）

4. Rujing Wang,  Lin Jiao,  Chengjun Xie,  Peng Chen*,  Du Jianming,  Li Rui, S-RPN: Sampling-balanced region proposal network for small crop pest detection. Computers and Electronics in Agriculture 2021, 187: 106290

5. Cheng Wang,  Jun Zhang,  Peng Chen*,  Bing Wang, Predicting Drug-Target Interactions Based on the Ensemble Models of Multiple Feature Pairs. International Journal of Molecular Sciences 2021, 22(12): 6598

6. Wenyan Wang,  Kun Lu,  Ziheng Wu,  Hongming Long,  Jun Zhang,  Peng Chen*,  Bing Wang, Surface Defects Classification of Hot Rolled Strip Based on Improved Convolutional Neural Network. Isij International 2021, Accepted

7. Qiang Hu,  Jun Zhang,  Peng Chen*,  Bing Wang, Compound identification via deep classification model for electron-ionization mass spectrometry. International Journal of Mass Spectrometry 2021, 463: 116540

8. Huimin Shen,  Youzhi Zhang,  Chun-Hou Zheng,  Bing Wang,  Peng Chen*. A Cascade Graph Convolutional Network for Predicting Protein–Ligand Binding Affinity. International Journal of Molecular Sciences 2021, 22(8), 4023

9. Cheng Lin Zhang,  You Zhi Zhang,  Bing Wang,  Peng Chen*, Prediction of Drug-Target Binding Affinity by An Ensemble Learning System with Network Fusion Information. Current Bioinformatics 2021, Accepted

10. Wenyan Wang,  Jun Zhang,  Fang Zhou,  Peng Chen*,  Bing Wang, Paper acceptance prediction at the institutional level based on the combination of individual and network features. Scientometrics 2021, 126: pages1581–1597

11. Peng Chen, Qingxin Xiao, Jun Zhang, Chengjun Xie, Bing Wang, Occurrence prediction of cotton pests and diseases by bidirectional long short-term memory networks with climate and atmosphere circulation. Computers and Electronics in Agriculture 2020, 176: 105612. (SCI, JCR一区）

12. ShanShan Hu, Peng Chen*, Jun Zhang, Bing Wang, Jinyan Li, A Deep Learning-Based Chemical System for QSAR Prediction, IEEE Journal of Biomedical and Health Informatics 2020, 24(10): 3020-3028.in print. (SCI, JCR一区）

13. Aijun Deng, Huan Zhang, Wenyan Wang, Jun Zhang, Dingdong Fan, Peng Chen*, and Bing Wang, Developing Computational Model to Predict Protein-Protein Interaction Sites Based on the XGBoost Algorithm. International Journal of Molecular Sciences 2020, 21(7), 2274. [Full paper]

14. 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 2020. in print. (SCI, JCR二区）

15. Kai-chao Miao, Ting-ting Han, Ye-qing Yao, Hui Lu, Peng Chen*, Bing Wang and Jun Zhang, Application of LSTM for Short Term Fog Forecasting based on Meteorological Elements, Neurocomputing 2020. Accepted. (SCI, JCR二区）

16. Bing Wang, Lili Peng, Nian Zhou, Peng Chen*, Jun Zhang, Inferring Protein-Protein Interaction Sites Using Sequence Profile and Hydrophobic Information, BMC Bioinformatics, 2020, Accepted.(SCI, JCR二区）

17. Ye Wang, Changqing Mei, Yuming Zhou, Yan Wang, Chunhou Zheng, Xiao Zhen, Yan Xiong, Peng Chen*, Jun Zhang and Bing Wang, Semi-supervised prediction of protein interaction sites from unlabeled sample information, BMC Bioinformatics 2019, 20(S25):699.

18. ShanShan Hu, Peng Chen*, Bing Wang and Jinyan Li, Predicting drug-target interactions from drug structure and protein sequence using novel convolutional neural networks. BMC Bioinformatics 2019, 20(S25):689.

19. 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 Bioinformatics 2019,  20(S25):688.

20. Jie Hang, Dexiang Zhang, Peng Chen*, Jun Zhang and Bing Wang, Classification of plant leaf diseases based on improved convolutional neural network. Sensors 2019, 19(19): 4083.

21. Yangyang Wang , Qingxin Xiao, Peng Chen*, Bing Wang, In silico Prediction of Drug-Induced Liver Injury Based on Ensemble Classifier Method. International Journal of Molecular Sciences 2019, 20(17), 4106. [Journal paper]

22. 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, 2019. (9): 7024.

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

24. Quanya Liu, Peng Chen*, Bing Wang, Jun Zhang, Jinyan Li, dbMPIKT: A kinetic and thermodynamic database of mutant protein interaction. BMC Bioinformatics 2018, 19:455.  (arXiv e-prints)

25. Quanya Liu, Bing Wang, Peng Chen*, Jinyan Li, Hot Spot prediction in protein-protein interactions by an ensemble learning. BMC Systems  Biology 2018, 12(S9): 132.

26. 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.

27. 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

28. 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.

29. 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.

30. 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]

31. 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.

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

33. 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

34. 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.

35. 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.  

36. 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.

37. 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

38. 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.

39. 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.

40. 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.

41. 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.

42. 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.

43. 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]

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

45. 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]

46. 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]

47. 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]

48. 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]

49. 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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