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基本信息 The basic information
姓名: 彭佳杰

学院: 计算机学院


学历: 博士研究生毕业

学位: 工学博士


职称: 副教授

职务:


学科: 计算机科学与技术-计算机应用技术





综合介绍 General Introduction
彭佳杰博士，现任西北工业大学副教授，博士生导师。哈尔滨工业大学计算机科学与技术专业博士，哈佛大学博士后，美国国家能源部-密西根州立大学植物研究实验室（PRL）联合培养博士。主要从事数据挖掘、人工智能、生物信息学、大数据算法学以及海量知识工程等方向的研究。近年来在《Nature Genetics》、《PNAS》、《Bioinformatics》、《Briefingsin Bioinformatics》、《Nucleic acids research》等期刊上发表论文50余篇，其中5篇入选ESI热点论文，6篇入选ESI高被引论文，主持国家自然科学基金面上项目等项目。担任中国计算机学会生物信息专业组委员；Biological ontologies and knowledge bases workshop 主席；《BMC Bioinformatics》《Frontiers in Genetics》《Journal of Biomedical Semantics》杂志客座编委；《Plos One》学术编辑；IJCAI、 BIBM、ECAI、GIW、InCoB、KEOD等国际会议program committee；担任TPAMI、Bioinformatics、Plos Genetics、BMC Bioinformatics、TCBB、Plos One、Frontier in Computer Science等国际知名期刊审稿人。
团队主页：http://www.nwpu-bioinformatics.com/
课题组：https://jiajiepeng.github.io/



招生信息 Admission Information
欢迎对生物信息学、数据挖掘、人工智能相关方向感兴趣的优秀本科生和研究生加入我们的团队！
（jiajiepeng （AT）nwpu.edu.cn）。
招生信息
长期招聘博士后，欢迎感兴趣的博士联系。课题组不安排博士生、博士后做工程项目。
现招收2022年9月入学计算机学院硕士研究生，2022春季、秋季入学博士生，欢迎感兴趣的同学提前邮件联系。

常年招收有志于继续深造的本科生（并不限于西北工业大学，并不限于计算机专业）与我们合作科研工作，欢迎感兴趣的同学与我邮件联系，会根据学生的特点开展相应的课题研究。





教育教学 Education And Teaching
本科生课程 《人工智能》 《人工智能与生物大数据分析交叉前沿》
研究生课程 《计算生物学》



科学研究 Scientific Research
研究方向
Machine learning: Deep Learning, Explainable AI, Network Analysis
Computational Biology and Medicine: Single Cell Biology, Network Biology, Biomedical Ontology


完整文章列表：https://scholar.google.com/citations?user=LZ1MiZwAAAAJ&hl=en
[#: equal contribution; ]


[43] GanqiangLiu, Jiajie Peng, Zhixiang Liao, ... Clemens Scherzer.Genome-wide survival study identifies a novel synaptic locus and polygenic score for cognitive progression in Parkinson’s disease.Nature Genetics,2021
[42]Jiajie Peng, Yuxian Wang, Jiaojiao Guan, Jingyi Li, Ruijiang Han, Jianye Hao, Zhongyu Wei, and Xuequn Shang.An end-to-end heterogeneous graph representation learning-based framework for drug–target interaction prediction.Briefings in Bioinformatics,2021
[41]Jiajie Peng, Tianyi Zhao. Reduction in TOM1 expression exacerbates Alzheimer’s disease. PNAS, 2020
[40]Tianpei Yang, Jianye Hao, Zhaopeng Meng, Zongzhang Zhang, Weixun Wang, Yujing Hu, Yingfeng Cheng, Changjie Fan, Zhaodong Wang, Jiajie Peng. Efficient Deep Reinforcement Learning through Policy Transfer. IJCAI, 2020
[39]Jiajie Peng#, Hansheng Xue#, Zhongyu Wei, Idil Tuncali, Jianye Hao, Xuequn Shang. Integrating multi-network topology for gene function prediction using deep neural networks. Briefings in Bioinformatics, 2020
[38]Tianyi Zhao#, Shuxuan Lyu#, Guilin Lu#, Liran Juan#, Xi Zeng, Zhongyu Wei, Jianye Hao, Jiajie Peng.SC2diseases: a manually curated database of Single-Cell Transcriptome for human diseases.Nucleic Acids Research, 2020
[37] Tianyi Zhao, Yang Hu, Jiajie Peng, Liang Cheng.GCN-CNN: A Novel Deep Learning Method for Prioritizing lncRNA Target Genes. Bioinformatics, 2020
[36]Jiajie Peng, Junya Lu, Donghee Hoh, Ayesha Dina, Xuequn Shang, David Kramer, Jin Chen. Identifying Emerging Phenomenon in Long Temporal Phenotyping Experiments. Bioinformatics, 2020
[35] Tianyi Zhao, Yang Hu, Tianyi Zang and Jiajie Peng. Identifying drug-target interactions based on Graph Convolutional Network and Deep Neural Network. Briefings in Bioinformatics, 2020
[34] Haotian Liao#, Yuxi Long#, Ruijiang Han, Wei Wang, Lin Xu, Mingheng Liao, Zhen Zhang, Zhenru Wu, Xuequn Shang, Xuefeng Li, Jiajie Peng, Kefei Yuan, Yong Zeng. Deep learning-based classification and mutation prediction from histopathological images of hepatocellular carcinoma.Clinical and translational medicine, 2020
[33]Haotian Liao, Tianyuan Xiong, Jiajie Peng, Lin Xu, Mingheng Liao, Zhen Zhang, Zhenru Wu, Kefei Yuan, Yong Zeng. Classification and Prognosis Prediction from Histopathological Images of Hepatocellular Carcinoma by a Fully Automated Pipeline Based on Machine Learning. Annals of Surgical Oncology, 2020
[32]J Peng, W Hui, Q Li, B Chen, J Hao, Q Jiang, X Shang, Z Wei.A learning-based framework for miRNA-disease association identification using neural networks. Bioinformatics, 2019
[31]J Peng, X Wang, X Shang.Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data. BMC Bioinformatics, 2019
[30] Peng, J., Lu, G., Xue, H., Wang, T., & Shang, X. TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology. BMC bioinformatics, 2019
[29] H Xue, J Peng, J Li, X Shang.Integrating Multi-Network Topology via Deep Semi-supervised Node Embedding. CIKM, 2019
[28]J Peng, L Zhu, Y Wang, J Chen.Mining Relationships among Multiple Entities in Biological Networks.IEEE/ACM transactions on computational biology and bioinformatics, 2019
[27]H Xue, J Peng, X Shang.Towards Gene Function Prediction via Multi-Networks Representation Learning. AAAI, 2019
[26]H Xue, J Peng, X Shang.Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO. BMC Systems Biology, 2019
[25]J Peng, J Guan, X Shang.Predicting Parkinson's disease genes based on node2vec and autoencoder.Frontiers in genetics, 2019
[24] Jiajie Peng, Weiwei Hui, Xuequn Shang. Measuring phenotype-phenotype similarity through the interactome. BMC Bioinformatics, 2018. （中科院二区 ，IF=2.30）
[23] Jiajie Peng, Xuanshuo Zhang, Weiwei Hui, Junya Lu, Qianqian Li, Shuhui Liu and Xuequn Shang. Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach. BMC Systems Biology, 2018. （中科院二区，IF=2.30）
[22] Liang Cheng, Yue Jiang, Hong Ju, Jie Sun, Jiajie Peng, Meng Zhou, Yang Hu. InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk . BMC Genomics , 2018. （中科院二区 ，IF=3.73）
[21] Jiajie Peng, Kun Bai, Xuequn Shang, Guohua Wang, Hansheng Xue, Shuilin Jin, Liang Cheng, Yadong Wang, and Jin Chen. Predicting disease-related genes using integrated biomedical networks . BMC Genomics, 2017. （中科院二区 ，IF=3.73）
[20] Jiajie Peng, Honggang Wang, Junya Lu, Weiwei Hui, Yadong Wang, Xuequn Shang. Identifying term relations cross different gene ontology categories . BMC Bioinformatics, 2017. （中科院二区 ，IF=3.80）
[19] Jiajie Peng, Qianqian Li, Xuequn Shang. Measuring phenotype-phenotype similarity through the interactome , Bioinformatics and Biomedicine (BIBM), 2017 IEEE International Conference on.（CCF B类会议）
[18] Jiajie Peng, Junya Lu, Xuequn Shang. Identifying consistent disease subnetworks using DNet. Methods, 2017. （中科院二区 ，IF=3.80）
[17] Jiajie Peng, Hansheng Xue, et al. A novel method to measure the semantic similarity of HPO terms. International Journal of Data Mining and Bioinformatics , 2017. （IF=0.62）
[16] Jiajie Peng, Qianqian Li, Xuequn Shang. Investigations on factors influencing HPO-based semantic similarity calculation, Journal of Biomedical Semantics, 2017.（IF=1.85）
[15] Jiajie Peng, Tao Wang, Jixuan Wang, Yadong Wang, Jin Chen. Extend Gene Ontology based on gene network data. Bioinformatics, (2016) 32 (8): 1185-1194.（中科院一区 ，IF=4.98）
[14] Jiajie Peng, Hongxiang Li, Yongzhuang Liu, Liran Juan, Qinghua Jiang, Yadong Wang and Jin Chen. InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology. BMC Genomics, (2016) 17 (5)（中科院二区 ，IF=3.99）
[13] Jiajie Peng, Hansheng Xue, Yukai Shao, Xuequn Shang, Yadong Wang, and Jin Chen, Measuring Phenotype Semantic Similarity using Human Phenotype Ontology. BIBM 2016 (CCF B类会议)
[12] Jiajie Peng, Tao Wang, Jianping Hu, Yadong Wang, Jin Chen. Constructing Networks of Organelle Functional Modules in Arabidopsis. Current Genomics, (2016) 17 (5), 427-438 （SCI收录，IF=2.34）
[11] Jiajie Peng, Sahra Uygun, Taehyong Kim,Yadong Wang, Seung Y. Rhee, Jin Chen. Measuring Genome-specific Semantic Similarities Using Gene Ontology and Gene Co-Function Networks [J]. BMC Bioinformatics, 2015,16: 44. （中科院二区 ，IF=2.58）
[10] Qinghua Jiang, Jixuan Wang, Xiaoliang Wu, Rui Ma, Shuilin Jin, Zhijie Han, Renjie Tan, Jiajie Peng, Guiyou Liu, Yu Li, Yadong Wang. LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression. Nucleic Acids Res, 2015. 43:D193-D196.（中科院一区 ，IF=9.11）
[9] Jiajie Peng, Hongxiang Li, Qinghua Jiang, Yadong Wang and Jin Chen. An Integrative Approach for Measuring Semantic Similarities using Gene Ontology [J]. BMC Systems Biology, 2014,8: S8. （中科院二区 ，IF=2.44）
[8] Jiajie Peng, Yadong Wang, and Jin Chen. Towards integrative gene functional similarity measurement. BMC bioinformatics, 2014, 15: S5 （中科院二区 ，IF=2.58）
[7] Jiajie Peng, Jin Chen, Yadong Wang. Identifying cross-category relations in gene ontology and constructing genome-specific term association networks. BMC bioinformatics, 2013, 14: S15（中科院二区 ，IF=2.58）
[6] Jiajie Peng, Hongxiang Li, Yongzhuang Liu, Liran Juan, Qinghua Jiang, Yadong Wang and Jin Chen. InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology[C]. BIOINFORMATICS RESEARCH AND APPLICATIONS (ISBRA 2015), 2015, 9096: 431-432.
[5] Jiajie Peng, Hongxiang Li, Yadong Wang and Jin Chen. A web tool for measuring gene semantic similarities by combining Gene Ontology and gene co-function networks[C]. proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology （ACM BCB）, 2015：678-679（DOI号为10.1145/**.**）
[4] Yongzhuang Liu, Jian Liu, Jianguo Lu, Jiajie Peng, Liran Juan, Xiaolin Zhu, Bingshan Li, Yadong Wang. Joint detection of copy number variations in the parent-offspring trio. Bioinformatics,（中科院一区 ，IF=4.98）
[3] Qinghua Jiang, Rui Ma, Jixuan Wang, Xiaoliang Wu, Shuilin Jin, Jiajie Peng, Renjie Tan, Tianjiao Zhang, Yu Li, Yadong Wang. LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data. BMC genomics, 2015. 16(S3):S2.（中科院二区 ，IF=3.99）
[2] Liang Cheng, Jie Li, Peng Ju, Jiajie Peng, and Yadong Wang. SemFunSim: A New Method for Measuring Disease Similarity by Integrating Semantic and Gene Functional Association. PloS one, 2014, 9(6): e99415（中科院三区 ，IF=3.23）
[1] Shuilin Jin, Renjie Tan, Qinghua Jiang, Li Xu, Jiajie Peng, Yong Wang, Yadong Wang. A Generalized Topological Entropy for Analyzing the Complexity of DNA Sequences. PLOS ONE, 2014, 9(2): e88519 （中科院三区 ，IF=3.23）





学术活动 Professional Activities
2021/05/12 与哈佛大学合作论文在nature genetics发表
2021/03/02 王余贤同学的论文在Briefings in Bioinformatics发表
2020/07/03 恭喜龙羽西和韩瑞江同学论文在《Clinical and translational medicine》发表
2020/04/21 "Efficient Deep Reinforcement Learning through Policy Transfer" is accepted by IJCAI 2020
2020/03/06 "Identifying drug-target interactions based on Graph Convolutional Network and Deep Neural Network" isaccepted by Briefings in Bioinformatics
2020/02/26 DeepMNE-CNN is accepted by Briefings in Bioinformatics
2020/02/10 “Reduction in TOM1 expression exacerbates Alzheimer’s disease” is accepted by PNAS.
2020/02/07 团队与华西医院合作的论文被《ANNALS OF SURGICAL ONCOLOGY》(外科肿瘤学年鉴)录用《Classification and Prognosis Prediction from Histopathological Images of Hepatocellular Carcinoma by a Fully Automated Pipeline Based on Machine Learning》
2020/02/07恭喜鲁桂林同学论文被《Curr Pharm Des》录用 《A Survey of Network Representation Learning Methods for Link Prediction in Biological Network》
2019/11/25 恭喜鲁桂林同学论文被BMC Bioinformatics录用《TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology》
2019/09/17 恭喜薛寒生同学在The Australian National University 开始新旅程. GOOD LUCK～
2019/08/09 恭喜薛寒生同学论文被CIKM录用 《Integrating Multi-Network Topology via Deep Semi-supervised Node Embedding》
2019/07/14 恭喜卢俊雅同学论文被Bioinformatics录用 《Identifying Emerging Phenomenon in Long Temporal Phenotyping Experiments》
2019/06/23 恭喜王晓昱同学论文被BMC Bioinformatics录用《Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data》
2019/4/3 恭喜惠薇薇和李倩倩同学论文被Bioinformatics录用 《A learning-based framework for miRNA-disease association identification using neural networks》
2019/3/12 恭喜管娇娇同学论文被Frontiers in Genetics 录用 《Predicting Parkinson's disease genes based on node2vec and autoencoder》

2019/3/11 恭喜俊雅和薇薇同学顺利通过硕士毕业答辩！Congrats！
2019/1/17 王晓昱同学参加APBC2019并作报告
2019/1/1 恭喜惠薇薇同学获得研究生国家奖学金
2018/12/1 恭喜薛寒生同学论文被AAAI录用
2018/4/12 惠薇薇同学的工作在BMC Bioinformatics期刊发表：《Measuring phenotype-phenotype similarity through the interactome》

2018/3/25 轩硕同学的工作在BMC Systems Biology期刊发表：《Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach》
2018/3/11恭喜倩倩顺利通过硕士生毕业答辩！




English Version