教师主页移动版

综合介绍 General Introduction 彭佳杰博士，现任西北工业大学长聘教授，博士生导师，国家级青年人才。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。主要从事人工智能、数据挖掘、生物信息学以及海量知识工程等方向的研究。近年来在《Nature Genetics》、《PNAS》、《Briefings in Bioinformatics》、《Bioinformatics》、NeurIPS、AAAI等期刊与会议上发表论文80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，入选2022全球华人AI青年学者 （生物计算领域中国大陆唯一）、陕西省青年科技新星、西北工业大学翱翔青年学者、西北工业大学翱翔新星等。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；AAAI、IJCAI、 BIBM、ECAI、GIW、InCoB、KEOD等国际会议program committee。团队主页：http://www.nwpu-bioinformatics.com/  个人相册

教育教学

教育教学 Education and teaching 招生信息 教育教学 欢迎对人工智能、生物信息学、数据挖掘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（计算机、人工智能、生命科学等相关方向），欢迎感兴趣的博士联系 （基础待遇详见：https://jsj.nwpu.edu.cn/snew/rczp.htm）。现招收2024年9月入学计算机学院硕士研究生（有考研名额），2024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。 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》

荣誉获奖

科学研究 Scientific Research 研究方向Machine learning: Deep Learning, Agent，Explainable AIComputational Biology and Medicine: Single Cell Biology, Network Biology, Brain Diseases完整文章列表：https://scholar.google.com/citations?user=LZ1MiZwAAAAJ&hl=en[#: equal contribution; ][49] Jingru Wang, Yihang Xiao, Xuequn Shang, and Jiajie Peng. Predicting drug–target binding affinity with cross-scale graph contrastive learning. Briefings in Bioinformatics, 2024.[48] Xi Zeng, Xiaotian Hao, Hongyao Tang, Zhentao Tang, Shaoqing Jiao, Dazhi Lu, Jiajie Peng. Designing Biological Sequences without Prior Knowledge Using Evolutionary Reinforcement Learning. AAAI, 2024.[47] Wang, Yongtian, Xinmeng Liu, Yewei Shen, Xuerui Song, Tao Wang, Xuequn Shang, and Jiajie Peng. Collaborative deep learning improves disease-related circRNA prediction based on multi-source functional information. Briefings in Bioinformatics, 2023.[46] Wang, Tao, Jinjin Yang, Yifu Xiao, Jingru Wang, Yuxian Wang, Xi Zeng, Yongtian Wang, and Jiajie Peng. DFinder: a novel end-to-end graph embedding-based method to identify drug–food interactions. Bioinformatics, 2023[45] Ganqiang Liu, 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[44] Wei Wang, Ruijiang Han, Menghan Zhang, Yuxian Wang, Tao Wang, Yongtian Wang, Xuequn Shang, and Jiajie Peng.  A network-based method for brain disease gene prediction by integrating brain connectome and molecular network. Briefings in Bioinformatics, 2021[43] Tao Wang, Yongzhuang Liu, Quanwei Yin, Jiaquan Geng, Jin Chen, Xipeng Yin, Yongtian Wang, Xuequn Shang, Chunwei Tian, Yadong Wang, Jiajie Peng. Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation. Briefings in Bioinformatics (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10.1145/2808719.2816835）[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）

科学研究

学术活动 Professional Activities 2023/12 祝贺曾檄等同学的论文被AAAI 2024录用！2023/12 祝贺王静茹等同学的论文被Briefings in Bioinformatics录用！2023/12 祝贺张梦涵等同学的论文被Computers in Biology and Medicine录用！2023/05 祝贺金金、彩伟、曾檄同学硕士毕业！2023/01 祝贺金金工作在Bioinformatics发表2022/10 祝贺余贤获西北工业大学优秀研究生毕业论文2022/08 祝贺彩伟、余贤、嘉泉的论文A review and performance evaluation of clustering frameworks for single-cell Hi-C data被Briefings in Bioinformatics录用2022/04 祝贺王余贤、彭景浩、李靖怡和韩璐同学硕士毕业！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 20202020/03/06 "Identifying drug-target interactions based on Graph Convolutional Network and Deep Neural Network" is accepted by Briefings in Bioinformatics2020/02/26 DeepMNE-CNN is accepted by Briefings in Bioinformatics2020/02/10 “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！

学术成果

综合介绍