>Selected Publications

• 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
• 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
• 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
• Jiajie Peng, Tianyi Zhao. Reduction in TOM1 expression exacerbates Alzheimer’s disease. PNAS, 2020
• 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
• Jiajie Peng, Junya Lu, Donghee Hoh, Ayesha Dina, Xuequn Shang, David Kramer, Jin Chen. Identifying Emerging Phenomenon in Long Temporal Phenotyping Experiments. Bioinformatics, 2020
• Hansheng Xue, Jiajie Peng, Xuequn Shang. Towards Gene Function Prediction via Multi-Networks Representation Learning. AAAI, 2019
• Hansheng Xue, Jiajie Peng, Jiying Li, Xuequn Shang. Integrating Multi-Network Topology via Deep Semi-supervised Node Embedding. CIKM, 2019
• L Liu, Y Ma, X Zhu, Y Yang, X Hao, L Wang, J Peng. Integrating Sequence and Network Information to Enhance Protein-Protein Interaction Prediction Using Graph Convolutional Networks. BIBM, 2019
• Jiajie Peng, Weiei Hui, Qianqian Li, Bolin Chen, Jianye Hao, Qinghua Jiang, Xuequn Shang, Zhongyu Wei. A learning-based framework for miRNA-disease association identification using neural networks. Bioinformatics, 2019
• 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
• 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
• Jiajie Peng, Tao Wang, Jixuan Wang, Yadong Wang, Jin Chen. Extend Gene Ontology based on gene network data. Bioinformatics, 2016
• 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, 2016
• 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. BMC Bioinformatics, 2015

>All Publications

Google Scholar: https://scholar.google.com/citations?user=LZ1MiZwAAAAJ&hl=en&oi=ao

2020~

• Jiajie Peng, Tianyi Zhao. Reduction in TOM1 expression exacerbates Alzheimer’s disease. PNAS, 2020
• 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
• Jiajie Peng, Junya Lu, Donghee Hoh, Ayesha Dina, Xuequn Shang, David Kramer, Jin Chen. Identifying Emerging Phenomenon in Long Temporal Phenotyping Experiments. Bioinformatics, 2020
• 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

2019~

• 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
• 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
• 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
• H Xue, J Peng, J Li, X Shang. Integrating Multi-Network Topology via Deep Semi-supervised Node Embedding. CIKM, 2019
• 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
• H Xue, J Peng, X Shang. Towards Gene Function Prediction via Multi-Networks Representation Learning. AAAI, 2019
• L Liu, Y Ma, X Zhu, Y Yang, X Hao, L Wang, J Peng. Integrating Sequence and Network Information to Enhance Protein-Protein Interaction Prediction Using Graph Convolutional Networks. BIBM, 2019
• J Peng, L Han, X Shang. A deconvolution method for predicting cell abundance based on single cell RNA-seq data. BIBM, 2019
• Y Wang, L Juan, J Peng, T Zang, Y Wang. LncDisAP: a computation model for LncRNA-disease association prediction based on multiple biological datasets. BMC bioinformatics, 2019
• T Wang, J Peng, Q Peng, Y Wang, J Chen. FSM: Fast and scalable network motif discovery for exploring higher-order network organizations. Methods, 2019
• J Peng, G Lu, X Shang. A Survey of Network Representation Learning Methods for Link Prediction in Biological Network. Current Pharmaceutical Design, 2019
• Y Wang, L Juan, J Peng, T Zang, Y Wang. Prioritizing candidate diseases-related metabolites based on literature and functional similarity. BMC bioinformatics, 2019
• T Wang, Q Peng, B Liu, X Liu, Y Liu, J Peng, Y Wang. eQTLMAPT: fast and accurate eQTL mediation analysis with efficient permutation testing approaches. Frontiers in Genetics, 2019
• H Xue, J Peng, X Shang. Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO. BMC Systems Biology, 2019
• J Peng, J Guan, X Shang. Predicting Parkinson's disease genes based on node2vec and autoencoder. Frontiers in genetics, 2019

2018~

• Jiajie Peng, Weiwei Hui, Xuequn Shang. Measuring phenotype-phenotype similarity through the interactome. BMC Bioinformatics, 2018.
• 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.
• 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. ）

2017~

• 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.
• Jiajie Peng, Honggang Wang, Junya Lu, Weiwei Hui, Yadong Wang, Xuequn Shang. Identifying term relations cross different gene ontology categories . BMC Bioinformatics, 2017.
• Jiajie Peng, Qianqian Li, Xuequn Shang. Measuring phenotype-phenotype similarity through the interactome , Bioinformatics and Biomedicine (BIBM), 2017 IEEE International Conference on.
• Jiajie Peng, Junya Lu, Xuequn Shang. Identifying consistent disease subnetworks using DNet. Methods, 2017.
• 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）
• Jiajie Peng, Qianqian Li, Xuequn Shang. Investigations on factors influencing HPO-based semantic similarity calculation, Journal of Biomedical Semantics, 2017.（IF=1.85）

2016~

• Jiajie Peng, Tao Wang, Jixuan Wang, Yadong Wang, Jin Chen. Extend Gene Ontology based on gene network data. Bioinformatics, (2016) 32 (8): 1185-1194.
• 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)
• Jiajie Peng, Hansheng Xue, Yukai Shao, Xuequn Shang, Yadong Wang, and Jin Chen, Measuring Phenotype Semantic Similarity using Human Phenotype Ontology. BIBM 2016
• 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

2015~

• 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）
• 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）
• 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.
• 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）
• 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）
• 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）

2014~

• 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）
• 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）
• 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）
• 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）

2013~

• 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）