Jiajie Peng - RankMe

90 papers A* 6A 2B 2Journal 65Unranked 15

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	BioRAGent: natural language biomedical querying with retrieval-augmented multiagent systems. Briefings Bioinform. Manlian Bi, Zhijie Bao, Dongna Xie, Xiaohan Xie, Changxiao Yang, Tao Wang, Yongtian Wang, Jiajie Peng
2025	J	`jnl`	EGA-Ploc: An Efficient Global-Local Attention Model for Multi-Label Protein Subcellular Localization Prediction on the Immunohistochemistry Images. IEEE J. Biomed. Health Informatics Boyang Wan, Xiaoyang Huang, Yang Qiao, Jiajie Peng, Fan Yang
2025	J	`jnl`	Integrative Graph-Based Framework for Predicting circRNA Drug Resistance Using Disease Contextualization and Deep Learning. IEEE J. Biomed. Health Informatics Yongtian Wang, Wenkai Shen, Yewei Shen, Shang Feng, Tao Wang, Xuequn Shang, Jiajie Peng
2025	J	`jnl`	MAEST: accurately spatial domain detection in spatial transcriptomics with graph masked autoencoder. Briefings Bioinform. Pengfei Zhu, Han Shu, Yongtian Wang, Xiaofeng Wang, Yuan Zhao, Jialu Hu, Jiajie Peng, Xuequn Shang, Zhen Tian, Jing Chen, Tao Wang
2025	J	`jnl`	Predicting CRISPR Cas9 Off-Target Activities With a Two-Stage Deep Learning Framework. IEEE Trans. Comput. Biol. Bioinform. Tianshan Zhang, Bei Jiang, Guang Yang, Zhijie Bao, Jiajie Peng
2025	A*	`conf`	SWAMamba: A Sliding Window Attention Mamba Framework for Predicting Translation Elongation Rates. AAAI Xi Zeng, Fei Ni, Shaoqing Jiao, Dazhi Lu, Jianye Hao, Jiajie Peng
2025	J	`jnl`	The rise and potential opportunities of large language model agents in bioinformatics and biomedicine. Briefings Bioinform. Tiantian Yang, Yihang Xiao, Zhijie Bao, Jianye Hao, Jiajie Peng
2025	J	`jnl`	cfMethylPre: deep transfer learning enhances cancer detection based on circulating cell-free DNA methylation profiling. Briefings Bioinform. Xuchao Zhang, Jing Chen, Yongtian Wang, Xiaofeng Wang, Jialu Hu, Jiajie Peng, Xuequn Shang, Yanpu Wang, Tao Wang
2025	J	`jnl`	scMamba: A Scalable Foundation Model for Single-Cell Multi-Omics Integration Beyond Highly Variable Feature Selection. CoRR Zhen Yuan, Shaoqing Jiao, Yihang Xiao, Jiajie Peng
2024	J	`jnl`	Accurately deciphering spatial domains for spatially resolved transcriptomics with stCluster. Briefings Bioinform. Tao Wang, Han Shu, Jialu Hu, Yongtian Wang, Jin Chen, Jiajie Peng, Xuequn Shang
2024	J	`jnl`	Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient Clustering. CoRR Shujian Jiao, Bingxuan Li, Lei Wang, Xiaojin Zhang, Wei Chen, Jiajie Peng, Zhongyu Wei
2024	J	`jnl`	CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis. CoRR Yihang Xiao, Jinyi Liu, Yan Zheng, Xiaohan Xie, Jianye Hao, Mingzhi Li, Ruitao Wang, Fei Ni, Yuxiao Li, Jintian Luo, Shaoqing Jiao, Jiajie Peng
2024	A*	`conf`	Designing Biological Sequences without Prior Knowledge Using Evolutionary Reinforcement Learning. AAAI Xi Zeng, Xiaotian Hao, Hongyao Tang, Zhentao Tang, Shaoqing Jiao, Dazhi Lu, Jiajie Peng
2024	—	`conf`	Identifying brain disease genes via integrating brain imaging and molecular network. BIBM Wei Wang, Yuxian Wang, Jiajie Peng
2024	J	`jnl`	Overview of the CAIL 2023 Argument Mining Track. CoRR Jingcong Liang, Junlong Wang, Xinyu Zhai, Yungui Zhuang, Yiyang Zheng, Xin Xu, Xiandong Ran, Xiaozheng Dong, Honghui Rong, Yanlun Liu, Hao Chen, Yuhan Wei, Donghai Li, Jiajie Peng, Xuanjing Huang, Chongde Shi, Yansong Feng, Yun Song, Zhongyu Wei
2024	J	`jnl`	PIORS: Personalized Intelligent Outpatient Reception based on Large Language Model with Multi-Agents Medical Scenario Simulation. CoRR Zhijie Bao, Qingyun Liu, Ying Guo, Zhengqiang Ye, Jun Shen, Shirong Xie, Jiajie Peng, Xuanjing Huang, Zhongyu Wei
2024	J	`jnl`	Predicting cell-type specific disease genes of diabetes with the biological network. Comput. Biol. Medicine Menghan Zhang, Jingru Wang, Wei Wang, Guang Yang, Jiajie Peng
2024	J	`jnl`	Predicting drug-target binding affinity with cross-scale graph contrastive learning. Briefings Bioinform. Jingru Wang, Yihang Xiao, Xuequn Shang, Jiajie Peng
2024	J	`jnl`	Vulnerability detection based on transformer and high-quality number embedding. Concurr. Comput. Pract. Exp. Yang Cao, Yunwei Dong, Jiajie Peng
2024	J	`jnl`	postGWAS: A web server for deciphering the causality post the genome-wide association studies. Comput. Biol. Medicine Tao Wang, Zhihao Yan, Yiming Zhang, Zhuofei Lou, Xiaozhu Zheng, Duoduo Mai, Yongtian Wang, Xuequn Shang, Bing Xiao, Jiajie Peng, Jin Chen
2023	J	`jnl`	A benchmark for automatic medical consultation system: frameworks, tasks and datasets. Bioinform. Wei Chen, Zhiwei Li, Hongyi Fang, Qianyuan Yao, Cheng Zhong, Jianye Hao, Qi Zhang, Xuanjing Huang, Jiajie Peng, Zhongyu Wei
2023	J	`jnl`	Collaborative deep learning improves disease-related circRNA prediction based on multi-source functional information. Briefings Bioinform. Yongtian Wang, Xinmeng Liu, Yewei Shen, Xuerui Song, Tao Wang, Xuequn Shang, Jiajie Peng
2023	J	`jnl`	DFinder: a novel end-to-end graph embedding-based method to identify drug-food interactions. Bioinform. Tao Wang, Jinjin Yang, Yifu Xiao, Jingru Wang, Yuxian Wang, Xi Zeng, Yongtian Wang, Jiajie Peng
2023	J	`jnl`	DISC-MedLLM: Bridging General Large Language Models and Real-World Medical Consultation. CoRR Zhijie Bao, Wei Chen, Shengze Xiao, Kuang Ren, Jiaao Wu, Cheng Zhong, Jiajie Peng, Xuanjing Huang, Zhongyu Wei
2023	J	`jnl`	DxFormer: a decoupled automatic diagnostic system based on decoder-encoder transformer with dense symptom representations. Bioinform. Wei Chen, Cheng Zhong, Jiajie Peng, Zhongyu Wei
2023	B	`conf`	HQProtoPNet: An Evidence-Based Model for Interpretable Image Recognition. IJCNN Jingqi Wang, Jiajie Peng, Zhiming Liu, Hengjun Zhao
2023	J	`jnl`	scMultiGAN: cell-specific imputation for single-cell transcriptomes with multiple deep generative adversarial networks. Briefings Bioinform. Tao Wang, Hui Zhao, Yungang Xu, Yongtian Wang, Xuequn Shang, Jiajie Peng, Bing Xiao
2022	J	`jnl`	A Benchmark for Automatic Medical Consultation System: Frameworks, Tasks and Datasets. CoRR Wei Chen, Zhiwei Li, Hongyi Fang, Qianyuan Yao, Cheng Zhong, Jianye Hao, Qi Zhang, Xuanjing Huang, Jiajie Peng, Zhongyu Wei
2022	B	`conf`	A Two Stage Adaptation Framework for Frame Detection via Prompt Learning. COLING Xinyi Mou, Zhongyu Wei, Changjian Jiang, Jiajie Peng
2022	J	`jnl`	A network-based method for brain disease gene prediction by integrating brain connectome and molecular network. Briefings Bioinform. Wei Wang, Ruijiang Han, Menghan Zhang, Yuxian Wang, Tao Wang, Yongtian Wang, Xuequn Shang, Jiajie Peng
2022	J	`jnl`	A review and performance evaluation of clustering frameworks for single-cell Hi-C data. Briefings Bioinform. Caiwei Zhen, Yuxian Wang, Jiaquan Geng, Lu Han, Jingyi Li, Jinghao Peng, Tao Wang, Jianye Hao, Xuequn Shang, Zhongyu Wei, Peican Zhu, Jiajie Peng
2022	J	`jnl`	Correction to: Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation. Briefings Bioinform. Tao Wang, Yongzhuang Liu, Quanwei Yin, Jiaquan Geng, Jin Chen, Xipeng Yin, Yongtian Wang, Xuequn Shang, Chunwei Tian, Yadong Wang, Jiajie Peng
2022	A*	`conf`	Deep Representation Debiasing via Mutual Information Minimization and Maximization (Student Abstract). AAAI Ruijiang Han, Wei Wang, Yuxi Long, Jiajie Peng
2022	—	`conf`	Discovering eQTL Regulatory Patterns Through eQTLMotif. BIBM Tao Wang, Hui Zhao, Yifu Xiao, Hanzi Yang, Xipeng Yin, Yongtian Wang, Bing Xiao, Xuequn Shang, Jiajie Peng
2022	J	`jnl`	DxFormer: A Decoupled Automatic Diagnostic System Based on Decoder-Encoder Transformer with Dense Symptom Representations. CoRR Wei Chen, Cheng Zhong, Jiajie Peng, Zhongyu Wei
2022	J	`jnl`	Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation. Briefings Bioinform. Tao Wang, Yongzhuang Liu, Quanwei Yin, Jiaquan Geng, Jin Chen, Xipeng Yin, Yongtian Wang, Xuequn Shang, Chunwei Tian, Yadong Wang, Jiajie Peng
2022	J	`jnl`	Flexibility and rigidity index for chromosome packing, flexibility and dynamics analysis. Frontiers Comput. Sci. Jiajie Peng, Jinjin Yang, D. Vijay Anand, Xuequn Shang, Kelin Xia
2022	J	`jnl`	Hierarchical reinforcement learning for automatic disease diagnosis. Bioinform. Cheng Zhong, Kangenbei Liao, Wei Chen, Qianlong Liu, Baolin Peng, Xuanjing Huang, Jiajie Peng, Zhongyu Wei
2022	—	`conf`	Hypergraph-based Gene Ontology Embedding for Disease Gene Prediction. BIBM Tao Wang, Hengbo Xu, Ranye Zhang, Yifu Xiao, Jiajie Peng, Xuequn Shang
2021	J	`jnl`	A novel method for predicting cell abundance based on single-cell RNA-seq data. BMC Bioinform. Jiajie Peng, Lu Han, Xuequn Shang
2021	J	`jnl`	A pipeline for RNA-seq based eQTL analysis with automated quality control procedures. BMC Bioinform. Tao Wang, Yongzhuang Liu, Junpeng Ruan, Xianjun Dong, Yadong Wang, Jiajie Peng
2021	J	`jnl`	An end-to-end heterogeneous graph representation learning-based framework for drug-target interaction prediction. Briefings Bioinform. Jiajie Peng, Yuxian Wang, Jiaojiao Guan, Jingyi Li, Ruijiang Han, Jianye Hao, Zhongyu Wei, Xuequn Shang
2021	A*	`conf`	Curriculum Learning for Vision-and-Language Navigation. NeurIPS Jiwen Zhang, Zhongyu Wei, Jianqing Fan, Jiajie Peng
2021	J	`jnl`	Curriculum Learning for Vision-and-Language Navigation. CoRR Jiwen Zhang, Zhongyu Wei, Jianqing Fan, Jiajie Peng
2021	—	`conf`	DCAE: Selecting Discriminative Genes on Single-cell RNA-seq Data for Cell-type Quantification. BIBM Shuhui Liu, Yupei Zhang, Jiajie Peng, Xuequn Shang
2021	J	`jnl`	ED2: An Environment Dynamics Decomposition Framework for World Model Construction. CoRR Cong Wang, Tianpei Yang, Jianye Hao, Yan Zheng, Hongyao Tang, Fazl Barez, Jinyi Liu, Jiajie Peng, Haiyin Piao, Zhixiao Sun
2021	J	`jnl`	Identifying drug-target interactions based on graph convolutional network and deep neural network. Briefings Bioinform. Tianyi Zhao, Yang Hu, Linda R. Valsdottir, Tianyi Zang, Jiajie Peng
2021	J	`jnl`	Integrating multi-network topology for gene function prediction using deep neural networks. Briefings Bioinform. Jiajie Peng, Hansheng Xue, Zhongyu Wei, Idil Tuncali, Jianye Hao, Xuequn Shang
2021	—	`conf`	Predicting Hepatoma-Related Genes Based on Representation Learning of PPI network and Gene Ontology Annotations. BIBM Tao Wang, Zhiyuan Shao, Yifu Xiao, Xuchao Zhang, Yitian Chen, Binze Shi, Siyu Chen, Yuxian Wang, Jiajie Peng, Xuequn Shang
2021	J	`jnl`	Prediction and collection of protein-metabolite interactions. Briefings Bioinform. Tianyi Zhao, Jinxin Liu, Xi Zeng, Wei Wang, Sheng Li, Tianyi Zang, Jiajie Peng, Yang Yang
2021	J	`jnl`	SC2disease: a manually curated database of single-cell transcriptome for human diseases. Nucleic Acids Res. Tianyi Zhao, Shuxuan Lyu, Guilin Lu, Liran Juan, Xi Zeng, Zhongyu Wei, Jianye Hao, Jiajie Peng
2020	J	`jnl`	A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network. BMC Bioinform. Jiajie Peng, Jingyi Li, Xuequn Shang
2020	—	`conf`	Automatic Term Name Generation for Gene Ontology: Task and Dataset. EMNLP (Findings) Yanjian Zhang, Qin Chen, Yiteng Zhang, Zhongyu Wei, Yixu Gao, Jiajie Peng, Zengfeng Huang, Weijian Sun, Xuanjing Huang
2020	J	`jnl`	Combining sequence and network information to enhance protein-protein interaction prediction. BMC Bioinform. Leilei Liu, Xianglei Zhu, Yi Ma, Haiyin Piao, Yaodong Yang, Xiaotian Hao, Yue Fu, Li Wang, Jiajie Peng
2020	J	`jnl`	DeepLGP: a novel deep learning method for prioritizing lncRNA target genes. Bioinform. Tianyi Zhao, Yang Hu, Jiajie Peng, Liang Cheng, Pier Luigi Martelli
2020	A	`conf`	Efficient Deep Reinforcement Learning through Policy Transfer. AAMAS Tianpei Yang, Jianye Hao, Zhaopeng Meng, Zongzhang Zhang, Yujing Hu, Yingfeng Chen, Changjie Fan, Weixun Wang, Zhaodong Wang, Jiajie Peng
2020	J	`jnl`	Efficient Deep Reinforcement Learning through Policy Transfer. CoRR Tianpei Yang, Jianye Hao, Zhaopeng Meng, Zongzhang Zhang, Weixun Wang, Yujing Hu, Yingfeng Chen, Changjie Fan, Zhaodong Wang, Jiajie Peng
2020	A*	`conf`	Efficient Deep Reinforcement Learning via Adaptive Policy Transfer. IJCAI Tianpei Yang, Jianye Hao, Zhaopeng Meng, Zongzhang Zhang, Yujing Hu, Yingfeng Chen, Changjie Fan, Weixun Wang, Wulong Liu, Zhaodong Wang, Jiajie Peng
2020	J	`jnl`	Identifying emerging phenomenon in long temporal phenotyping experiments. Bioinform. Jiajie Peng, Junya Lu, Donghee Hoh, Ayesha S. Dina, Xuequn Shang, David M. Kramer, Jin Chen
2020	J	`jnl`	Mining Relationships among Multiple Entities in Biological Networks. IEEE ACM Trans. Comput. Biol. Bioinform. Jiajie Peng, Linjiao Zhu, Yadong Wang, Jin Chen
2019	—	`conf`	A deconvolution method for predicting cell abundance based on single cell RNA-seq data. BIBM Jiajie Peng, Lu Han, Xuequn Shang
2019	J	`jnl`	A learning-based framework for miRNA-disease association identification using neural networks. Bioinform. Jiajie Peng, Weiwei Hui, Qianqian Li, Bolin Chen, Jianye Hao, Qinghua Jiang, Xuequn Shang, Zhongyu Wei
2019	J	`jnl`	Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data. BMC Bioinform. Jiajie Peng, Xiaoyu Wang, Xuequn Shang
2019	A	`conf`	Integrating Multi-Network Topology via Deep Semi-supervised Node Embedding. CIKM Hansheng Xue, Jiajie Peng, Jiying Li, Xuequn Shang
2019	—	`conf`	Integrating Sequence and Network Information to Enhance Protein-Protein Interaction Prediction Using Graph Convolutional Networks. BIBM Leilei Liu, Yi Ma, Xianglei Zhu, Yaodong Yang, Xiaotian Hao, Li Wang, Jiajie Peng
2019	J	`jnl`	LncDisAP: a computation model for LncRNA-disease association prediction based on multiple biological datasets. BMC Bioinform. Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang, Yadong Wang
2019	J	`jnl`	Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO. BMC Syst. Biol. Hansheng Xue, Jiajie Peng, Xuequn Shang
2019	J	`jnl`	Prioritizing candidate diseases-related metabolites based on literature and functional similarity. BMC Bioinform. Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang, Yadong Wang
2019	J	`jnl`	TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology. BMC Bioinform. Jiajie Peng, Guilin Lu, Hansheng Xue, Tao Wang, Xuequn Shang
2019	A*	`conf`	Towards Gene Function Prediction via Multi-Networks Representation Learning. AAAI Hansheng Xue, Jiajie Peng, Xuequn Shang
2018	J	`jnl`	Deep Feature Learning of Multi-Network Topology for Node Classification. CoRR Hansheng Xue, Jiajie Peng, Xuequn Shang
2018	—	`conf`	Identifying Representative Network Motifs for Inferring Higher-order Structure of Biological Networks. BIBM Tao Wang, Jiajie Peng, Yadong Wang, Jin Chen
2018	J	`jnl`	Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach. BMC Syst. Biol. Jiajie Peng, Xuanshuo Zhang, Weiwei Hui, Junya Lu, Qianqian Li, Shuhui Liu, Xuequn Shang
2018	J	`jnl`	Measuring phenotype-phenotype similarity through the interactome. BMC Bioinform. Jiajie Peng, Weiwei Hui, Xuequn Shang
2018	—	`conf`	Predicting candidate disease-related lncRNAs based on network random walk. BIBM Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang, Yadong Wang
2018	—	`conf`	TSGOE: A web tool for tissue-specific gene ontology enrichment. BIBM Jiajie Peng, Guilin Lu, Hansheng Xue, Tao Wang, Xuequn Shang
2017	J	`jnl`	A novel method to measure the semantic similarity of HPO terms. Int. J. Data Min. Bioinform. Jiajie Peng, Hansheng Xue, Yukai Shao, Xuequn Shang, Yadong Wang, Jin Chen
2017	J	`jnl`	Identifying term relations cross different gene ontology categories. BMC Bioinform. Jiajie Peng, Honggang Wang, Junya Lu, Weiwei Hui, Yadong Wang, Xuequn Shang
2017	J	`jnl`	Investigations on factors influencing HPO-based semantic similarity calculation. J. Biomed. Semant. Jiajie Peng, Qianqian Li, Xuequn Shang
2017	—	`conf`	Measuring phenotype-phenotype similarity through the interactome. BIBM Jiajie Peng, Weiwei Hui, Xuequn Shang
2016	—	`conf`	Analyzing factors involved in the HPO-based semantic similarity calculation. BIBM Jiajie Peng, Qianqian Li, Bolin Chen, Jialu Hu, Xuequn Shang
2016	J	`jnl`	Extending gene ontology with gene association networks. Bioinform. Jiajie Peng, Tao Wang, Jixuan Wang, Yadong Wang, Jin Chen
2016	J	`jnl`	Joint detection of copy number variations in parent-offspring trios. Bioinform. Yongzhuang Liu, Jian Liu, Jianguo Lu, Jiajie Peng, Liran Juan, Xiaolin Zhu, Bingshan Li, Yadong Wang
2016	—	`conf`	Measuring phenotype semantic similarity using Human Phenotype Ontology. BIBM Jiajie Peng, Hansheng Xue, Yukai Shao, Xuequn Shang, Yadong Wang, Jin Chen
2015	—	`conf`	A web tool for measuring gene semantic similarities by combining gene ontology and gene co-function networks. BCB Jiajie Peng, Hongxiang Li, Yadong Wang, Jin Chen
2015	J	`jnl`	LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression. Nucleic Acids Res. Qinghua Jiang, Jixuan Wang, Xiaoliang Wu, Rui Ma, Tianjiao Zhang, Shuilin Jin, Zhijie Han, Renjie Tan, Jiajie Peng, Guiyou Liu, Yu Li, Yadong Wang
2015	J	`jnl`	Measuring semantic similarities by combining gene ontology annotations and gene co-function networks. BMC Bioinform. Jiajie Peng, Sahra Uygun, Taehyong Kim, Yadong Wang, Seung Y. Rhee, Jin Chen
2014	J	`jnl`	An integrative approach for measuring semantic similarities using gene ontology. BMC Syst. Biol. Jiajie Peng, Hongxiang Li, Qinghua Jiang, Yadong Wang, Jin Chen
2014	J	`jnl`	Towards integrative gene functional similarity measurement. BMC Bioinform. Jiajie Peng, Yadong Wang, Jin Chen
2013	J	`jnl`	Identifying cross-category relations in gene ontology and constructing genome-specific term association networks. BMC Bioinform. Jiajie Peng, Jin Chen, Yadong Wang