Identifying cross-category relations in gene ontology and constructing genome-specific term association networks. - Jiajie Peng; Jin Chen 004; Yadong Wang 001 (BMC Bioinform., 2013)

Towards integrative gene functional similarity measurement. - Jiajie Peng; Yadong Wang 001; Jin Chen 004 (BMC Bioinform., 2014)

An integrative approach for measuring semantic similarities using gene ontology. - Jiajie Peng; Hongxiang Li; Qinghua Jiang; Yadong Wang 001; Jin Chen 004 (BMC Syst. Biol., 2014)

A web tool for measuring gene semantic similarities by combining gene ontology and gene co-function networks. - Jiajie Peng; Hongxiang Li; Yadong Wang 001; Jin Chen 004 (BCB, 2015)

Measuring semantic similarities by combining gene ontology annotations and gene co-function networks. - Jiajie Peng; Sahra Uygun; Taehyong Kim; Yadong Wang 001; Seung Y. Rhee; Jin Chen 004 (BMC Bioinform., 2015)

LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression. - Qinghua Jiang; Jixuan Wang; Xiaoliang Wu; Rui Ma; Tianjiao Zhang; Shuilin Jin; Zhijie Han 002; Renjie Tan; Jiajie Peng; Guiyou Liu; Yu Li; Yadong Wang 001 (Nucleic Acids Res., 2015)

Analyzing factors involved in the HPO-based semantic similarity calculation. - Jiajie Peng; Qianqian Li; Bolin Chen; Jialu Hu; Xuequn Shang 001 (BIBM, 2016)

Measuring phenotype semantic similarity using Human Phenotype Ontology. - Jiajie Peng; Hansheng Xue; Yukai Shao; Xuequn Shang 001; Yadong Wang 001; Jin Chen 004 (BIBM, 2016)

Joint detection of copy number variations in parent-offspring trios. - Yongzhuang Liu; Jian Liu; Jianguo Lu; Jiajie Peng; Liran Juan; Xiaolin Zhu 002; Bingshan Li; Yadong Wang 001 (Bioinform., 2016)

Extending gene ontology with gene association networks. - Jiajie Peng; Tao Wang 082; Jixuan Wang; Yadong Wang 001; Jin Chen 004 (Bioinform., 2016)

Investigations on factors influencing HPO-based semantic similarity calculation. - Jiajie Peng; Qianqian Li; Xuequn Shang 001 (J. Biomed. Semant., 2017)

Identifying term relations cross different gene ontology categories. - Jiajie Peng; Honggang Wang; Junya Lu; Weiwei Hui; Yadong Wang 001; Xuequn Shang 001 (BMC Bioinform., 2017)

A novel method to measure the semantic similarity of HPO terms. - Jiajie Peng; Hansheng Xue; Yukai Shao; Xuequn Shang 001; Yadong Wang 001; Jin Chen 004 (Int. J. Data Min. Bioinform., 2017)

TSGOE: A web tool for tissue-specific gene ontology enrichment. - Jiajie Peng; Guilin Lu; Hansheng Xue; Tao Wang 082; Xuequn Shang 001 (BIBM, 2018)

Predicting candidate disease-related lncRNAs based on network random walk. - Yongtian Wang; Liran Juan; Jiajie Peng; Tianyi Zang; Yadong Wang 001 (BIBM, 2018)

Identifying Representative Network Motifs for Inferring Higher-order Structure of Biological Networks. - Tao Wang 082; Jiajie Peng; Yadong Wang 001; Jin Chen 004 (BIBM, 2018)

Measuring phenotype-phenotype similarity through the interactome. - Jiajie Peng; Weiwei Hui; Xuequn Shang 001 (BMC Bioinform., 2018)

Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach. - Jiajie Peng; Xuanshuo Zhang; Weiwei Hui; Junya Lu; Qianqian Li; Shuhui Liu; Xuequn Shang 001 (BMC Syst. Biol., 2018)

Deep Feature Learning of Multi-Network Topology for Node Classification. - Hansheng Xue; Jiajie Peng; Xuequn Shang 001 (CoRR, 2018)

Towards Gene Function Prediction via Multi-Networks Representation Learning. - Hansheng Xue; Jiajie Peng; Xuequn Shang 001 (AAAI, 2019)

Integrating Sequence and Network Information to Enhance Protein-Protein Interaction Prediction Using Graph Convolutional Networks. - Leilei Liu; Yi Ma 005; Xianglei Zhu; Yaodong Yang 002; Xiaotian Hao; Li Wang; Jiajie Peng (BIBM, 2019)

A deconvolution method for predicting cell abundance based on single cell RNA-seq data. - Jiajie Peng; Lu Han; Xuequn Shang 001 (BIBM, 2019)

Integrating Multi-Network Topology via Deep Semi-supervised Node Embedding. - Hansheng Xue; Jiajie Peng; Jiying Li; Xuequn Shang 001 (CIKM, 2019)

A learning-based framework for miRNA-disease association identification using neural networks. - Jiajie Peng; Weiwei Hui; Qianqian Li; Bolin Chen; Jianye Hao; Qinghua Jiang; Xuequn Shang 001; Zhongyu Wei (Bioinform., 2019)

TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology. - Jiajie Peng; Guilin Lu; Hansheng Xue; Tao Wang 082; Xuequn Shang 001 (BMC Bioinform., 2019)

Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data. - Jiajie Peng; Xiaoyu Wang; Xuequn Shang 001 (BMC Bioinform., 2019)

Prioritizing candidate diseases-related metabolites based on literature and functional similarity. - Yongtian Wang; Liran Juan; Jiajie Peng; Tianyi Zang; Yadong Wang 001 (BMC Bioinform., 2019)

LncDisAP: a computation model for LncRNA-disease association prediction based on multiple biological datasets. - Yongtian Wang; Liran Juan; Jiajie Peng; Tianyi Zang; Yadong Wang 001 (BMC Bioinform., 2019)

Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO. - Hansheng Xue; Jiajie Peng; Xuequn Shang 001 (BMC Syst. Biol., 2019)

Efficient Deep Reinforcement Learning through Policy Transfer. - Tianpei Yang; Jianye Hao; Zhaopeng Meng; Zongzhang Zhang; Yujing Hu; Yingfeng Chen; Changjie Fan; Weixun Wang; Zhaodong Wang; Jiajie Peng (AAMAS, 2020)

Automatic Term Name Generation for Gene Ontology: Task and Dataset. - Yanjian Zhang; Qin Chen 001; Yiteng Zhang; Zhongyu Wei; Yixu Gao; Jiajie Peng; Zengfeng Huang; Weijian Sun; Xuanjing Huang 001 (EMNLP (Findings), 2020)

Efficient Deep Reinforcement Learning via Adaptive Policy Transfer. - Tianpei Yang; Jianye Hao; Zhaopeng Meng; Zongzhang Zhang; Yujing Hu; Yingfeng Chen; Changjie Fan; Weixun Wang; Wulong Liu; Zhaodong Wang; Jiajie Peng (IJCAI, 2020)

Identifying emerging phenomenon in long temporal phenotyping experiments. - Jiajie Peng; Junya Lu; Donghee Hoh; Ayesha S. Dina; Xuequn Shang 001; David M. Kramer 001; Jin Chen 004 (Bioinform., 2020)

DeepLGP: a novel deep learning method for prioritizing lncRNA target genes. - Tianyi Zhao; Yang Hu 008; Jiajie Peng; Liang Cheng 006; Pier Luigi Martelli (Bioinform., 2020)

Combining sequence and network information to enhance protein-protein interaction prediction. - Leilei Liu; Xianglei Zhu; Yi Ma 005; Haiyin Piao; Yaodong Yang 002; Xiaotian Hao; Yue Fu; Li Wang; Jiajie Peng (BMC Bioinform., 2020)

A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network. - Jiajie Peng; Jingyi Li; Xuequn Shang 001 (BMC Bioinform., 2020)

Mining Relationships among Multiple Entities in Biological Networks. - Jiajie Peng; Linjiao Zhu; Yadong Wang 001; Jin Chen 004 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

DCAE: Selecting Discriminative Genes on Single-cell RNA-seq Data for Cell-type Quantification. - Shuhui Liu; Yupei Zhang; Jiajie Peng; Xuequn Shang 001 (BIBM, 2021)

Predicting Hepatoma-Related Genes Based on Representation Learning of PPI network and Gene Ontology Annotations. - Tao Wang 082; Zhiyuan Shao; Yifu Xiao; Xuchao Zhang; Yitian Chen; Binze Shi; Siyu Chen; Yuxian Wang; Jiajie Peng; Xuequn Shang 001 (BIBM, 2021)

Curriculum Learning for Vision-and-Language Navigation. - Jiwen Zhang; Zhongyu Wei; Jianqing Fan; Jiajie Peng (NeurIPS, 2021)

An end-to-end heterogeneous graph representation learning-based framework for drug-target interaction prediction. - Jiajie Peng; Yuxian Wang; Jiaojiao Guan; Jingyi Li; Ruijiang Han; Jianye Hao; Zhongyu Wei; Xuequn Shang 001 (Briefings Bioinform., 2021)

Integrating multi-network topology for gene function prediction using deep neural networks. - Jiajie Peng; Hansheng Xue; Zhongyu Wei; Idil Tuncali; Jianye Hao; Xuequn Shang 001 (Briefings Bioinform., 2021)

Identifying drug-target interactions based on graph convolutional network and deep neural network. - Tianyi Zhao; Yang Hu 008; Linda R. Valsdottir; Tianyi Zang; Jiajie Peng (Briefings Bioinform., 2021)

Prediction and collection of protein-metabolite interactions. - Tianyi Zhao; Jinxin Liu; Xi Zeng; Wei Wang; Sheng Li; Tianyi Zang; Jiajie Peng; Yang Yang (Briefings Bioinform., 2021)

A novel method for predicting cell abundance based on single-cell RNA-seq data. - Jiajie Peng; Lu Han; Xuequn Shang 001 (BMC Bioinform., 2021)

A pipeline for RNA-seq based eQTL analysis with automated quality control procedures. - Tao Wang 082; Yongzhuang Liu; Junpeng Ruan; Xianjun Dong; Yadong Wang 001; Jiajie Peng (BMC Bioinform., 2021)

ED2: An Environment Dynamics Decomposition Framework for World Model Construction. - Cong Wang; Tianpei Yang; Jianye Hao; Yan Zheng 002; Hongyao Tang; Fazl Barez; Jinyi Liu 002; Jiajie Peng; Haiyin Piao; Zhixiao Sun (CoRR, 2021)

SC2disease: a manually curated database of single-cell transcriptome for human diseases. - Tianyi Zhao; Shuxuan Lyu; Guilin Lu; Liran Juan; Xi Zeng; Zhongyu Wei; Jianye Hao; Jiajie Peng (Nucleic Acids Res., 2021)

Deep Representation Debiasing via Mutual Information Minimization and Maximization (Student Abstract). - Ruijiang Han; Wei Wang; Yuxi Long; Jiajie Peng (AAAI, 2022)

Hypergraph-based Gene Ontology Embedding for Disease Gene Prediction. - Tao Wang 082; Hengbo Xu; Ranye Zhang; Yifu Xiao; Jiajie Peng; Xuequn Shang 001 (BIBM, 2022)

Discovering eQTL Regulatory Patterns Through eQTLMotif. - Tao Wang 082; Hui Zhao; Yifu Xiao; Hanzi Yang; Xipeng Yin; Yongtian Wang; Bing Xiao 001; Xuequn Shang 001; Jiajie Peng (BIBM, 2022)

A Two Stage Adaptation Framework for Frame Detection via Prompt Learning. - Xinyi Mou; Zhongyu Wei; Changjian Jiang; Jiajie Peng (COLING, 2022)

A network-based method for brain disease gene prediction by integrating brain connectome and molecular network. - Wei Wang; Ruijiang Han; Menghan Zhang; Yuxian Wang; Tao Wang 082; Yongtian Wang; Xuequn Shang 001; Jiajie Peng (Briefings Bioinform., 2022)

Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation. - Tao Wang 082; Yongzhuang Liu; Quanwei Yin; Jiaquan Geng; Jin Chen 004; Xipeng Yin; Yongtian Wang; Xuequn Shang 001; Chunwei Tian; Yadong Wang 001; Jiajie Peng (Briefings Bioinform., 2022)

Correction to: Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation. - Tao Wang 082; Yongzhuang Liu; Quanwei Yin; Jiaquan Geng; Jin Chen 004; Xipeng Yin; Yongtian Wang; Xuequn Shang 001; Chunwei Tian; Yadong Wang 001; Jiajie Peng (Briefings Bioinform., 2022)

A review and performance evaluation of clustering frameworks for single-cell Hi-C data. - Caiwei Zhen; Yuxian Wang; Jiaquan Geng; Lu Han; Jingyi Li; Jinghao Peng; Tao Wang 082; Jianye Hao; Xuequn Shang 001; Zhongyu Wei; Peican Zhu; Jiajie Peng (Briefings Bioinform., 2022)

Hierarchical reinforcement learning for automatic disease diagnosis. - Cheng Zhong; Kangenbei Liao; Wei Chen 088; Qianlong Liu; Baolin Peng; Xuanjing Huang 001; Jiajie Peng; Zhongyu Wei (Bioinform., 2022)

Flexibility and rigidity index for chromosome packing, flexibility and dynamics analysis. - Jiajie Peng; Jinjin Yang; D. Vijay Anand; Xuequn Shang 001; Kelin Xia (Frontiers Comput. Sci., 2022)

HQProtoPNet: An Evidence-Based Model for Interpretable Image Recognition. - Jingqi Wang; Jiajie Peng; Zhiming Liu 001; Hengjun Zhao (IJCNN, 2023)

DISC-MedLLM: Bridging General Large Language Models and Real-World Medical Consultation. - Zhijie Bao; Wei Chen 088; Shengze Xiao; Kuang Ren; Jiaao Wu; Cheng Zhong; Jiajie Peng; Xuanjing Huang 001; Zhongyu Wei (CoRR, 2023)

A benchmark for automatic medical consultation system: frameworks, tasks and datasets. - Wei Chen 088; Zhiwei Li; Hongyi Fang; Qianyuan Yao; Cheng Zhong; Jianye Hao; Qi Zhang 001; Xuanjing Huang 001; Jiajie Peng; Zhongyu Wei (Bioinform., 2023)

DxFormer: a decoupled automatic diagnostic system based on decoder-encoder transformer with dense symptom representations. - Wei Chen 088; Cheng Zhong; Jiajie Peng; Zhongyu Wei (Bioinform., 2023)

DFinder: a novel end-to-end graph embedding-based method to identify drug-food interactions. - Tao Wang 082; Jinjin Yang; Yifu Xiao; Jingru Wang; Yuxian Wang; Xi Zeng; Yongtian Wang; Jiajie Peng (Bioinform., 2023)

Collaborative deep learning improves disease-related circRNA prediction based on multi-source functional information. - Yongtian Wang; Xinmeng Liu; Yewei Shen; Xuerui Song; Tao Wang 082; Xuequn Shang 001; Jiajie Peng (Briefings Bioinform., 2023)

scMultiGAN: cell-specific imputation for single-cell transcriptomes with multiple deep generative adversarial networks. - Tao Wang 082; Hui Zhao; Yungang Xu; Yongtian Wang; Xuequn Shang 001; Jiajie Peng; Bing Xiao 001 (Briefings Bioinform., 2023)

Designing Biological Sequences without Prior Knowledge Using Evolutionary Reinforcement Learning. - Xi Zeng; Xiaotian Hao; Hongyao Tang; Zhentao Tang; Shaoqing Jiao; Dazhi Lu; Jiajie Peng (AAAI, 2024)

Identifying brain disease genes via integrating brain imaging and molecular network. - Wei Wang; Yuxian Wang; Jiajie Peng (BIBM, 2024)

Accurately deciphering spatial domains for spatially resolved transcriptomics with stCluster. - Tao Wang 082; Han Shu; Jialu Hu; Yongtian Wang; Jin Chen 004; Jiajie Peng; Xuequn Shang 001 (Briefings Bioinform., 2024)

Predicting drug-target binding affinity with cross-scale graph contrastive learning. - Jingru Wang; Yihang Xiao; Xuequn Shang 001; Jiajie Peng (Briefings Bioinform., 2024)

postGWAS: A web server for deciphering the causality post the genome-wide association studies. - Tao Wang 082; Zhihao Yan; Yiming Zhang; Zhuofei Lou; Xiaozhu Zheng; Duoduo Mai; Yongtian Wang; Xuequn Shang 001; Bing Xiao 001; Jiajie Peng; Jin Chen 004 (Comput. Biol. Medicine, 2024)

Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient Clustering. - Shujian Jiao; Bingxuan Li; Lei Wang; Xiaojin Zhang 002; Wei Chen 088; Jiajie Peng; Zhongyu Wei (CoRR, 2024)

Overview of the CAIL 2023 Argument Mining Track. - Jingcong Liang; Junlong Wang; Xinyu Zhai; Yungui Zhuang; Yiyang Zheng; Xin Xu; Xiandong Ran; Xiaozheng Dong; Honghui Rong; Yanlun Liu; Hao Chen; Yuhan Wei; et al. (CoRR, 2024)

CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis. - Yihang Xiao; Jinyi Liu 002; Yan Zheng 002; Xiaohan Xie; Jianye Hao; Mingzhi Li; Ruitao Wang; Fei Ni 001; Yuxiao Li; Jintian Luo; Shaoqing Jiao; Jiajie Peng (CoRR, 2024)

PIORS: Personalized Intelligent Outpatient Reception based on Large Language Model with Multi-Agents Medical Scenario Simulation. - Zhijie Bao; Qingyun Liu 012; Ying Guo; Zhengqiang Ye; Jun Shen; Shirong Xie; Jiajie Peng; Xuanjing Huang 001; Zhongyu Wei (CoRR, 2024)

Predicting cell-type specific disease genes of diabetes with the biological network. - Menghan Zhang; Jingru Wang; Wei Wang; Guang Yang; Jiajie Peng (Comput. Biol. Medicine, 2024)

Vulnerability detection based on transformer and high-quality number embedding. - Yang Cao; Yunwei Dong; Jiajie Peng (Concurr. Comput. Pract. Exp., 2024)

SWAMamba: A Sliding Window Attention Mamba Framework for Predicting Translation Elongation Rates. - Xi Zeng; Fei Ni 001; Shaoqing Jiao; Dazhi Lu; Jianye Hao; Jiajie Peng (AAAI, 2025)

cfMethylPre: deep transfer learning enhances cancer detection based on circulating cell-free DNA methylation profiling. - Xuchao Zhang; Jing Chen; Yongtian Wang; Xiaofeng Wang; Jialu Hu; Jiajie Peng; Xuequn Shang 001; Yanpu Wang; Tao Wang 082 (Briefings Bioinform., 2025)

MAEST: accurately spatial domain detection in spatial transcriptomics with graph masked autoencoder. - Pengfei Zhu; Han Shu; Yongtian Wang; Xiaofeng Wang; Yuan Zhao; Jialu Hu; Jiajie Peng; Xuequn Shang 001; Zhen Tian; Jing Chen; Tao Wang 082 (Briefings Bioinform., 2025)

scMamba: A Scalable Foundation Model for Single-Cell Multi-Omics Integration Beyond Highly Variable Feature Selection. - Zhen Yuan; Shaoqing Jiao; Yihang Xiao; Jiajie Peng (CoRR, 2025)