Esub8: A novel tool to predict protein subcellular localizations in eukaryotic organisms. - Qinghua Cui; Tianzi Jiang; Bing Liu 008; Songde Ma (BMC Bioinform., 2004)

A combinational feature selection and ensemble neural network method for classification of gene expression data. - Bing Liu 008; Qinghua Cui; Tianzi Jiang; Songde Ma (BMC Bioinform., 2004)

Characterizing the dynamic connectivity between genes by variable parameter regression and Kalman filtering based on temporal gene expression data. - Qinghua Cui; Bing Liu 008; Tianzi Jiang; Songde Ma (Bioinform., 2005)

Protein evolution on a human signaling network. - Qinghua Cui; Enrico O. Purisima; Edwin Wang (BMC Syst. Biol., 2009)

Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases. - Dong Wang; Juan Wang 018; Ming Lu; Fei Song; Qinghua Cui (Bioinform., 2010)

TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs. - Ming Lu; Bing Shi; Juan Wang 018; Qun Cao; Qinghua Cui (BMC Bioinform., 2010)

microRNA evolution in a human transcription factor and microRNA regulatory network. - Chengxiang Qiu; Juan Wang 018; Pengying Yao; Edwin Wang; Qinghua Cui (BMC Syst. Biol., 2010)

TransmiR: a transcription factor-microRNA regulation database. - Juan Wang 018; Ming Lu; Chengxiang Qiu; Qinghua Cui (Nucleic Acids Res., 2010)

miREnvironment Database: providing a bridge for microRNAs, environmental factors and phenotypes. - Qingqing Yang; Chengxiang Qiu; Jie Yang; Qing Wu; Qinghua Cui (Bioinform., 2011)

miR2Gene: pattern discovery of single gene, multiple genes, and pathways by enrichment analysis of their microRNA regulators. - Chengxiang Qiu; Juan Wang 018; Qinghua Cui (BMC Syst. Biol., 2011)

The relationship between rational drug design and drug side effects. - Juan Wang 018; Zhi-xin Li; Chengxiang Qiu; Dong Wang; Qinghua Cui (Briefings Bioinform., 2012)

SpliceDisease database: linking RNA splicing and disease. - Juan Wang 018; Jie Zhang; Kaibo Li; Wei Zhao; Qinghua Cui (Nucleic Acids Res., 2012)

LncRNADisease: a database for long-non-coding RNA-associated diseases. - Geng Chen; Ziyun Wang; Dongqing Wang; Chengxiang Qiu; Mingxi Liu; Xing Chen 001; Qipeng Zhang; Guiying Yan; Qinghua Cui (Nucleic Acids Res., 2013)

HMDD v2.0: a database for experimentally supported human microRNA and disease associations. - Yang Li; Chengxiang Qiu; Jian Tu; Bin Geng; Jichun Yang; Tianzi Jiang; Qinghua Cui (Nucleic Acids Res., 2014)

LncTar: a tool for predicting the RNA targets of long noncoding RNAs. - Jianwei Li; Wei Ma; Pan Zeng; Junyi Wang; Bin Geng; Jichun Yang; Qinghua Cui (Briefings Bioinform., 2015)

Drug-Path: a database for drug-induced pathways. - Hui Zeng; Chengxiang Qiu; Qinghua Cui (Database J. Biol. Databases Curation, 2015)

PPUS: a web server to predict PUS-specific pseudouridine sites. - Yan-Hui Li; Gaigai Zhang; Qinghua Cui (Bioinform., 2015)

An analysis of human microbe-disease associations. - Wei Ma; Lu Zhang; Pan Zeng; Chuanbo Huang; Jianwei Li; Bin Geng; Jichun Yang; Wei Kong; Xuezhong Zhou; Qinghua Cui (Briefings Bioinform., 2017)

NmSEER: A Prediction Tool for 2'-O-Methylation (Nm) Sites Based on Random Forest. - Yiran Zhou; Qinghua Cui; Yuan Zhou (ICIC (1), 2018)

Identification and analysis of the human sex-biased genes. - Sisi Guo; Yuan Zhou; Pan Zeng; Guoheng Xu; Guoqing Wang; Qinghua Cui (Briefings Bioinform., 2018)

AGD: Aneurysm Gene Database. - Ruya Sun; Chunmei Cui; Yuan Zhou; Qinghua Cui (Database J. Biol. Databases Curation, 2018)

Identification and Analysis of Human Sex-biased MicroRNAs. - Chunmei Cui; Weili Yang; Jiangcheng Shi; Yong Zhou; Jichun Yang; Qinghua Cui; Yuan Zhou 018 (Genom. Proteom. Bioinform., 2018)

PTMD: A Database of Human Disease-associated Post-translational Modifications. - Hao-Dong Xu; Yongbo Wang; Shaofeng Lin; Wankun Deng; Di Peng; Qinghua Cui; Yu Xue 001 (Genom. Proteom. Bioinform., 2018)

Comparative Analysis of Human Genes Frequently and Occasionally Regulated by m6A Modification. - Yuan Zhou 018; Qinghua Cui (Genom. Proteom. Bioinform., 2018)

TAM 2.0: tool for MicroRNA set analysis. - Jianwei Li; Xiaofen Han; Yanping Wan; Shan Zhang; Yingshu Zhao; Rui Fan; Qinghua Cui; Yuan Zhou (Nucleic Acids Res., 2018)

miES: predicting the essentiality of miRNAs with machine learning and sequence features. - Fei Song; Chunmei Cui; Lin Gao 006; Qinghua Cui (Bioinform., 2019)

NmSEER V2.0: a prediction tool for 2′-O-methylation sites based on random forest and multi-encoding combination. - Yiran Zhou; Qinghua Cui; Yuan Zhou (BMC Bioinform., 2019)

Combining network topology with transcriptomic data for identifying radiosensitive gene signatures. - Qinghua Cui; Tingting Sun; Zongyao Nie (J. Comput. Methods Sci. Eng., 2019)

LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. - Zhenyu Bao; Zhen Yang 030; Zhou Huang; Yiran Zhou; Qinghua Cui; Dong Dong (Nucleic Acids Res., 2019)

HMDD v3.0: a database for experimentally supported human microRNA-disease associations. - Zhou Huang; Jiangcheng Shi; Yuanxu Gao; Chunmei Cui; Shan Zhang; Jianwei Li; Yuan Zhou; Qinghua Cui (Nucleic Acids Res., 2019)

MISIM v2.0: a web server for inferring microRNA functional similarity based on microRNA-disease associations. - Jianwei Li; Shan Zhang; Yanping Wan; Yingshu Zhao; Jiangcheng Shi; Yuan Zhou; Qinghua Cui (Nucleic Acids Res., 2019)

TransmiR v2.0: an updated transcription factor-microRNA regulation database. - Zhan Tong; Qinghua Cui; Juan Wang 018; Yuan Zhou (Nucleic Acids Res., 2019)

Annotation and curation of the causality information in LncRNADisease. - Kaiwen Jia; Yuanxu Gao; Jiangcheng Shi; Yuan Zhou; Yong Zhou; Qinghua Cui (Database J. Biol. Databases Curation, 2020)

smORFunction: a tool for predicting functions of small open reading frames and microproteins. - Xiangwen Ji; Chunmei Cui; Qinghua Cui (BMC Bioinform., 2020)

m6Acorr: an online tool for the correction and comparison of m6A methylation profiles. - Jianwei Li; Yan Huang; Qinghua Cui; Yuan Zhou 018 (BMC Bioinform., 2020)

Defining the functional divergence of orthologous genes between human and mouse in the context of miRNA regulation. - Chunmei Cui; Yuan Zhou; Qinghua Cui (Briefings Bioinform., 2021)

Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores. - Rui Fan; Qinghua Cui (Bioinform., 2021)

Comparative analysis of aneurysm subtypes associated genes based on protein-protein interaction network. - Ruya Sun; Yuan Zhou; Qinghua Cui (BMC Bioinform., 2021)

A layer-stress learning framework universally augments deep neural network tasks. - Shihao Shao; Yong Liu; Qinghua Cui (CoRR, 2021)

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. - Yongbiao Xue; Yiming Bao; Zhang Zhang 002; Wenming Zhao; Jing-Fa Xiao; Shunmin He; Guoqing Zhang 006; Yixue Li; Guoping Zhao; Runsheng Chen; Shuhui Song; Lina Ma; et al. (Nucleic Acids Res., 2021)

AGTR2, One Possible Novel Key Gene for the Entry of SARS-CoV-2 Into Human Cells. - Chunmei Cui; Chuanbo Huang; Wanlu Zhou; Xiangwen Ji; Fenghong Zhang; Liang Wang; Yuan Zhou; Qinghua Cui (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

1st Place Solution in Google Universal Images Embedding. - Shihao Shao; Qinghua Cui (CoRR, 2022)

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. - Yongbiao Xue; Yiming Bao; Zhang Zhang 002; Wenming Zhao; Jing-Fa Xiao; Shunmin He; Guoqing Zhang 006; Yixue Li; Guoping Zhao; Runsheng Chen; Jingyao Zeng; Yadong Zhang; et al. (Nucleic Acids Res., 2022)

Global Features are All You Need for Image Retrieval and Reranking. - Shihao Shao; Kaifeng Chen; Arjun Karpur; Qinghua Cui; André Araújo 001; Bingyi Cao (ICCV, 2023)

MicroRNA-Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice. - Yicong Shen; Yuanxu Gao; Jiangcheng Shi; Zhou Huang; Rongbo Dai; Yi Fu; Yuan Zhou 018; Wei Kong; Qinghua Cui (Genom. Proteom. Bioinform., 2023)

Deciphering gene contributions and etiologies of somatic mutational signatures of cancer. - Xiangwen Ji; Edwin Wang; Qinghua Cui (Briefings Bioinform., 2023)

Solution Structures of an Electrical Transmission Line Model with Bifurcation and Chaos in Hamiltonian Dynamics. - Jianming Qi; Qinghua Cui; Le Zhang; Yiqun Sun (Int. J. Bifurc. Chaos, 2023)

Defining the single base importance of human mRNAs and lncRNAs. - Rui Fan; Xiangwen Ji; Jianwei Li; Qinghua Cui; Chunmei Cui (Briefings Bioinform., 2023)

A fusion framework of deep learning and machine learning for predicting sgRNA cleavage efficiency. - Yu Liu; Rui Fan; Jingkun Yi; Qinghua Cui; Chunmei Cui (Comput. Biol. Medicine, 2023)

Ratio law: mathematical descriptions for a universal relationship between AI performance and input samples. - Boming Kang; Qinghua Cui (CoRR, 2024)

High-Rank Irreducible Cartesian Tensor Decomposition and Bases of Equivariant Spaces. - Shihao Shao; Yikang Li; Zhouchen Lin; Qinghua Cui (CoRR, 2024)

FreeCG: Free the Design Space of Clebsch-Gordan Transform for Machine Learning Force Fields. - Shihao Shao; Haoran Geng; Zun Wang; Qinghua Cui (ICLR, 2025)

Comprehensive prediction and analysis of human protein essentiality based on a pretrained large language model. - Boming Kang; Rui Fan; Chunmei Cui; Qinghua Cui (Nat. Comput. Sci., 2025)