Biography
Education
Admission Information
Work Experience
Social Position
Research Areas
Scientific research
I was the project leader of the National Key Research and Development Program and one of the early researchers engaged in genome in China. As the class director of the first Genome Science Innovation class in 2009, with the opportunity of the joint training of master's and doctor's degree by South China University of Technology and BGI, I have trained more than 100 high-throughput sequencing research and application talents, who play a key role in leading gene testing enterprises such as BGI, Golden Testing, and Daan Gene. So far, I have hosted or participated in more than 20 national key research and development projects, major special projects and scientific and technological support projects. I have published more than 70 SCI papers, with a total citation of more than 2500 times, in Nat Biotechnol, Bioinformatics, Frontiers in Immunology, Journal of Chemical Information and Modeling, Computational and Structural Biotechnology Journal, Cancers, Front Psychol and other internationally renowned journals. Ten invention patents were applied, 4 were authorized, 16 software Copyrights were obtained, and 1 provincial second prize of scientific and technological progress was awarded.
Research interests:
(1) Development and application of multi-omics big data analysis technology based on artificial intelligence;
(2) mechanism discovery and therapeutic target identification of tumors and infectious diseases based on tissue, single cell, spatiotemporal multi-omics big data and system life regulation;
(3) high-throughput small molecule drug screening and modified siRNA drug design based on artificial intelligence;
(4) Development and application of diagnostic methods and tools for early diagnosis and precision medicine of tumors based on omics.
Courses Taught
Teaching and learning
Undergraduate teaching: Genomics, Systems biology
Graduate teaching: Molecular genetics, molecular biology
Research Project
Selected Publications
- Yin, Feng;Yang, Jing;Luo, Hao;Yu, Tiantian;Lu, Wenhua;Zhao, Mingyue;Du, Hongli;Wen, Shijun;Huang, Peng;Hu, Yumin,Targeting oncogenic activation of FLT3/SREBP/FASN promotes the therapeutic effect of quizartinib involving disruption of mitochondrial phospholipids,Cell Death & Disease,2025
- Tan, Wenchong;Dai, Mingshu;Ye, Shimin;Tang, Xin;Jiang, Dawei;Chen, Dong;Du, Hongli,ENsiRNA: A Multimodality Method for siRNA-mRNA and Modified siRNA Efficacy Prediction Based on Geometric Graph Neural Network,Journal of Molecular Biology,2025
- Yang, Zhengning; Meng, Zhongxuan; Liu, Shangyuan; Chen, Yuxin; Gan, Xuhong; Zhang, Zi-Mei; Luo, Xiaoshan; Yan, Jiahong; Chen, Huijin; Huang, Danqing; Huang, Lihong; Zeng, Xiaomin; Ma, Wenyu; Liu, Jun; Wang, Linlin; Huang, Haotian; Yang, Xinyi; Hu, Mei; Chen, Lin; Du, Hongli,LTO1 and YAE1 regulate MHC-I expression via nonsense-mediated RNA decay in tumor cells,Journal for ImmunoTherapy of Cancer,2025
- Xi, Binbin;Hua, Zhihao;Jiang, Dawei;Chen, Zixi;Wei, Jinfen;Meng, Yuhuan;Du, Hongli,Within-Host Fitness and Antigenicity Shift Are Key Factors Influencing the Prevalence of Within-Host Variations in the SARS-CoV-2 S Gene,Viruses-Basel,2025
- 张利刚;唐冬生;杜红丽,铜代谢和铜死亡的分子机制及相关疾病治疗研究,佛山科学技术学院学报(自然科学版),2025
- Cai, Yi;Zhang, Qian;Tan, Wenchong;Li, Jing;Chen, Dong;Lu, Xiaoyun;Du, Hongli,Comprehensive Drug-Likeness Prediction Using a Pretrained Transformer Model and Multitask Learning,Journal of Chemical Information and Modeling,2025
- Xie, Jianling; Shen, Kaikai; Liang, Wenken; Kuang, Zijian; Shrestha, Raj K.; Hanson, Adrienne R.; Townley, Scott L.; He, Meiling; Yu, Sishu; Zhou, Peiwen; Zhu, Liangzhen; Gong, Zhiwen; Ao, Xiang; Rao, Sushma R.; Zhang, Qing; Chen, Kaijie; Wei, Jinfen; Marri, Shashikanth; Snel, Marten F.; Irani, Swati,Protein disulfide isomerases regulate androgen receptor stability and promote prostate cancer cell growth and survival,Proceedings of the National Academy of Sciences of the United States of America,2025
- Jiang Dawei;Chen Zixi;Du Hongli,Cyclic peptide membrane permeability prediction using deep learning model based on molecular attention transformer,Frontiers in Bioinformatics,2025
- Wan, Yanbin;Huang, Caimei;Feng, Dongyan;Wang, Lv;Lin, Xiding;Zhao, Xuanye;Han, Liya;Zhu, Yanyu;Hao, Lijing;Du, Hongli;Huang, Lizhen*,Characterizing the collateral activity of CRISPR/Cas13 in mammalian cells: Implications for RNA editing and therapeutic applications,International Journal of Biological Macromolecules,2024
- Gong, Xiaocheng;Liu, Yunfei;Liang, Keying;Chen, Zixi;Ding, Ke;Qiu, Li;Wei, Jinfen;Du, Hongli,Cucurbitacin I exerts its anticancer effects by inducing cell cycle arrest via the KAT2a-ube2C/E2F1 pathway and inhibiting HepG2-induced macrophage M2 polarization,Biochemical and Biophysical Research Communications,2024
- Zhang, Ligang;Deng, Ruiting;Guo, Raoqing;Jiang, Yawen;Guan, Yichen;Chen, Caiyue;Zhao, Wudi;Huang, Guobin;Liu, Lian;Du, Hongli;Tang, Dongsheng,Recent progress of methods for cuproptosis detection,Frontiers in Molecular Biosciences,2024
- Zhang, Ligang;Deng, Ruiting;Liu, Lian;Du, Hongli;Tang, Dongsheng,Novel insights into cuproptosis inducers and inhibitors,Frontiers in Molecular Biosciences,2024
- Fu, Shuying;Gong, Xiaocheng;Liang, Keying;Ding, Ke;Qiu, Li;Cen, Huice;Du, Hongli,KLF3 impacts insulin sensitivity and glucose uptake in skeletal muscle,American Journal of Physiology - Cell Physiology,2024
- Yang, Fang;Lin, Qianmeng;Song, Xiaojuan;Huang, Huisi;Chen, Xiaojuan;Tan, Jianwen;Li, Yun;Zhou, Yang;Tu, Zhengchao;Du, Hongli;Zhang, Zhi-min;Ortega, Raquel;Lin, Xiaojing;Patterson, Adam V.;Smaill, Jeff B.;Chen, Yongheng;Lu, Xiaoyun,Discovery of 6-Formylpyridyl Urea Derivatives as Potent Reversible-Covalent Fibroblast Growth Factor Receptor 4 Inhibitors with Improved Anti-Hepatocellular Carcinoma Activity,Journal of Medicinal Chemistry,2024
- Qu, Yimo;Gong, Xiaocheng;Zhao, Ziyuan;Zhang, Zimei;Zhang, Qian;Huang, Yuting;Xie, Qingsong;Liu, Yunfei;Wei, Jinfen;Du, Hongli,Establishment and Validation of Novel Prognostic Subtypes in Hepatocellular Carcinoma Based on Bile Acid Metabolism Gene Signatures Using Bulk and Single-Cell RNA-Seq Data,International Journal of Molecular Sciences,2024
- Jiang, Dawei;Xi, Binbin;Tan, Wenchong;Chen, Zixi;Wei, Jinfen;Hu, Meiling;Lu, Xiaoyun;Chen, Dong;Cai, Hongmin;Du, Hongli,NeoaPred: a deep-learning framework for predicting immunogenic neoantigen based on surface and structural features of peptide-human leukocyte antigen complexes,Bioinformatics,2024
- Gong, Xiaocheng;Liu, Yunfei;Zhang, Qian;Liang, Keying;Wei, Jinfen;Du, Hongli,LHFPL2 Serves as a Potential Biomarker for M2 Polarization of Macrophages in Renal Cell Carcinoma,International Journal of Molecular Sciences,2024
- Zhang, Zi-Mei;Huang, Yuting;Liu, Guanghao;Yu, Wenqi;Xie, Qingsong;Chen, Zixi;Huang, Guanda;Wei, Jinfen;Zhang, Haibo;Chen, Dong;Du, Hongli,Development of machine learning-based predictors for early diagnosis of hepatocellular carcinoma,Scientific Reports,2024
- Wei Jinfen;Yu Wenqi;Chen Juanzhi;Huang Guanda;Zhang Lingjie;Chen Zixi;Hu Meiling;Gong Xiaocheng;Du Hongli,Single-cell and spatial analyses reveal the association between gene expression of glutamine synthetase with the immunosuppressive phenotype of APOE+CTSZ+TAM in cancers,Molecular Oncology,2023
- Lin, Cailing;Chen, Feng;Huang, Dongchao;Li, Wenyan;He, Changsheng;Tang, Yingjun;Li, Xueping;Liu, Can;Han, Liya;Yang, Yunpeng;Zhu, Yongchong;Chen, Ruikang;Shi, Yuanju;Xia, Chenglai;Yan, Zhibin;Du, Hongli;Huang, Lizhen,A universal all-in-one RPA-Cas12a strategy with de novo autodesigner and its application in on-site ultrasensitive detection of DNA and RNA viruses,Biosensors and Bioelectronics,2023
- Liang, Keying;Wang, Qian;Qiu, Li;Gong, Xiaocheng;Chen, Zixi;Zhang, Haibo;Ding, Ke;Liu, Yunfei;Wei, Jinfen;Lin, Shudai;Fu, Shuying;Du, Hongli,Combined Inhibition of UBE2C and PLK1 Reduce Cell Proliferation and Arrest Cell Cycle by Affecting ACLY in Pan-Cancer,International Journal of Molecular Sciences,2023
- Lin Cailing;Chen Feng;Huang Dongchao;Li Wenyan;He Changsheng;Tang Yingjun;Li Xueping;Liu Can;Han Liya;Yang Yunpeng;Zhu Yongchong;Chen Ruikang;Shi Yuanju;Xia Chenglai;Yan Zhibin;Du Hongli;Huang Lizhen,A universal all-in-one RPA-Cas12a strategy with de novo autodesigner and its application in on-site ultrasensitive detection of DNA and RNA viruses,Biosensors and Bioelectronics,2023
- Wei, Jinfen;Yu, Wenqi;Wu, Lei;Chen, Zixi;Huang, Guanda;Hu, Meiling;Du, Hongli,Intercellular Molecular Crosstalk Networks within Invasive and Immunosuppressive Tumor Microenvironment Subtypes Associated with Clinical Outcomes in Four Cancer Types,Biomedicines,2023
- Xi Binbin;Zeng Xi;Chen Zixi;Zeng Jiong;Huang Lizhen;Du Hongli,SARS-CoV-2 within-host diversity of human hosts and its implications for viral immune evasion.,mBio,2023
- Xi, Binbin;Zeng, Xi;Chen, Zixi;Zeng, Jiong;Huang, Lizhen;Du, Hongli,SARS-CoV-2 within-host diversity of human hosts and its implications for viral immune evasion,mBio,2023
- Yao Yao;Wang Xueping;Guan Jian;Xie Chuanbo;Zhang Hui;Yang Jing;Luo Yao;Chen Lili;Zhao Mingyue;Huo Bitao;Yu Tiantian;Lu Wenhua;Liu Qiao;Du Hongli;Liu Yuying;Huang Peng;Luan Tiangang;Liu Wanli;Hu Yumin,Metabolomic differentiation of benign vs malignant pulmonary nodules with high specificity via high-resolution mass spectrometry analysis of patient sera,Nature Communications,2023
- Cao, Yanan; Chen, Lingling; Chen, Hua; Cun, Yupeng; Dai, Xiaofeng; Du, Hongli; Gao, Feng; Guo, Fengbiao; Guo, Yalong; Hao, Pei; He, Shunmin; He, Shunping; He, XiongLei; Hu, Zheng; Hoh, Boon-Peng; Jin, Xin; Jiang, Qian; Jiang, Qinghua; Khan, Asifullah; Kong, Hong-Zhi,Was Wuhan the early epicenter of the COVID-19 pandemic?-A critique,National Science Review,2023
- Yao, Yao;Wang, Xueping;Guan, Jian;Xie, Chuanbo;Zhang, Hui;Yang, Jing;Luo, Yao;Chen, Lili;Zhao, Mingyue;Huo, Bitao;Yu, Tiantian;Lu, Wenhua;Liu, Qiao;Du, Hongli;Liu, Yuying;Huang, Peng;Luan, Tiangang;Liu, Wanli;Hu, Yumin,Metabolomic differentiation of benign vs malignant pulmonary nodules with high specificity via high-resolution mass spectrometry analysis of patient sera,Nature Communications,2023
- Gong, Xiaocheng;Liu, Yunfei;Liang, Keying;Chen, Zixi;Ding, Ke;Qiu, Li;Wei, Jinfen;Du, Hongli,Cucurbitacin I Reverses Tumor-Associated Macrophage Polarization to Affect Cancer Cell Metastasis,International Journal of Molecular Sciences,2023
- Yanan Cao; Lingling Chen; Hua Chen; Yupeng Cun; Xiaofeng Dai; Hongli Du; Feng Gao; Fengbiao Guo; Yalong Guo; Pei Hao; Shunmin He; Shunping He; XiongLei He; Zheng Hu; Boon-Peng Hoh; Xin Jin; Qian Jiang; Qinghua Jiang; Asifullah Khan; Hong-Zhi Kong,Was Wuhan the early epicenter of the COVID-19 pandemic?——a critique,National Science Review,2023
- Yanan Cao; Lingling Chen; Hua Chen; Yupeng Cun; Xiaofeng Dai; Hongli Du; Feng Gao; Fengbiao Guo; Yalong Guo; Pei Hao; Shunmin He; Shunping He; XiongLei He; Zheng Hu; Boon-Peng Hoh; Xin Jin; Qian Jiang; Qinghua Jiang; Asifullah Khan; Hong-Zhi Kong,Was Wuhan the early epicenter of the COVID-19 pandemic?——a critiqueOA,National Science Review,2023
- Lu Shaohua;Lu Hong;Zheng Tingkai;Yuan Huiming;Du Hongli;Gao Youhe;Liu Yongtao;Pan Xuanzhen;Zhang Wenlu;Fu Shuying;Sun Zhenghua;Jin Jingjie;He QingYu;Chen Yang;Zhang Gong,A multi-omics dataset of human transcriptome and proteome stable reference.,Scientific data,2023
- Wei Jinfen;Yu Wenqi;Chen Juanzhi;Huang Guanda;Zhang Lingjie;Chen Zixi;Hu Meiling;Gong Xiaocheng;Du Hongli,Single-cell and spatial analyses reveal the association between gene expression of glutamine synthetase with the immunosuppressive phenotype of APOE+CTSZ+TAM in cancers.,Molecular oncology,2023
- Lu, Shaohua;Lu, Hong;Zheng, Tingkai;Yuan, Huiming;Du, Hongli;Gao, Youhe;Liu, Yongtao;Pan, Xuanzhen;Zhang, Wenlu;Fu, Shuying;Sun, Zhenghua;Jin, Jingjie;He, Qing-Yu;Chen, Yang;Zhang, Gong,A multi-omics dataset of human transcriptome and proteome stable reference,Scientific Data,2023
- Wei, Jinfen;Yu, Wenqi;Chen, Juanzhi;Huang, Guanda;Zhang, Lingjie;Chen, Zixi;Hu, Meiling;Gong, Xiaocheng;Du, Hongli,Single-cell and spatial analyses reveal the association between gene expression of glutamine synthetase with the immunosuppressive phenotype of APOE plus CTSZ plus TAM in cancers,Molecular Oncology,2023
- Xi, Binbin;Meng, Yuhuan;Jiang, Dawei;Bai, Yunmeng;Chen, Zixi;Qu, Yimo;Li, Shuhua;Wei, Jinfen;Huang, Lizhen;Du, Hongli,Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2,Viruses-Basel,2022
- Lin, Shudai;Qiu, Li;Liang, Keying;Zhang, Haibo;Xian, Mingjian;Chen, Zixi;Wei, Jinfen;Fu, Shuying;Gong, Xiaocheng;Ding, Ke;Zhang, Zihao;Hu, Bowen;Zhang, Xiquan;Duan, Yuyou;Du, Hongli,KAT2A/E2F1 Promotes Cell Proliferation and Migration via Upregulating the Expression of UBE2C in Pan-Cancer,Genes,2022
- Lai, Yanzhen;Wang, Yu;Wu, Yaxian;Wu, Meng;Xing, Shan;Xie, Ying;Chen, Shulin;Li, Xiaohui;Zhang, Ao;He, Yi;Li, Huilan;Dai, Shuqin;Wang, Junye;Lin, Shudai;Bai, Yunmeng;Du, Hongli;Liu, Wanli,Identification and Validation of Serum CST1 as a Diagnostic Marker for Differentiating Early-Stage Non-Small Cell Lung Cancer from Pulmonary Benign Nodules,Cancer Control,2022
- Tang, Deyou;Li, Yucheng;Tan, Daqiang;Fu, Juan;Tang, Yelei;Lin, Jiabin;Zhao, Rong;Du, Hongli;Zhao, Zhongming,KCOSS: an ultra-fast k-mer counter for assembled genome analysis,Bioinformatics,2022
- Wei, Jinfen;Xie, Qingsong;Qu, Yimo;Huang, Guanda;Chen, Zixi;Du, Hongli,scWizard: A web-based automated tool for classifying and annotating single cells and downstream analysis of single-cell RNA-seq data in cancers,Computational and Structural Biotechnology Journal,2022
- He, Changsheng;Lin, Cailing;Mo, Guosheng;Xi, Binbin;Li, Anan;Huang, Dongchao;Wan, Yanbin;Chen, Feng;Liang, Yufeng;Zuo, Qingxia;Xu, Wanqing;Feng, Dongyan;Zhang, Guanting;Han, Liya;Ke, Changwen;Du, Hongli;Huang, Lizhen,Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform,Biosensors and Bioelectronics,2022
- Xu, Wanqing;Zuo, Qingxia;Feng, Dongyan;He, Changsheng;Lin, Cailing;Huang, Dongchao;Wan, Yanbin;Chen, Feng;Mo, Guosheng;Sun, Qi;Du, Hongli;Huang, Lizhen,Validation Study to Determine the Accuracy of Widespread Promoterless EGFP Reporter at Assessing CRISPR/Cas9-Mediated Homology Directed Repair,Current Issues in Molecular Biology,2022
- Wei, Jinfen;Hu, Meiling;Du, Hongli,Improving Cancer Immunotherapy: Exploring and Targeting Metabolism in Hypoxia Microenvironment,Frontiers in Immunology,2022
- Jin, Jingjie;Chen, Zixi;Liu, Jinchao;Du, Hongli;Zhang, Gong,Towards an accurate and robust analysis pipeline for somatic mutation calling,Frontiers in Genetics,2022
- Zuo, Qingxia;Xu, Wanqing;Wan, Yanbin;Feng, Dongyan;He, Changsheng;Lin, Cailing;Huang, Dongchao;Chen, Feng;Han, Liya;Sun, Qi;Chen, Dong;Du, Hongli;Huang, Lizhen,Efficient generation of a CYP3A4-T2A-luciferase knock-in HepaRG subclone and its optimized differentiation,Biomedicine & Pharmacotherapy,2022
- Wei Jinfen;Hu Meiling;Du Hongli,Improving Cancer Immunotherapy: Exploring and Targeting Metabolism in Hypoxia Microenvironment,Frontiers in Immunology,2022
- Ding Ke;He Youhua;Wei Jinfen;Fu Shuying;Wang Jiajian;Chen Zixi;Zhang Haibo;Qu Yimo;Liang Keying;Gong Xiaocheng;Qiu Li;Chen Dong;Xiao Botao;Du Hongli,A score of DNA damage repair pathway with the predictive ability for chemotherapy and immunotherapy is strongly associated with immune signaling pathway in pan-cancer,Frontiers in Immunology,2022
- Ding, Ke;He, Youhua;Wei, Jinfen;Fu, Shuying;Wang, Jiajian;Chen, Zixi;Zhang, Haibo;Qu, Yimo;Liang, Keying;Gong, Xiaocheng;Qiu, Li;Chen, Dong;Xiao, Botao;Du, Hongli,A score of DNA damage repair pathway with the predictive ability for chemotherapy and immunotherapy is strongly associated with immune signaling pathway in pan-cancer,Frontiers in Immunology,2022
- He Changsheng;Lin Cailing;Mo Guosheng;Xi Binbin;Li An′an;Huang Dongchao;Wan Yanbin;Chen Feng;Liang Yufeng;Zuo Qingxia;Xu Wanqing;Feng Dongyan;Zhang Guanting;Han Liya;Ke Changwen;Du Hongli;Huang Lizhen,Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform,Biosensors and Bioelectronics,2022
- Wei Jinfen;Xie Qingsong;Qu Yimo;Huang Guanda;Chen Zixi;Du Hongli,scWizard: A web-based automated tool for classifying and annotating single cells and downstream analysis of single-cell RNA-seq data in cancers,Computational and Structural Biotechnology Journal,2022
Achievements
Patent
Honor
Software achievement