姓名：陈实富
学历/职称：工学博士/教授级高级工程师
出生年月：1984年12月
毕业学校：中国科学院大学
学科专业：模式识别与智能系统
电话/微信：13510427830
mail：chen@haplox.com
个人简历：
陈实富，博士，正高级工程师。海普洛斯集团创始人兼首席技术官，赣南医科大学特聘教授，广东省肿瘤基因组学和肿瘤生物信息学工程技术中心主任。2019年深圳市青年科技奖获得者，获评2022广东省创新达人，以项目负责人身份获2022深圳科技进步奖，以核心成员获中国图象图形学学会自然科学二等奖，连续四年入选全球前2%顶尖科学家榜单（全学科年度榜单前5000名，肿瘤学和生物信息学方向）和中国高被引作者（计算机科学方向）。曾任英伟达系统工程师，发起了开源项目组OpenGene，开发了超过10款热门生物信息学软件，在STTT, iMeta, Nat Comm, Can Res, BIB, Bioinformatics等著名期刊发表论文60余篇，含近年中国生物医学领域最高引用论文（单篇引用2万多次，第一作者兼通讯作者）。在生物信息学和肿瘤标志物领域拥有数十项发明专利和软件著作权。主持多项广东省和深圳市重点研发项目，主持项目获批经费超过2000万元。参与创立高水平国际期刊《iMeta》(IF=33.2)并任执行副主编，任《International Open Medical Journal》副主编，《Research》青年编委，是中国抗癌协会基因诊断专业委员会委员，肿瘤测序及大数据分析专委会委员，中国工业与应用数学学会“数学与产业专业委员会”委员。
研究方向：生物信息学，高性能计算，医学人工智能
科研项目：
(1) 中华人民共和国科学技术部, 国家重大科技专项,结直肠癌多组学数据集构建,
2025-11 至 2028-10, 300万元, 在研, 参与
(2) 中华人民共和国科学技术部, 国家重大科技专项, 于肿瘤整体生态观的结直肠癌免疫
治疗方案优化研究, 2024-08 至 2028-07, 414万元, 在研, 参与
(3) 广东省科学技术厅, 广东省重点领域研发计划, 粤科资字〔2023〕121号, 基于液体活检的肿瘤实时监测分子诊断产品研发项目, 2023-05 至 2026-05, 500万元, 在研, 主持
一作或通讯代表性论文（*为通讯作者）：
Huaichao Luo, et al, Shifu Chen*, Large-Scale TCR Repertoire Profiling Unveils Tumor-Specific Signals for Diagnosing Indeterminate Pulmonary Nodules, Cancer Research, 2025.
Huanming Shen, Zhongchun Zhou, Xiaoni Zhang, Mingyan Xu, Xiaofang Jiang, Wenjian Qin, Shifu Chen*, Comparative analysis of pyrosequencing and next-generation sequencing for assessing MGMT methylation in glioma patients, Journal of Neuro-Oncology, 2025
Weihua Xiao, Qiong Chen, Chunjiao Liu, Yueer Yu, Tianliang Liu, Yang Jin, Haifen Ma, Shifu Chen*, Chao Jiang, Gut microbiota in cancer: From molecular mechanisms to precision medicine applications. iMeta, 2025
Xuebin Wan, Dan Wang, Xiaoni Zhang, Mingyan Xu, Yuying Huang, Wenjian Qin, Shifu Chen*, Unleashing the power of urine‑based biomarkers in diagnosis, prognosis and monitoring of bladder cancer, International Journal of Oncology, 2025
Ming Liu, Tianhao Mu, Jia Gu, Mingyan Xu, Shifu Chen*, The Method of Minimal Residual Disease Detection With Circulating Tumor DNA and Its Clinical Applications in Colorectal Cancer. Cancer Reports, 2025
Defeng Bai et al, Shifu Chen*, et al, Yongxin Liu, EasyMetagenome: A user‐friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research. iMeta. 2025
Yao Wang et al, Shifu Chen*, et al, Yongxin Liu, iMeta Conference 2024: Building an innovative scientific research ecosystem for microbiome and One Health. iMeta. 2024
Yujie Shi, Bo Hu, Mingyan Xu, Yunhan Yao, Shuaiqiang Gao, Xiang Xia, Xikai Deng, Jianfeng Liu, Jia Gu, Shifu Chen*. Application of Quantitative Histomorphometric Features in Computational Pathology. Interdisciplinary Medicine. 2024.
Mingyao Lai, Tianhao Mu, Ming Liu, Qingjun Hu, Juan Li, Tanxiao Huang, Yingmei Li, Shifu Chen*, Linbo Cai. Personalized therapy guided by longitudinal liquid biopsies for treatment of leptomeningeal disease from lung adenocarcinoma: A case report. Oncology Letters. 2024.
Bosen Zhu, Ming Liu, Tianhao Mu, Wentao Li, Junqi Ren, Xiangtao Li, Yi Liang, Ziyi Yang, Yulin Niu, Shifu Chen*, Junqiong Lin. Quadruple primary tumors in a lynch syndrome patient surviving more than 26 years with genetic analysis: a case report and literature review. Frontiers in Oncology. 2024.
Shifu Chen*, Yaru Chen, Zhouyang Wang, Wenjian Qin, Jing Zhang, Heera Nand, Jishuai Zhang, Jun Li, Xiaoni Zhang, Xiaoming Liang and Mingyan Xu, Efficient sequencing data compression and FPGA acceleration based on a two-step framework, Frontiers in Genetics.
Limin Xu, Jing Zhang, Yiqian He, Qianqian Yang, Tianhao Mu, Qiushi Guo, Yingqiang Li, Tian Tong, Shifu Chen*, Richard D. Ye*, ScRNAPip: A systematic and dynamic pipeline for single-cell RNA sequencing analysis, iMeta, 2023.
Shifu, Chen*, Ultrafast one pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta (2023): e107.
Guowu, Wu, et al., Shifu Chen*, The genomic characteristics of RET fusion positive tumors in Chinese non-small cell lung cancer (NSCLC) patients. Journal of Cancer Research and Clinical Oncology 149.3 (2023): 1019-1028.
Huaichao Luo, Ruiling Zu, Ziru Huang, Yingqiang Li, Yulin Liao, Wenxin Luo, Peng Zhou, Dongsheng Wang, Shifu Chen*, Weimin Li* & Jian Huang*, Characteristics and significance of peripheral blood T-cell receptor repertoire features in patients with indeterminate lung nodules. Signal Transduction and Targeted Therapy.
Qi Zhao#, Feng Wang#, Yan-Xing Chen#, Shifu Chen# et al , Comprehensive profiling of 1015 patients’ exomes reveals genomic-clinical associations in colorectal cancer. Nature Communications, 2022.
Shifu Chen* et al. A Computational Toolset for Rapid Identification of SARS-CoV-2, other Viruses, and Microorganisms from Sequencing Data. Briefing in Bioinformatics
Shaokun Liu et al, Shifu Chen*. The Genomic Characteristics of ALK Fusion Positive Tumors in Chinese NSCLC Patients. Frontiers in Oncology, 2020.
Jixian Li et al., Shifu Chen*, Da Wu*. Targeted deep sequencing helps distinguish independent primary tumors from intrapulmonary metastasis for lung cancer diagnosis. Journal of Cancer Research and Clinical Oncology, 2020.
Jingxian Duan et al. Shifu Chen*, Genetic Biomarkers For Hepatocellular Carcinoma In The Era Of Precision Medicine, Journal of hepatocellular carcinoma, 2019.
Kaibin Huang et al, Shifu Chen*, Ligang Xia. Circulating tumor DNA sequencing for colorectal cancers: A comparative analysis of colon cancer and rectal cancer data. Cancer Biomarkers 2019, DOI: 10.3233/CBM-190257
Jingxian Duan et al, Shifu Chen*. Genetic Biomarkers For Hepatocellular Carcinoma In The Era Of Precision Medicine. Journal of Hepatocellular Carcinoma, 2019, DOI: 10.2147/JHC.S224849
Shifu Chen*, Yanqing, Yaru Chen, et al. gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data. BMC Bioinformatics, 2019, DOI: 10.1186/s12859-019-3280-9
Shifu Chen*, Yanqing Zhou, Yaru Chen, Jia Gu. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bionformatics, 2018. DOI10.1093/bioinformatics/bty560.
Shifu Chen*, Ming Liu, Tanxiao Huang, Wenting Liao, Mingyan Xu, Jia Gu. GeneFuse: detection and visualization of target gene fusions from DNA sequencing data. International Journal of Biological Sciences; 14(8):843-848. doi:10.7150/ijbs.24626..
Shifu Chen*, Ming Liu, Yanqing Zhou. Bioinformatics Analysis for Cell-Free Tumor DNA Sequencing Data. Computational Systems Biology: Methods and Protocols, Methods in Molecular Biology, vol. 1754. 2018. DOI 10.1007/978-1-4939-7717-8.
Xiao Sun, Tanxiao Huang, Fangsheng Cheng, Kaibing Huang, Ming Liu, Wan He, Mingwei Li, Xiaoni Zhang, Mingyan Xu, Shifu Chen*, Ligang Xia. Monitoring colorectal cancer following surgery using plasma circulating tumor DNA. Oncology Letters, 2018.
Ruilian Xu, Guolin Zhong, Tanxiao Huang, Wan He, Cheng Kong, Xiaoni Zhang, Ying Wang, Ming Liu, Mingyan Xu, Shifu Chen*. Sequencing of circulating tumor DNA for dynamic monitoring of gene mutations in advanced non-small cell lung cancer. Oncology Letters, 15, 3726-3734. 2018
Shifu Chen*, Tanxiao Huang, Tiexiang Wen, Hong Li, Mingyan Xu, Jia Gu. MutScan: Fast detection and visualization of target mutations by scanning FASTQ data. Jan 2018, BMC Bioinformatics 19(1)
Shifu Chen, Tanxiao Huang, Yanqing Zhou, Yue Han, Mingyan Xu and Jia Gu. AfterQC: automatic filtering, trimming, error removing and quality control for fastq data. BMC Bioinformatics Vol 18 Suppl 4, 2017.
Shifu Chen, Ming Liu, Xiaoni Zhang, Renwen Long, Yixing Wang, Yue Han, Shiwei Zhang and Jia Gu. SeqMaker: A Study of Cell-free DNA Fragmentation Pattern and Its Application in DNA Sample Type Classification. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2017
发明专利：
一种基于单肿瘤样本检测微卫星不稳定性的微卫星位点组合及其应用, ZL 2023 1 1818272.8
一种测序样本的标识方法及其应用, ZL2018 1 0579424.6
