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个人简介

张靖,男,模式识别与智能系统博士,北京航空航天大学医学科学与工程学院教授、博导、“国家青年**计划”获得者(海外优青),生物信息与智能计算学科带头人,世界华人生物医学工程学会青年委员,中国科学院青年创新促进会成员。 2002年6月和2005年6月于哈尔滨理工大学分别获得自动控制学士学位和计算机应用技术硕士学位,2009年博士毕业于中国科学院自动化研究所、模式识别与智能系统国家重点实验室。于2009年7月入职中国科学院北京基因组所任助理研究员,2014年1月升任副研究员。2014年获得中国科学院“卓越青年科学家人才”,入选中国科学院青年创新促进会,获得2014年度“卢嘉锡青年人才奖”。2015年7月入职美国哥伦比亚大学(Columbia University)任Associate Research Scientist。2019年入职北京航空航天大学任教授。 多年来一直从事数据挖掘、机器学习、人工智能方法的研究以及在生物医药领域的应用。主要集中在如何开发、应用机器学习方法从充满噪音的高通量、高纬度的海量数据中提取特征,挖掘有用信息,以解决肿瘤发生发展、疫苗研发方面的实际问题。发表SCI论文30多篇,累计引用1200多次,其中一作、并列一作或通讯作者论文18篇,代表作包括世界顶级刊物Cell(封面文章,IF=41.582),Brain (IF=13.501),Annals of Oncology(IF=32.976), Neuro Oncology(2篇,其中一篇封面文章,IF=12.300),Cell Research(IF=25.617), Nucleic Acid Research (IF=16.971), National Science Review(IF=12.413)等刊物。先后承担国家自然科学基金、国家级人才项目、部级人才项目,成果已先后开始应用于临床诊疗(TMZ化疗效果预测标记物miR-181d已经被列入卫健委-《脑胶质瘤临床诊疗指南2022版》)。多次受邀出席国际会议作基因组大数据挖掘与机器学习的报告。2019年从美国哥伦比亚大学全职回国组建实验室,目前已建立了一支由博士、硕士、本科生不同梯队组成的研究队伍;与中国人民解放军总医院、北京大学肿瘤医院、北京天坛医院、美国哥伦比亚大学建立起全方位的合作。 教育背景 2005.9-2009.6 中国科学院自动化研究所 控制科学与工程 博士学位 博士研究生毕业 2002.9-2005.6 哈尔滨理工大学 计算机科学与技术 硕士学位 硕士研究生毕业 1998.9-2002.6 哈尔滨理工大学 控制科学与工程 学士学位 大学本科毕业 工作经历 2019.6-至今 北京航空航天大学 教授 2015.7-2019.6 Columbia University Associate Research Scientist 2014.1-2015.6 中国科学院北京基因组研究所 副研究员 2009.7-2013.12 中国科学院北京基因组研究所 助理研究员 社会兼职 2014.1 -- 至今 中国科学院青年创新促进会成员 2020.12 -- 至今 世界华人生物医学工程协会青年委员

研究领域

[1] 深度学习方法开发,以解决肿瘤发生发展,预后,免疫相关科学问题 集中在开发深度学习(Deep Learning)模型和方法,特别是概率模型和新颖的推断方法,通过新的深度学习方法学习实体肿瘤多组学数据的内在规律和表示层次,解决肿瘤发生发展,预后,免疫相关的科学问题。 [2] 机器学习方法应用,研究免疫系统与肿瘤发生发展之间的交互作用关系 机器学习(Machine Learning)是人工智能技术的核心,主要集中在开展各种机器学习方法的应用,通过挖掘多组学数据研究免疫系统如何与肿瘤细胞之间相互作用,开发出能杀死肿瘤细胞的疫苗。 [3] 机器学习方法开发,开发针对肿瘤和病毒的多肽疫苗 新的机器学习方法的开发,主要集中在开发新的机器学习方法,从高通量组学数据中进行特征提取与模式识别,鉴定具有高质量免疫原性的肿瘤疫苗、病毒疫苗等,并进行体外、动物实验,开发疫苗,防止重大疾病和传染病的产生。 [4] 转基因动物模型构建, 从分子生物学的机制层面研究肿瘤免疫、多肽疫苗相关的科学问题构建转基因动物模型,在活体动物上验证大规模计算发现。 [5] 生物医学诊疗平台的开发 开发生物医学诊疗平台,实现人工智能个性化治疗。

近期论文

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Lin Li,Zhongpeng Zhao,Xiaolan Yang,Zhongyi Su,Wendong Li,Shaolong Chen,Lu Wang,Ting Sun,Chen Du,Ziyi Li,Zeqian Yang,Min Li,Tiecheng Wang.A Newly Identified Spike Protein Targeted Linear B‐Cell Epitope Based Dissolvable Microneedle Array Successfully Eliciting Neutralizing Activities against SARS‐CoV‐2 Wild‐Type Strain in Mice:Advanced Science,2023:e2207474 Ting Sun,Yuchen Wang,Xiaoyu Song,Ruili Li,Fanghua Mei,Mengliu Yang,Xiaojie Huang,Yan Li,Xuwei Zhou,Haoyu Wang,Wendong Li,Jing Li,Lu Wang.Impaired Humoral Immunity Identified in Inactivated SARS-CoV-2 Vaccine Recipients without Anti-Spike RBD Antibodies:Microbiology Spectrum,2023(e0278322) Jia Liu,Zhuojun Liu,Jing Zhang,Xiaofang Chen,Junge Chen.Ibrutinib inhibits angiogenesis and tumorigenesis in a BTK-independent manner:Pharmaceutics,2022,14(9):1876 Qiao Zhang,Qingzu Jia.Neoantigens in precision cancer immunotherapy: from identification to clinical applications:Chinese Medical Journal,2022 Guanzhang Li,Lin Li,Yiming Li,Zenghui Qian,Fan Wu,Yufei He,Haoyu Jiang,Renpeng Li,Di Wang,You Zhai,Zhiliang Wang,Tao Jiang.An MRI radiomics approach to predict survival and tumour-infiltrating macrophages in gliomas:Brain,2022,145(3):1151-1161 Wendong Li,Ting Sun,Muyang Li,Yufei He,Lin Li,Lu Wang,Haoyu Wang,Jing Li,Hao Wen,Yong Liu,Yifan Chen.GNIFdb: a neoantigen intrinsic feature database for glioma.[期刊]:Database-Oxford,2022:baac0 Zixuan Xiao,Wei Zhang,Guanzhang Li,Wendong Li,Lin Li,Ting Sun,Yufei He,Guang Liu,Lu Wang,Xiaohan Han,Hao Wen,Yong Liu,Yifan Chen,Haoyu Wang,Jing Li.Multiomics Analysis Reveals the Prognostic Non-tumor Cell Landscape in Glioblastoma Niches.[期刊]:Frontiers in Genetics,2021,12:741325 Ting Sun,Yufei He,Wendong Li,Guang Liu,Lin Li,Lu Wang,Zixuan Xiao,Xiaohan Han,Hao Wen,Yong Liu,Yifan Chen,Haoyu Wang,Jing Li.neoDL: a novel neoantigen intrinsic feature-based deep learning model identifies IDH wild-type glioblastomas with the longest survival.[期刊]:BMC Bioinformatics,2021,22(1):382 Wendong Li,Lin Li,Ting Sun,Yufei He,Guang Liu,Zixuan Xiao.Spike protein-based epitopes predicted against SARS-CoV-2 through literature mining.[期刊]:Medicine in Novel Technology and Devices,2020 Lin Li,Ting Sun,Yufei He,Wendong Li.Epitope-based peptide vaccines predicted against novel coronavirus disease caused by SARS-CoV-2.[期刊]:Virus Research,2020 Francesca Pia Caruso,Luciano Garofano,Fulvio D'Angelo,Kai Yu,Fuchou Tang,Jinzhou Yuan,Jing Zhang,Luigi Cerulo,Stefano M Pagnotta,Davide Bedognetti,Peter A Sims,Mario Suvà,Anna Lasorella,Xiao-Dong Su.A map of tumor-host interactions in glioma at single-cell resolution.[期刊]:Gigascience,2020,9(10):giaa109 Xiaocui Xu,Guoqiang Li,Congru Li,Jing Zhang,Qiang Wang,David K Simmons,Xuepeng Chen,Naveen Wijesena,Wei Zhu,Zhanyang Wang,Zhenhua Wang,Bao Ju,Weimin Ci,Xuemei Lu,Daqi Yu,Qian-fei Wang,Neelakanteswar Aluru,Paola Oliveri,Yong E Zhang,Mark Q Martindale.Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis.[期刊]:National Science Review,2019,nwz064 Jing Zhang,Francesca P. Caruso,Jason K. Sa,Sune Justesen,Do-Hyun Nam,Peter Sims.The combination of neoantigen quality and T lymphocyte infiltrates identifies glioblastomas with the longest survival.[期刊]:Communications Biology,2019,2:135 Fulvio D'Angelo,Michele Ceccarelli,Tala,Luciano Garofano,Jing Zhang,Véronique Frattini,Francesca P Caruso,Genevieve Lewis,Kristin D Alfaro,Luc Bauchet,Giulia Berzero,David Cachia,Mario Cangiano,Laurent Capelle,John de Groot,Francesco DiMeco,Fran?ois Ducray,Walid Farah,Gaetano Finocchiaro,Stéphane Goutagny,Carlos Kamiya-Matsuoka,Cinzia Lavarino,Hugues Loiseau,Véronique Lorgis,Carlo E Marras,Ian McCutcheon,Do-Hyun Nam,Susanna Ronchi,Veronica Saletti,Romuald Seizeur,John Slopis,Mariona Su?ol,Fanny Vandenbos,Pascale Varlet,Dominique Vidaud,Colin Watts,David E Reuss,Seung-Ki Kim,Viviane Tabar,David Meyronet,Karima Mokhtari,Héctor Salvador,Krishna P. Bhat,Marica Eoli,Marc Sanson.The molecular landscape of glioma in patients with Neurofibromatosis 1.[期刊]:Nature Medicine,2018,25(1):176-187 Yu Ren,Yun-fei Wang,Jing Zhang,Qi-xue Wang,Lei Han.Targeted design and identification of AC1NOD4Q to block activity of HOTAIR by abrogating the scaffold interaction with EZH2.[期刊]:Clinical Epigenetics,2019,11(29) Jason K. Sa,Seung Won Choi,Junfei Zhao,Yeri Lee,Jing Zhang,Doo‐Sik Kong,Jung Won Choi,Ho Jun Seol,Jung‐Il Lee,Antonio Iavarone,Raul Rabadan.Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations.[期刊]:International Journal of Cancer,2019,144(12):3023-3030 FapingShen,ChunyanSong,YunmianLiu,JingZhang.IGFBP2 Promotes Neural Stem Cell Maintenance and Proliferation Differentially Associated with Glioblastoma Subtypes.[期刊]:Brain Research,2019,1704:174-186 Qixue Wang,Jinquan Cai,Chuan Fang,Chao Yang,Junhu Zhou,Yanli Tan,Yunfei Wang,Yansheng Li,Xiangqi Meng,Kai Zhao,Kaikai Yi,Sijing Zhang,Jianning Zhang.Mesenchymal glioblastoma constitutes a major ceRNA signature in the TGF-β pathway.[期刊]:Theranostics,2018,8(17):4733-4749 Véronique Frattini,Stefano M. Pagnotta,Tala,Jerry J. Fan,Marco V. Russo,Sang Bae Lee,Luciano Garofano,Jing Zhang,Peiguo Shi,Genevieve Lewis,Heloise Sanson,Vanessa Frederick,Angelica M. Castano,Luigi Cerulo,Delphine C. M. Rolland,Raghvendra Mall,Karima Mokhtari,Kojo S.J. Elenitoba-Johnson,Marc Sanson,Xi Huang,Michele Ceccarelli.A metabolic function of FGFR3-TACC3 gene fusions in cancer.[期刊]:Nature,2018,553(7687):222-227 Qin Jinhua,Wang Shuyong,Zhang Wencheng,Duan Jialei,Zhang Jing,Wang Xin,Yan Fang,Chang Mingyang,Liu Xiaofang,Feng Bo,Liu Jiang.Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules.[期刊]:Cell stem cell,2016,19(4):449-461 Chen Ke,Zhang Jing,Guo Zhongqiang,Ma Qin,Xu Zhengzheng,Zhou Yuanyuan,Xu Ziying,Li Zhongwu,Liu Yiqiang,Ye Xiongjun,Li Xuesong,Yuan Bifeng,Ke Yuwen,He Chuan.Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer.[期刊]:Cell Research,2015,26:103-118 Han Haibo,Du Yantao,Zhao Wei,Li Sheng,Chen Dongji,Zhang Jing,Liu Jiang,Suo Zhenhe,Bian Xiuwu,Xing Baocai.PBX3 is targeted by multiple miRNAs and is essential for liver tumour-initiating cells.[期刊]:Nature Communications,2015:8271 Zhou Xuan,Ren Yu,Zhang Jing,Zhang Chuanbao,Zhang Kailiang,Han Lei,Kong Lingping,Wei Jianwei,Chen Luyue,Yang Jingxuan,Wang Qixue,Zhang Jianning,Yang Yuqi.HOTAIR is a therapeutic target in glioblastoma.[期刊]:Oncotarget,2015,6:8353-8365 Zou Dong,Sun Shixiang,Zhang Zhang,Li Rujiao,Liu Jiang.MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.[期刊]:Nucleic Acids Research,2015,43(Database issue):D54-D58 Wang Lu,Zhang Jun,Duan Jialei,Gao Xinxing,Zhu Wei,Lu Xingyu,Yang Lu,Zhang Jing,Li Guoqiang,Ci Weimin,Li Wei,Zhou Qi,Aluru Neel,Tang Fuchou,He Chuan.Programming and inheritance of parental DNA methylomes in mammals.[期刊]:Cell,2015,157(4) Li Guoqiang,Ci Weimin,Karmakar Subhradip,Chen Ke,Dhar Ruby,Fan Zhixiang,Guo Zhongqiang,Zhang Jing,Ke Yuwen,Wang Lu,Zhuang Min,Hu Shengdi,Li Xuesong,Zhou Liqun,Li Xianghong,Calabrese MatthewF,Watson EdmondR,Prasad SandipM,Rinker-Schaeffer Carrie,Eggener ScottE,Stricker Thomas,Tian Yong,Schulman BrendaA.SPOP promotes tumorigenesis by acting as a key regulatory hub in kidney cancer.[期刊]:Cancer Cell,2015,25(4):455-468 Lin Yi,Zhang Guozhen,Zhang Jing,Gao Guangzu,Li Min,Chen Yong,Wang Jiangfei,Li Guilin,Song Sonya-Wei,Qiu Xiaoguang,Wang Yunjie.A panel of four cytokines predicts the prognosis of patients with malignant gliomas.[期刊]:Journal of Neuro-Oncology,2013,114(2):199-208 Jiang Lan,Zhang Jing,Wang Jing-Jing,Wang Lu,Zhang Li,Li Guoqiang,Yang Xiaodan,Ma Xin,Sun Xin,Cai Jun,Zhang Jun,Huang Xingxu,Yu Miao,Wang Xuegeng,Liu Feng,Wu Chung-I,He Chuan,Zhang Bo.Sperm, but Not Oocyte, DNA Methylome Is Inherited by Zebrafish Early Embryos.[期刊]:Cell,2013,153(4):773-784 Zhang Wei,Zhang Jing,Yan Wei,You Gan,Bao Zhaoshi,Li Shouwei,Kang Chunsheng,Jiang Chuanlu,You Yongping,Zhang Yuxiang,Chen ClarkC.Whole-genome microRNA expression profiling identifies a 5-microRNA signature as a prognostic biomarker in Chinese patients with primary glioblastoma multiforme.[期刊]:Cancer,2013,119(4):814-824 Zhang Jun-Xia,Zhang Jing,Yan Wei,Wang Ying-Yi,Han Lei,Yue Xiao,Liu Ning,You Yong-Ping.Unique genome-wide map of TCF4 and STAT3 targets using ChIP-seq reveals their association with new molecular subtypes of glioblastoma.[期刊]:Neuro-Oncology,2013,15(3):712-719 Zhang Wei,Zhang Jing,Hoadley Katherine,Kushwaha Deepa,Ramakrishnan Valya,Li Shouwei,Kang Chunsheng,You Yongping,Jiang Chuanlu.MiR-181d: Predictive glioblastoma biomarker that downregulates MGMT expression.[期刊]:Neuro-Oncology,2012,14(6):712-719 Li Yuchen,Jiang Tao,Zhang Jing,Zhang Bin,Yang Wei,You Gan,Xu Kaiyu,Wu Jing,Luo Chenghua.Elevated serum antibodies against insulin-like growth factor-binding protein-2 allow detecting early-stage cancers: evidences from glioma and colorectal carcinoma studies.[期刊]:Annals of Oncology,2012,23(9):2415-2422 Tao Yong,Ruan Jue,Yeh Shiou-Hwei,Lu Xuemei,Wang Yu,Zhai Weiwei,Cai Jun,Ling Shaoping,Gong Qiang,Chong Zecheng,Qu Zhengzhong,Li Qianqian,Liu Jiang,Yang Jin,Zheng Caihong,Zeng Changqing,Wang Hurng-Yi,Zhang Jing,Wang Sheng-Han,Hao Lingtong,Dong Lili,Li Wenjie,Sun Min,Zou Wei,Yu Caixia,Liu Guojing,Jiang Lan,Xu Jin,Huang Huanwei,Li Chunyan,Mi Shuangli,Zhang Bing,Zhao Wenming,Hu Songnian,Zhuang Shi-Mei,Shen Yang,Shi Suhua,Brown Christopher,White Kevin P.,Chen Pei-Jer.Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data.[期刊]:Proc Natl Acad Sci U S A,2011,108(29):12042-12047 Fan Ming,Liu Bing,Jiang Xingpeng,Zhao Huizhi,Zhang Jing.Meta-analysis of the Association between the Monoamine Oxidase-A Gene and Mood Disorders.[期刊]:Psychiatric Genetics,2010,20(1):1-7 Zhao Huizhi,Wang Dong,Liu Bing,Jiang Xingpeng,Zhang Jing,Fan Ming,Fan Zhenjie,Chen Ying,Song SonyaWei,Gao Wei.Recombination rates of human microRNA.[期刊]:Biochem Biophys Res Commun,2009,379(3):702-705 Zhang Jing,Liu Bing,Jiang Xingpeng,Zhao Huizhi,Fan Ming,Fan Zhenjie,Lee J.Jack,Jiang Tao.A Systems Biology-Based Gene Expression Classifier of Glioblastoma Predicts Survival with Solid Tumors.[期刊]:PLoS ONE,2009,4(7):e6274 Jiang Xingpeng,Liu Bing,Jiang Jiefeng,Zhao Huizhi,Fan Ming,Zhang Jing,Fan Zhenjie.Modularity in the genetic disease-phenotype network.[期刊]:FEBS Lett,2008,582(17):2549-2554 Zhang Jing,Liu Bing,Jiang Xingpeng,Zhao Huizhi.Systematic benchmarking of microarray data feature extraction and classification.[期刊]:International Journal of Computer Mathematics,2008,85(5):803-811 Liu Bing,Ma Songde,Zhao Huizhi,Li Jun,Jiang Xingpeng,Zhang Jing.Exploring candidate genes for human brain diseases from a brain-specific gene network.[期刊]:Biochem Biophys Res Commun,2006,349(4):1308-1314 Zhang Jing.Hotspot clustering for ad hoc network.[会议录]:Proceedings of International Conference on Wireless Communications, Networking and Mobile Computing,2005,2

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