基本信息
靳文菲  男    中国科学院上海营养与健康研究所
电子邮件: jinwf@sinh.ac.cn
通信地址: 上海市岳阳路320号生科大楼347
邮政编码: 200031

研究方向

研究组致力于开发和整合组学技术和生物信息手段提升精准医学。即基于多种组学技术刻画人的衰老和癌症样本,通过建立新的人工智能算法和模型解析生物学过程,鉴定关键信号和分子靶点。主要研究方向:
(1)开发组学技术和组学计算方法,尤其是单细胞多组学技术及其分析方法;
(2)多组学数据整合,构建全息细胞图谱解析细胞解析细胞对外界刺激的应答;
(3)利用单细胞技术解析肿瘤微环境和肿瘤微进化,发展精准免疫治疗。


招生方向

0710Z1-基因组学,基因组研究方法

0710Z2-计算生物学,生物信息

1001Z1-精准医学,肿瘤免疫


教育背景

2006-09--2012-01   中国科学院上海生命科学研究院   博士
2001-09--2006-07   郑州大学   学士

工作经历

2023-10~现在, 中国科学院上海营养和健康研究所, 研究员
2017-03~2024-02,南方科技大学, 副教授,研究员
2013-01~2017-03,美国国立卫生研究院(NIH), 博士后
2012-01~2012-12,中国科学院上海生命科学研究院, 助理研究员


学术兼职
2023-11-01-今,中国遗传学会, 三维基因组学专委会委员
2023-05-31-今,中国生物信息学学会(筹), 表观遗传信息学专委会委员
2023-05-01-今,广东省生物信息学会, 常务理事
2023-04-01-今,中国生物信息学学会(筹), 非编码RNA与RNA信息学专业委员会委员
2021-03-01-今,中国生物工程学会, 系统生物医学专业委员会委员

专利与奖励

   
奖励信息
(1) 南方科技大学优秀研究生导师, , 研究所(学校), 2022
(2) 南方科技大学“良师益友”优秀研究生导师, 研究所(学校), 2022
(3) 广东省珠江人才计划青年拔尖, , 省级, 2019
专利成果
[1] 陈曦, 靳文菲, 徐玮, 洪旎. 一种单细胞开放染色质和转录组共测序文库的构建方法. CN: CN116694730A, 2023-09-05.
[2] 袁昕, 余胜, 洪旎, 靳文菲. 一种单细胞文库的构建方法. CN: CN113584598A, 2021-11-02.

出版信息

   
发表论文
(1) Decreased GATA3 levels cause changed mouse cutaneous innate lymphoid cell fate, facilitating hair follicle recycling, Dev Cell, 2024, 第 1 作者  通讯作者
(2) Sirp�� on tumor-associated myeloid cells restrains antitumor immunity in colorectal cancer independent of its interaction with CD47, Nature Cancer, 2024, 第 1 作者  通讯作者
(3) Single cell analyses of cancer cells identified two regulatorily and functionally distinct categories in differentially expressed genes among tumor subclones, HELIYON, 2024, 第 10 作者  通讯作者
(4) Anti-PD-1 therapy achieves favorable outcomes in HBV-positive non-liver cancer, ONCOGENESIS, 2023, 第 19 作者  通讯作者
(5) Exploring the dynamics and influencing factors of CD4 Tcell activation using single-cell RNA-seq, ISCIENCE, 2023, 第 10 作者  通讯作者
(6) The bone-liver interaction modulates immune and hematopoietic function through Pinch-Cxcl12-Mbl2 pathway, CELL DEATH AND DIFFERENTIATION, 2023, 第 12 作者
(7) Glucose-induced CRL4COP1-p53 axis amplifies glycometabolism to drive tumorigenesis, MOLECULAR CELL, 2023, 第 21 作者
(8) Proline uptake promotes activation of lymphoid tissue inducer cells to maintain gut homeostasis, NATURE METABOLISM, 2023, 第 15 作者
(9) A fast and globally optimal solution for RNA-seq quantification, BRIEFINGS IN BIOINFORMATICS, 2023, 第 4 作者  通讯作者
(10) ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells, NATURE METHODS, 2022, 第 10 作者  通讯作者
(11) Reinvestigation of Classic T Cell Subsets and Identification of Novel Cell Subpopulations by Single-Cell RNA Sequencing, JOURNAL OF IMMUNOLOGY, 2022, 第 8 作者  通讯作者
(12) Single-Cell RNA Sequencing Unravels Upregulation of Immune Cell Crosstalk in Relapsed Pediatric Ependymoma, FRONTIERS IN IMMUNOLOGY, 2022, 第 8 作者  通讯作者
(13) Dissecting Complex Traits Using Omics Data: A Review on the Linear Mixed Models and Their Application in GWAS, PLANTS-BASEL, 2022, 第 4 作者  通讯作者
(14) Comprehensive mapping of alternative polyadenylation site usage and its dynamics at single-cell resolution, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2022, 第 10 作者  通讯作者
(15) A topology-preserving dimensionality reduction method for single-cell RNA-seq data using graph autoencoder, SCIENTIFIC REPORTS, 2021, 第 4 作者  通讯作者
(16) Integrated decoding hematopoiesis and leukemogenesis using single-cell sequencing and its medical implication, CELL DISCOVERY, 2021, 第 12 作者  通讯作者
(17) Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis, GENOME BIOLOGY, 2021, 第 4 作者  通讯作者
(18) Cross-Tissue Characterization of Heterogeneities of Mesenchymal Stem Cells and Their Differentiation Potentials, FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY, 2021, 第 9 作者  通讯作者
(19) A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility, NATURE PROTOCOLS, 2021, 第 6 作者
(20) A Comprehensive Characterization of Monoallelic Expression During Hematopoiesis and Leukemogenesis via Single-Cell RNA-Sequencing, FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY, 2021, 第 7 作者  通讯作者
(21) The Tyrosine Kinase-Driven Networks of Novel Long Non-coding RNAs and Their Molecular Targets in Myeloproliferative Neoplasms, FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY, 2021, 第 8 作者
(22) Focal adhesion protein Kindlin-2 regulates bone homeostasis in mice, Focal adhesion protein Kindlin-2 regulates bone homeostasis in mice, BONE RESEARCH, 2020, 第 7 作者
(23) H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells, DEVELOPMENT, 2020, 第 3 作者
(24) Diploid genome architecture revealed by multi-omic data of hybrid mice, GENOME RESEARCH, 2020, 第 8 作者  通讯作者
(25) Kindlin-2 regulates skeletal homeostasis by modulating PTH1R in mice, Kindlin-2 regulates skeletal homeostasis by modulating PTH1R in mice, SIGNAL TRANSDUCTION AND TARGETED THERAPY, 2020, 第 14 作者
(26) Single-Cell Transcriptome Analysis Reveals Six Subpopulations Reflecting Distinct Cellular Fates in Senescent Mouse Embryonic Fibroblasts, FRONTIERS IN GENETICS, 2020, 第 12 作者  通讯作者
(27) Inhibition of Glycolysis in Pathogenic T(H)17 Cells through Targeting a miR-21-Peli1-c-Rel Pathway Prevents Autoimmunity, JOURNAL OF IMMUNOLOGY, 2020, 第 9 作者
(28) Exploring the changing landscape of cell-to-cell variation after CTCF knockdown via single cell RNA-seq, BMC GENOMICS, 2019, 第 4 作者  通讯作者
(29) Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing (vol 562, pg 281, 2018), NATURE, 2018, 第 6 作者
(30) Trac-looping measures genome structure and chromatin accessibility, NATURE METHODS, 2018, 第 3 作者
(31) Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing, NATURE, 2018, 第 6 作者
(32) Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells, IMMUNITY, 2018, 第 7 作者
(33) CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression, MOLECULAR CELL, 2017, 第 2 作者
(34) Genome-wide identification of histone H2A and histone variant H2A.Z-interacting proteins by bPPI-seq, CELL RESEARCH, 2017, 第 5 作者
(35) Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3 (vol 14, R121, 2013), GENOME BIOLOGY, 2016, 第 2 作者
(36) Evaluating information content of SNPs for sample-tagging in re-sequencing projects, SCIENTIFIC REPORTS, 2015, 第 3 作者
(37) Copy number variations and genetic admixtures in three *** ethnic minority groups, EUROPEANJOURNALOFHUMANGENETICS, 2015, 第 3 作者
(38) Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples, NATURE, 2015, 第 1 作者
(39) Y Chromosomes of 40% Chinese Descend from Three Neolithic Super-Grandfathers, PLOS ONE, 2014, 第 12 作者
(40) Distribution of ancestral chromosomal segments in admixed genomes and its implications for inferring population history and admixture mapping, EUROPEAN JOURNAL OF HUMAN GENETICS, 2014, 第 1 作者
(41) A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese, EUROPEAN JOURNAL OF HUMAN GENETICS, 2014, 第 3 作者
(42) Association of Two Variants in SMAD7 with the Risk of Congenital Heart Disease in the Han Chinese Population, PLOS ONE, 2013, 第 2 作者
(43) Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3, GENOME BIOLOGY, 2013, 第 2 作者
(44) A systematic characterization of genes underlying both complex and Mendelian diseases, HUMAN MOLECULAR GENETICS, 2012, 第 1 作者
(45) Genome-wide detection of natural selection in African Americans pre- and post-admixture, GENOME RESEARCH, 2012, 第 1 作者
(46) Exploring Population Admixture Dynamics via Empirical and Simulated Genome-wide Distribution of Ancestral Chromosomal Segments, AMERICAN JOURNAL OF HUMAN GENETICS, 2012, 第 1 作者
(47) A Map of Copy Number Variations in Chinese Populations, PLOS ONE, 2011, 第 6 作者
(48) A Genome-Wide Search for Signals of High-Altitude Adaptation in Tibetans, MOLECULAR BIOLOGY AND EVOLUTION, 2011, 第 6 作者
(49) Haplotype-Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors, MOLECULAR BIOLOGY AND EVOLUTION, 2009, 第 2 作者
(50) Genomic Dissection of Population Substructure of Han Chinese and Its Implication in Association Studies, AMERICAN JOURNAL OF HUMAN GENETICS, 2009, 第 4 作者
发表著作
(1) 混合人群的混合动态、自然选择与疾病, Admixture Dynamics, Natural Selection and Diseases in Admixed Populations, 施普林格, 2015-10, 第 1 作者

科研活动

   
科研项目
( 1 ) 整合多种单细胞技术解析肿瘤浸润免疫细胞的耗竭机制, 负责人, 国家任务, 2019-01--2022-12
( 2 ) 发展单细胞多组学技术在单细胞水平研究基因调控, 负责人, 国家任务, 2022-01--2025-12
( 3 ) 开发多模态单细胞数据整合方法在单细胞水平解析基因调控和发育, 负责人, 国家任务, 2024-01--2027-12
( 4 ) 单细胞测序数据计算方法开发和数据挖掘, 负责人, 国家任务, 2018-01--2018-12
( 5 ) 新型可遗传获得性性状和表观载体的筛选, 负责人, 国家任务, 2018-12--2021-11
( 6 ) 细胞多重分子特征多维度分析、建模及癌变预警应用, 负责人, 国家任务, 2021-12--2024-11
( 7 ) 基于单细胞测序和染色质开放位点分析的肿瘤浸润淋巴细胞耗竭过程研究, 负责人, 地方任务, 2018-05--2021-05
( 8 ) 基于个体化肿瘤数字模型的结直肠癌精准诊疗研发团队, 参与, 地方任务, 2019-11--2024-10
( 9 ) 肿瘤免疫微环境三维高精度分析算法研究, 负责人, 地方任务, 2022-10--2025-10
( 10 ) 真核生物人工染色体的设计建造与功能研究, 参与, 国家任务, 2021-12--2026-12
( 11 ) 整合Stereo-seq和单细胞转录组构建单细胞分辨率的三维肿瘤微环境, 负责人, 境内委托项目, 2023-01--2024-12
( 12 ) 单细胞多组学技术在辅助生殖中的应用, 参与, 地方任务, 2023-05--2026-05