个人简介：

方晓东，生物信息学博士，南方科技大学医学院人类细胞生物和遗传学系教授，博士生导师。曾任华大研究院副院长，国内首批高通量测序数据分析挖掘技术人员，深度参与炎黄基因组、千人基因组、千种动植物基因组、国际肿瘤基因组、人类时空图谱等国内外重大科研项目。长期深耕大规模组学数据采集、分析挖掘工作，覆盖基因组学、细胞组学、时空组学等技术，熟悉组学技术特点、数据特征、分析思路和科研设计；推动多组学与AI融合，构建多模态多组学大数据智能分析系统，探索生物适应性演化、疾病发生机制和干预方法，重点聚焦中药-菌群-宿主互作、肿瘤免疫微环境和组织器官发育等方向，挖掘关键调控靶点与分子标志物，为精准诊疗、药物研发提供智能化解决方案。主持及参与国家、省市区级项目几十项，累计获批经费超9000万元；以共同一作、共同通讯作者身份在Cell、Nature、Science、Nature Biotechnology、Nature Genetics、Nature Communications、Sig Transduct Target Ther、iMeta、PNAS、JCI、Microbiome、ISME 等期刊发表论文几十篇。多次从头组建团队负责基因组中心和生信平台搭建、技术研发、运营管理和产业推广，具有丰富的基础研究和产业转化全链条实战经验，带领团队累计获得超10亿产业收入。

研究领域：

1. 方法和平台构建：高通量多组学数据采集、分析和挖掘，开发AI驱动的多模态多组学数据整合和自主科学发现的方法和平台；

2. 生物基础机理研究：依托多组学大数据与AI技术，探索生物适应性演化、组织器官发育的分子调控机制

3. 稳态医学研究：构建稳态医学量化指标体系，开发疾病风险评估模型。关注重大疾病与精准医学研究，聚焦中药-菌群-宿主互作研究、肿瘤免疫微环境及重大疾病发生发展，鉴定疾病诊疗标志物，助力精准诊疗与药物研发。

教育背景：

2012.09—2015.10，哥本哈根大学，博士
2003.09—2006.07，海南大学，硕士
1999.09—2003.07，海南大学， 学士

工作经历：

2026.03—现在，南方科技大学医学院，人类细胞生物和遗传学系，教授

2020.10—2026.02，深圳华大生命科学研究院副院长

2013.01—2020.10，深圳华大基因科技服务有限公司 首席技术官

2007.05—2012.12，深圳华大基因研究院 生物信息中心副主管

2006.06—2007.05，北京华大基因研究中心 生物信息分析员

获奖情况及荣誉：

2010—2015，深圳市国家级领军人才

2016—2021，深圳市海外高层次B类人才

2022年，   广东省科技进步一等奖

学术任职或杂志编委会委员：

中国科学院大学 博士生导师

香港中文大学  兼职副教授

第二届广东省抗癌协会遗传性肿瘤专委会委员

中国医疗器械行业协会智慧及移动医疗分会委员

广东省中药标准化技术委员会（GD/TC 36）委员

发表论文：

1. Xie P^*, Shen J^*, Yang Y^*, Wang X^*, Liu W^*, Cao H^*, Zheng Y, Wu C, Mao G, Chen L, He J, Zheng W, Yang Z, Zhang X, Jiang X, Yang X, Fang K, Zhang Z, Xue X, Chen X, Wang C, Liu X, Liu L, Yao X, Jing N, Xie W, Liu J^#, Cao H^#, Luo Z^#, Fang X^#, Lin C^#. Digital reconstruction of full embryos during early mouse organogenesis. Cell. 2025 Aug 21;188(17):4754-4772.e18. DOI: 10.1016/j.cell.2025.05.035. Epub 2025 Jun 18. PMID: 40920635.

2. Wang X^*, Wang Z^*, Liao Q^*, Yuan P^*, Mei J^*, Zhang Y^*, Wu C, Kang X, Zheng S, Yang C, Liu J, Shang Q, Li J, Wang B, Li L, Liu H, Hu W, Dong Z, Zhao J, Wang L, Liu T, Den Y, Wang C, Han L, Chen Q, Yang H, Xu X, He J, Yue Z^#, Sun N^#, Fang X^#, Ying J^#. Spatially resolved atlas of breast cancer uncovers intercellular machinery of venular niche governing lymphocyte extravasation. Nat Commun. 2025 Apr 9;16(1):3348. DOI: 10.1038/s41467-025-58511-0. PMID: 40199901.

3. Liu C, Wang K, Mei J, Zhao R, Shen J, Zhang W, Li L, Roy B^#, Fang X^#. Integrative single-cell and spatial transcriptome analysis reveals heterogeneity of human liver progenitor cells. Hepatol Commun. 2025 Feb 26;9(3):e0662. DOI: 10.1097/HC9.0000000000000662. PMID: 40008906.

4. Shen J^*, Liang W^*, Zhao R^*, Chen Y^*, Liu Y^*, Cheng W^*, Chai T, Zhang Y, Chen S, Liu J, Chen X, Deng Y, Zhang Z, Huang Y, Yang H, Pang L, Qiu Q, Deng H, Pan S, Wang L, Ye J, Luo W, Jiang X, Huang X, Li W, Leung EL, Zhang L, Huang L, Yang Z, Chen R, Mei J, Yue Z, Wei H^#, Karsten K^#, Han L^#, Fang X^#. Cross-tissue multi-omics analyses reveal the gut microbiota's absence impacts organ morphology, immune homeostasis, bile acid and lipid metabolism. Imeta. 2025 Feb 14;4(1):e272. DOI: 10.1002/imt2.272. Erratum in: Imeta. 2025 Nov 16;4(6):e70092. DOI: 10.1002/imt2.70092. PMID: 40027481.

5. Li H^*, Chen X^*, Wang JJ^*, Shen J^*, Abuduwufuer K, Zhang Z, Dong Z, Wen Z, He J, Chen S, Li W, Chen C, Li F, Fang X^#, Wang DW^#. Spatiotemporal transcriptomics elucidates the pathogenesis of fulminant viral myocarditis. Signal Transduct Target Ther. 2025 Feb 10;10(1):59. DOI: 10.1038/s41392-025-02143-9. PMID: 39924580.

6. Chai T, Shen J, Sheng Y, Huang Y, Liang W, Zhang Z, Zhao R, Shang H, Cheng W, Zhang H, Chen X, Huang X, Zhang Y, Liu J, Yang H, Wang L, Pan S, Chen Y, Han L, Qiu Q, Gao A, Wei H^#, Fang X^#. Effects of flora deficiency on the structure and function of the large intestine. iScience. 2024 Jan 17;27(2):108941. DOI: 10.1016/j.isci.2024.108941. PMID: 38333708.

7. Yang C^*, Zhang Z^*, Huang Y, Xie X, Liao H, Xiao J, Veldsman WP, Yin K, Fang X^#, Zhang L^#. LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome. Gigascience. 2024 Jan 2;13:giae028. DOI: 10.1093/gigascience/giae028. PMID: 3886914.

8. Zhao R, Cheng W, Shen J, Liang W, Zhang Z, Sheng Y, Chai T, Chen X, Zhang Y, Huang X, Yang H, Song C, Pang L, Nan C, Zhang Y, Chen R, Mei J, Wei H^#, Fang X^#. Single-cell and spatiotemporal transcriptomic analyses reveal the effects of microorganisms on immunity and metabolism in the mouse liver. Comput Struct Biotechnol J. 2023 Jun 30;21:3466-3477. DOI: 10.1016/j.csbj.2023.06.020. PMID: 38152123.

9. Zhang Y, Shen J, Cheng W, Roy B, Zhao R, Chai T, Sheng Y, Zhang Z, Chen X, Liang W, Hu W, Liao Q, Pan S, Zhuang W, Zhang Y, Chen R, Mei J, Wei H^#, Fang X^#. Microbiota-mediated shaping of mouse spleen structure and immune function characterized by scRNA-seq and Stereo-seq. J Genet Genomics. 2023 Sep;50(9):688-701. DOI: 10.1016/j.jgg.2023.04.012. Epub 2023 May 6. PMID: 37156441.

10. Huang Y^*, Jiang P^*, Liang Z, Chen R, Yue Z, Xie X, Guan C^#*, Fang X^#. Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing. Front Microbiol. 2023 May 5;14:1145315. DOI: 10.3389/fmicb.2023.1145315. PMID: 37213501.

11. Han L^*, Zhao L^*, Zhou Y^*, Yang C^*, Xiong T^*, Lu L^*, Deng Y, Luo W, Chen Y, Qiu Q, Shang X, Huang L, Mo Z, Huang S, Huang S, Liu Z, Yang W, Zhai L, Ning Z, Lin C, Huang T, Cheng C, Zhong LLD, Li S^#, Bian Z^#, Fang X^#. Altered metabolome and microbiome features provide clues in understanding irritable bowel syndrome and depression comorbidity. ISME J. 2022 Apr;16(4):983-996. DOI: 10.1038/s41396-021-01123-5. Epub 2021 Nov 8. PMID: 34750528.

12. Zhao J^*, Tian X^*, Zhu Y^*, Zhang Z, Rydkina E, Yuan Y, Zhang H, Roy B, Cornwell A, Nevo E, Shang X, Huang R, Kristiansen K, Seluanov A^#, Fang X^#, Gorbunova V^#. Reply to: Transformation of naked mole-rat cells. Nature. 2020 Jul;583(7814):E8-E13. DOI: 10.1038/s41586-020-2411-9. PMID: 32612220.

13. Zhao L^*, Yang W^*, Chen Y^*, Huang F^*, Lu L, Lin C, Huang T, Ning Z, Zhai L, Zhong LL, Lam W, Yang Z, Zhang X, Cheng C, Han L, Qiu Q, Shang X, Huang R, Xiao H, Ren Z, Chen D, Sun S, El-Nezami H, Cai Z, Lu A^#, Fang X^#, Jia W^#, Bian Z^#. A Clostridia-rich microbiota enhances bile acid excretion in diarrhea-predominant irritable bowel syndrome. J Clin Invest. 2020 Jan 2;130(1):438-450. DOI: 10.1172/JCI130976. PMID: 31815740.

14. Xing R^#*, Zhou Y^*, Yu J^*, Yu Y^*, Nie Y^*, Luo W^*, Yang C^*, Xiong T, Wu WKK, Li Z, Bing Y, Lin S, Zhang Y, Hu Y, Li L, Han L, Yang C, Huang S, Huang S, Zhou R, Li J, Wu K, Fan D, Tang G, Dou J, Zhu Z, Ji J^#, Fang X^#, Lu Y^#. Whole-genome sequencing reveals novel tandem-duplication hotspots and a prognostic mutational signature in gastric cancer. Nat Commun. 2019 May 2;10(1):2037. DOI: 10.1038/s41467-019-09644-6. PMID: 31048690.

15. Liu Z^*, Yang C^*, Li X, Luo W, Roy B, Xiong T, Zhang X, Yang H, Wang J, Ye Z, Chen Y, Song J, Ma S, Zhou Y^#, Yang M^#, Fang X^#, Du J^#. The landscape of somatic mutation in sporadic Chinese colorectal cancer. Oncotarget. 2018 Jun 8;9(44):27412-27422. DOI: 10.18632/oncotarget.25287. PMID: 29937994.

16. Zhang L^#*, Fang X^*, Liao H^*, Zhang Z, Zhou X, Han L, Chen Y, Qiu Q, Li SC^#. A comprehensive investigation of metagenome assembly by linked-read sequencing. Microbiome. 2020 Nov 11;8(1):156. DOI: 10.1186/s40168-020-00929-3. PMID: 33176883.

17. Ai H^*, Fang X^*, Yang B^*, Huang Z, Chen H, Mao L, Zhang F, Zhang L, Cui L, He W, Yang J, Yao X, Zhou L, Han L, Li J, Sun S, Xie X, Lai B, Su Y, Lu Y, Yang H, Huang T, Deng W, Nielsen R^#, Ren J^#, Huang L^#. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet. 2015 Mar;47(3):217-25. DOI: 10.1038/ng.3199. Epub 2015 Jan 26. PMID: 25621459.

18. Fang X^*, Seim I^*, Huang Z, Gerashchenko MV, Xiong Z, Turanov AA, Zhu Y, Lobanov AV, Fan D, Yim SH, Yao X, Ma S, Yang L, Lee SG, Kim EB, Bronson RT, Šumbera R, Buffenstein R, Zhou X, Krogh A, Park TJ, Zhang G, Wang J^#, Gladyshev VN^#. Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes. Cell Rep. 2014 Sep 11;8(5):1354-64. DOI: 10.1016/j.celrep.2014.07.030. Epub 2014 Aug 28. PMID: 25176646.

19. Fang X^*, Nevo E^*#, Han L^*, Levanon EY^*, Zhao J^*, Avivi A^*, Larkin D^*, Jiang X^*, Feranchuk S, Zhu Y, Fishman A, Feng Y, Sher N, Xiong Z, Hankeln T, Huang Z, Gorbunova V, Zhang L, Zhao W, Wildman DE, Xiong Y, Gudkov A, Zheng Q, Rechavi G, Liu S, Bazak L, Chen J, Knisbacher BA, Lu Y, Shams I, Gajda K, Farré M, Kim J, Lewin HA, Ma J, Band M, Bicker A, Kranz A, Mattheus T, Schmidt H, Seluanov A, Azpurua J, McGowen MR, Ben Jacob E, Li K, Peng S, Zhu X, Liao X, Li S, Krogh A, Zhou X^#, Brodsky L^#, Wang J^#. Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nat Commun. 2014 Jun 3;5:3966. DOI: 10.1038/ncomms4966. Erratum in: Nat Commun. 2015 Aug 12;6:8051. DOI: 10.1038/ncomms9051. PMID: 24892994.

20. Seim I^*, Fang X^*, Xiong Z, Lobanov AV, Huang Z, Ma S, Feng Y, Turanov AA, Zhu Y, Lenz TL, Gerashchenko MV, Fan D, Hee Yim S, Yao X, Jordan D, Xiong Y, Ma Y, Lyapunov AN, Chen G, Kulakova OI, Sun Y, Lee SG, Bronson RT, Moskalev AA, Sunyaev SR, Zhang G, Krogh A, Wang J^#, Gladyshev VN^#. Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii. Nat Commun. 2013;4:2212. DOI: 10.1038/ncomms3212. PMID: 23962925.

21. Zhang G^*#, Fang X^*, Guo X^*#, Li L^*, Luo R^*, Xu F^*, Yang P^*, Zhang L^*, Wang X^*, Qi H, Xiong Z, Que H, Xie Y, Holland PW, Paps J, Zhu Y, Wu F, Chen Y, Wang J, Peng C, Meng J, Yang L, Liu J, Wen B, Zhang N, Huang Z, Zhu Q, Feng Y, Mount A, Hedgecock D, Xu Z, Liu Y, Domazet-Lošo T, Du Y, Sun X, Zhang S, Liu B, Cheng P, Jiang X, Li J, Fan D, Wang W, Fu W, Wang T, Wang B, Zhang J, Peng Z, Li Y, Li N, Wang J, Chen M, He Y, Tan F, Song X, Zheng Q, Huang R, Yang H, Du X, Chen L, Yang M, Gaffney PM, Wang S, Luo L, She Z, Ming Y, Huang W, Zhang S, Huang B, Zhang Y, Qu T, Ni P, Miao G, Wang J, Wang Q, Steinberg CE, Wang H, Li N, Qian L, Zhang G, Li Y, Yang H, Liu X, Wang J, Yin Y^#, Wang J^#. The oyster genome reveals stress adaptation and complexity of shell formation. Nature. 2012 Oct 4;490(7418):49-54. DOI: 10.1038/nature11413. Epub 2012 Sep 19. PMID: 22992520.

22. Fang X^*, Mou Y, Huang Z, Li Y, Han L, Zhang Y, Feng Y, Chen Y, Jiang X, Zhao W, Sun X, Xiong Z, Yang L, Liu H, Fan D, Mao L, Ren L, Liu C, Wang J, Li K, Wang G, Yang S, Lai L, Zhang G, Li Y, Wang J, Bolund L, Yang H, Wang J, Feng S^#, Li S^#, Du Y^#. The sequence and analysis of a Chinese pig genome. Gigascience. 2012 Nov 15;1(1):16. DOI: 10.1186/2047-217X-1-16. PMID: 23587058.

23. Yan G^*#, Zhang G^*, Fang X^*, Zhang Y^*, Li C^*, Ling F^*, Cooper DN, Li Q, Li Y, van Gool AJ, Du H, Chen J, Chen R, Zhang P, Huang Z, Thompson JR, Meng Y, Bai Y, Wang J, Zhuo M, Wang T, Huang Y, Wei L, Li J, Wang Z, Hu H, Yang P, Le L, Stenson PD, Li B, Liu X, Ball EV, An N, Huang Q, Zhang Y, Fan W, Zhang X, Li Y, Wang W, Katze MG, Su B, Nielsen R, Yang H, Wang J, Wang X^#, Wang J^#. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol. 2011 Oct 16;29(11):1019-23. DOI: 10.1038/nbt.1992. PMID: 22002653.

24. Kim EB^*, Fang X^*, Fushan AA^*, Huang Z^*, Lobanov AV, Han L, Marino SM, Sun X, Turanov AA, Yang P, Yim SH, Zhao X, Kasaikina MV, Stoletzki N, Peng C, Polak P, Xiong Z, Kiezun A, Zhu Y, Chen Y, Kryukov GV, Zhang Q, Peshkin L, Yang L, Bronson RT, Buffenstein R, Wang B, Han C, Li Q, Chen L, Zhao W, Sunyaev SR, Park TJ, Zhang G^#, Wang J^#, Gladyshev VN^#. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature. 2011 Oct 12;479(7372):223-7. DOI: 10.1038/nature10533. PMID: 21993625.

25. Liu P^*, Fang X^*, Feng Z^*, Guo YM, Peng RJ, Liu T, Huang Z, Feng Y, Sun X, Xiong Z, Guo X, Pang SS, Wang B, Lv X, Feng FT, Li DJ, Chen LZ, Feng QS, Huang WL, Zeng MS, Bei JX, Zhang Y, Zeng YX^#. Direct sequencing and characterization of a clinical isolate of Epstein-Barr virus from nasopharyngeal carcinoma tissue by using next-generation sequencing technology. J Virol. 2011 Nov;85(21):11291-9. DOI: 10.1128/JVI.00823-11. Epub 2011 Aug 31. PMID: 21880770.

26. Fang X^*, Zhang Y^*, Zhang R^*, Yang L, Li M, Ye K, Guo X, Wang J^#, Su B^#. Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque. Genome Biol. 2011 Jul 6;12(7):R63. DOI: 10.1186/gb-2011-12-7-r63. PMID: 21733155.