PERSONAL PROFILE：

Professor Fang Xiaodong has been deeply involved in major domestic and international research initiatives, including the YanHuang Genome Project, the 1000 Genomes Project, the International Cancer Genome Consortium, the 1,000 Plants and Animals Genome Project, and the Human Spatiotemporal Atlas. He has long been dedicated to large-scale multi-omics data acquisition, analysis, and mining, with expertise spanning genomics, cellomics, and spatiotemporal omics. He possesses a thorough understanding of the technical characteristics, data features, analytical approaches, and scientific design of omics research project.

Professor Fang has been instrumental in advancing the integration of multi-omics with artificial intelligence, developing intelligent analysis systems for multimodal multi-omics data. His research focuses on exploring biological adaptive evolution, disease mechanisms, and intervention strategies, with particular emphasis on drug–microbiota–host interactions, tissue and organ development, and the tumor immune microenvironment. He aims to identify key regulatory targets and molecular biomarkers to enable intelligent solutions for precision diagnostics and drug development.

He has led or participated in dozens of research projects at national, provincial, and municipal levels, securing over 90 million RMB in cumulative funding. As co-first author or co-corresponding author, he has published more than tens of papers in academic journals such as Cell, Nature, Science, Nature Biotechnology, Nature Genetics, Nature Communications, Signal Transduction and Targeted Therapy, iMeta, PNAS, JCI, Microbiome, and The ISME Journal.

Professor Fang has repeatedly built teams from the ground up to establish and manage genomics core facilities, overseeing platform development, technology innovation, operations, and research collaborations. With extensive hands-on experience spanning the full continuum from fundamental research to industrial translation, he has led teams to generate over one billion RMB in industrial revenue.

RESEARCH:

1. Methods and Platform Development
High-throughput multi-omics data acquisition, analysis, and mining; development of AI-driven multimodal multi-omics data integration methods and platforms to facilitate autonomous scientific discovery.

2. Fundamental Mechanisms in Biology
Leveraging multi-omics big data and AI technologies to investigate molecular regulatory mechanisms underlying biological adaptive evolution and tissue and organ development.

3. Homeostasis Medicine Research
Development of a quantitative evaluation framework for homeostasis medicine and establishment of disease risk assessment models. Focus on diseases and precision medicine research, with emphasis on the tumor immune microenvironment and the interplay among traditional Chinese medicine, microbiota, and host. Identification of diagnostic and therapeutic biomarkers to support precision diagnostics and drug development.

EDUCATION:

2012.09–2015.10 University of Copenhagen, Ph.D.
2003.09–2006.07 Hainan University, M.Sc.
1999.09–2003.07 Hainan University, B.Sc.

WOKRING EXPERIENCE:

2026.03–Present Professor, Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology
2020.10–2026.02 Vice President, Shenzhen BGI-Research
2013.01–2020.10 Chief Technology Officer, Shenzhen BGI Technology Services Co., Ltd.
2007.05–2012.12 Deputy Head, Bioinformatics Center, BGI-Research
2006.06–2007.05 Bioinformatician, BGI-Research Beijing Center                   

HONORS AND AWARDS:

2010–2015 State-Level Leading Talent of Shenzhen
2016–2021 Overseas High-Caliber Talent (Class B), Shenzhen
2022 First Prize for Scientific and Technological Progress, Guangdong Province

PUBLICATIONS：

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.