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BAI, Fan
Office Address: Integrated Science Research Center,Peking University, No.5 Yiheyuan Road, Haidian District,Beijing, P.R.China 100871
Lab Address: Integrated Science Research Center,Peking University, No.5 Yiheyuan Road, Haidian District,Beijing, P.R.China 100871
Lab Homepage: http://
Personal Homepage: http://
Representative Peer-Reviewed Publications
Single cell and cancer genomics:
27. Li Y#, Li X#, Li H#, Zhao Y#, Liu Z#, Sun K, Zhu X, Qi Q, An B, Shen D, Li R, Liu T, Mi J, Wang L, Yang F*, Bai F*, Wang J*, Genomic characterisation of pulmonary subsolid nodules: mutational landscape and radiological features, European Respiratory Journal (2019), DOI:10.1183/13993003.01409-2019 (*corresponding author)
26. Xue R#, Chen L#, Zhang C#, Fujita m#, ..., Nakagawa H*, Zeng M*, Bai F*, Zhang N*, Genomic and transcriptomic profiling of combined hepatocellular and intrahepatic cholangiocarcinoma reveals distinct molecular subtypes, Cancer Cell (2019) 35, pp.932-947(*corresponding author)
Highlighted by preview `The Worst from Both Worlds: cHCC-ICC`, Cancer Cell (2019) 35, pp. 823-824
25. Jiang Y,...Bai F, Wang P*, Shi L*, Huang W*, Shao Z*, Genomic and transcriptomic landscape of triple-negative breast cancers: subtypes and treatment strategies, Cancer Cell (2019) 35, pp.428-440.e5
24. Su z, Wang Z, Ni X, Duan J, Gao Y, Zhuo M, Li R, Zhao J, Ma Q, Bai H, Chen H, Wang S, Chen X, An T, Wang Y, Tian Y, Yu J, Wang D, Xie X*, Bai F*, Wang J*, Inferring evolution and progression of small-cell lung cancer by single-cell sequencing of circulating tumor cells, Clinical Cancer Research (2019) 25, pp. 5049-5060 (*corresponding author)
23. Zhang J#, Chen H#, Li R, Yao G, Bai F*, Xing J*, Spatial clustering and common regulatory elements correlate with coordinated gene expression, PLOS Computational Biology (2019) 15, pp.e1006786 (*corresponding author)

22. Fujimaki K#, Li R#, Chen H, Della Croce K, Zhang H, Xing J, Bai F*, Yao G*, Graded regulation of cellular quiescence depth between proliferation and senescence by a lysosomal dimmer switch, PNAS (2019) 116, pp.22624-22634 (*corresponding author)
21. Zhao H, Tian X, He L, Li Y, Pu W, Liu Q, Tang J, Wu J, Cheng X, Liu Y, Zhou Q, Tan Z, Bai F, Xu F, Smart N, Zhou B*, Apj+ vessels drive tumor growth and represent a tractable therapeutic target, Cell Reports 25 (2018), pp. 1241-1254
20.Li Z#,Li S#,Li R#, Zhu H, Guo X, Mu L, Cai J, Bai F*, Chen G*, Hong D*, Leukaemic alterations of IKZF1 prime stemness and malignancy programs in human lymphocytes, Cell Death and Disease 9 (2018), pp. 526 (*corresponding author)
19.Liu M#, Liu Y#, Deng L#, Wang D, He X, Zhou L, Wicha M, Bai F*, Liu S*, Transcriptional profiles of different states of cancer stem cells in triple-negative breast cancer, Molecular Cancer 17(2018), pp. 65 (*corresponding author)
18.Xue R, Li J, Bai F, Wang XW, Ji J, Lu Y, A Race to uncover a panoramic view of the liver cancer genome, Cancer Biol Med (2018), in press doi: 10.20892/j.issn.2095-3941. 2017.0112.

17.Liu M#, Liu Y#, Di J#, Su Z, Yang H, Jiang B, Wang Z, Zhuang M, Bai F*, Su X*, Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer, BMC Cancer 17 (2017), pp.787 (*corresponding author)
16.Li R#, Li X#, Xue R#, Yang F#, Wang S, Li Y, Shen D, Sun K, Chen K, Weng W, Bai F*, Wang J*, Early metastasis detected in patients with multifocal pulmonary ground-glass opacities (GGOs), Thorax 73 (2018), pp. 290-292(*corresponding author)
15.Li Y, Wu S, Bai F*, Molecular characterization of circulating tumor cells—from bench to bedside, Seminars in Cell & Developmental Biology 75 (2018), pp. 88-97(*corresponding author)
14.Chen X#, Yan S#, Liu Y#, Zhong Q#, Chen Z#, Jin S#, Xia T, Li R, Zhou A, Su Z, Huang Y, Huang Q, Huang L, Zhang X, Zhao Y, Yun J, Wu Q, Lin D, Bai F*, Zeng M*, Genomic comparison of esophageal squamous cell carcinoma and its precursor lesions by multi-region whole exome sequencing, Nature Communications 8 (2017), pp.524 doi: 10.1038/s41467-017-00650-0(*corresponding author)
13.Li J#, Liu K#, Chen H#, Li R, Drechsler M, Bai F*, Huang J*, Tang B*, Yan Y*, Functional build-in template directed siliceous fluorescent supramolecular vesicles as diagnostics, ACS Applied Materials & Interfaces 9 (2017), pp. 21706-21714(*corresponding author)
12.Fang Y#, Su Z#, Xie J#, Xue R, Ma Q, Lu X, Wang X, Wen C, Shi M, Tang X, Chen H, Zhan Q, Li H, Deng X, Peng C, Bai F*, Shen B*, Genomic signatures of adenosquamous carcinoma of pancreas in Chinese population,Journal of Pathology 243 (2017), pp. 155-159(*corresponding author)
Highlighted by Invited Commentaries `Recent advances in genomic profiling of adenosquamous carcinoma of the pancreas` of the same issue
11.Gao Y#, Ni X#, Guo H#, Su Z#, Ba Y#, Tong Z, Guo Z, Yao X, Chen X, Yin J, Yan Z, Guo L, Liu Y, Bai F*, Xie S*, Zhang N*, Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumour cells, Genome Research 27 (2017), pp. 1312-1322(*corresponding author)
10. Du Y#, Li R#, Chen Z#, Wang X, Xu T*, Bai F*, Mutagenic factors and complex clonal relationship of multifocal urothelial cell carcinoma, European Urology 71 (2017), pp. 841–843 (*corresponding author)

9. Xue R, Li R, Zhang N*, Bai F*, Understanding intra-tumor heterogeneity and tumor evolution to facilitate hepatocellular carcinoma therapy, Translational Cancer Research 3 (2016), pp. S604-S605 (*corresponding author)
8. Xue R#, Li R#, Guo H#, Guo L#, Su Z, Ni X, Qi L, Zhang T, Li Q, Zhang Z, Xie XS, Bai F*, Zhang N*, Variable extent of intra-tumor heterogeneity revealed by genomic sequencing of multiple lesions in patients with hepatocellular carcinoma, Gastroenterology 150 (2016), pp. 998-1008 (*corresponding author)
Highlighted by Editorial `Heterogeneity among liver cancer-a hurdle to optimizing therapy` of the same issue,
Highlighted by `The genetic heterogeneity of hepatocellular carcinoma and the implications for personalised medicine` Translational Cancer Research 5,(Suppl 1):S1-S4 (2016).

7. Chen XX, Bai F*, Single-cell analyses of circulating tumor cells, Cancer Biology & Medicine 12 (2015), pp. 184-192 (*corresponding author)

6. Zhang J, Tian X, Zhang H, Teng Y, Li R, Bai F, Elankumaran S*, Xing J*, TGF-β–induced epithelial-to-mesenchymal transition proceeds through stepwise activation of multiple feedback loops, Science Signaling 7 (2014), ra91
5. Xue R, Li R, Bai F*, Single cell sequencing: technique, application and future development , Science Bulletin (2014), doi: 10.1007/ s11434-014-0634-6 (*corresponding author)

4. He Y, Tsutsui M, Scheicher RH, Bai F, Taniguchi M, Kawai T, Thermophoretic manipulation of DNA translocation through nanopores, ACS Nano 7 (2013), pp. 538–546
3. Ni X#, Zhuo M#, Su Z#, Duan J#, Gao Y#, Wang Z#, Zong C#, Bai H, Chapman A, Zhao J, Xu L, An T, Ma Q, Wang Y, Wu M, Sun Y, Wang S, Li Z, Yang X, Yong J, Su X, Lu Y, Bai F*, Xie XS*, Wang J*, Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients, Proceedings of the National Academy of Sciences USA 110 (2013), pp. 21083-21088 (*corresponding author)
Highlighted by `Singled out for sequencing`, Nature Methods 11 (2014), pp. 13–17

2. Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, Chen Z, Mu D, Zhang H, Li N, Yue Z, Bai F, Li H, Fan W*, pIRS: Profile based illumina pair-end reads simulator, Bioinformatics 28 (2012), pp. 1533-1535
1. Lu S#, Zong C#, Fan W#, Yang M#, Li J, Chapman A, Zhu P, Hu X, Xu L, Yan L, Bai F, Qiao J, Tang F, Li R*, Xie XS*, Probing meiotic recombination and aneuploidy of single sperm cells by whole genome sequencing, Science 338 (2012), pp. 1627-1630

Bacterial biophysics and drug tolerance:
26. Wang Y#, Tian T#, Zhang J#, Jin X#, Yue H, Zhang X, Du L, Bai F*, Indole reverses the intrinsic antibiotic resistance of Lysobacter by promoting the expression of a novel dual-function importer, mBio (2019) 10, pp.e00676-19 (*corresponding author)
25. Tong H, Wang X, Dong Y, Hu Q, Zhao Z, Zhu Y, Dong L, Bai F, Dong X, A bacterial aquaporin acts as peroxiporin for efflux cellular hydrogen peroxide and alleviation of oxidative stress, Journal of Biological Chemistry (2019), in press

24. Pu Y#, Li Y#, Jin X#, Tian T#, Ma Q, Zhao Z, Lin S, Chen Z, Li B, Leake MC, Lo CJ, Bai F*, ATP-dependent dynamic protein aggregation regulates bacterial dormancy depth critical for antibiotic tolerance, Molecular Cell 73 (2019), pp. 1-14 (11.21.2018 online)(*corresponding author)
23. Zhao Z#, Zhao Y#, Zhuang X#, Lo W, Baker MA, Lo C*, Bai F*, Frequent pauses in Escherichia coli flagella elongation revealed by single cell real-time fluorescence imaging, Nature Communications 9 (2018), pp. 1885 (*corresponding author)
Highlighted by `Filming flagella and pili in action`, Nature Reviews Microbiology 16 (2018), pp. 584

22. Jin X, Guo X*, Xu D, Zhao Y, Bai F*, Single-cell real-time visualization and quantification of perylene bioaccumulation in microorganisms, Environmental Science & Technology 51 (2017),pp. 6211–6219(*corresponding author)
21. Chen M#, Zhao Z#, Yang J#, Peng K, Baker M, Bai F*, Lo C*, Length-dependent flagellar growth of Vibrio alginolyticus revealed by real time fluorescent imaging, eLIFE (2017), DOI: http://dx.doi.org/10.7554/eLife.22140(*corresponding author)
Highlighted by `Flagellum length control: how long is long enough`, Current Biology 27 (2017), pp. R413-415
20. Pu Y, Ke Y*, Bai F*, Active efflux in dormant bacterial cells – new insights into antibiotic persistence, Drug Resistance Updates 30 (2017), pp. 7-14 (*corresponding author)

19. Buda R#, Liu Y#, Yang J#, Hegde S#, Stevenson K, Bai F* and Pilizota T*, Dynamics of Escherichia coli`s passive response to a sudden decreases in external osmolarity, Proceedings of the National Academy of Sciences USA 113 (2016), pp. E5838-E5846 (*corresponding author)
18. Zhu J, Li H, Feng L, Yang M, Yang R, Yang L, Li L, Li R, Liu M, Hou S, Ke Y*, Li W*, Bai F*, Severe chronic osteomyelitis caused by Morganella morganii with high population diversity, International Journal of Infectious Diseases 50 (2016), pp. 44-47 (*corresponding author)
17. Pu Y#, Zhao Z#, Li Y#, Zou J, Ma Q, Zhao Y, Ke Y, Zhu Y, Chen H, Baker A.B. M, Ge H, Sun Y, Xie XS*, Bai F*, Enhanced efflux activity facilitates drug tolerance in dormant bacterial cells, Molecular Cell 62 (2016), pp. 284-294 (*corresponding author)
Highlighted by `Microbiology:Pumping persisters`, Nature 534 (2016), pp. 41–42
Highlighted by `Persisters are under the pump`, Nature Reviews Microbiology 14 (2016), pp. 332–333
16. Ma Q, Sowa Y, Baker M*, Bai F*, Conformational spread in the flagellar motor switch in response to CheY-P regulation and motor structural alterations, Biophysical Journal 110 (2016), pp. 1411-1420 (*corresponding author)

15. Xue R, Ma Q, Baker M*, Bai F*, A delicate nanoscale motor made by nature-the bacterial flagellar motor, Advanced Science 2 (2015), pp. 1500129(*corresponding author)
14. Guo X*, Jin X, Lv X, Pu Y, Bai F*, Real time visualization of perylene nano-clusters (PNCs) in water and their partitioning to graphene surface and macrophage cells, Environmental Science & Technology 49 (2015), pp. 7926-7933 (*corresponding author)

13. Bai F, Morimoto Y, Yoshimura S, Hara N, Kami-ike N, Namba K*, Minamino T*, Assembly dynamics and the roles of FliI ATPase of the bacterial flagellar type III export apparatus, Scientific Reports 4 (2014), Article number: 6528
12. Liu Y, Yang J, Zhao Z, Pu Y*, Bai F*, Bacterial persistence, Science China Chemistry 57 (2014), pp. 1625-1633 (*corresponding author)
11. Morimoto Y, Ito M, Hiraoka K, Che YS, Bai F, Kami-ike N, Namba K, Minamino T, Assembly and stoichiometry of FliF and FlhA in Salmonella flagellar basal body, Molecular Microbiology 91 (2014), pp. 1214-1226

10. Bai F, Che YS, Kami-ike N, Ma Q, Minamino T, Sowa Y, Namba K, Populational heterogeneity vs. temporal fluctuation in Escherichia coli flagellar motor switching, Biophysical Journal 105 (2013), pp. 2123-2129

9. Bai F, Minamino T, Wu Z, Namba K, Xing J, Coupling between switching regulation and torque generation in bacterial flagellar motor, Physical Review Letters 108 (2012), pp. 178105
8. Ma Q, Nicolau D, Berry R, Maini P. Bai F*, Conformational spread in the flagellar motor switch: a model study, PLoS Computational Biology 8 (2012), pp. e1002523

7. Mora T#, Bai F#, Che Y, Minamino T, Namba K, Wingreen N, Non-genetic individuality in Escherichia coli motor switching, Physical Biology (Communication) 8 (2011), pp. 024001 (#equal contribution)
6. Little M, Steel B, Bai F, Sowa Y, Bilyard T, Mueller D, Berry R, Jones N*, Steps and bumps: precision extraction of discrete states of molecular machines using physically-based, high-throughput time series analysis, Biophysical Journal 101 (2011), pp. 477-485

5. Bai F#, Branch R#, Nicolau D#, Pilizota T, Steel, B, Maini P, Berry R*, Conformational spread as a mechanism for cooperativity in the bacterial flagellar switch, Science 327 (2010), pp. 685-689
Highlighted by Perspective `An Ensemble View of Allostery` of the same issue

4. Bai F, Lo C, Berry R, Xing J*, Model studies on the dynamics of bacterial flagellar motor, Biophysical Journal 96 (2009), pp. 3154-3167

3. Pilizota T, Bilyard T, Bai F, Futai M, Hosokawa H, Berry R*, A programmable optical angle clamp for rotary molecular motors, Biophysical Journal 93 (2007), pp. 264-275

2. Leake MC, Chandler JH, Wadhams GH, Bai F, Berry RM, Armitage JP*, Stoichiometry and turnover in single, functioning membrane protein complexes, Nature 443 (2006), pp. 355-358
1. Xing J, Bai F, Berry R, Oster G*, Torque-speed relationship of the bacterial flagellar motor, Proceedings of the National Academy of Sciences USA 103 (2006), pp. 1260-1265
Laboratory Introduction