Selected Publications
(*indicates corresponding or co-corresponding authors, # indicates equal contributed first authors)

Single-cell Sequencing and Cancer Genomics
1. Wang J#, Xu Y#, Chen Z#, Liang J#, Lin Z#, Liang H#, ……, Bai F*, Xia H*, Wen Z*, Zhang Y*, Liver immune profiling reveals pathogenesis and therapeutics for biliary atresia, Cell 183 (2020), pp. 1867-1883
2. Li R#, Du Y#, Chen Z#, Xu D#, Lin T#, Jin S, Wang G, Liu Z, Lu M, Chen X, Xu T*, Bai F*, Macroscopic somatic clonal expansion in morphologically normal human urothelium, Science 370 (2020), pp. 82-89
3. Jin S#, Li R#, Chen M#, Yu C#, Tang L#, …….., Mai H, Gewurz B, Zhao B, Young L, Zhong Q*, Bai F*, Zeng M*, Single-cell transcriptomic analysis defines the interplay between tumor cells, viral infection, and the microenvironment in nasopharyngeal carcinoma, Cell Research 30 (2020), pp. 950-965
4. Zhang J#, Wang X#, Xing X#, Xu Z#, ……., Zhang Y, Zumla A, Maeurer M, Bai F*, Wang F*, Single-cell landscape of immunological responses in patients with COVID-19, Nature Immunology 21 (2020), pp. 1107-1118
5. Zhang C#, Zhang L#, Xu T#, Xue R#, Yu L#, Zhu Y, Wu Y, Zhang Q, Li D, Shen S, Tan D, Bai F*, Zhang H*, Mapping the spreading routes of lymphatic metastases in human colorectal cancer, Nature Communications 11 (2020), 1993
6. Wang X#, Lu Y#, Song Y#, Dong J#, Li R, Wang G, Wang X, Zhang S, Dong Z, Lu M, Wang S, Ge L, Luo G, Ma R, Rozen S, Bai F*, Wu D*, Ma L*, Integrative genomic study of Chinese clear cell renal cell carcinoma reveals features associated with thrombus, Nature Communications 11 (2020), 739
7. Huang B#, Chen Z#, Geng L#, Wang J#, Liang H#, ......, Gong S*, Bai F*, Yang M*, Zhang Y*, Mucosal profiling of pediatric-onset colitis and IBD reveals common pathogenics and therapeutic pathways, Cell 179 (2019), pp. 1160-1176
8. 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, Proceedings of the National Academy of Sciences USA 116 (2019), pp. 22624-22634
9. 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 25 (2019), pp. 5049-5060
10. 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 35 (2019), pp. 932-947
11. Jiang Y#, Ma D#, Suo C#, Shi J#, Xue M#, Liu Y, Xiao Y, Hu X, Yu Y, Zhang J, Li B, Li X, Zheng Y, Ren L, Hou W, Zhao S, Gong Y, Ren Y, Zhang C, Niu Z, Bai F, Yu K, Wang P*, Shi L*, Huang W*, Shao Z*, The genomic and transcriptomic landscape of triple-negative breast cancer suggests subtype-specific treatment strategies in Chinese population, Cancer Cell 35 (2019), pp.428-440.e5
12. 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
13. 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
14. 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 tumor cells, Genome Research 27 (2017), pp. 1312-1322
15. 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
16. 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
17. 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 X*, 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
18. 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 X*, Probing meiotic recombination and aneuploidy of single sperm cells by whole genome sequencing, Science 338 (2012), pp. 1627-1630

Bacterial Physiology and Antibiotic Tolerance
1. Zhuang X#, Guo S#, Li Z#, Zhao Z#, Kojima S, Homma M, Wang P, Lo C*, Bai F*, Live-cell fluorescence imaging reveals dynamic production and loss of bacterial flagella, Molecular Microbiology (2020), (April 07, 2020 online)
2. 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 10 (2019), e00676-19
3. 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 (November 21, 2018 online)
4. 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
5. 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
6. 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 (invited review)
7. Buda R#, Liu Y#, Yang J#, Hegde S#, Stevenson K, Bai F*, Pilizota T*, Dynamics of Escherichia coli’s passive response to a sudden decrease in external osmolarity, Proceedings of the National Academy of Sciences USA 113 (2016), pp. E5838-E5846
8. 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
9. 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
10. 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 (invited review)
11. 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
12. 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
13. 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
14. 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
15. Bai F, Lo C, Berry R, Xing J*, Model studies on the dynamics of bacterial flagellar motor, Biophysical Journal 96 (2009), pp. 3154-3167
16. 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　
17. 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