Yuan Bifeng

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Research

Bi-Feng  Yuan studied biochemistry and biophysics at Wuhan University in China,  where he received his BSc and Ph.D. degrees in 2001 and 2006,  respectively. From 2006-2007 and 2007-2010, he worked as a postdoctoral  researcher in the Department of Biological Sciences at National  University of Singapore and in the Department of Chemistry at University  of California Riverside, respectively. He joined Wuhan University in  2011 and is currently a Professor in the School of Public Health.

1. Environmental epigenetics

Epigenetic  modifications of nucleic acids play a crucial role in gene regulation  and are key players in the development of various diseases, including  cancer. Our research is dedicated to investigating the physiological  functions of epigenetic modifications of nucleic acids by establishing  sensitive and specific analytical methods such as mass spectrometry and  sequencing techniques. Additionally, we explore the impact and  mechanisms of environmental factors on epigenetic modifications, aiming  to provide new strategies and insights for the prevention and treatment  of related diseases.

2. Metabolomics

We  are dedicated to developing metabolomics research methods based on mass  spectrometry technology, in conjunction with appropriate biological  approaches, to identify disease biomarkers. Our research aims to  comprehensively explore the vital physiological functions of metabolites  in disease occurrence and progression, while also investigating the  impact and mechanisms of environmental factors on life metabolism. Our  goal is to provide novel strategies and insights for the prevention,  diagnosis, and treatment of related diseases.

3. Investigation of Environmental Pollutants and Their Impact on Health

Develop  new technologies for the detection of environmental pollutants with  high sensitivity and wide coverage, and explore the impact of  environmental pollutants on human health. Through correlation analysis  of environmental pollutants and health outcomes, identify key  environmental factors that significantly affect human health.


Selected publications

1.         Wang, M., Xie, N.B., Gang, F.Y., Zhang, S., Zeng, L., Ji, T.T., Xiong, J., Guo, X., Hao, Y.,  Liu, Y., and Yuan, B.F.* (2024) Bisulfite-Free Whole-Genome Mapping of 5-Methylcytosine at Single-Base Resolution by NTD-seq. Sci China Life Sci, DOI:10.1007/s11427-024-2702-8.

2.         Xiong, J., Wu, J., Liu, Y., Feng, Y.J. and Yuan, B.F.* (2024) Quantification and mapping of RNA modifications. TrAC-Trend Anal Chem, 172, 117606.

3.         Xie, N.B., Wang, M., Ji, T.T., Guo, X., Gang, F.Y., Hao, Y., Zeng, L., Wang, Y.F., Feng, Y.Q. and Yuan, B.F.*  (2024) Simultaneous detection of 5-methylcytosine and  5-hydroxymethylcytosine at specific genomic loci by engineered  deaminase-assisted sequencing. Chem Sci, 15, 10073-10083.

4.         Min, Y.H., Shao, W.X., Hu, Q.S., Xie, N.B., Zhang, S., Feng, Y.Q., Xing, X.W.* and Yuan, B.F.*  (2024) Simultaneous Detection of Adenosine-to-Inosine Editing and  N(6)-Methyladenosine at Identical RNA Sites through Deamination-Assisted  Reverse Transcription Stalling. Anal Chem, 96, 8730-8739.

5.         Gu, Y.H., Chen, Y., Li, Q., Xie, N.B., Xing, X., Xiong, J., Hu, M., Li, T.Z., Yuan, K.Y., Liu, Y., Tang, T.*, He, F.* and Yuan, B.F.*  (2024) Metabolome profiling by widely-targeted metabolomics and  biomarker panel selection using machine-learning for patients in  different stages of chronic kidney disease. Chin Chem Lett, 35, 109627.

6.         Xiong, J., Chen, K.K., Xie, N.B., Chen, W., Shao, W.X., Ji, T.T., Yu, S.Y., Feng, Y.Q. and Yuan, B.F.* (2024) Demethylase-assisted site-specific detection of N1-methyladenosine in RNA. Chin Chem Lett, 35, 108953.

7.         Ding, J.H., Li, G., Xiong, J., Liu, F.L., Xie, N.B., Ji, T.T., Wang, M., Guo, X., Feng, Y.Q., Ci, W.* and Yuan, B.F.*  (2024) Whole-Genome Mapping of Epigenetic Modification of  5-Formylcytosine at Single-Base Resolution by Chemical Labeling  Enrichment and Deamination Sequencing. Anal Chem, 96, 4726-4735.

8.         Guo, X., Xie, N.B., Chen, W., Ji, T.T., Xiong, J., Feng, T., Wang, M., Zhang, S., Gu, S.Y., Feng, Y.Q.* and Yuan, B.F.*  (2024) AlkB-Facilitated Demethylation Enables Quantitative and  Site-Specific Detection of Dual Methylation of Adenosine in RNA. Anal Chem, 96, 847-855.

9.         Feng, T., Gao, Y.L., Hu, D., Yuan, K.Y., Gu, S.Y., Gu, Y.H., Yu, S.Y., Xiong, J., Feng, Y.Q., Wang, J.* and Yuan, B.F.*  (2024) Chronic sleep deprivation induces alterations in DNA and RNA  modifications by liquid chromatography-mass spectrometry analysis. Chin Chem Lett, 35, 109259.

10.      Chen, Y.Y., Gui, Z., Hu, D., Chen, M.Y., He, J.G., Yu, S.Y., Feng, Y.Q., Wang, J. and Yuan, B.F.*  (2024) Adolescent alcohol exposure changes RNA modifications in adult  brain by mass spectrometry-based comprehensive profiling analysis. Chin Chem Lett, 34, 108522.

11.      Xie, N.B., Wang, M., Chen, W., Ji, T.T., Guo, X., Gang, F.Y., Wang, Y.F., Feng, Y.Q., Liang, Y.,* Ci, W.,* and Yuan, B.F.* (2023) Whole-Genome Sequencing of 5Hydroxymethylcytosine at Base Resolution by Bisulfite-Free Single-Step Deamination with Engineered Cytosine Deaminase, ACS Cent Sci, 9, 2315-2325.

12.      Ma,  C.J., Li, G., Shao, W.X., Min, Y.H., Wang, P., Ding, J.H., Xie, N.B.,  Wang, M., Tang, F., Feng, Y.Q., Ci, W.,* Wang, Y.,* and Yuan, B.F.* (2023) Single-Nucleotide Resolution Mapping of N6‑Methyladenine in Genomic DNA. ACS Cent Sci, 9, 1799-1809.

13.      Shao, W.X., Min, Y.H., Chen, W., Xiong, J., Guo, X., Xie, N.B., Zhang, S., Yu, S.Y., Xie, C., Feng, Y.Q. and Yuan, B.F.* (2023) Single-Base Resolution Detection of N(6)-Methyladenosine in RNA by Adenosine Deamination Sequencing. Anal Chem, 95, 10588-10594.

14.      Ji, T.T., Xie, N.B., Ding, J.H., Wang, M., Guo, X., Chen, Y.Y., Yu, S.Y., Feng, Y.Q. and Yuan, B.F.*  (2023) Enzymatic Cleavage-Mediated Extension Stalling Enables Accurate  Recognition and Quantification of Locus-Specific Uracil Modification in  DNA. Anal Chem, 95, 8384-8392.

15.      Wang, M., Xie, N.B., Chen, K.K., Ji, T.T., Xiong, J., Guo, X., Yu, S.Y., Tang, F., Xie, C., Feng, Y.Q. and Yuan, B.F.*  (2023) Engineered APOBEC3C Sequencing Enables Bisulfite-Free and Direct  Detection of DNA Methylation at a Single-Base Resolution. Anal Chem, 95, 1556-1565.

16.      Ding, J.H., Chen, M.Y., Xie, N.B., Xie, C., Xiong, N., He, J.G., Wang, J., Guo, C., Feng, Y.Q. and Yuan, B.F.*  (2023) Quantitative and site-specific detection of inosine modification  in RNA by acrylonitrile labeling-mediated elongation stalling. Biosens Bioelectron, 219, 114821.

17.      Tao, W.B., Xie, N.B., Cheng, Q.Y., Feng, Y.Q. and Yuan, B.F.*  (2023) Sensitive determination of inosine RNA modification in single  cell by chemical derivatization coupled with mass spectrometry analysis.  Chin Chem Lett, 34, 108243.

18.      Xiong, J., Wang, P., Shao, W.X., Li, G.J., Ding, J.H., Xie, N.B., Wang, M., Cheng, Q.Y., Xie, C.H., Feng, Y.Q., Ci, W.M.* and Yuan, B.F.* (2022) Genome-wide mapping of N-4-methylcytosine at single-base resolution by APOBEC3A-mediated deamination sequencing. Chem Sci, 13, 9960-9972.

19.      Xiong, J., Chen, K.K., Xie, N.B., Ji, T.T., Yu, S.Y., Tang, F., Xie, C., Feng, Y.Q. and Yuan, B.F.*  (2022) Bisulfite-Free and Single-Base Resolution Detection of  Epigenetic DNA Modification of 5-Methylcytosine by  Methyltransferase-Directed Labeling with APOBEC3A Deamination  Sequencing. Anal Chem, 94, 15489-15498.

20.      You, X.J., Zhang, S., Chen, J.J., Tang, F., He, J., Wang, J., Qi, C.B., Feng, Y.Q., Yuan, B.F.* (2022) Formation and removal of 1,N6-dimethyladenosine in mammalian transfer RNA. Nucleic Acids Res. 50, 9858-9872.

21.      Tang, F., Yuan, J., Yuan, B.F.* and Wang, Y.* (2022) DNA−Protein Cross-Linking Sequencing for Genome-Wide Mapping of Thymidine Glycol. J Am Chem Soc, 144, 454-462.

22.      Chen, J.J., You, X.J., Li, L., Xie, N.B., Ding, J.H., Yuan, B.F.*  and Feng, Y.Q. (2022) Single-Base Resolution Detection of  Adenosine-to-Inosine RNA Editing by Endonuclease-Mediated Sequencing. Anal Chem, 94, 8740-8747..

23.      Xie, N.B., Wang, M., Ji, T.T., Guo, X., Ding, J.H., Yuan, B.F.*  and Feng, Y.Q. (2022) Bisulfite-free and single-nucleotide resolution  sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine  using engineered deaminase. Chem Sci, 13, 7046–7056.

24.      Feng, Y.J., You, X.J., Ding, J.H., Zhang, Y.F., Yuan, B.F.*  and Feng, Y.Q. (2022) Identification of Inosine and 2'-O-Methylinosine  Modifications in Yeast Messenger RNA by Liquid Chromatography-Tandem  Mass Spectrometry Analysis. Anal Chem, 94, 4747-4755.

25.      Chen, M.Y., Qi, C.B., Tang, X.M., Ding, J.H., Yuan, B.F.*  and Feng, Y.Q. (2022) Comprehensive profiling and evaluation of the  alteration of RNA modifications in thyroid carcinoma by liquid  chromatography-tandem mass spectrometry. Chin Chem Lett, 33, 3772-3776.

26.      Chen, M.Y., Gui, Z., Chen, K.K., Ding, J.H., He, J.G., Xiong, J., Li, J.L., Wang, J., Yuan, B.F.*  and Feng, Y.Q. (2022) Adolescent alcohol exposure alters DNA and RNA  modifications in peripheral blood by liquid chromatography-tandem mass  spectrometry analysis. Chin Chem Lett, 33, 2086-2090.

27.      Ma, C.J., Li, L., Shao, W.X., Ding, J.H., Cai, X., Lun, Z., Yuan, B.F.* and Feng, Y.Q. (2021) Enzyme-mediated bioorthogonal labeling method for genome-wide mapping of 5-hydroxymethyluracil. Chem Sci, 12, 14126-14132.

28.      Feng, Y., Chen, J.J., Xie, N.B., Ding, J.H., You, X.J., Tao, W.B., Zhang, X., Yi, C., Zhou, X., Yuan, B.F.*  and Feng, Y.Q. (2021) Direct decarboxylation of Ten-eleven  translocation-produced 5-carboxylcytosine in mammalian genomes forms a  new mechanism for active DNA demethylation. Chem Sci, 12, 11322-11329.

29.      Cheng, M.Y., You, X.J., Ding, J.H., Dai, Y., Chen, M.Y., Yuan, B.F.* and Feng, Y.Q. (2021) Novel dual methylation of cytidines in RNA of mammals. Chem Sci, 12, 8149–8156.

30.      Dai, Y., Yuan, B.F.* and Feng, Y.Q. (2021) Quantification and mapping of DNA modifications. RSC Chem Biol, 2, 1096–1114.

31.      Dai, Y., Qi, C.B., Feng, Y., Cheng, Q.Y., Liu, F.L., Cheng, M.Y., Yuan, B.F.*  and Feng, Y.Q. (2021) Sensitive and Simultaneous Determination of  Uridine Thiolation and Hydroxylation Modifications in Eukaryotic RNA by  Derivatization Coupled with Mass Spectrometry Analysis. Anal Chem. 93, 6938-6946.

32.      Liu, F.L., Ye, T.T., Ding, J.H., Yin, X.M., Yang, X.K., Huang, W.H., Yuan, B.F.*  and Feng, Y.Q. (2021) Chemical Tagging Assisted Mass Spectrometry  Analysis Enables Sensitive Determination of Phosphorylated Compounds in a  Single Cell. Anal Chem, 93, 6848-6856.

33.      Wang, Q., Ding, J.H., Xiong, J., Feng, Y., Yuan, B.F.*  and Feng, Y.Q. (2021) Site-specific quantification of  5-carboxylcytosine in DNA by chemical conversion coupled with  ligation-based PCR. Chin Chem Lett, 32, 3426-3430.

34.      Jeschke, J., Collignon, E., Al Wardi, C., Krayem, M., … Yuan, B.F.,  Willard-Gallo, K., Sotiriou, C., Marine, J.C. and Fuks, F.* (2021)  Downregulation of the FTO m(6)A RNA demethylase promotes EMT-mediated  progression of epithelial tumors and sensitivity to Wnt inhibitors. Nat Cancer, 2, 611-628.

35.      Feng, Y., Xie, N.B., Tao, W.B., Ding, J.H., You, X.J., Ma, C.J., Zhang, X., Yi, C., Zhou, X., Yuan, B.F.*  and Feng, Y.Q. (2020) Transformation of 5-Carboxylcytosine to Cytosine  Through C–C Bond Cleavage in Human Cells Constitutes a Novel Pathway for  DNA Demethylation. CCS Chem, 2, 994-1008.

36.      Cheng, Q.Y., Xiong, J., Ma, C.J., Dai, Y., Ding, J.H., Liu, F.L., Yuan, B.F.* and Feng, Y. Q. (2020) Chemical tagging for sensitive determination of uridine modifications in RNA, Chem Sci, 11, 1878-1891.

37.      Ding, J.H., Ma, C.J., Chen, M.Y., Chen, B., Yuan, B.F.*  and Feng, Y.Q. (2020) Quantification and single-base resolution  analysis of N1-methyladenosine in mRNA by ligation-assisted  differentiation. Anal Chem, 92, 2612-2619.

38.      Liu, F.L, Qi, C.B., Cheng, Q.Y., Ding, J.H., Yuan, B.F.*  and Feng, Y.Q. (2020) Diazo reagent labeling with mass spectrometry  analysis for sensitive determination of ribonucleotides in living  organisms. Anal Chem, 92, 2301-2309.

39.      Lan, J., Rajan, N., Bizet, M., Penning, A.,… Yuan, B.F. and Fuks, F.* (2020) Functional role of Tet-mediated RNA hydroxymethylcytosine in mouse ES cells and during differentiation. Nat Commun, 11, 4956.

40.      You, X.J., Liu, T., Ma, C.J., Qi, C.B., Tong, Y., Zhao, X., Yuan, B.F.* and Feng, Y.Q. (2019) Determination of RNA hydroxylmethylation in mammals by mass spectrometry analysis. Anal Chem, 91, 10477-10483.

41.      Tang, F., Liu, S., Li, Q.Y., Yuan, J., Li, L., Wang, Y., Yuan, B.F.* and Feng, Y.Q. (2019) Location analysis of 8-oxo-7,8-dihydroguanine in DNA by polymerase-mediated differential coding. Chem Sci, 10, 4272–4281.

42.      Xiong, J., Ye, T.T., Ma, C.J., Cheng, Q.Y., Yuan, B.F.* and Feng, Y.Q. (2019) N6-Hydroxymethyladenine: a hydroxylation derivative of N6-methyladenine in genomic DNA of mammals. Nucleic Acids Res, 47, 1268-1277.

43.      Chen, B., Yuan, B.F.* and Feng, Y.Q. (2019) Analytical Methods for Deciphering RNA Modifications. Anal Chem, 91, 743-756.

44.      Xu, J., Zhang, Q.F., Zheng, J., Yuan, B.F.* and Feng, Y.Q.* (2019) Mass spectrometry-based fecal metabolome analysis. TrAC-Trend Anal Chem, 112, 161-174.

45.      Ma, C.J., Ding, J.H., Ye, T.T., Yuan, B.F.* and Feng, Y.Q. (2019) AlkB Homologue 1 Demethylates N(3)-Methylcytidine in mRNA of Mammals. ACS Chem Biol, 14, 1418-1425.

46.      Qi, C.B., Jiang, H.P., Xiong, J., Yuan, B.F.*,  and Feng, Y.Q. (2019) On-line trapping/capillary  hydrophilic-interaction liquid chromatography/mass spectrometry for  sensitive determination of RNA modifications from human blood. Chin Chem Lett, 30, 553-557.

47.      Qi, C.B., Ding, J.H., Yuan, B.F.*, and Feng, Y.Q. (2019) Analytical methods for locating modifications in nucleic acids. Chin Chem Lett, 30, 1618-1626.

48.      Lan, M.D., Yuan, B.F.*, and Feng, Y.Q. (2019) Deciphering nucleic acid modifications by chemical derivatization-mass spectrometry analysis. Chin Chem Lett, 30, 1-6.

49.      Li, Q.Y., Xie, N.B., Xiong, J., Yuan, B.F.*  and Feng, Y.Q. (2018) Single-Nucleotide Resolution Analysis of  5-Hydroxymethylcytosine in DNA by Enzyme-Mediated Deamination in  Combination with Sequencing. Anal Chem, 90, 14622-14628.

50.      Chu, J.M., Ye, T.T., Ma, C.J., Lan, M.D., Liu, T., Yuan, B.F.*  and Feng, Y.Q. (2018) Existence of Internal N7-Methylguanosine  Modification in mRNA Determined by Differential Enzyme Treatment Coupled  with Mass Spectrometry Analysis. ACS Chem Biol. 13, 3243−3250

51.      Jiang, H.P., Xiong, J., Liu, F.L., Ma, C.J., Tang, X.L., Yuan, B.F.* and Feng, Y.Q. (2018) Modified nucleoside triphosphates exist in mammals. Chem Sci, 9, 4160-4167.

52.      Yuan, B.F.,  Zhu, Q.F., Guo, N., Zheng, S.J., Wang, Y.L., Wang, J., Xu, J., Liu,  S.J., He, K., Hu, T., Zheng, Y.W., Xu, F.Q. and Feng, Y.Q.* (2018)  Comprehensive Profiling of Fecal Metabolome of Mice by Integrated  Chemical Isotope Labeling-Mass Spectrometry Analysis. Anal Chem, 90, 3512-3520.

53.      Lan, M.D., Xiong, J., You, X.J., Weng, X.C., Zhou, X., Yuan, B.F.* and Feng, Y.Q. (2018) Existence of Diverse Modifications in Small-RNA Species Composed of 16-28 Nucleotides. Chem-Eur J, 24, 9949-9956.

54.      Cheng, Q. Y., Xiong, J., Wang, F., Yuan, B.F.*,  and Feng, Y. Q. (2018) Chiral derivatization coupled with liquid  chromatography/mass spectrometry for determining ketone metabolites of  hydroxybutyrate enantiomers, Chin Chem Lett 29, 115-118.

55.      Zeng, H., Qi, C.B., Liu, T., Xiao, H.M., Cheng, Q.Y., Jiang, H.P., Yuan, B.F.*  and Feng, Y.Q. (2017) Formation and Determination of Endogenous  Methylated Nucleotides in Mammals by Chemical Labeling Coupled with Mass  Spectrometry Analysis. Anal Chem, 89, 4153-4160.

56.      Xiong, J., Liu, X., Cheng, Q.Y., Xiao, S., Xia, L.X., Yuan, B.F.* and Feng, Y.Q. (2017) Heavy Metals Induce Decline of Derivatives of 5-Methycytosine in Both DNA and RNA of Stem Cells. ACS Chem Biol, 12, 1636-1643.

57.      Tang, F., Yu, Q.W., Yuan, B.F.* and Feng, Y.Q.* (2017) Hydrophilic materials in sample pretreatment. TrAC-Trend Anal Chem, 86, 172-184.

58.      Huang, W., Lan, M.D., Qi, C.B., Zheng, S.J., Wei, S.Z., Yuan, B.F.* and Feng, Y.Q. (2016). Formation and determination of the oxidation products of 5-methylcytosine in RNA. Chem Sci. 2016, 7, 5495-5502.

59.      Zhang, H.Y., Xiong, J., Qi, B.L., Feng, Y.Q.* and Yuan, B.F.* (2016) The existence of 5-hydroxymethylcytosine and 5-formylcytosine in both DNA and RNA in mammals. Chem Commun (Camb), 52, 737-740

60.      Huang, W., Qi, C.B., Lv, S.W., Xie, M., Feng, Y.Q.*, Huang, W.H.* and Yuan, B.F.* (2016) Determination of DNA and RNA Methylation in Circulating Tumor Cells by Mass Spectrometry. Anal Chem. 88, 1378-1384.

61.      Xu, J., Wu, P., Ye, E.C., Yuan, B.F.* and Feng, Y.Q.* (2016) Metal oxides in sample pretreatment. TrAC-Trend Anal Chem, 80, 41-56.

62.      Li, X.S., Yuan, B.F.* and Feng, Y.Q.* (2016) Recent advances in phosphopeptide enrichment: Strategies and techniques. TrAC-Trend Anal Chem, 78, 70-83.

63.      Chen, K., Zhang, J., Guo, Z., Ma, Q., Xu, Z., Zhou, Y., Xu, Z., Li, Z., Liu, Y., Ye, X., Li, X., Yuan, B.F.,  Ke, Y., He, C., Zhou, L., Liu, J. and Ci, W.* (2016) Loss of  5-hydroxymethylcytosine is linked to gene body hypermethylation in  kidney cancer. Cell Res, 26, 103-118.

64.      Tang, Y., Zheng, S.J., Qi, C.B., Feng, Y.Q.* and Yuan, B.F.*  (2015) Sensitive and simultaneous determination of 5-methylcytosine and  its oxidation products in genomic DNA by chemical derivatization  coupled with liquid chromatography-tandem mass spectrometry analysis. Anal Chem, 87, 3445-3452.

65.      Chu, J.M., Qi, C.B., Huang, Y.Q., Jiang, H.P., Hao, Y.H., Yuan, B.F.*  and Feng, Y.Q.* (2015) Metal Oxide-Based Selective Enrichment Combined  with Stable Isotope Labeling-Mass Spectrometry Analysis for Profiling of  Ribose Conjugates. Anal Chem, 87, 7364-7372.

66.      Shen, F., Huang, W., Huang, J.T., Xiong, J., Yang, Y., Wu, K., Jia, G.F., Chen, J., Feng, Y.Q.*, Yuan, B.F.*,  Liu, S.M.* (2015) Decreased N(6)-Methyladenosine in Peripheral Blood  RNA From Diabetic Patients Is Associated With FTO Expression Rather Than  ALKBH5. J Clin Endocrinol Metab, 100, E148-154.

67.      Li, X.M., Zheng, K.W., Zhang, J.Y., Liu, H.H., He, Y.D., Yuan, B.F., Hao, Y.H. and Tan, Z.* (2015) Guanine-vacancy-bearing G-quadruplexes responsive to guanine derivatives. Proc Natl Acad Sci U S A. 112, 14581-14586

68.      Yuan, B.F.* and Feng, Y.Q. (2014) Recent advances in the analysis of 5-methylcytosine and its oxidation products. TrAC-Trend Anal Chem, 54, 24-35.

69.      Xing, X.W., Tang, F., Wu, J., Chu, J.M., Feng, Y.Q., Zhou, X.* and Yuan, B.F.* (2014) Sensitive detection of DNA methyltransferase activity based on exonuclease-mediated target recycling. Anal Chem, 86, 11269-11274.

70.      Tang, Y., Xiong, J., Jiang, H.P., Zheng, S.J., Feng, Y.Q.* and Yuan, B.F.*  (2014) Determination of oxidation products of 5-methylcytosine in  plants by chemical derivatization coupled with liquid  chromatography/tandem mass spectrometry analysis. Anal Chem, 86, 7764-7772.

71.      Qi, B.L., Liu, P., Wang, Q.Y., Cai, W.J., Yuan, B.F.* and Feng, Y.Q.* (2014) Derivatization for liquid chromatography-mass spectrometry. TrAC-Trend Anal Chem, 59, 121-132.

72.      Liu, P., Huang, Y.Q., Cai, W.J., Yuan, B.F.*  and Feng, Y.Q.* (2014) Profiling of thiol-containing compounds by  stable isotope labeling double precursor ion scan mass spectrometry. Anal Chem, 86, 9765-9773.

73.      Liang,  Q., Dexheimer, T.S., Zhang, P., Rosenthal, A.S., Villamil, M.A., You,  C., Zhang, Q., Chen, J., Ott, C.A., Sun, H., Luci, D.K., Yuan, B.F.,  Simeonov, A., Jadhav, A., Xiao, H., Wang, Y., Maloney, D.J. and Zhuang,  Z.* (2014) A selective USP1-UAF1 inhibitor links deubiquitination to  DNA damage responses. Nat Chem Biol, 10, 298-304.

74.      Wang, S.T., Huang, W., Lu, W., Yuan, B.F.*  and Feng, Y.Q.* (2013) TiO2-Based Solid Phase Extraction Strategy for  Highly Effective Elimination of Normal Ribonucleosides before Detection  of 2'-Deoxynucleosides/Low-Abundance 2'-O-Modified Ribonucleosides. Anal Chem, 85, 10512-10518.

75.      Tang, Y., Chu, J.M., Huang, W., Xiong, J., Xing, X.W., Zhou, X., Feng, Y.Q.* and Yuan, B.F.*  (2013) Hydrophilic material for the selective enrichment of  5-hydroxymethylcytosine and its liquid chromatography-tandem mass  spectrometry detection. Anal Chem, 85, 6129-6135.

76.      Chen, M.L., Shen, F., Huang, W., Qi, J.H., Wang, Y., Feng, Y.Q.*, Liu, S.M.* and Yuan, B.F.*  (2013) Quantification of 5-Methylcytosine and 5-Hydroxymethylcytosine  in Genomic DNA from Hepatocellular Carcinoma Tissues by Capillary  Hydrophilic-Interaction Liquid Chromatography/Quadrupole TOF Mass  Spectrometry. Clin Chem, 59, 824-832.

77.      Chen, M.L., Liu, Y.L., Xing, X.W., Zhou, X., Feng, Y.Q.* and Yuan, B.F.*  (2013) Preparation of a Hyper-cross-linked Polymer Monolithic Column  and Its Application to the Sensitive Determination of Genomic DNA  Methylation. Chem-Eur J, 19, 1035-1041.

78.      Cao, Z., Yu, Y., Wu, Y., Hao, P.,… Yuan, B.F.,  Feng, Y., Huang, W., Xing, X., Zhao, G., Li, X., Li, Y. and Li, W.*  (2013) The genome of Mesobuthus martensii reveals a unique adaptation  model of arthropods. Nat Commun, 4, 2602.

79.      Tang, Y., Gao, X.D., Wang, Y., Yuan, B.F.*  and Feng, Y.Q.* (2012) Widespread existence of Cytosine methylation in  yeast DNA measured by gas chromatography/mass spectrometry. Anal Chem, 84, 7249-7255.

80.      You, C., Dai, X., Yuan, B.F.,  Wang, J., Wang, J., Brooks, P.J., Niedernhofer, L.J. and Wang, Y.*  (2012) A quantitative assay for assessing the effects of DNA lesions on  transcription. Nat Chem Biol, 8, 817-822.

81.      Yuan, B.F.,  Zhang, J., Wang, H., Xiong, L., Cai, Q., Wang, T., Jacobsen, S.,  Pradhan, S. and Wang, Y.* (2011) 6-Thioguanine reactivates  epigenetically silenced genes in acute lymphoblastic leukemia cells by  facilitating proteasome-mediated degradation of DNMT1. Cancer Res, 71, 1904-1911.

82.      Yuan, B.F.,  Wang, J., Cao, H., Sun, R. and Wang, Y.* (2011) High-throughput  analysis of the mutagenic and cytotoxic properties of DNA lesions by  next-generation sequencing. Nucleic Acids Res, 39, 5945-5954.

83.      Yuan, B.F.,  You, C., Andersen, N., Jiang, Y., Moriya, M., O'Connor, T.R. and Wang,  Y.* (2011) The roles of DNA polymerases kappa and iota in the error-free  bypass of N2-carboxyalkyl-2'-deoxyguanosine lesions in mammalian cells.  J Biol Chem, 286, 17503-17511.

84.      Yuan, B.F., O'Connor, T.R. and Wang, Y.* (2010) 6-Thioguanine and S(6)-Methylthioguanine Are Mutagenic in Human Cells. ACS Chem. Biol., 5, 1021-1027.

85.      Yuan, B.F.,  Jiang, Y. and Wang, Y.* (2010) Efficient formation of the tandem  thymine glycol/8-oxo-7,8-dihydroguanine lesion in isolated DNA and the  mutagenic and cytotoxic properties of the tandem lesions in Escherichia  coli cells. Chem Res Toxicol, 23, 11-19.

86.      Yuan, B.F., Cao, H., Jiang, Y., Hong, H. and Wang, Y.* (2008) Efficient and accurate bypass of N2-(1-carboxyethyl)-2'-deoxyguanosine by DinB DNA polymerase in vitro and in vivo. Proc. Natl. Acad. Sci. U S A., 105, 8679-8684.

87.      Yuan, B.F.  and Wang, Y.* (2008) Mutagenic and cytotoxic properties of 6-thioguanine, S6-methylthioguanine, and guanine-S6-sulfonic acid. J Biol Chem, 283, 23665-23670.

88.      Yuan, B.F., Zhuang, X.Y., Hao, Y.H. and Tan, Z.* (2008) Kinetics of base stacking-aided DNA hybridization. Chem Commun (Camb), 6600-6602.

89.      Yuan, B.F.,  Hao, Y.H. and Tan, Z.* (2004) Universal sensing strategy for the  detection of nucleic acid targets by optical biosensor based on surface  plasmon resonance. Clin Chem, 50, 1057-1060.

 

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