代表性文章：
1. Ting Wu#, Shang-Tong Li#, Yu Ran#, Yinuo Lin, Lu Liu, Xiajun Zhang, Lianqi Zhou, Long Zhang, Donghai Wu, Bing Yang, Shibing Tang, Mapping protein direct interactome of oxidoreductases with small molecular chemical cross-linkers in live cells, Redox Biology, 2023, 61, 102642, https://doi.org/10.1016/j.redox.2023.102642. (# These authors contribute equally)
2. Shu X#, Liao QQ#, Li ST#, Liu L, Zhang X, Zhou L, Zhang L, Coin I, Wang L, Wu H, Yang B. Detecting Active Deconjugating Enzymes with Genetically Encoded Activity-Based Ubiquitin and Ubiquitin-like Protein Probes. Anal Chem. 2023;95(2):846-853.
3 Shu X#, Asghar S#, Yang F, Li ST, Wu H, Yang B. Uncover New Reactivity of Genetically Encoded Alkyl Bromide Non-Canonical Amino Acids. Front Chem. 2022; 10:815991. Published 2022 Feb 18.
4. Liu C#, Wu T#, Shu X#, Li ST#, Wang DR#, Wang N#, Zhou R, Yang H, Jiang H, Hendriks IA, Gong P, Zhang L, Nielsen ML, Li K, Wang L, Yang B. Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa. Adv Biol (Weinh). 2021 Mar;5(3): e2000308.
5. Yang B#, Wang N#, Schnier PD#, Zheng F#, Zhu H#, Polizzi NF,Ittuveetil A,Saikam V,DeGrado WF,Wang Q,Wang PG and Wang L. Genetically Introducing Biochemically Reactive Amino Acids Dehydroalanine and Dehydrobutyrine in Proteins. J Am Chem Soc. 2019 May 15;141(19):7698-7703. (# these authors contributed equally)
6. Yang B#, Wu H#, Schnier PD#, Liu Y#, Liu J, Wang N, DeGrado WF, and Wang L. Proximity-enhanced SuFEx chemical cross-linker for specific and multitargeting cross-linking mass spectrometry. Proc Natl Acad Sci U S A. October 30, 2018 115 (44) 11162-11167. (# these authors contributed equally)
7. Wang N#, Yang B#, Fu C#, Zhu H, Zheng F, Kobayashi T, Liu J, Li S, Ma C, Wang PG, Wang Q, Wang L. Genetically Encoding Fluorosulfate-l-tyrosine To React with Lysine, Histidine, and Tyrosine via SuFEx in Proteins in Vivo. J Am Chem Soc. 2018 Apr 18;140(15):4995-4999. (# these authors contributed equally)
8. Yang B#, Tang Shibing#, Ma C#, Li ST, Shao GC, Dang B, DeGrado WF, Dong MQ, Wang PG, Ding S, Wang L. Spontaneous and specific chemical cross-linking in live cells to capture and identify protein interactions. Nat Commun. 2017 Dec 21;8(1):2240. (# these authors contributed equally)
9. Lu S#, Fan SB#, Yang B#, Li XY, Meng JM, Wu L, Li P, Wang HT, Zhang K, Zhang MJ, Luo JC, Du LL, Sun RX, He SM, Dong MQ. Mapping native disulfide bonds at a proteome scale.Nat Methods.Nat Methods. 2015 Apr;12(4):329-31. (# these authors contributed equally)
10. Yang B#, Wu YJ#, Zhu M#, Fan SB#, Lin JZ, Li S, Luo SK, Zhang K, Xiu LY, Li YX, Chen S, Ye KQ, He SM, Dong MQ. Identification of cross-linked peptides from complex samples.Nat Methods.2012 Sep;9(9):904-906. (# these authors contributed equally)
11. Yang B#, Ying W#, Gong Y, Zhang Y, Cai Y, Dong H, Qian X. Using cross-correlation normalized for peptide length to optimize peptide identification in shotgun proteomics. Rapid Commun Mass Spectrom. 2005;19(20):2983-2985. (# these authors contributed equally)
发表文章：
1. Zhang Z, Du J, Wang S, Shao L, Jin K, Li F, Wei B, Ding W, Fu P, van Dam H, Wang A, Jin J, Ding C, Yang B, Zheng M, Feng XH, Guan KL, Zhang L.OTUB2 Promotes Cancer Metastasis via Hippo-Independent Activation of YAP and TAZ. Mol Cell. 2019 Jan 3;73(1):7-21.e7.
2. Yang B, Wang N, Schnier PD, Zheng F, Zhu H, Polizzi NF, Ittuveetil A, Saikam V, DeGrado WF, Wang Q, Wang PG, Wang L.Genetically Introducing Biochemically Reactive Amino Acids Dehydroalanine and Dehydrobutyrine in Proteins.J Am Chem Soc. 2019 May 15;141(19):7698-7703.
3. Liu J, Li S, Aslam NA, Zheng F, Yang B, Cheng R, Wang N, Rozovsky S, Wang PG, Wang Q, Wang L.Genetically Encoding Photocaged Quinone Methide to Multitarget Protein Residues Covalently in Vivo.J Am Chem Soc. 2019 Jun 19;141(24):9458-9462.
4. Zuzow N, Ghosh A, Leonard M, Liao J,Yang B, Bennett EJ.Mapping the mammalian ribosome quality control complex interactome using proximity labeling approaches.Mol Biol Cell. 2018 May 15;29(10):1258-1269.
5. Wang N, Yang B, Fu C, Zhu H, Zheng F, Kobayashi T, Liu J, Li S, Ma C, Wang PG, Wang Q, Wang L. Genetically Encoding Fluorosulfate-l-tyrosine To React with Lysine, Histidine, and Tyrosine via SuFEx in Proteins in Vivo. J Am Chem Soc. 2018 Apr 18;140(15):4995-4999.
6. Yang B, Wu H, Schnier PD, Liu Y, Liu J, Wang N, DeGrado WF, Wang L. Proximity-enhanced SuFEx chemical cross-linker for specific and multitargeting cross-linking mass spectrometry. Proc Natl Acad Sci U S A. 2018 Oct 30;115(44):11162-11167.
7. Gao L, Wang L, Dai T,Jin K, Zhang Z, Wang S, Xie F,2, Fang P,Yang B, Huang H, van Dam H, Zhou F, Zhang L.Tumor-derived exosomes antagonize innate antiviral immunity.Nat Immunol. 2018 Mar;19(3):233-245.
8. Dai T, Wu L, Wang S, Wang J, Xie F, Zhang Z, Fang X, Li J, Fang P, Li F, Jin K, Dai J, Yang B, Zhou F, van Dam H, Cai D, Huang H, Zhang L.FAF1 Regulates Antiviral Immunity by Inhibiting MAVS but Is Antagonized by Phosphorylation upon Viral Infection.Cell Host Microbe. 2018 Dec 12;24(6):776-790.e5.
9. Xie F, Jin K, Shao L, Fan Y, Tu Y, Li Y, Yang B, van Dam H, Ten Dijke P, Weng H, Dooley S, Wang S, Jia J, Jin J, Zhou F, Zhang L. FAF1 phosphorylation by AKT accumulates TGF-β type II receptor and drives breast cancer metastasis. Nat Commun. 2017 Apr 26;8:15021.
10. Hoppmann C, Wong A, Yang B, Li S, Hunter T, Shokat KM, Wang L. Site-specific incorporation of phosphotyrosine using an expanded genetic code. Nat Chem Biol. 2017 Aug;13(8):842-844.
11. Wang S, Xie F, Chu F, Zhang Z, Yang B, Dai T, Gao L, Wang L, Ling L, Jia J, van Dam H, Jin J, Zhang L, Zhou F.YAP antagonizes innate antiviral immunity and is targeted for lysosomal degradation through IKKb-mediated phosphorylation.Nat Immunol. 2017 Jul;18(7):733-743.
12. Yang B, Tang S, Ma C, Li ST, Shao GC, Dang B, DeGrado WF, Dong MQ, Wang PG, Ding S, Wang L. Spontaneous and specific chemical cross-linking in live cells to capture and identify protein interactions. Nat Commun. 2017 Dec 21;8(1):2240.
13. Zhang Z, Fan Y, Xie F, Zhou H, Jin K, Shao L, Shi W, Fang P, Yang B, van Dam H, Ten Dijke P, Zheng X, Yan X, Jia J, Zheng M, Jin J, Ding C, Ye S, Zhou F, Zhang L. Breast cancer metastasis suppressor OTUD1 deubiquitinates SMAD7. Nat Commun. 2017 Dec 13;8(1):2116.
14. Tan D, Li Q, Zhang MJ, Liu C, Ma C, Zhang P, Ding YH, Fan SB, Tao L, Yang B, Li X, Ma S, Liu J, Feng B, Liu X, Wang HW, He SM, Gao N, Ye K, Dong MQ, Lei X. Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states. Elife. 2016 Mar 8;5:e12509.
15. Gendron JM, Webb K, Yang B, Rising L, Zuzow N, Bennett EJ. Using the Ubiquitin-modified Proteome to Monitor Distinct and Spatially Restricted Protein Homeostasis Dysfunction. Mol Cell Proteomics. 2016 Aug;15(8):2576-93.
16. Ren H, Yang B, Ma C, Hu YS, Wang PG, Wang L. Cysteine Sulfoxidation Increases the Photostability of Red Fluorescent Proteins. ACS Chem Biol. 2016 Oct 21;11(10):2679-2684.
17. Kobayashi T, Hoppmann C, Yang B, Wang L. Using Protein-Confined Proximity To Determine Chemical Reactivity. J Am Chem Soc. 2016 Nov 16;138(45):14832-14835.
18. Zhou F, Li F, Fang P, Dai T, Yang B, van Dam H, Jia J, Zheng M, Zhang L.Ubiquitin-Specific Protease 4 Antagonizes Osteoblast Differentiation Through Dishevelled.J Bone Miner Res. 2016 Oct;31(10):1888-1898.
19. Chi H, He K, Yang B, Chen Z, Sun RX, Fan SB, Zhang K, Liu C, Yuan ZF, Wang QH, Liu SQ, Dong MQ, He SM.pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data.J Proteomics. 2015 Jul 1;125:89-97.
20. Lu S, Fan SB, Yang B, Li YX, Meng JM, Wu L, Li P, Zhang K, Zhang MJ, Fu Y, Luo J, Sun RX, He SM, Dong MQ.Mapping native disulfide bonds at a proteome scale.Nat Methods. 2015 Apr;12(4):329-31.
21. Facette MR, Park Y, Sutimantanapi D, Luo A, Cartwright HN, Yang B, Bennett EJ, Sylvester AW, Smith LG.The SCAR/WAVE complex polarizes PAN receptors and promotes division asymmetry in maize.Nat Plants. 2015 Jan 26;1:14024.
22. Higgins R, Gendron JM, Rising L, Mak R, Webb K, Kaiser SE, Zuzow N, Riviere P, Yang B, Fenech E, Tang X, Lindsay SA, Christianson JC, Hampton RY, Wasserman SA, Bennett EJ. The Unfolded Protein Response Triggers Site-Specific Regulatory Ubiquitylation of 40S Ribosomal Proteins. Mol Cell. 2015 Jul 2;59(1):35-49.
23. Hendriks IA, D'Souza RC, Yang B, Verlaan-de Vries M, Mann M, Vertegaal AC. Uncovering global SUMOylation signaling networks in a site-specific manner. Nat Struct Mol Biol. 2014 Oct;21(10):927-36.
24. Fan SB , Wu YJ , Yang B , Chi H, Meng JM, Lu S, Zhang K, Wu L, Sun RX, Dong MQ. A New Approach to Protein Structure and Interaction Research: Chemical Cross-linking in Combination With Mass Spectrometry[J]. Progress in Biochemistry & Biophysics, 2014, 41(11):1109-1125.
25. Fu C, Kobayashi T, Wang N, Hoppmann C, Yang B, Irannejad R, Wang L.Genetically encoding quinoline reverses chromophore charge and enables fluorescent protein brightening in acidic vesicles.J Am Chem Soc. 2018 Sep 5;140(35):11058-11066.
26. Sun LL, Li M, Suo F, Liu XM, Shen EZ, Yang B, Dong MQ, He WZ, Du LL. Global analysis of fission yeast mating genes reveals new autophagy factors. PLoS Genet. 9(8):e1003715.
27. Yang B, Wu YJ, Zhu M, Fan SB, Lin J, Zhang K, Li S, Chi H, Li YX, Chen HF, Luo SK, Ding YH, Wang LH, Hao Z, Xiu LY, Chen S, Ye K, He SM, Dong MQ.Identification of cross-linked peptides from complex samples.Nat Methods. 2012 Sep;9(9):904-6.
28. Chi H, Chen H, He K, Wu L, Yang B, Sun RX, Liu J, Zeng WF, Song CQ, He SM, Dong MQ.pNovo+: de novo peptide sequencing using complementary HCD and ETD tandem mass spectra. J Proteome Res. 2013 Feb 1;12(2):615-25.
29. Qu M, Yang B, Tao L, Yates JR 3rd, Russell P, Dong MQ, Du LL. Phosphorylation-dependent interactions between Crb2 and Chk1 are essential for DNA damage checkpoint. PLoS Genet. 8(7):e1002817.
30. Li S, Duan J, Li D, Yang B, Dong M, Ye K. Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase. Genes Dev. 2011 Nov 15;25(22):2409-21.
31. Chi H, Sun RX, Yang B, Song CQ, Wang LH, Liu C, Fu Y, Yuan ZF, Wang HP, He SM, Dong MQ.pNovo: de novo peptide sequencing and identification using HCD spectra.J Proteome Res. 2010 May 7;9(5):2713-24.
32. Sun RX, Dong MQ, Song CQ, Chi H, Yang B, Xiu LY, Tao L, Jing ZY, Liu C, Wang LH, Fu Y, He SM.Improved peptide identification for proteomic analysis based on comprehensive characterization of electron transfer dissociation spectra.J Proteome Res. 2010 Dec 3;9(12):6354-67.
33. Sun RX, Dong MQ, Chi H, Yang B, Xiu LY, Wang LH, Fu Y, He SM. ECD/ETD-based Tandem Mass Spectrometry in Proteomics*[J]. Progress in Biochemistry and Biophysics, 2010, 37(1):94-102.
34. Coffman K, Yang B, Lu J, Tetlow AL, Pelliccio E, Lu S, Guo DC, Tang C, Dong MQ, Tamanoi F. Characterization of the Raptor/4E-BP1 interaction by chemical cross-linking coupled with mass spectrometry analysis. J Biol Chem. 2014 Feb 21;289(8):4723-34.
35. Chen M, Yang B, Ying W, He F, Qian X.Annotation of non-synonymous single polymorphisms in human liver proteome by mass spectrometry.Protein Pept Lett. 2010 Mar;17(3):277-86.
36. Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ, HUPO Test Sample Working Group. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat Methods. 2009 Jun;6(6):423-30.
37. Sui S, Wang J, Yang B, Song L, Zhang J, Chen M, Liu J, Lu Z, Cai Y, Chen S, Bi W, Zhu Y, He F, Qian X.Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy.Proteomics. 2008 May;8(10):2024-34.
38. Chen M, Ying W, Song Y, Liu X, Yang B, Wu S, Jiang Y, Cai Y, He F, Qian X.Analysis of human liver proteome using replicate shotgun strategy.Proteomics. 2007 Jul;7(14):2479-88.
39. Liu J, Cai Y, Wang J, Zhou Q, Yang B, Lu Z, Jiao L, Zhang D, Sui S, Jiang Y, Ying W, Qian X.Phosphoproteome profile of human liver Chang's cell based on 2-DE with fluorescence staining and MALDI-TOF/TOF-MS.Electrophoresis. 2007 Dec;28(23):4348-58.
40. Gong Y, Li X, Yang B, Ying W, Li D, Zhang Y, Dai S, Cai Y, Wang J, He F, Qian X.Different immunoaffinity fractionation strategies to characterize the human plasma proteome.J Proteome Res. 2006 Jun;5(6):1379-87.
41. Dai J, Wang J, Zhang Y, Lu Z, Yang B, Li X, Cai Y, Qian X.Enrichment and identification of cysteine-containing peptides from tryptic digests of performic oxidized proteins by strong cation exchange LC and MALDI-TOF/TOF MS.Anal Chem. 2005 Dec 1;77(23):7594-604.
42. Yang B, Ying W, Gong Y, Zhang Y, Cai Y, Dong H, Qian X.Using cross-correlation normalized for peptide length to optimize peptide identification in shotgun proteomics.Rapid Commun Mass Spectrom. 2005;19(20):2983-5.