A Targeted Quantitative Proteomic Approach for Probing Altered Protein Expression of Small GTPases Associated with Colorectal Cancer Metastasis
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Anal. Chem. 2019, in press.
Targeted Quantitative Kinome Analysis Identifies PRPS2 as a Promoter for Colorectal Cancer Metastasis
Miao, W.; Wang Y.*
J Proteome Res. 2019, in press.
Location analysis of 8-oxo-7,8-dihydroguanine in DNA by polymerase-mediated differential coding.
Tang, F.; Liu, S.; Li, Q.Y.; Yuan, J.; Li, L.; Wang, Y.; Yuan, B.F.;* Feng, Y.
Chem. Sci., 2019, in press.
Human DNA polymerase η has reverse transcriptase activity in cellular environments.
Su, Y.; Ghodke, P.P.; Egli, M.; Li, L.; Wang, Y. and Guengerich, F.P.*
J. Biol. Chem., 2019, in press.
Cytotoxic and mutagenic properties of C1' and C3'-epimeric lesions of 2'-deoxyribonucleosides in human cells.
Du, H.; Wang, P.; Li, L.; Amato, N.; Wang Y.*
ACS Chem. Biol. 2019, 14, 478-485
Imatinib-induced changes in protein expression and ATP-binding affinities of kinases in chronic myelocytic leukemia cells.
Miao, W.; Guo, L.; Wang Y.*
Anal. Chem. 2019, 91, 3209-3214.
Dual regulation of Arabidopsis AGO2 by arginine methylation.
Hu, P.; Zhao, H.; Zhu, P.; Xiao, Y.; Miao, W.; Wang, Y. and Jin, H.*
Nat. Commun. 2019, 10, 844.
Quantification of DNA lesions induced by 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol in mammalian cells.
Guo, S.; Leng, J.; Tan, Y.; Price, N. E. and Wang, Y.*
Chem. Res. Toxicol., 2019, in press.
DNA replication studies of N-nitroso compound-induced O6-alkyl-2'-deoxyguanosine lesions in Escherichia coli.
Wang, P.; Leng, J. and Wang, Y.*
J. Biol. Chem. 2019, 294, 3894-3908.
Targeted profiling of heat shock proteome in radioresistant breast cancer cells.
Miao, W.; Fan, M. Huang, M.; Li, J.J. and Wang, Y.*
Chem. Res. Toxicol., 2019, 32, 326-332.
Integrated genomic and proteomic analyses reveal novel mechanisms of the methyltransferase SETD2 in renal cell carcinoma development.
Li, L.; Miao, W.; Huang, M.; Williams, P. and Wang, Y.*
Mol. Cell. Proteomics, 2019, 18, 437-447.
Normalized retention time for targeted analysis of the DNA adductome.
Cui, Y.; Wang, P.; Yu, Y.; Yuan, J. and Wang, Y.*
Anal. Chem., 2018, 90, 14111-14115.
N6-methyladenine DNA Modification in Glioblastoma
Xie Q.; Wu, T.P.; Gimple, R.C.; Li, Z.; Prager, B.C.; Wu, Q.; Yu, Y.; Wang, P.; Wang Y.; Gorkin, D.U.; Zhang, C.; Dowiak, A.V.; Lin, K.; Zeng, C.; Sui, Y.; Kim, L.J.Y.; Miller, T.E.; Jiang, L.; Lee, C.H.; Huang, Z.; Fang, X.; Zhai, K.; Mack, S.C.; Sander, M.; Bao, S.; Kerstetter-Fogle, A.E.; Sloan, A.E.; Xiao, A.Z.*; Rich, J.N.*
Cell, 2018, 175, 1228-1243.
Role of small GTPases in acquired tamoxifen resistance in MCF-7 cells revealed by targeted, quantitative proteomic analysis.
Huang, M. and Wang, Y.*
Anal. Chem. 2018, 90, 14551-14560.
Targeted quantitative profiling of GTP-binding proteins in cancer cells using isotope-coded GTP probes.
Cai, R.; Huang, M. and Wang, Y.*
Anal. Chem. 2018, 90, 14339-14346.
Identification of helicase proteins as clients for HSP90.
Miao, W.; Li, L. and Wang, Y.*
Anal. Chem., 2018, 90, 11751-11755.
Bypassing a 8,5-cyclo-2'-deoxyadenosine lesion by human DNA polymerase &eta at the atomic resolution.
Weng, P.; Gao, Y.; Gregory, M.T.; Wang, P.; Wang, Y.* and Yang, W.*
Proc. Natl. Acad. Sci. USA, 2018, 115, 10660-10665.
Pyruvate kinase M2 regulates homologous recombination-mediated DNA double-strand break repair.
Sizemore, S.; Zhang, M.; Cho, J.H.; Sizemore, G.; Hurwitz, B.; Kaur, B.; Lehman, N.; Ostrowski, M.; Robe, P.; Miao, W.; Wang, Y.; Chakravarti, A. and Xia, F.*
Cell Res., 2018, 28, 1090-1102.
Cytotoxic and mutagenic properties of O6-alkyl-2'-deoxyguanosine lesions in Escherichia coli cells.
Wang, P. and Wang, Y.*
J. Biol. Chem., 2018, 293, 15033-15042.
A novel malic acid-enhanced method for analysis of 5-methyl-2'-deoxycytidine, 5-hydroxymethyl-2'-deoxycytidine, 5-methylcytidine and 5-hydroxymethylcytidine in human urine using hydrophilic interaction liquid chromatography-tandem mass spectrometry.
Guo, C.*; Xie, C.; Chen, Q.; Cao, X.; Guo, M.; Zheng, S. and Wang, Y.*
Anal. Chim. Acta, 2018, 1034, 110-118.
Dysregulation of DAF-16/FOXO3-mediated stress responses accelerates oxidative DNA damage induced aging.
Gurkar, A.U.; Robinson, A.R.; Cui, Y., Li, X.; Allani, S.K.; Webster, A.; Muravia, M.; Fallahi, M.; Weissbach, H.; Robbins, P.D.; Wang, Y.; Kelley, E.E.; St. Croix, C.M.; Niedernhofer, L.J. and Gill, M.S.*
Redox Biol. 2018, 18, 191-199.
A targeted quantitative proteomic approach assesses the reprogramming of small GTPases during melanoma metastasis.
Huang, M.; Qi, T.F.; Li, L.; Zhang, G. and Wang, Y.*
Cancer Res. 2018, 78, 5431-5445.
Identification of YTH domain-containing proteins as the readers for N1-methyladenosine in RNA.
Dai, X.; Wang, T.; Gonzalez, G. and Wang, Y.*
Anal. Chem. 2018, 90, 6380-6384.
Impact of tobacco-specific nitrosamine–derived DNA adducts on the efficiency and fidelity of DNA replication in human cells
Du, H.; Leng, J.; Wang, P.; Li, L. and Wang, Y.*
J. Biol. Chem. 2018, 293, 11100-11108.
A targeted proteomic approach for heat shock proteins reveals DNAJB4 as a suppressor for melanoma metastasis.
Miao, W.; Li, L. and Wang, Y.*
Anal. Chem. 2018, 90, 6835-6842.
Arsenite targets the RING finger domain of Rbx1 E3 ubiquitin ligase to inhibit proteasome-mediated degradation of Nrf2.
Jiang, J.; Tam, L.M.; Wang, P. and Wang, Y.*
Chem. Res. Toxicol., 2018, 31, 380-387.
Cytotoxic and mutagenic properties of minor-groove O2-alkylthymidine lesions in human cells.
Wu, J.; Wang, P.; Li, L.; You, C. and Wang, Y.*
J. Biol. Chem., 2018, 293, 8638-8644.
Spontaneous DNA damage to the nuclear genome promotes senescence and aging.
Robinson, A.R.; Yousefzadeh, M.J.; Rozgaja, T. A.; Wang, J.; Li, X.; Tilstra, J. S.; Feldman, C. H.; Gregg, S. Q.; Johnson, C.H.; Skoda, E.M.; Frantz, M.-C.; Bell-Temin, H.; Pope-Varsalona, H.; Gurkar, A.U.; Nasto, L.A.; Robinson, R.A.S.; Fuhrmann-Stroissnigg, H.; Czerwinska, J.; McGowan, S. J.; Cantu-Medellin, S.; Harris, J.B.; Maniar, S.; Ross, M. A.; Trussoni, C. E.; LaRusso, N. F.; Cifuentes-Pagano, E.; Pagano, P. J.; Tudek, B.; Vo, N. V.; Rigatti, L. H.; Opresko, P. L.; Beer-Stolz, D.; Watkins, S. C.; Burd, C. E.; Croix, C. M. S.; Siuzdak, G.; Yates, N. A.; Robbins, P. D.; Wang, Y.; Wipf, P.; Kelley, E. E.*; Niedernhofer, L. J.*
Redox Biol., 2018, 17, 259-273.
An effector from the Huanglongbing-associated pathogen targets citrus proteases.
Clark, K.; Franco, J.; Schwizer, S.; Pang, Z.; Hawara, E.; Liebrand, T.; Pagliaccia, D.; Zeng, L.; Gurung, F.; Wang, P.; Shi, J.; Wang, Y.; Ancona, V.; van der Hoorn, R.; Wang, N.; Coaker, G. and Ma, W.
Nat. Commun., 2018, 9, 1718.
Nuclear genomic instability and aging.
Niedernhofer, L.J.*; Gurkar, A.U.; Wang, Y., Vijg, J.; Hoeijmakers, J. and Robbins, P.D.
Ann. Rev. Biochem., 2018,, 87, 295-322.
Cytotoxic and mutagenic properties of alkyl phosphotriester lesions in Escherichia coli cells.
Wu, J.; Wang, P. and Wang, Y.*
Nucleic Acids Res., 2018, 46, 4013-4021.
Structural basis for DNMT3A-mediated de novo DNA methylation.
Zhang, Z.-M.; Lu, R.; Wang, P.; Yu, Y.; Chen, D.L.; Gao, L.; Liu, S.; Ji, D.; Rothbart, S.B.; Wang, Y.; Wang, G.G.* and Song, J.*
Nature, 2018, 554,387-391
Chemical analysis of DNA damage.
Yu, Y.; Wang, P.; Cui. Y. and Wang, Y.*
Anal. Chem. 2018, 90, 556-576.
Photocatalytic degradation of norfloxacin on different TiO2-X polymorphs under visible light in water.
Yang, H.; Mei, L.; Wang, P.; Genereux, J.; Wang, Y.; Yi, B.; Au, C.; Dang, L. and Feng, P.*
RSC Adv., 2017, 7, 47521.
Transcription coupling: Direct interactions of RNA polymerase with ribosomes and ribosomal subunits.
Fan, H.; Conn, A.B.; Williams, P.B.; Diggs, S.; Hahm, J.; Wang, Y. and Blaha, G.M.*
Nucleic Acids Res. 2017, 45, 11043-11055.
Identification of SLIRP as a G quadruplex-binding protein.
Williams, P.; Li, L.; Dong, X. and Wang, Y.*
J. Am. Chem. Soc., 2017, 139, 12426–12429.
Arsenite binds to the zinc finger motif of TIP60 histone acetyltransferase and induces its degradation via the 26S proteasome.
Tam, L.M.; Jiang, J.; Wang, P.; Lin, L.; Miao, W.; Dong, X. and Wang, Y.*
Chem. Res. Toxicol., 2017, 30, 1685-1693.
1HNMR metabolic profiling of earthworm (Eisenia fetida) coelomic fluid, coelomocytes and tissue: Identification of a new metabolite - malylglutamate.
Griffith, C.M.; Williams, P.B.; Tinoco, L.W.; Dinges, M.M.; Wang, Y. and Larive, C.K.*
J. Proteome Res., 2017, 16, 3407-3418.
Site-selective sensing of histone methylation enzyme activity via an arrayed supramolecular tandem assay.
Liu, Y.; Perez, L.; Gill, A.; Mettry, M.; Li, L.; Wang, Y.; Hooley, R.* and Zhong, W.*
J. Am. Chem. Soc., 2017, 139, 10964-10967.
Liquid chromatography-tandem mass spectrometry for the quantification of tobacco-specific nitrosamine-induced DNA adducts in mammalian cells.
Leng, J. and Wang, Y.*
Anal. Chem. 2017, 89, 9124-9130.
Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis.
Xu, L.; Wang, W.; Wu, J.; Shina, J.H.; Wand, P.; Unartae, I.C.; Jenny, C.; Wang, Y.* and Wang, D.*
Proc. Natl. Acad. Sci. USA, 2017, 114, E7082-E7091.
Cytotoxic and mutagenic properties of C3′-epimeric lesions of 2′-deoxyribonucleosides in Escherichia coli cells.
Wang, P.; Amato, N. and Wang, Y.*
Biochemistry 2017, 56, 3725-3732.
Position-dependent effects of regioisomeric methylated adenine and guanine ribonucleosides on translation.
You, C.; Dai, X. and Wang, Y.*
Nucleic Acids Res., 2017, 45, 9059-9067.
Arsenite binds to the RING finger domain of FANCL E3 ubiquitin ligase and inhibits DNA interstrand cross-link repair.
Jiang, J.; Bellani, M.; Li, L.; Wang, P.; Seidman, M.M. and Wang, Y.*
ACS Chem. Biol., 2017, 12, 1858-1866.
Crosstalk between the pK36me3 and H4K16ac histone epigenetic marks in DNA double-strand break repair.
Li, L. and Wang, Y.*
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Structure-activity relationship investigation for benzonaphthyridinone derivatives as novel potent Bruton's tyrosine kinase irreversible inhibitors.
Wang, B.; Deng, Y.; Chen, Y.; Yu, K.; Wang, A.; Liang, Q.; Wang, W.; Chen, C.; Wu, H.; Hu, C.; Miao, W.; Hur, W.; Wang, W.; Hu, Z.; Weisberg, E.L.; Wang, J.; Ren, T.; Wang, Y.; Gray, N.S.; Liu, Q.; Liu, J.*
Eur. J. Med. Chem. 2017, 137, 545-557.
Replication and repair of a reduced 2′-deoxyguanosine-abasic site interstrand cross-link in human cells.
Price, N.E.; Li, L.; Gates, K.S.* and Wang, Y.*
Nucleic Acids Res. 2017, 45, 6486-6493.
Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA.
Yang, Z.; Price, N.E.; Johnson, K.M.; Wang, Y. and Gates, K.S.*
Nucleic Acids Res. 2017, 45, 6275-6283.
Replicative bypass studies of α-anomeric lesions of 2′-deoxyribonucleosides in vitro.
Williams, N.L.; Amato, N.J. and Wang, Y.*
Chem. Res. Toxicol. 2017, 30, 1127-1133.
Discovery of 2-((3-Acrylamido-4-methylphenyl)amino)-N-(2-methyl-5-(3,4,5-trimethoxybenzamido)phenyl)-4-(methylamino)pyrimidine-5-carboxamide (CHMFL-BMX-078) as a highly potent and selective type II irreversible bone marrow kinase in the X chromosome kinase inhibitor.
Liang, X.; Lv, F.; Wang, B.; Yu, K.; Wu, H.; Qi, Z.; Jiang, Z.; Chen, C.; Wang, A.; Miao, W.; Wang, W.; Hu, Z.; Liu, J.; Liu, X.; Zhao, Z.; Wang, L.; Zhang, S.; Ye, Z.; Wang, C.; Ren, T.; Wang, Y.; Liu, Q.; Liu, J.
J. Med. Chem. 2017, 60, 1793-1816.
A role for the base excision repair enzyme NEIL3 in replication-dependent repair of interstrand DNA cross-links derived from psoralen and abasic sites.
Yang, Z.; Nejad, M. I.; Varela, J. G.; Price, N.; Wang, Y. and Gates, K.S.*
DNA Repair, 2017, 52, 1-11.
Replication studies of carboxymethylated DNA lesions in human cells.
Wu, J.; Wang, P.; Li, L.; Williams, N.L., Ji, D.; Zahurancik, W.J.; You, C.; Wang, J.; Suo, Z. and Wang, Y.*
Nucleic Acids Res., 2017, 45, 7276-7284.
AMPK promotes mitochondrial biogenesis and function by phosphorylating the epigenetic factors DNMT1, RBBP7, and HAT1
Marin, T.L.; Gongol, B.; Zhang, F.; Martin, M.; Johnson, D. A.; Xiao, H.; Wang, Y.; Subramaniam, S.; Chien, S. and Shyy, J. Y.-J.*
Sci. Signaling, 2017, 10, eaaf7478.
SILAC-based quantitative proteomic analysis unveiled the arsenite-induced perturbation of multiple pathways in human skin fibroblast cells.
Zhang, F.; Xiao, Y. and Wang, Y.*
Chem. Res. Toxicol., 2017, 30, 1006-1014.
Distinct cellular and molecular environments support aging-related DNA methylation changes in the substantia nigra.
Fasolino, M.; Liu, S.; Wang, Y.* and Zhou, Z.*
Epigenomics, 2017, 9, 21-31.
The melanoma-linked "redhead" MC1R influences dopaminergic neuron survival.
Chen, X.*; Chen, H.; Cai, W.; Maguire, M.; Ya, B.; Zuo, F.; Logan, R.; Li, H.; Robinson, K.; Vanderburg, C.R.; Yu, Y; Wang, Y.; Fisher, D.E. and Schwarzschild, M.A.
Ann. Neurol. 2017, 81, 395-406.
Global discovery of protein kinases and other nucleotide-binding proteins by mass spectrometry.
Xiao, Y. and Wang, Y.*
Mass Spectrom. Rev., 2016, 35, 601-619.
Comprehensive assessment of oxidatively induced modifications of DNA in a rat model of human Wilson’s disease.
Yu, Y.; Guerrero, C.R.; Liu, S.; Sharma, Y.; Gupta, S. and Wang, Y.*
Mol. Cell. Proteomics, 2016, 15, 810-817.
Base J glucosyltransferase does not regulate the sequence specificity of J synthesis in Trypanosomatid telomeric DNA.
Bullard, W.; Cliff, L.; Wang, P.; Wang, Y. and Sabatini, R.*
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Mass spectrometry-based quantitative strategies for assessing the biological consequences and repair of DNA adducts.
You, C. and Wang, Y.*
Acc. Chem. Res. 2016, 49, 205-213.
Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells.
Lichinchi, G.; Gao, Y.; Saletore, Y.; Gonzalez, G.M.; Bansal, V.; Wang, Y.; Mason, C. and Rana, T.M.*
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Roles of Aag, Alkbh2, and Alkbp in the repair of carboxymethylated and ethylated thymidine lesions.
You, C.; Wang, P.; Nay, S.L.; Wang, J.; Dai, X.; O’Connor, T.R. and Wang, Y.*
ACS Chem. Biol., 2016, 11, 1332-1338.
In vitro lesion bypass studies of O4-alkylthymidines with human DNA polymerase κ.
Williams, N.; Wang, P.; Wu, J. and Wang, Y.*
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Phosphorylation of human DNA polymerase η at Ser687 is required for UV damage tolerance.
Dai, X.; You, C. and Wang, Y.*
Mol. Cell. Proteomics, 2016, 15, 1913-1920.
Photochemical generation of benzyl cations that selectively cross-link guanine and cytosine in DNA.
Wang Y.; Liu, S.; Lin, Z.; Fan, Y.; Wang, Y.; Peng, X.*
Org. Lett. 2016, 18, 2544-2547.
Translesion synthesis of O4-alkylthymidine lesions in human cells.
Wu, J.; Li, L.; Wang, P.; You, C.; Williams, N. and Wang, Y.*
Nucleic Acids Res., 2016, 44, 9256-9265.
Quantification of azaserine-induced carboxymethylated and methylated DNA lesions in cells by nanoflow liquid chromatography-nanoelectrospray ionization tandem mass spectrometry coupled with the stable isotope-dilution method.
Yu, Y.; Wang, J.; Wang, P. and Wang, Y.*
Anal. Chem., 2016, 88, 8036-8042.
Tris(1,3-dichloro-2-propyl) phosphate induces genome-wide hypomethylation within early zebrafish embryos.
Volz, D.*; Leet, J. K; Chen, A.; Stapleton, H.; Katiyar, N.; Kaundal, R.; Yu, Y. and Wang, Y.
Environ. Sci. Technol., 2016, 50, 10255-63.
A high-throughput targeted proteomic approach for comprehensive profiling of methylglyoxal-induced perturbations of the human kinome.
Miao, W.; Xiao, Y.; Guo, L.; Jiang, X.; Huang, M. and Wang, Y.*
Anal. Chem., 2016, 88, 9773-9779.
Reversible regulation of promoter and enhancer histone landscape by DNA methylation in mouse embryonic stem cells.
King, A.D.; Huang, K.; Rubbi, L.; Liu, S.; Wang, C.Y.; Wang, Y.; Pellegrini, M.; Fan, G.*
Cell Rep. 2016, 17, 289-302.
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Williams, N.L.; Wang, P. and Wang, Y.*
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AMP-activated protein kinase and sirtuin 1 coregulation of cortactin contributes to endothelial function.
Shentu, T.P.; He, M.; Sun, X.; Zhang, J.; Zhang, F.; Gongo, B.; Marin, T.L.; Zhang, J.; Wen, L.; Wang, Y.; Geary, G.G.; Zhu, Y.; Johnson, D.A. and Shyy, J. Y.-J.*
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Occurrence, biological consequences, and human health relevance of oxidative stress-induced DNA damage.
Yu, Y.; Cui, Y.; Niedernhofer, L.J. and Wang, Y.*
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Profiling global kinome signatures of the radioresistant MCF-7/C6 breast cancer cells using MRM-based targeted proteomics.
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Transcriptional inhibition and mutagenesis induced by N-nitroso compounds-derived carboxymethylated thymidine adducts in DNA.
You, C.; Wang, J.; Dai, X. and Wang, Y.*
Nucleic Acids Res., 2015, 43, 1012-1018.
Chemical and structural characterization of interstrand cross-links formed between abasic sites and adenine residues in duplex DNA.
Price, N. E; Catalano, M.; Liu, S.; Wang, Y.; Gates, K. S.*
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Chemical structure and properties of the interstrand cross-link formed by the reaction of abasic sites with guanine residues in duplex DNA.
Catalano, M.; Liu, S.; Andersen, N.; Yang, Z.; Johnson, K. M.; Price, N.E.; Wang, Y. and Gates, K.S.*
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Identification and functional characterizations of N-terminal α-N-methylation and phosphorylation of serine 461 in human poly(ADP-ribose) polymerase 3.
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Crystal structure of human DNA methyltransferase 1
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In vivo detection and replication studies of -anomeric lesions of 2′-deoxyribonucleosides.
Amato, N. J.; Zhai, Q., Navarro, D. C.; Niedernhofer, L. J. and Wang, Y.*
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Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes
Pfeifer, G.P.; Dunwell, J.M.; Wamaedeesa, R.; Ullah, I.; Wang, Y.; Hu, S.*
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An allosteric interaction links USP7 to deubiquitination and chromatin targeting of UHRF1.
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Facile discovery of cell-surface protein targets of cancer cell aptamers.
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Hu, L.; Lu, J.; Cheng, J.; Rao, Q.; Li, Z.; Hou, H.; Lou, Z.; Zhang, L.; Li, W.; Gong, W.; Liu, M.; Sun, C.; Yin, X.; Li, J.; Tan, X.; Wang, P.; Wang, Y.; Fang, D.; Cui, Q.; Yang, P.; He, C.; Jiang, H.; Luo, C.* and Xu, Y.*
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Arsenite targets the zinc finger domains of Tet proteins and inhibits Tet-mediated oxidation of 5-methylcytosine.
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Cai, Q.; Fu, L.; Wang, Z.; Gan, N.; Dai, X. and Wang, Y.* a-N-methylation of damaged DNA-binding protein 2 (DDB2) and its function in nucleotide excision repair. J. Biol. Chem., 2014, 289, 16046-16056.
Bullard, W.; da Rosa-Spiegler, J.L.; Liu, S.; Wang, Y. and Sabatini, R.* Identification of the glucosyltransferase that converts hydroxymethyluracil to base J in the trypanosomatid genome. J. Biol. Chem., 2014, 289, 20273-20282.
Fu, L.; Guerrero, C.R.; Zhong, N.; Amato, N.J.; Liu, Y.; Liu, S.; Cai, Q.; Ji, D.; Jin, S.G.; Niedernhofer, L.J.; Pfeifer, G.P.; Xu, G.L.; Wang Y.* Tet-mediated formation of 5-hydroxymethylcytosine in RNA.; J. Am. Chem. Soc., 2014, 136, 11582-11585.
Ji, D. and Wang, Y.* Facile enzymatic synthesis of base J-containing oligodeoxyribonucleotides and an analysis of the impact of base J on DNA replication in cells.; PLoS One, 2014, 9, e103335.
Liu, S.; Ji, D.; Cliffe, L.; Sabatini, R. and Wang, Y.* Quantitative mass spectrometry-based analysis of β-D-glucosyl-5-hydroxymethyluracil in genomic DNA of Trypanosoma brucei.; J. Am. Soc. Mass Spectrom., 2014, 25, 1763-1770.
Ji, D.; You, C.; Wang, P. and Wang, Y.* Effects of Tet-induced oxidation products of 5-methylcytosine on DNA replication in mammalian cells. ;Chem. Res. Toxicol., 2014, 27, 1304-1309.
Zhang, F.; Paramasivam, M.; Cai, Q.; Dai, X.; Wang, P.; Lin, K.; S, J.; Seidman, M.M. and Wang, Y.* Arsenite binds to the RING finger domains of RNF20-RNF40 histone E3 ubiquitin ligase and inhibits DNA double-strand break repair. J. Am. Chem. Soc., 2014, 136, 12884-12887.
Zhai, Q.; Wang, P.; Cai, Q. and Wang, Y.* Syntheses and characterizations of the in-vivo replicative bypass and mutagenic properties of the minor-groove O2-alkylthymidine lesions. Nucleic Acids Res., 2014, 42, 10529-10537.
Yu, Q.-W.; Li, X.-S.; Xiao, Y.; Guo, L.; Zhang, F.; Cai, Q.; Feng, Y.-Q.; Yuan, B.-F. and Wang, Y.* Sequential enrichment with titania-coated magnetic mesoporous hollow silica microspheres and zirconium arsenate-modified magnetic nanoparticles for the study of phosphoproteome of HL60 cells. J. Chromatogr. A, 2014, 1365, 54-60.
Guo, L.; Xiao, Y. and Wang, Y.* The application of ATP affinity probe and scheduled MRM analysis for profiling global kinome in human cells in response to arsenite treatment. Anal. Chem., 2014, 86, 10700-7.
You, C.; Ji, D.; Dai, X. and Wang, Y.* Effects of Tet-mediated oxidation products of 5-methylcytosine on DNA transcription in vitro and in mammalian cells. Sci. Rep., 2014, 4, 7052.
Chavez, L.; Huang, Y.; Luong, K.; Agarwal, S.; Iyer, L.M.; Pastor, W.A.; Hench, V.K.; Frazier-Bowers, S.A.; Korol, E.; Liu, S.; Tahiliani, M.; Wang, Y.; Clark, T.A.; Korlach, J.; Pukkila, P.J.; Aravind, L.; and Rao, A.* Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea.; Proc. Natl. Acad. Sci. USA, 2014, 111, E5149-58.
You, C.; Dai, X. and Wang, Y.* Transcriptional bypass of regioisomeric ethylated thymidine lesions by T7 RNA polymerase and human RNA polymerase II. Nucleic Acids Res., 2014, 42, 13706-13713.
Yuan, B. Zhang, J. Wang, H. Xiong, L. Cai, Q. Wang, T. Jacobsen, S. Pradhane, S. and Wang, Y.* 6-Thioguanine reactivates epigenetically silenced genes in acute lymphoblastic leukemia cells by facilitating proteasome-mediated degradation of DNMT1, Cancer Res., 2011, 71, 1904-1911.
Xiong, L. Zhang, J. Yuan, B. Dong, X. Jiang, X. and Wang, Y.* Global proteome quantification for discovering imatinib-induced perturbation of multiple biological pathways in K562 human chronic myeloid leukemia cells. J. Proteome Res., 2010, 9, 6007-6015.
Wang, P. Jiang, Y. Wang, Y. Shyy, J. Y. and DeFea, K.A.* b-Arrestin inhibits CAMKKb-dependent AMPK activation downstream of protease-activated-receptor-2. BMC Biochemistry, 2010, 11:36.
Yuan, B. O&rsquoConnor;, T. R. and Wang, Y.* 6-Thioguanine and S6-methylthioguanine are mutagenic in human cells. ACS Chem. Biol., 2010, 5, 1021-1027.
Dong, X. Xiong, L. Jiang, X. and Wang, Y.* Quantitative proteomic analysis reveals the perturbation of multiple cellular pathways in Jurkat-T cells induced by doxorubicin. J. Proteome Res., 2010, 9, 5943&ndash5951;.
Weng, M. Zheng, Y. Jasti, V. Champeil, E. Tomasz, M. Wang, Y. Basu, A. and Tang, M.* Repair of mitomycin C mono- and interstrand cross-linked DNA adducts by UvrABC: a new model. Nucleic Acids Res., 2010, 38, 6976-84.
Dong, X. Cheng, J. Li, J.* and Wang, Y.* Graphene as a novel matrix for the analysis of small molecules by MALDI-TOF MS. Anal. Chem., 2010, 82, 6208-6214.
Wang, H. and Wang, Y.* LC-MS/MS coupled with stable isotope dilution method for the quantification of 6-thioguanine and S6-methylthioguanine in genomic DNA of human cancer cells treated with 6-thioguanine. Anal. Chem., 2010, 82, 5797-5803.
Wang, J. and Wang, Y.* Synthesis and characterization of oligodeoxyribonucleotides containing a site-specifically incorporated N6-carboxymethyl-2&rsquo-deoxyadenosine or N4-carboxymethyl-2’-deoxycytidine. Nucleic Acids Res., 2010, 38, 6774-6784.
Xiong, L. Adhvaryu, K. K. Selker, E. U. and Wang, Y.* Mapping of lysine methylation and acetylation in core histones of Neurospora crassa. Biochemistry, 2010, 49, 5236-5243.
Lin, G. Zhang, J. Luo, H.* and Wang, Y.* Conformation-dependent formation of the G[8-5]U intrastrand cross-link in 5-bromouracil-containing G-quadruplex DNA induced by UVA irradiation. Biochemistry, 2010, 49, 2346-2350.
Li, P. Wang, D. Yao, H. Doret, P. Hao, G. Shen, Q. Qiu, H. Zhang, X. Wang, Y. Chen, G. and Wang, Y.* Coordination of PAD4 and HDAC2 in the regulation of p53 target gene expression. Oncogene, 2010, 29, 3153-3162.
Xiong, L. and Wang, Y.* Quantitative proteomic analysis reveals the perturbation of multiple cellular pathways in HL-60 cells induced by arsenite treatment. J. Proteome Res., 2010, 9, 1129-1137.
Yuan, B. Jiang, Y. Wang, Y. and Wang, Y.* Mutagenic and cytotoxic properties of tandem lesions containing neighboring thymidine glycol and 8-oxo-7,8-dihydro-2’-deoxyguanosine. Chem. Res. Toxicol., 2010, 23, 11-19.
Wang, H. Cao, H. and Wang, Y.* Quantification of N2-carboxymethyl-2’-deoxyguanosine in calf-thymus DNA and cultured human kidney epithelial cells by capillary LC tandem mass spectrometry coupled with stable isotope-dilution method. Chem. Res. Toxicol., 2010, 23, 74-81.
Jiang, D. Li, X. Williams, R.T. Patel, S. Men, L. Wang, Y. and Zhou, F.* Fe(III)- and Fe-nitrilotriacetic acid complexes of amyloid-β(1−16): Binding affinities, redox properties, and relevance to iron-induced oxidative stress in Alzheimer&rsquos; disease, Biochemistry, 2009, 48, 7939-7947.
Zhang, Q. and Wang, Y.* HMG modifications and nuclear function. Biochim. Biophys. Acta, 2010, 1799, 28-36.
Cao, H., Jiang, Y. and Wang, Y.* Kinetics of deamination and Cu/H2O2/ascorbate-induced formation of 5-methylcytosine glycol at CpG sites in duplex DNA. Nucleic Acids Res., 2009, 37, 6635-6643.
Xiong, L. Ping, L. Yuan, B. and Wang, Y.* Methyl group migration during the fragmentation of singly charged ions of trimethyllysine-containing peptides: Precaution of using MS/MS of singly charged ions for interrogating peptide methylation. J. Am. Soc. Mass Spectrom., 2009, 20, 1172-1181.
Rempel-Hester, M. A. Hong, H. Wang, Y. Deng, X. Armstrong, J. Gully, J. and Schlenk, D.* Site-specific effects of 17β-estradiol in hornyhead turbot (Pleuronichthys verticalis) collected from a wastewater outfall and reference location. Environ. Res., 2009, 109, 552-558.
Qiu, H. and Wang, Y.* Exploring DNA-binding proteins with in vivo chemical cross-linking and mass spectrometry. J. Proteome Res., 2009, 8, 1983-1991.
Wang, H. and Wang, Y.* 6-Thioguanine perturbs cytosine methylation at CpG dinucleotide site by DNA methyltransferases in vitro and acts as a DNA demethylating agent in vivo. Biochemistry, 2009, 48, 2290-2299.
Rempel, M. A. Hester, B. DeHaro, H. Hong, H. Wang, Y. and Schlenk, D.* Effects of 17β-estradiol, and its metabolite, 4-hydroxyestradiol on the spermatozoa of the sand dollar (Dendraster excentricus): Effects on fertilization, embryo development and oxidative DNA damage. Sci. Tot. Environ., 2009, 407, 2209-15.
Jiang, Y. Wang, Y. and Wang, Y.* In-vitro replication and repair studies of tandem lesions containing neighboring thymidine glycol and 8-oxo-7,8-dihydro-2’-deoxyguanosine. Chem. Res. Toxicol., 2009, 22, 574-583.
Cao, H. and Wang, Y.* Fragmentation of isomeric intrastrand cross-link lesions of DNA in an ion-trap mass spectrometer. J. Am. Soc. Mass Spectrom., 2009, 20, 611-617.
Wang, J. and Wang, Y.* Chemical synthesis of oligodeoxynucleotides containing N3- and O4-carboxymethylthymidine and their formation in DNA. Nucleic Acids Res., 2009, 37, 336-345.
Lai, C. Cao, H. Hearst, J. Corash, L. Luo, H. and Wang, Y.* Quantitative analysis of DNA interstrand cross-links and monoadducts formed in human cells induced by psoralens and UVA irradiation. Anal. Chem., 2008, 80, 8790-8798.
Rempel, M. A. Wang, Y. Armstrong, J. Schlenk, D.* Uptake of estradiol from sediment by hornyhead turbot (Pleuronichthys verticalis) and effects on oxidative DNA damage in male gonads. Mar. Environ. Res. 2008, 66, 111-112.
Yuan, B. and Wang, Y.* Mutagenic and cytotoxic properties of 6-thioguanine, S6-methylthioguanine and guanine-S6-sulfonic acid. J. Biol. Chem., 2008, 283, 23665-23670.
Zhang, Q. and Wang, Y.* High mobility group proteins and their post-translational modifications. Biochim. Biophys. Acta, 2008, 1784, 1159-1166.
Yuan, B. Cao, H. Jiang, Y. Hong, H. and Wang, Y.* Efficient and accurate bypass of N2-(1-carboxyethyl)-2’-deoxyguanosine by DinB DNA polymerase in vitro and in vivo. Proc. Natl. Acad. Sci. USA., 2008, 105, 8679-8684.
Qiu, H. and Wang, Y.* Quantitative analysis of surface plasma membrane proteins of primary and metastatic melanoma cells. J. Proteome Res., 2008, 7, 1904-1915.
Cao, H. Hearst, J. E. Corash, L. Wang, Y.* LC-MS/MS for the detection of DNA interstrand cross-links formed by 8-methoxypsoralen and UVA irradiation in human cells. Anal. Chem., 2008, 80, 2932-2938.
Wang, Y.* Bulky DNA lesions induced by reactive oxygen species. Chem. Res. Toxicol, 2008, 21, 276-281.
Zhang, Q. and Wang, Y.* Homeodomain-interacting protein kinase-2 (HIPK2) phosphorylates HMGA1a at Ser-35, Thr-52, and Thr-77 and modulates its DNA binding affinity. J. Proteome Res., 2007, 6, 4711-4719.
Hong, H. Cao, H. and Wang, Y.* Formation and genotoxicity of a guanine-cytosine intrastrand cross-link lesion in vivo. Nucleic Acids Res., 2007, 35, 7118-7127.
Jiang, Y. Hong, H. Cao, H. and Wang, Y.* In-vivo formation and in-vitro replication of a guanine-thymine intrastrand cross-link lesion. Biochemistry, 2007, 46, 12757-12763.
Gao, Y. and Wang, Y.* A method to determine the ionization efficiency change of peptides caused by phosphorylation. J. Am. Soc. Mass Spectrom., 2007, 19, 1973-1976.
Cao, H. Jiang, Y. and Wang, Y.* Stereospecific synthesis and characterizations of oligodeoxyribonucleotides containing N2-(1-carboxyethyl)-2’-deoxyguanosine. J. Am. Chem. Soc., 2007, 129, 12123-12130.
Men, L. Roginskaya, M. Zou, Y. and Wang, Y.* Redox-dependent formation of disulfide bonds in human replication protein A. Rapid Commun. Mass Spectrom., 2007, 21, 2743-2749.
Cao, H. and Wang, Y.* Quantification of oxidative single-base and intrastrand cross-link lesions in unmethylated and CpG-methylated DNA induced by Fenton-type reagents. Nucleic Acids Res., 2007, 35, 4833-4844.
Zhang, Q. Zhang, K. Zou, Y. Perna, A. D. and Wang, Y.* A quantitative study on the in-vitro and in-vivo acetylation of high mobility group A1 proteins. J. Am. Soc. Mass Spectrom., 2007, 19, 1569-1578.
Jiang, D Men, L. Wang, J. Zhang, Y Chickenyen, S. Wang, Y. and Zhou, F.* Redox reactions of copper complexes formed with different b-amyloid peptides and their neuropathalogical relevance. Biochemistry, 2007, 46, 9270-9282.
Qiu, H. and Wang, Y.* Probing adenosine nucleotide-binding proteins with an affinity labeled-nucleotide probe and mass spectrometry. Anal. Chem., 2007, 79, 5547-5556.
Zeng, Y. and Wang, Y.* UVB-induced formation of intrastrand crosslink products of DNA in MCF-7 cells treated with 5-bromo-2’-deoxyuridine. Biochemistry, 2007, 46, 8189-8195.
Zou, Y. Webb, K. Perna, A. D. Zhang, Q. Clarke, S. and Wang, Y.* A mass spectrometric study on the in-vitro methylation of HMGA1a and HMGA1b proteins by PRMTs: methylation specificity, the effect of binding to AT-rich duplex DNA and the effect of C-terminal phosphorylation. Biochemistry, 2007, 46, 7896-7906.
Gu, C. Wang, Y.* In-vitro replication and thermodynamic studies of methylation and oxidation modifications of 6-thioguanine. Nucleic Acids Res., 2007, 35, 3693-3704.
Zou, Y. Wang, Y.* Mass spectrometric analysis of high-mobility group proteins and their post-translational modifications in normal and cancerous human breast tissues. J. Proteome Res. 2007, 6, 2304-2314.
Hong, H. and Wang, Y.* Derivatization with Girard reagent T combined with LC-MS/MS for the sensitive detection of 5-formyl-2’-deoxyuridine in cellular DNA. Anal. Chem., 2007, 79, 322-326.
Men, L. and Wang, Y.* The oxidation of yeast alcohol dehydrogenase-1 by hydrogen peroxide in vitro. J. Proteome Res., 2007, 6, 216-225.
Gao, Y. and Wang, Y.* Site-selective modifications of arginine residues in human hemoglobin induced by methylglyoxal. Biochemistry, 2006, 45, 15654-15660.
Zeng, Y. and Wang, Y.* Sequence-dependent formation of intrastrand crosslink products from the UVB irradiation of duplex DNA containing a 5-bromo-2’-deoxyuridine or 5-bromo-2’-deoxycytidine. Nucleic Acids Res., 2006, 34, 6521-6529.
Sun, W. Lee, T. S. Zhu, M. Gu, C. Wang, Y. Zhu, Y. and Shyy, J. Y.* Statins activate AMP-activated protein kinase in vitro and in vivo. Circulation, 2006, 114, 2655-2662.
Gu, C. Zhang, Q. Yang, Z. Wang, Y. Zou, Y. and Wang, Y.* Recognition and incision of oxidative intrastrand cross-link lesions by UvrABC nuclease. Biochemistry, 2006, 45, 10739-46.
Cao, H. and Wang, Y.* Collisionally activated dissociation of protonated 2’-deoxycytidine, 2’-deoxyuridine and their oxidatively damaged derivatives. J. Am. Soc. Mass Spectrom., 2006, 17, 1335-1341.
Wang, Y. and Wang, Y.* Synthesis and thermodynamic studies of oligodeoxyribonucleotides containing tandem lesions of thymidine glycol and 8-oxo-2’-deoxyguanosine. Chem. Res. Toxicol., 2006, 19, 837-843.
Jiang, X. and Wang, Y.* Acetylation and phosphorylation of high-mobility group A1 proteins in PC-3 human tumor cells. Biochemistry, 2006, 45, 7194-7201.
Jiang, X. and Wang, Y.* Phosphorylation of human high mobility group N1 protein by protein kinase CK2. Biochem. Biophys. Res. Commun., 2006, 345, 1497-1503.
Zhang, Q. and Wang, Y.* Differentiation of 2’-O- and 3’-O-methylated ribonucleosides by tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 2006, 17, 1096-1099.
Zeng, Y. and Wang, Y.* Facile photocyclization chemistry of 5-phenylthio-2’-deoxyuridine in duplex DNA. Org. Lett., 2006, 8, 2527-2530.
Hong, H. Cao, H. Wang, Y. and Wang, Y.* Identification and quantification of a guanine-thymine intrastrand crosslink lesion induced by Cu/H2O2/ascorbate. Chem. Res. Toxicol., 2006, 19, 614-621.
Gao, Y. and Wang, Y.* The photochemistry of 5-BrdCpdC, dCp5-BrdCpdA, and dCp5-BrdCdT in aqueous solution. Nucleosides, Nucleotides & Nucleic Acids, 2006, 25, 279-287.
Men, L. and Wang, Y.* Fragmentation of the deprotonated ions of peptides containing cysteine, cysteine sulfinic acid, cysteine sulfonic acid, aspartic acid, and glutamic acid. Rapid Commun. Mass Spectrom., 2006, 20, 777-784.
Zhang, Q. and Wang, Y.* The reactivity of the 5-hydroxy-5,6-dihydrothymidin-6-yl radical in oligodeoxyribonucleotides. Chem. Res. Toxicol., 2005, 18, 1897-1906.
Hong, H. and Wang, Y.* Formation of intrastrand crosslink products between cytosine and adenine from UV irradiation of d(BrCA) and duplex DNA containing a 5-bromocytosine. J. Am. Chem. Soc., 2005, 127, 13969-13977.
Gu, C. and Wang, Y.* Thermodynamic and in-vitro replication studies of an intrastrand crosslink lesion G[8-5]C. Biochemistry, 2005, 44, 8883-8889.
Zou, Y. and Wang, Y.* Tandem mass spectrometry for the examination of the post-translational modifications of high-mobility group A1 proteins: Symmetric and asymmetric dimethylation of Arg25 in HMGA1a protein. Biochemistry, 2005, 44, 6293-6301.
Zhang, Q. and Wang, Y.* Generation of 5-(2’-deoxycytidinyl)methyl radical and the formation of intrastrand cross-link lesions in oligodeoxyribonucleotides. Nucleic Acids Res., 2005, 33, 1593-1603.
Men, L. and Wang, Y.* Further studies on the fragmentation of protonated ions of peptides containing aspartic acid, glutamic acid, cysteine sulfinic acid, and cysteine sulfonic acid. Rapid Commun. Mass Spectrom., 2005, 19, 23-30.
Jiang, X. and Wang, Y.* b-elimination combined with tandem mass spectrometry for the identification of the in vivo and in vitro sites of phosphorylation of dehydrin DHN1 protein. Biochemistry, 2004, 43, 15567-15576.
Liu, Z. Gao, Y. Zeng, Y. Fang, F. Chi, D. Wang, Y.* Isolation and characterization of a novel crosslink lesion in d(CpC) induced by one-electron photooxidation. Photochem. Photobiol. 2004, 80, 209-215.
Zhang, Q. and Wang, Y.* Independent generation of the 5-hydroxy-5,6-dihydrothymidin-6-yl radical and its reactivity in dinucleoside monophosphates. J. Am. Chem. Soc. 2004, 126, 13287-13297.
Wang, Y., Zhang, Q. and Wang, Y.* Tandem mass spectrometry for the determination of the sites of DNA interstrand crosslink. J. Am. Soc. Mass Spectrom. 2004, 15, 1565-1571.
Zeng, Y. and Wang, Y.* Facile formation of an intrastrand crosslink lesion between cytosine and guanine upon Pyrex-filtered UV light irradiation of d(BrCG) and duplex DNA containing 5-bromocytosine. J. Am. Chem. Soc. 2004, 126, 6552-6553.
Gu, C. and Wang, Y.* LC-MS/MS identification and yeast polymerase h bypass of a novel g-irradiation-induced intrastrand crosslink lesion G[8-5]C. Biochemistry 2004, 43, 6745-6750.
Zou, Y. Jiang, X. Wang, Y.* Identification of novel in vivo phosphorylation sites in high mobility group N1 protein from the MCF-7 human breast cancer cells. Biochemistry 2004, 43, 6322-6329.
Wang, Y.*, Vivekananda, S., Men, L., and Zhang, Q. Fragmentation of protonated ions of peptides containing cysteine, cysteine sulfinic acid, and cysteine sulfonic acid. J. Am. Soc. Mass Spectrom. 2004, 15, 697-702.
Wang, Y. and Wang, Y.* Structure elucidation of DNA interstrand crosslink lesions by a combination of nuclease P1 digestion with mass spectrometry. Anal. Chem. 2003, 75, 6306-6313.
Zhang, Q. and Wang, Y.* Independent generation of 5-(2’-deoxycytidinyl)methyl radical and the formation of a novel crosslink lesion between 5-methylcytosine and guanine. J. Am. Chem. Soc. 2003, 125, 12795-12802.
Liu, Z., Gao, Y. and Wang, Y.* Identification and characterization of a novel crosslink lesion in d(CpC) upon 365 nm-irradiation in the presence of 2-methyl-1,4-naphthoquinone. Nucleic Acids Res. 2003, 31, 5413-5424.
Wang, Y.* and Liu, Z. Mechanisms for the formation of major oxidation products of adenine upon 365-nm irradiation with 2-methyl-1,4-naphthoquinone as a sensitizer. J. Org. Chem., 2002, 67, 8507-8512.
Wang, Y.*, Men, L., and Vivekananda, S. Fragmentation of deprotonated ions of oligodeoxynucleotides carrying a 5-formyluracil or 2-aminoimidazolone. J. Am. Soc. Mass Spectrom. 2002, 13, 1190-1194.
Wang, Y.*, Vivekananda, S, and Zhang, K. ESI-MS/MS for the differentiation of diastereomeric pyrimidine glycols in mononucleosides. Anal. Chem. 2002, 74, 4505-4512.
Wang, Y.*, Liu, Z., and Dixon, C. Major adenine products from 2-methyl-1,4-naphthoquinone-sensitized photoirradiation at 365 nm. Biochem. Biophys. Res. Commun. 2002, 291, 1252-1257.
Wang, Y.*. HPLC isolation and mass spectrometric characterization of two isomers of thymine glycols in oligodeoxynucleotides. Chem. Res. Toxicol., 2002, 15, 671-676.