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Chuan He

TitlePROFESSOR
InstitutionUniversity of Chicago
DepartmentChemistry
AddressChicago IL 60637
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    Chuan He is the John T. Wilson Distinguished Service Professor in the Department of Chemistry and Director of the Institute for Biophysical Dynamics at the University of Chicago.He received his B.S. (1994) from the University of Science and Technology of China. He received his Ph. D. degree from Massachusetts Institute of Technology in chemistry in 2000. After being trained as a Damon-Runyon postdoctoral fellow at Harvard University from 2000-2002, he joined the University of Chicago as an Assistant Professor, and was promoted to Associate Professor in 2008, Professor in 2010 and John T. Wilson Distinguished Service Professor in 2014. He is also a member of the Cancer Research Center at the University of Chicago. His research spans a broad range of chemical biology, epigenetics, cell biology, molecular biology, biochemistry, structural biology, and genomics. His recent research concerns reversible RNA and DNA methylation in biological regulation. His research group discovered the first RNA demethylase and showed that reversible RNA methylation significantly affects post-transcriptional gene expression regulation.


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    2013HHMI Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Hsu PJ, Shi H, Zhu AC, Lu Z, Miller N, Edens BM, Ma YC, He C. The RNA-binding protein FMRP facilitates the nuclear export of N6-methyladenosine-containing mRNAs. J Biol Chem. 2019 Nov 21. PMID: 31753916.
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    2. Chiu BC, Zhang Z, You Q, Zeng C, Stepniak E, Bracci PM, Yu K, Venkataraman G, Smith SM, He C, Zhang W. Prognostic implications of 5-hydroxymethylcytosines from circulating cell-free DNA in diffuse large B-cell lymphoma. Blood Adv. 2019 Oct 08; 3(19):2790-2799. PMID: 31570490.
      View in: PubMed
    3. Zhou H, Rauch S, Dai Q, Cui X, Zhang Z, Nachtergaele S, Sepich C, He C, Dickinson BC. Evolution of a reverse transcriptase to map N1-methyladenosine in human messenger RNA. Nat Methods. 2019 Dec; 16(12):1281-1288. PMID: 31548705.
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    4. Wei J, He C. Site-specific m6A editing. Nat Chem Biol. 2019 09; 15(9):848-849. PMID: 31383973.
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    5. Zhou KI, Shi H, Lyu R, Wylder AC, Matuszek Z, Pan JN, He C, Parisien M, Pan T. Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG. Mol Cell. 2019 Oct 03; 76(1):70-81.e9. PMID: 31445886.
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    6. Zhao S, Liu J, Nanga P, Liu Y, Cicek AE, Knoblauch N, He C, Stephens M, He X. Detailed modeling of positive selection improves detection of cancer driver genes. Nat Commun. 2019 07 30; 10(1):3399. PMID: 31363082.
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    7. Edens BM, Vissers C, Su J, Arumugam S, Xu Z, Shi H, Miller N, Rojas Ringeling F, Ming GL, He C, Song H, Ma YC. FMRP Modulates Neural Differentiation through m6A-Dependent mRNA Nuclear Export. Cell Rep. 2019 Jul 23; 28(4):845-854.e5. PMID: 31340148.
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    8. Yang S, Wei J, Cui YH, Park G, Shah P, Deng Y, Aplin AE, Lu Z, Hwang S, He C, He YY. m6A mRNA demethylase FTO regulates melanoma tumorigenicity and response to anti-PD-1 blockade. Nat Commun. 2019 06 25; 10(1):2782. PMID: 31239444.
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    9. Hu L, Liu Y, Han S, Yang L, Cui X, Gao Y, Dai Q, Lu X, Kou X, Zhao Y, Sheng W, Gao S, He X, He C. Jump-seq: Genome-Wide Capture and Amplification of 5-Hydroxymethylcytosine Sites. J Am Chem Soc. 2019 Jun 05; 141(22):8694-8697. PMID: 31117646.
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    10. Jeong JJ, Gu X, Nie J, Sundaravel S, Liu H, Kuo WL, Bhagat TD, Pradhan K, Cao J, Nischal S, McGraw KL, Bhattacharyya S, Bishop MR, Artz A, Thirman MJ, Moliterno A, Ji P, Levine RL, Godley LA, Steidl U, Bieker JJ, List AF, Saunthararajah Y, He C, Verma A, Wickrema A. Cytokine-Regulated Phosphorylation and Activation of TET2 by JAK2 in Hematopoiesis. Cancer Discov. 2019 May 17. PMID: 31101629.
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    11. Shi H, Wei J, He C. Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers. Mol Cell. 2019 05 16; 74(4):640-650. PMID: 31100245.
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    12. Applebaum MA, Barr EK, Karpus J, Nie J, Zhang Z, Armstrong AE, Uppal S, Sukhanova M, Zhang W, Chlenski A, Salwen HR, Wilkinson E, Dobratic M, Grossman R, Godley LA, Stranger BE, He C, Cohn SL. 5-Hydroxymethylcytosine Profiles Are Prognostic of Outcome in Neuroblastoma and Reveal Transcriptional Networks That Correlate With Tumor Phenotype. JCO Precis Oncol. 2019; 3. PMID: 31179414.
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    13. Liu J, Luo G, Sun J, Men L, Ye H, He C, Ren D. METTL14 is essential for ß-cell survival and insulin secretion. Biochim Biophys Acta Mol Basis Dis. 2019 Sep 01; 1865(9):2138-2148. PMID: 31029827.
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    14. Zhang LS, Liu C, Ma H, Dai Q, Sun HL, Luo G, Zhang Z, Zhang L, Hu L, Dong X, He C. Transcriptome-wide Mapping of Internal N7-Methylguanosine Methylome in Mammalian mRNA. Mol Cell. 2019 Jun 20; 74(6):1304-1316.e8. PMID: 31031084.
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    15. Jeong JJ, Gu X, Nie J, Sundaravel S, Liu H, Kuo WL, Bhagat TD, Pradhan K, Cao J, Nischal S, McGraw KL, Bhattacharyya S, Bishop MR, Artz A, Thirman MJ, Moliterno A, Ji P, Levine RL, Godley LA, Steidl U, Bieker JJ, List AF, Saunthararajah Y, He C, Verma A, Wickrema A. Cytokine-Regulated Phosphorylation and Activation of TET2 by JAK2 in Hematopoiesis. Cancer Discov. 2019 Jun; 9(6):778-795. PMID: 30944118.
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    16. Liu J, Harada BT, He C. Regulation of Gene Expression by N6-methyladenosine in Cancer. Trends Cell Biol. 2019 Jun; 29(6):487-499. PMID: 30940398.
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    17. Karginova O, Weekley CM, Raoul A, Alsayed A, Wu T, Lee SS, He C, Olopade OI. Inhibition of Copper Transport Induces Apoptosis in Triple-Negative Breast Cancer Cells and Suppresses Tumor Angiogenesis. Mol Cancer Ther. 2019 05; 18(5):873-885. PMID: 30824611.
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    18. He C. Special Issue on Regulating the Central Dogma. Biochemistry. 2019 02 05; 58(5):295-296. PMID: 30717600.
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    19. He PC, He C. mRNA acetylation: a new addition to the epitranscriptome. Cell Res. 2019 02; 29(2):91-92. PMID: 30631155.
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    20. Hsu PJ, He C. High-Resolution Mapping of N 6-Methyladenosine Using m6A Crosslinking Immunoprecipitation Sequencing (m6A-CLIP-Seq). Methods Mol Biol. 2019; 1870:69-79. PMID: 30539547.
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    21. Wang X, Li Y, Chen W, Shi H, Eren AM, Morozov A, He C, Luo GZ, Pan T. Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome. Cell Res. 2019 02; 29(2):167-170. PMID: 30559439.
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    22. Zhao BS, Roundtree IA, He C. Publisher Correction: Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol. 2018 Dec; 19(12):808. PMID: 30341428.
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    23. Hsu PJ, Fei Q, Dai Q, Shi H, Dominissini D, Ma L, He C. Single base resolution mapping of 2'-O-methylation sites in human mRNA and in 3' terminal ends of small RNAs. Methods. 2019 03 01; 156:85-90. PMID: 30471344.
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    24. Zhong X, Yu J, Frazier K, Weng X, Li Y, Cham CM, Dolan K, Zhu X, Hubert N, Tao Y, Lin F, Martinez-Guryn K, Huang Y, Wang T, Liu J, He C, Chang EB, Leone V. Circadian Clock Regulation of Hepatic Lipid Metabolism by Modulation of m6A mRNA Methylation. Cell Rep. 2018 11 13; 25(7):1816-1828.e4. PMID: 30428350.
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    25. Shi H, Zhang X, Weng YL, Lu Z, Liu Y, Lu Z, Li J, Hao P, Zhang Y, Zhang F, Wu Y, Delgado JY, Su Y, Patel MJ, Cao X, Shen B, Huang X, Ming GL, Zhuang X, Song H, He C, Zhou T. m6A facilitates hippocampus-dependent learning and memory through YTHDF1. Nature. 2018 11; 563(7730):249-253. PMID: 30401835.
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    26. Frye M, Harada BT, Behm M, He C. RNA modifications modulate gene expression during development. Science. 2018 09 28; 361(6409):1346-1349. PMID: 30262497.
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    27. Nachtergaele S, He C. Chemical Modifications in the Life of an mRNA Transcript. Annu Rev Genet. 2018 11 23; 52:349-372. PMID: 30230927.
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    28. Wei J, Liu F, Lu Z, Fei Q, Ai Y, He PC, Shi H, Cui X, Su R, Klungland A, Jia G, Chen J, He C. Differential m6A, m6Am, and m1A Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm. Mol Cell. 2018 09 20; 71(6):973-985.e5. PMID: 30197295.
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    29. Liu J, Eckert MA, Harada BT, Liu SM, Lu Z, Yu K, Tienda SM, Chryplewicz A, Zhu AC, Yang Y, Huang JT, Chen SM, Xu ZG, Leng XH, Yu XC, Cao J, Zhang Z, Liu J, Lengyel E, He C. m6A mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer. Nat Cell Biol. 2018 09; 20(9):1074-1083. PMID: 30154548.
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    30. Koranda JL, Dore L, Shi H, Patel MJ, Vaasjo LO, Rao MN, Chen K, Lu Z, Yi Y, Chi W, He C, Zhuang X. Mettl14 Is Essential for Epitranscriptomic Regulation of Striatal Function and Learning. Neuron. 2018 07 25; 99(2):283-292.e5. PMID: 30056831.
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    31. Cheng JX, Chen L, Li Y, Cloe A, Yue M, Wei J, Watanabe KA, Shammo JM, Anastasi J, Shen QJ, Larson RA, He C, Le Beau MM, Vardiman JW. Author Correction: RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia. Nat Commun. 2018 06 06; 9(1):2286. PMID: 29875356.
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    32. Cheng JX, Chen L, Li Y, Cloe A, Yue M, Wei J, Watanabe KA, Shammo JM, Anastasi J, Shen QJ, Larson RA, He C, Le Beau MM, Vardiman JW. RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia. Nat Commun. 2018 03 21; 9(1):1163. PMID: 29563491.
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    33. Shi H, He C. Phasing Gene Expression: mRNA N6-Methyladenosine Regulates Temporal Progression of Mammalian Cortical Neurogenesis. Biochemistry. 2018 02 20; 57(7):1055-1056. PMID: 29384655.
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    34. Hsu PJ, He C. Identifying the m6A Methylome by Affinity Purification and Sequencing. Methods Mol Biol. 2018; 1649:49-57. PMID: 29130189.
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    35. Zhao BS, Nachtergaele S, Roundtree IA, He C. Our views of dynamic N6-methyladenosine RNA methylation. RNA. 2018 03; 24(3):268-272. PMID: 29222116.
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    36. Hsu PJ, He C. Making Changes: N6-Methyladenosine-Mediated Decay Drives the Endothelial-to-Hematopoietic Transition. Biochemistry. 2017 11 21; 56(46):6077-6078. PMID: 29112411.
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    37. Harada BT, He C. Epigenetics: Making your mark on DNA. Nat Chem. 2017 Oct 24; 9(11):1040-1042. PMID: 29064503.
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    38. Hsu PJ, Shi H, He C. Epitranscriptomic influences on development and disease. Genome Biol. 2017 10 23; 18(1):197. PMID: 29061143.
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    39. Roundtree IA, Luo GZ, Zhang Z, Wang X, Zhou T, Cui Y, Sha J, Huang X, Guerrero L, Xie P, He E, Shen B, He C. YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs. Elife. 2017 10 06; 6. PMID: 28984244.
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    40. Zhao BS, He C. "Gamete On" for m6A: YTHDF2 Exerts Essential Functions in Female Fertility. Mol Cell. 2017 Sep 21; 67(6):903-905. PMID: 28938096.
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    41. Hsu PJ, Zhu Y, Ma H, Guo Y, Shi X, Liu Y, Qi M, Lu Z, Shi H, Wang J, Cheng Y, Luo G, Dai Q, Liu M, Guo X, Sha J, Shen B, He C. Ythdc2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis. Cell Res. 2017 Sep; 27(9):1115-1127. PMID: 28809393.
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    42. Roundtree IA, Evans ME, Pan T, He C. Dynamic RNA Modifications in Gene Expression Regulation. Cell. 2017 Jun 15; 169(7):1187-1200. PMID: 28622506.
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    43. Luo GZ, He C. DNA N6-methyladenine in metazoans: functional epigenetic mark or bystander? Nat Struct Mol Biol. 2017 Jun 06; 24(6):503-506. PMID: 28586322.
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    44. Dai Q, Moshitch-Moshkovitz S, Han D, Kol N, Amariglio N, Rechavi G, Dominissini D, He C. Nm-seq maps 2'-O-methylation sites in human mRNA with base precision. Nat Methods. 2017 Jul; 14(7):695-698. PMID: 28504680.
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    45. Karpus J, Bosscher M, Ajiboye I, Zhang L, He C. Chromate Binding and Removal by the Molybdate-Binding Protein ModA. Chembiochem. 2017 04 04; 18(7):633-637. PMID: 28150901.
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    46. Zhao BS, Wang X, Beadell AV, Lu Z, Shi H, Kuuspalu A, Ho RK, He C. m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition. Nature. 2017 02 23; 542(7642):475-478. PMID: 28192787.
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    47. Shi H, Wang X, Lu Z, Zhao BS, Ma H, Hsu PJ, Liu C, He C. YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. Cell Res. 2017 Mar; 27(3):315-328. PMID: 28106072.
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    48. Ma L, Zhao B, Chen K, Thomas A, Tuteja JH, He X, He C, White KP. Evolution of transcript modification by N6-methyladenosine in primates. Genome Res. 2017 03; 27(3):385-392. PMID: 28052920.
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    49. Weekley CM, He C. Developing drugs targeting transition metal homeostasis. Curr Opin Chem Biol. 2017 Apr; 37:26-32. PMID: 28040658.
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    50. Li Z, Weng H, Su R, Weng X, Zuo Z, Li C, Huang H, Nachtergaele S, Dong L, Hu C, Qin X, Tang L, Wang Y, Hong GM, Huang H, Wang X, Chen P, Gurbuxani S, Arnovitz S, Li Y, Li S, Strong J, Neilly MB, Larson RA, Jiang X, Zhang P, Jin J, He C, Chen J. FTO Plays an Oncogenic Role in Acute Myeloid Leukemia as a N6-Methyladenosine RNA Demethylase. Cancer Cell. 2017 01 09; 31(1):127-141. PMID: 28017614.
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    51. Nachtergaele S, He C. The emerging biology of RNA post-transcriptional modifications. RNA Biol. 2017 02; 14(2):156-163. PMID: 27937535.
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    52. Zhao BS, Roundtree IA, He C. Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol. 2017 01; 18(1):31-42. PMID: 27808276.
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    53. Liu F, Clark W, Luo G, Wang X, Fu Y, Wei J, Wang X, Hao Z, Dai Q, Zheng G, Ma H, Han D, Evans M, Klungland A, Pan T, He C. ALKBH1-Mediated tRNA Demethylation Regulates Translation. Cell. 2016 Oct 20; 167(3):816-828.e16. PMID: 27745969.
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    54. Liu J, Zhu Y, Luo GZ, Wang X, Yue Y, Wang X, Zong X, Chen K, Yin H, Fu Y, Han D, Wang Y, Chen D, He C. Abundant DNA 6mA methylation during early embryogenesis of zebrafish and pig. Nat Commun. 2016 10 07; 7:13052. PMID: 27713410.
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    55. Shi H, He C. A glance at N(6)-methyladenosine in transcript isoforms. Nat Methods. 2016 07 28; 13(8):624-5. PMID: 27467725.
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    56. Han D, Lu X, Shih AH, Nie J, You Q, Xu MM, Melnick AM, Levine RL, He C. A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations. Mol Cell. 2016 08 18; 63(4):711-719. PMID: 27477909.
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    57. Yang YA, Zhao JC, Fong KW, Kim J, Li S, Song C, Song B, Zheng B, He C, Yu J. FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function. Nucleic Acids Res. 2016 09 30; 44(17):8153-64. PMID: 27257062.
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    58. Luo GZ, Wang F, Weng X, Chen K, Hao Z, Yu M, Deng X, Liu J, He C. Characterization of eukaryotic DNA N(6)-methyladenine by a highly sensitive restriction enzyme-assisted sequencing. Nat Commun. 2016 Apr 15; 7:11301. PMID: 27079427.
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    59. Roundtree IA, He C. Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. Trends Genet. 2016 06; 32(6):320-321. PMID: 27050931.
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    60. Ji Q, Chen PJ, Qin G, Deng X, Hao Z, Wawrzak Z, Yeo WS, Quang JW, Cho H, Luo GZ, Weng X, You Q, Luan CH, Yang X, Bae T, Yu K, Jiang H, He C. Structure and mechanism of the essential two-component signal-transduction system WalKR in Staphylococcus aureus. Nat Commun. 2016 Mar 18; 7:11000. PMID: 26987594.
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    61. Dominissini D, Nachtergaele S, Moshitch-Moshkovitz S, Peer E, Kol N, Ben-Haim MS, Dai Q, Di Segni A, Salmon-Divon M, Clark WC, Zheng G, Pan T, Solomon O, Eyal E, Hershkovitz V, Han D, Doré LC, Amariglio N, Rechavi G, He C. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature. 2016 Feb 25; 530(7591):441-6. PMID: 26863196.
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    62. Chen K, Zhao BS, He C. Nucleic Acid Modifications in Regulation of Gene Expression. Cell Chem Biol. 2016 Jan 21; 23(1):74-85. PMID: 26933737.
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    63. Huang H, Jiang X, Wang J, Li Y, Song CX, Chen P, Li S, Gurbuxani S, Arnovitz S, Wang Y, Weng H, Neilly MB, He C, Li Z, Chen J. Identification of MLL-fusion/MYC?miR-26?TET1 signaling circuit in MLL-rearranged leukemia. Cancer Lett. 2016 Mar 28; 372(2):157-65. PMID: 26791235.
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    64. Dai Q, Sanstead PJ, Peng CS, Han D, He C, Tokmakoff A. Weakened N3 Hydrogen Bonding by 5-Formylcytosine and 5-Carboxylcytosine Reduces Their Base-Pairing Stability. ACS Chem Biol. 2016 Feb 19; 11(2):470-7. PMID: 26641274.
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    65. Roundtree IA, He C. RNA epigenetics--chemical messages for posttranscriptional gene regulation. Curr Opin Chem Biol. 2016 Feb; 30:46-51. PMID: 26625014.
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    66. Hu L, He C. Detecting hepatocellular carcinoma in blood. Cell Res. 2015 Dec; 25(12):1279-80. PMID: 26596784.
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    67. Wang J, Luo C, Shan C, You Q, Lu J, Elf S, Zhou Y, Wen Y, Vinkenborg JL, Fan J, Kang H, Lin R, Han D, Xie Y, Karpus J, Chen S, Ouyang S, Luan C, Zhang N, Ding H, Merkx M, Liu H, Chen J, Jiang H, He C. Inhibition of human copper trafficking by a small molecule significantly attenuates cancer cell proliferation. Nat Chem. 2015 Dec; 7(12):968-79. PMID: 26587712.
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    68. Luo GZ, Blanco MA, Greer EL, He C, Shi Y. DNA N(6)-methyladenine: a new epigenetic mark in eukaryotes? Nat Rev Mol Cell Biol. 2015 Dec; 16(12):705-10. PMID: 26507168.
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    69. He C. Chemical decaging in living systems. Natl Sci Rev. 2015 Sep; 2(3):250-251. PMID: 26413369.
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    70. Zheng G, Qin Y, Clark WC, Dai Q, Yi C, He C, Lambowitz AM, Pan T. Efficient and quantitative high-throughput tRNA sequencing. Nat Methods. 2015 Sep; 12(9):835-837. PMID: 26214130.
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    71. Chen K, Luo GZ, He C. High-Resolution Mapping of N6-Methyladenosine in Transcriptome and Genome Using a Photo-Crosslinking-Assisted Strategy. Methods Enzymol. 2015; 560:161-85. PMID: 26253971.
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    72. Yu M, Ji L, Neumann DA, Chung DH, Groom J, Westpheling J, He C, Schmitz RJ. Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing. Nucleic Acids Res. 2015 Dec 02; 43(21):e148. PMID: 26184871.
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    73. Yue Y, Liu J, He C. RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation. Genes Dev. 2015 Jul 01; 29(13):1343-55. PMID: 26159994.
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    74. He C. Decoding the transcriptome and DNA methylome of human primordial germ cells. Sci China Life Sci. 2015 Jul; 58(7):729-30. PMID: 26059858.
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    75. Wang X, Zhao BS, Roundtree IA, Lu Z, Han D, Ma H, Weng X, Chen K, Shi H, He C. N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency. Cell. 2015 Jun 04; 161(6):1388-99. PMID: 26046440.
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    76. Cheglakov Z, Cronin TM, He C, Weizmann Y. Live Cell MicroRNA Imaging Using Cascade Hybridization Reaction. J Am Chem Soc. 2015 May 20; 137(19):6116-9. PMID: 25932784.
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    77. Fu Y, Luo GZ, Chen K, Deng X, Yu M, Han D, Hao Z, Liu J, Lu X, Dore LC, Weng X, Ji Q, Mets L, He C. N6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas. Cell. 2015 May 07; 161(4):879-892. PMID: 25936837.
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    78. Liu J, Yue Y, He C. Preparation of Human Nuclear RNA m6A Methyltransferases and Demethylases and Biochemical Characterization of Their Catalytic Activity. Methods Enzymol. 2015; 560:117-30. PMID: 26253968.
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    79. He C, Cole P. Introduction: epigenetics. Chem Rev. 2015 Mar 25; 115(6):2223-4. PMID: 25804907.
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    80. Liu N, Dai Q, Zheng G, He C, Parisien M, Pan T. N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature. 2015 Feb 26; 518(7540):560-4. PMID: 25719671.
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    81. Lu X, Zhao BS, He C. TET family proteins: oxidation activity, interacting molecules, and functions in diseases. Chem Rev. 2015 Mar 25; 115(6):2225-39. PMID: 25675246.
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    82. Lu X, Han D, Zhao BS, Song CX, Zhang LS, Doré LC, He C. Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics. Cell Res. 2015 Mar; 25(3):386-9. PMID: 25591929.
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    83. Chen X, Velmurugu Y, Zheng G, Park B, Shim Y, Kim Y, Liu L, Van Houten B, He C, Ansari A, Min JH. Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Nat Commun. 2015 Jan 06; 6:5849. PMID: 25562780.
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    84. Chen K, Lu Z, Wang X, Fu Y, Luo GZ, Liu N, Han D, Dominissini D, Dai Q, Pan T, He C. High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing. Angew Chem Int Ed Engl. 2015 Jan 26; 54(5):1587-90. PMID: 25491922.
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    85. He C. Visualizing a protein's sugars. Natl Sci Rev. 2014 Dec; 1(4):480-481. PMID: 26114009.
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    86. Luo GZ, MacQueen A, Zheng G, Duan H, Dore LC, Lu Z, Liu J, Chen K, Jia G, Bergelson J, He C. Unique features of the m6A methylome in Arabidopsis thaliana. Nat Commun. 2014 Nov 28; 5:5630. PMID: 25430002.
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    87. Yu M, Song CX, He C. Detection of mismatched 5-hydroxymethyluracil in DNA by selective chemical labeling. Methods. 2015 Jan 15; 72:16-20. PMID: 25462560.
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    88. Zhao BS, He C. Pseudouridine in a new era of RNA modifications. Cell Res. 2015 Feb; 25(2):153-4. PMID: 25367125.
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    89. Wang X, He C. Dynamic RNA modifications in posttranscriptional regulation. Mol Cell. 2014 Oct 02; 56(1):5-12. PMID: 25280100.
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    90. Deng X, Liang H, Chen K, He C, Lan L, Tang X. Molecular mechanisms of two-component system RhpRS regulating type III secretion system in Pseudomonas syringae. Nucleic Acids Res. 2014 Oct; 42(18):11472-86. PMID: 25249629.
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    91. Cheng Y, Dai Q, Morshed RA, Fan X, Wegscheid ML, Wainwright DA, Han Y, Zhang L, Auffinger B, Tobias AL, Rincón E, Thaci B, Ahmed AU, Warnke PC, He C, Lesniak MS. Blood-brain barrier permeable gold nanoparticles: an efficient delivery platform for enhanced malignant glioma therapy and imaging. Small. 2014 Dec 29; 10(24):5137-50. PMID: 25104165.
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    92. Zheng G, Cox T, Tribbey L, Wang GZ, Iacoban P, Booher ME, Gabriel GJ, Zhou L, Bae N, Rowles J, He C, Olsen MJ. Synthesis of a FTO inhibitor with anticonvulsant activity. ACS Chem Neurosci. 2014 Aug 20; 5(8):658-65. PMID: 24834807.
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    102. Madzo J, Liu H, Rodriguez A, Vasanthakumar A, Sundaravel S, Caces DBD, Looney TJ, Zhang L, Lepore JB, Macrae T, Duszynski R, Shih AH, Song CX, Yu M, Yu Y, Grossman R, Raumann B, Verma A, He C, Levine RL, Lavelle D, Lahn BT, Wickrema A, Godley LA. Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis. Cell Rep. 2014 Jan 16; 6(1):231-244. PMID: 24373966.
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    108. Lu X, He C. Nonenzymatic labeling of 5-hydroxymethylcytosine in nanopore sequencing. Chembiochem. 2013 Jul 22; 14(11):1289-90. PMID: 23780928.
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    113. Deng X, Weerapana E, Ulanovskaya O, Sun F, Liang H, Ji Q, Ye Y, Fu Y, Zhou L, Li J, Zhang H, Wang C, Alvarez S, Hicks LM, Lan L, Wu M, Cravatt BF, He C. Proteome-wide quantification and characterization of oxidation-sensitive cysteines in pathogenic bacteria. Cell Host Microbe. 2013 Mar 13; 13(3):358-70. PMID: 23498960.
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    123. Jiang X, Huang H, Li Z, Li Y, Wang X, Gurbuxani S, Chen P, He C, You D, Zhang S, Wang J, Arnovitz S, Elkahloun A, Price C, Hong GM, Ren H, Kunjamma RB, Neilly MB, Matthews JM, Xu M, Larson RA, Le Beau MM, Slany RK, Liu PP, Lu J, Zhang J, He C, Chen J. Blockade of miR-150 maturation by MLL-fusion/MYC/LIN-28 is required for MLL-associated leukemia. Cancer Cell. 2012 Oct 16; 22(4):524-35. PMID: 23079661.
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    124. Brugarolas P, Movahedzadeh F, Wang Y, Zhang N, Bartek IL, Gao YN, Voskuil MI, Franzblau SG, He C. The oxidation-sensing regulator (MosR) is a new redox-dependent transcription factor in Mycobacterium tuberculosis. J Biol Chem. 2012 Nov 02; 287(45):37703-12. PMID: 22992749.
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    125. Wang J, Karpus J, Zhao BS, Luo Z, Chen PR, He C. A selective fluorescent probe for carbon monoxide imaging in living cells. Angew Chem Int Ed Engl. 2012 Sep 17; 51(38):9652-6. PMID: 22930547.
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    126. Sun F, Ding Y, Ji Q, Liang Z, Deng X, Wong CC, Yi C, Zhang L, Xie S, Alvarez S, Hicks LM, Luo C, Jiang H, Lan L, He C. Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance. Proc Natl Acad Sci U S A. 2012 Sep 18; 109(38):15461-6. PMID: 22927394.
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    127. Hendrickx AP, Poor CB, Jureller JE, Budzik JM, He C, Schneewind O. Isopeptide bonds of the major pilin protein BcpA influence pilus structure and bundle formation on the surface of Bacillus cereus. Mol Microbiol. 2012 Jul; 85(1):152-63. PMID: 22624947.
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    129. Sun F, Liang H, Kong X, Xie S, Cho H, Deng X, Ji Q, Zhang H, Alvarez S, Hicks LM, Bae T, Luo C, Jiang H, He C. Quorum-sensing agr mediates bacterial oxidation response via an intramolecular disulfide redox switch in the response regulator AgrA. Proc Natl Acad Sci U S A. 2012 Jun 05; 109(23):9095-100. PMID: 22586129.
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    130. Ji Q, Zhang L, Sun F, Deng X, Liang H, Bae T, He C. Staphylococcus aureus CymR is a new thiol-based oxidation-sensing regulator of stress resistance and oxidative response. J Biol Chem. 2012 Jun 15; 287(25):21102-9. PMID: 22553203.
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    131. Dai Q, Lu X, Zhang L, He C. Synthesis of DNA oligos containing 2'-deoxy-2'-fluoro-D-arabinofuranosyl-5-carboxylcytosine as hTDG inhibitor. Tetrahedron. 2012 Jul 01; 68(26):5145-5151. PMID: 22711938.
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    132. Liang H, Deng X, Ji Q, Sun F, Shen T, He C. The Pseudomonas aeruginosa global regulator VqsR directly inhibits QscR to control quorum-sensing and virulence gene expression. J Bacteriol. 2012 Jun; 194(12):3098-108. PMID: 22505688.
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    133. Zhang L, Lu X, Lu J, Liang H, Dai Q, Xu GL, Luo C, Jiang H, He C. Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Nat Chem Biol. 2012 Feb 12; 8(4):328-30. PMID: 22327402.
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    134. Deng X, Sun F, Ji Q, Liang H, Missiakas D, Lan L, He C. Expression of multidrug resistance efflux pump gene norA is iron responsive in Staphylococcus aureus. J Bacteriol. 2012 Apr; 194(7):1753-62. PMID: 22267518.
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    135. Sun F, Ji Q, Jones MB, Deng X, Liang H, Frank B, Telser J, Peterson SN, Bae T, He C. AirSR, a [2Fe-2S] cluster-containing two-component system, mediates global oxygen sensing and redox signaling in Staphylococcus aureus. J Am Chem Soc. 2012 Jan 11; 134(1):305-14. PMID: 22122613.
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    136. Dai Q, He C. Preparation of DNA containing 5-hydroxymethyl-2'-deoxycytidine modification through phosphoramidites with TBDMS as 5-hydroxymethyl protecting group. Curr Protoc Nucleic Acid Chem. 2011 Dec; Chapter 4:Unit 4.47.1-18. PMID: 22147420.
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    138. Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, Yi C, Lindahl T, Pan T, Yang YG, He C. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol. 2011 Oct 16; 7(12):885-7. PMID: 22002720.
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    139. Capretto DA, Brouwer C, Poor CB, He C. Gold(I)-catalyzed formation of 3-pyrazolines through cycloaddition of diaziridine to alkynes. Org Lett. 2011 Nov 04; 13(21):5842-5. PMID: 21988670.
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    140. Qian Y, Karpus J, Kabil O, Zhang SY, Zhu HL, Banerjee R, Zhao J, He C. Selective fluorescent probes for live-cell monitoring of sulphide. Nat Commun. 2011 Oct 11; 2:495. PMID: 21988911.
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    142. Aryal BP, Brugarolas P, He C. Binding of ReO4(-) with an engineered MoO4(2-)-binding protein: towards a new approach in radiopharmaceutical applications. J Biol Inorg Chem. 2012 Jan; 17(1):97-106. PMID: 21861186.
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    143. Özçubukçu S, Mandal K, Wegner S, Jensen MP, He C. Selective recognition of americium by peptide-based reagents. Inorg Chem. 2011 Sep 05; 50(17):7937-9. PMID: 21819087.
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    144. Brugarolas P, Duguid EM, Zhang W, Poor CB, He C. Structural and biochemical characterization of N5-carboxyaminoimidazole ribonucleotide synthetase and N5-carboxyaminoimidazole ribonucleotide mutase from Staphylococcus aureus. Acta Crystallogr D Biol Crystallogr. 2011 Aug; 67(Pt 8):707-15. PMID: 21795812.
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    145. Song CX, Sun Y, Dai Q, Lu XY, Yu M, Yang CG, He C. Detection of 5-hydroxymethylcytosine in DNA by transferring a keto-glucose by using T4 phage ß-glucosyltransferase. Chembiochem. 2011 Jul 25; 12(11):1682-5. PMID: 21656634.
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    146. Dai Q, He C. Syntheses of 5-formyl- and 5-carboxyl-dC containing DNA oligos as potential oxidation products of 5-hydroxymethylcytosine in DNA. Org Lett. 2011 Jul 01; 13(13):3446-9. PMID: 21648398.
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    147. Dolan KT, Duguid EM, He C. Crystal structures of SlyA protein, a master virulence regulator of Salmonella, in free and DNA-bound states. J Biol Chem. 2011 Jun 24; 286(25):22178-85. PMID: 21550983.
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    152. Wegner SV, Sun F, Hernandez N, He C. The tightly regulated copper window in yeast. Chem Commun (Camb). 2011 Mar 07; 47(9):2571-3. PMID: 21180717.
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    154. He C. Grand challenge commentary: RNA epigenetics? Nat Chem Biol. 2010 Dec; 6(12):863-5. PMID: 21079590.
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    155. Fu Y, Dai Q, Zhang W, Ren J, Pan T, He C. The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA. Angew Chem Int Ed Engl. 2010 Nov 15; 49(47):8885-8. PMID: 20583019.
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    156. Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C. Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature. 2010 Nov 11; 468(7321):330-3. PMID: 21068844.
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    157. Saikia M, Fu Y, Pavon-Eternod M, He C, Pan T. Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs. RNA. 2010 Jul; 16(7):1317-27. PMID: 20484468.
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    158. Lan L, Cheng A, Dunman PM, Missiakas D, He C. Golden pigment production and virulence gene expression are affected by metabolisms in Staphylococcus aureus. J Bacteriol. 2010 Jun; 192(12):3068-77. PMID: 20400547.
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    159. Lu L, Yi C, Jian X, Zheng G, He C. Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system. Nucleic Acids Res. 2010 Jul; 38(13):4415-25. PMID: 20223766.
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    160. Wegner SV, Arslan H, Sunbul M, Yin J, He C. Dynamic copper(I) imaging in mammalian cells with a genetically encoded fluorescent copper(I) sensor. J Am Chem Soc. 2010 Mar 03; 132(8):2567-9. PMID: 20131768.
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    161. Sun F, Li C, Jeong D, Sohn C, He C, Bae T. In the Staphylococcus aureus two-component system sae, the response regulator SaeR binds to a direct repeat sequence and DNA binding requires phosphorylation by the sensor kinase SaeS. J Bacteriol. 2010 Apr; 192(8):2111-27. PMID: 20172998.
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    162. Lan L, Murray TS, Kazmierczak BI, He C. Pseudomonas aeruginosa OspR is an oxidative stress sensing regulator that affects pigment production, antibiotic resistance and dissemination during infection. Mol Microbiol. 2010 Jan; 75(1):76-91. PMID: 19943895.
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    163. Budzik JM, Poor CB, Faull KF, Whitelegge JP, He C, Schneewind O. Intramolecular amide bonds stabilize pili on the surface of bacilli. Proc Natl Acad Sci U S A. 2009 Nov 24; 106(47):19992-7. PMID: 19903875.
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    164. Jian X, Wasinger EC, Lockard JV, Chen LX, He C. Highly sensitive and selective gold(I) recognition by a metalloregulator in Ralstonia metallidurans. J Am Chem Soc. 2009 Aug 12; 131(31):10869-71. PMID: 19606897.
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    165. Poor CB, Chen PR, Duguid E, Rice PA, He C. Crystal structures of the reduced, sulfenic acid, and mixed disulfide forms of SarZ, a redox active global regulator in Staphylococcus aureus. J Biol Chem. 2009 Aug 28; 284(35):23517-24. PMID: 19586910.
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    166. Yi C, Yang CG, He C. A non-heme iron-mediated chemical demethylation in DNA and RNA. Acc Chem Res. 2009 Apr 21; 42(4):519-29. PMID: 19852088.
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    167. Lin Y, Zhao T, Jian X, Farooqui Z, Qu X, He C, Dinner AR, Scherer NF. Using the bias from flow to elucidate single DNA repair protein sliding and interactions with DNA. Biophys J. 2009 Mar 04; 96(5):1911-7. PMID: 19254550.
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    168. Wegner SV, Boyaci H, Chen H, Jensen MP, He C. Engineering a uranyl-specific binding protein from NikR. Angew Chem Int Ed Engl. 2009; 48(13):2339-41. PMID: 19199314.
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    169. Yang S, Li Z, Jian X, He C. Platinum(II)-catalyzed intramolecular cyclization of o-substituted aryl alkynes through sp3 C-H activation. Angew Chem Int Ed Engl. 2009; 48(22):3999-4001. PMID: 19402084.
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    170. He C. Chemical methods to study protein-nucleic acid interactions. Nucleic Acids Symp Ser (Oxf). 2009; (53):43. PMID: 19749251.
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    171. Shigdel UK, He C. A new 1'-methylenedisulfide deoxyribose that forms an efficient cross-link to DNA cytosine-5 methyltransferase (DNMT). J Am Chem Soc. 2008 Dec 31; 130(52):17634-5. PMID: 19108695.
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    172. Richter S, Anderson VJ, Garufi G, Lu L, Budzik JM, Joachimiak A, He C, Schneewind O, Missiakas D. Capsule anchoring in Bacillus anthracis occurs by a transpeptidation reaction that is inhibited by capsidin. Mol Microbiol. 2009 Jan; 71(2):404-20. PMID: 19017271.
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    174. Qiu Z, Lu L, Jian X, He C. A diazirine-based nucleoside analogue for efficient DNA interstrand photocross-linking. J Am Chem Soc. 2008 Nov 05; 130(44):14398-9. PMID: 18842048.
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    176. Chen H, Hu J, Chen PR, Lan L, Li Z, Hicks LM, Dinner AR, He C. The Pseudomonas aeruginosa multidrug efflux regulator MexR uses an oxidation-sensing mechanism. Proc Natl Acad Sci U S A. 2008 Sep 09; 105(36):13586-91. PMID: 18757728.
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    177. Li Z, Brouwer C, He C. Gold-catalyzed organic transformations. Chem Rev. 2008 Aug; 108(8):3239-65. PMID: 18613729.
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    179. Chen PR, He C. Selective recognition of metal ions by metalloregulatory proteins. Curr Opin Chem Biol. 2008 Apr; 12(2):214-21. PMID: 18258210.
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    181. Durek T, Zhang J, He C, Kent SB. Synthesis of photoactive analogues of a cystine knot trypsin inhibitor protein. Org Lett. 2007 Dec 20; 9(26):5497-500. PMID: 18041846.
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    182. Chen PR, Wasinger EC, Zhao J, van der Lelie D, Chen LX, He C. Spectroscopic insights into lead(II) coordination by the selective lead(II)-binding protein PbrR691. J Am Chem Soc. 2007 Oct 17; 129(41):12350-1. PMID: 17880216.
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    183. Li Z, Capretto DA, Rahaman RO, He C. Gold(III)-catalyzed nitrene insertion into aromatic and benzylic C-H groups. J Am Chem Soc. 2007 Oct 10; 129(40):12058-9. PMID: 17880068.
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    184. Wegner SV, Okesli A, Chen P, He C. Design of an emission ratiometric biosensor from MerR family proteins: a sensitive and selective sensor for Hg2+. J Am Chem Soc. 2007 Mar 28; 129(12):3474-5. PMID: 17335208.
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    185. Li Z, Capretto DA, Rahaman R, He C. Silver-catalyzed intermolecular amination of C--H groups. Angew Chem Int Ed Engl. 2007; 46(27):5184-6. PMID: 17535005.
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    186. Chen PR, Bae T, Williams WA, Duguid EM, Rice PA, Schneewind O, He C. An oxidation-sensing mechanism is used by the global regulator MgrA in Staphylococcus aureus. Nat Chem Biol. 2006 Nov; 2(11):591-5. PMID: 16980961.
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    187. Li Z, Zhang J, Brouwer C, Yang CG, Reich NW, He C. Brønsted acid catalyzed addition of phenols, carboxylic acids, and tosylamides to simple olefins. Org Lett. 2006 Sep 14; 8(19):4175-8. PMID: 16956180.
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    188. Li Z, Ding X, He C. Nitrene transfer reactions catalyzed by gold complexes. J Org Chem. 2006 Aug 04; 71(16):5876-80. PMID: 16872166.
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    189. Brouwer C, He C. Efficient gold-catalyzed hydroamination of 1,3-dienes. Angew Chem Int Ed Engl. 2006 Mar 03; 45(11):1744-7. PMID: 16453358.
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    190. Zhang J, Yang CG, He C. Gold(I)-catalyzed intra- and intermolecular hydroamination of unactivated olefins. J Am Chem Soc. 2006 Feb 15; 128(6):1798-9. PMID: 16464072.
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    191. Mishina Y, He C. Oxidative dealkylation DNA repair mediated by the mononuclear non-heme iron AlkB proteins. J Inorg Biochem. 2006 Apr; 100(4):670-8. PMID: 16469386.
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    192. Mishina Y, Duguid EM, He C. Direct reversal of DNA alkylation damage. Chem Rev. 2006 Feb; 106(2):215-32. PMID: 16464003.
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    193. Mishina Y, Yang CG, He C. Direct repair of the exocyclic DNA adduct 1,N6-ethenoadenine by the DNA repair AlkB proteins. J Am Chem Soc. 2005 Oct 26; 127(42):14594-5. PMID: 16231911.
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    194. Yang CG, Reich NW, Shi Z, He C. Intramolecular additions of alcohols and carboxylic acids to inert olefins catalyzed by silver(I) triflate. Org Lett. 2005 Oct 13; 7(21):4553-6. PMID: 16209477.
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    195. Duguid EM, Rice PA, He C. The structure of the human AGT protein bound to DNA and its implications for damage detection. J Mol Biol. 2005 Jul 22; 350(4):657-66. PMID: 15964013.
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    196. Yang CG, He C. Gold(I)-catalyzed intermolecular addition of phenols and carboxylic acids to olefins. J Am Chem Soc. 2005 May 18; 127(19):6966-7. PMID: 15884936.
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    197. Chen P, Greenberg B, Taghavi S, Romano C, van der Lelie D, He C. An exceptionally selective lead(II)-regulatory protein from Ralstonia metallidurans: development of a fluorescent lead(II) probe. Angew Chem Int Ed Engl. 2005 Apr 29; 44(18):2715-9. PMID: 15800869.
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    198. Mishina Y, Chen LX, He C. Preparation and characterization of the native iron(II)-containing DNA repair AlkB protein directly from Escherichia coli. J Am Chem Soc. 2004 Dec 29; 126(51):16930-6. PMID: 15612731.
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    199. Shi Z, He C. Direct functionalization of arenes by primary alcohol sulfonate esters catalyzed by gold(III). J Am Chem Soc. 2004 Oct 27; 126(42):13596-7. PMID: 15493899.
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    200. Cui Y, He C. A silver-catalyzed intramolecular amidation of saturated C--h bonds. Angew Chem Int Ed Engl. 2004 Aug 13; 43(32):4210-2. PMID: 15307089.
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    201. Shi Z, He C. Efficient functionalization of aromatic C-H bonds catalyzed by gold(III) under mild and solvent-free conditions. J Org Chem. 2004 May 28; 69(11):3669-71. PMID: 15152995.
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    202. Shi Z, He C. An Au-catalyzed cyclialkylation of electron-rich arenes with epoxides to prepare 3-chromanols. J Am Chem Soc. 2004 May 19; 126(19):5964-5. PMID: 15137751.
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    203. He C, Mishina Y. Modeling non-heme iron proteins. Curr Opin Chem Biol. 2004 Apr; 8(2):201-8. PMID: 15062782.
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    204. Mishina Y, Lee CH, He C. Interaction of human and bacterial AlkB proteins with DNA as probed through chemical cross-linking studies. Nucleic Acids Res. 2004; 32(4):1548-54. PMID: 15004242.
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    205. Chen P, He C. A general strategy to convert the MerR family proteins into highly sensitive and selective fluorescent biosensors for metal ions. J Am Chem Soc. 2004 Jan 28; 126(3):728-9. PMID: 14733542.
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    206. Cui Y, He C. Efficient aziridination of olefins catalyzed by a unique disilver(I) compound. J Am Chem Soc. 2003 Dec 31; 125(52):16202-3. PMID: 14692757.
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    207. Duguid EM, Mishina Y, He C. How do DNA repair proteins locate potential base lesions? a chemical crosslinking method to investigate O6-alkylguanine-DNA alkyltransferases. Chem Biol. 2003 Sep; 10(9):827-35. PMID: 14522053.
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    208. Mishina Y, He C. Probing the structure and function of the Escherichia coli DNA alkylation repair AlkB protein through chemical cross-linking. J Am Chem Soc. 2003 Jul 23; 125(29):8730-1. PMID: 12862460.
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