39. Wang, P.Y., Sexton, A.N., Culligan, W.J. and Simon, M.D. (2018) Carbodiimide reagents for the chemical probing of RNA structure in cells. RNA. doi: 10.1261/rna.067561.118. (Pubmed)
38. Duffy, E.E., Schofield, J.A. and Simon, M.D. (2018) Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine. Wiley Interdiscip Rev RNA. doi: 10.1002/wrna.1513 (Pubmed)
37. Kiefer, L., Schofield, J.A. and Simon, M.D. (2018) Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-thioguanosine. J. Am. Chem. Soc., doi: 10.1021/jacs.8b08554 (Pubmed)
36. Duffy, E.E., Canzio, D., Maniatis, T., Simon, M.D. (2018) Solid phase chemistry to covalently and reversibly capture thiolated RNA. Nucleid Acids Research, 46(21), 6996-7005 (Pubmed)
35. Schofield, J.A., Duffy, E.E., Kiefer, L., Sullivan, M.C., and Simon, M.D. (2018) TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding. Nature Methods, doi:10.1038/nmeth.4582 (Pubmed)
34. Machyna, M. and Simon, M.D. (2017) Catching RNAs on chromatin using hybridization capture methods. Brief Funct Genomics, PMID: 29126220. (Pubmed)
33. Sexton, A.N., Wang, P.Y., Rutenberg-Schoenberg, M., and Simon, M.D. (2017) Interpreting reverse transcriptase termination and mutation events for greater insight into the chemical probing of RNA. Biochemistry, 56(35), 4713-4721. PMID: 28820243. (Pubmed)
32. Li, H., Tong, Y., Zhu, S., Batista, P.J., Duffy, E.E., Zhao, J., Bailis, W., Cao, G., Kroehling, L., Chen, Y., Wang, G., Chen, Y.G., Broughton, J.P., Kluger, Y., Simon, M.D., Chang, H.Y., Yin, Z. and Flavell, R. (2017) m6A mRNA methylation controls T cell homeostasis by targeting IL-7/STAT/SOCS pathway. Nature, 548(7667), 338-342. PMID: 28792938. (Pubmed)
31. Duffy, E.E., and Simon M.D. (2016) Enriching s4U-RNA Using Methane Thiosulfonate (MTS) Chemistry. Curr Protoc Chem Bio, 8(4), 234-250. PMID: 27925666. (Pubmed)
30. Rutenberg-Schoenberg, M., Sexton, A.N., Simon, M.D. (2016) The Properties of Long Noncoding RNAs That Regulate Chromatin. Annu Rev Genom Hum Genet, 17, 69-94. PMID: 27147088 (Pubmed)
29. Simon, M.D. (2016) Insight into lncRNA biology using hybridization capture analyses. Biochim Biophys Acta, 1859(1), 121-127. PMID: 26381323. (Pubmed)
28. Sexton, A., Machyna, M., and Simon, M.D. Capture Hybridization Analysis of RNA Targets (CHART-seq) (2016) Methods Molecular Biology, 1480, 87-97. PMID: 27659977 (Pubmed)
27. Fang, R.*, Moss, W.N.*, Rutenberg-Schoenberg, M. and Simon, M.D. (2015) Probing Xist RNA structure in cells using Targeted Structure-Seq. PLoS Genetics, 11(12):e1005668. PMID: 26646615 *equal contributions (Pubmed)
26. Du ffy, E.E., Rutenberg-Schoenberg, M., Stark, C.D., Kitchen, R.R., Gerstein, M.B., and Simon M.D. Tracking distinct RNA populations using effcient and reversible covalent chemistry. (2015) Mol Cell, 59(5), 858-66. PMID: 26340425.(Pubmed)
25. West, J.A., Davis, C.P., Sunwoo, H., Simon, M.D., Sadreyev, R.I., Wang, P.I., Tolstorukov, M.Y., and Kingston, R.E. The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. (2014) Mol Cell, 55(5), 791-802. PMID: 25155612.(Pubmed)
24. Alpatov, R., Lesch, B.J., Nakamoto-Kinoshita, M., Blanco, A., Chen, S., Stützer, A., Armache, K.J., Simon, M.D., Xu, C., Ali, M., Murn, J., Prisic, S., Kutateladze, T.G., Vakoc, C.R., Min, J., Kingston, R.E., Fischle, W., Warren, S.T., Page, D.C., Shi, Y. (2014) Cell 157, 869-81. PMID: 24813610. (Pubmed)
23. Simon, M. D.#,*, Pinter, S. F.*, Fang, R.*, Sarma, K., Rutenberg-Schoenberg, M., Bowman, S. K., Kesner, B. A., Maier, V.K., Kingston, R.E.#, Lee, J.T.# (2013) High resolution Xist binding maps reaveal two-step spreading durring X-chromosome inactivation. Nature 504, 465-9. (Pubmed) #corresponding authors; *equal contributions.
22. Bowman, S. K., Simon, M. D., Deaton, A. M., Tolstorukov, M., Borowsky, M. L., Kingston, R. E. Multiplexed Illumina sequencing libraries from picogram quantities of DNA. (2013) BMC Genomics 14, 466. PMID:23837789. (Pubmed)
21. Simon, M. D. (2013) Capture Hybridization Analysis of RNA Targets (CHART), Curr Protoc Mol Biol Chapter 21, Unit 21 21.25. PMID:23288463. (Pubmed)
20. Simon, M. D., and Shokat, K. M. (2012) A method to site-specifically incorporate methyl-lysine analogues into recombinant proteins, Methods Enzymol 512, 57-69. PMID:22910202. (Pubmed)
19. Fang, R., Chen, F., Dong, Z., Hu, D., Barbera, A. J., Clark, E. A., Fang, J., Yang, Y., Mei, P., Rutenberg, M., Li, Z., Zhang, Y., Xu, Y., Yang, H., Wang, P., Simon, M. D., Zhou, Q., Li, J., Marynick, M. P., Li, X., Lu, H., Kaiser, U. B., Kingston, R. E., Xu, Y., and Shi, Y. G. (2012) LSD2/KDM1B and Its Cofactor NPAC/GLYR1 Endow a Structural and Molecular Model for Regulation of H3K4 Demethylation, Mol Cell 49, 558-70. PMID:23260659. (Pubmed)
18. Simon, M. D., Wang, C. I., Kharchenko, P. V., West, J. A., Chapman, B. A., Alekseyenko, A. A., Borowsky, M. L., Kuroda, M. I., and Kingston, R. E. (2011) The genomic binding sites of a noncoding RNA, Proc Natl Acad Sci U S A 108, 20497-20502. PMID:22143764. (Pubmed)
17. Canzio, D., Chang, E. Y., Shankar, S., Kuchenbecker, K. M., Simon, M. D., Madhani, H. D., Narlikar, G. J., and Al-Sady, B. (2011) Chromodomain-mediated oligomerization of HP1 suggests a nucleosome-bridging mechanism for heterochromatin assembly, Mol Cell 41, 67-81. PMID:21211724. (Pubmed)
16. Simon, M. D. (2010) Installation of site-specific methylation into histones using methyl lysine analogs, Curr Protoc Mol Biol Chapter 21, Unit 21 18 21-10. PMID:20373501. (Pubmed)
15. Millet, Y. A., Danna, C. H., Clay, N. K., Songnuan, W., Simon, M. D., Werck-Reichhart, D., and Ausubel, F. M. (2010) Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns, Plant Cell 22, 973-990. PMID:20348432. (Pubmed)
14. Shen, X., Kim, W., Fujiwara, Y., Simon, M. D., Liu, Y., Mysliwiec, M. R., Yuan, G. C., Lee, Y., and Orkin, S. H. (2009) Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells, Cell 139, 1303-1314. PMID:20064376. (Pubmed)
13. Li, B., Jackson, J., Simon, M. D., Fleharty, B., Gogol, M., Seidel, C., Workman, J. L., and Shilatifard, A. (2009) Histone H3 lysine 36 dimethylation (H3K36me2) is sufficient to recruit the Rpd3s histone deacetylase complex and to repress spurious transcription, J Biol Chem 284, 7970-7976. PMID:19155214. (Pubmed)
12. Hung, T., Binda, O., Champagne, K. S., Kuo, A. J., Johnson, K., Chang, H. Y., Simon, M. D., Kutateladze, T. G., and Gozani, O. (2009) ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation, Mol Cell 33, 248-256. PMID:19187765. (Pubmed)
11. Francis, N. J., Follmer, N. E., Simon, M. D., Aghia, G., and Butler, J. D. (2009) Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro, Cell 137, 110-122. PMID:19303136. (Pubmed)
10. Lu, X., Simon, M. D., Chodaparambil, J. V., Hansen, J. C., Shokat, K. M., and Luger, K. (2008) The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure, Nat Struct Mol Biol 15, 1122-1124. PMID:18794842. (Pubmed)
9. Simon, M. D., Chu, F., Racki, L. R., de la Cruz, C. C., Burlingame, A. L., Panning, B., Narlikar, G. J., and Shokat, K. M. (2007) The site-specific installation of methyl-lysine analogs into recombinant histones, Cell 128, 1003-1012. PMID:17350582. (Pubmed)
8. de la Cruz, C. C., Kirmizis, A., Simon, M. D., Isono, K., Koseki, H., and Panning, B. (2007) The polycomb group protein SUZ12 regulates histone H3 lysine 9 methylation and HP1 alpha distribution, Chromosome Res 15, 299-314. PMID:17406994. (Pubmed)
7. Simon, M.D. and Shokat, K.M. Revealing biological specify by engineering protein-ligand interactions. Chemical Biology: From Small Molecules to System Biology and Drug Discovery, Wiley, 2006.
6. Simon, M. D.*, Feldman, M. E.*, Rauh, D., Maris, A. E., Wemmer, D. E., and Shokat, K. M. (2006) Structure and properties of a re-engineered homeodomain protein-DNA interface, ACS Chem Biol 1, 755-760. PMID:17240973. (Pubmed)*equal contributions.
5. Simon, M. D., and Shokat, K. M. (2004) Adaptability at a protein-DNA interface: re-engineering the engrailed homeodomain to recognize an unnatural nucleotide, J Am Chem Soc 126, 8078-8079. PMID:15225024. (Pubmed)
4. Simon, M. D., Sato, K., Weiss, G. A., and Shokat, K. M. (2004) A phage display selection of engrailed homeodomain mutants and the importance of residue Q50, Nucleic Acids Res 32, 3623-3631. PMID:15247345. (Pubmed)
3. Sato, K., Simon, M. D., Levin, A. M., Shokat, K. M., and Weiss, G. A. (2004) Dissecting the Engrailed homeodomain-DNA interaction by phage-displayed shotgun scanning, Chem Biol11, 1017-1023. PMID:15271360. (Pubmed)
2. Zahn, T., Eilers, M., Guo, Z., Ksebati, M., Simon, M., Scholten, J., Smith, S., and Gibbs, R. (2000) Evaluation of isoprenoid conformation in solution and in the active site of protein-farnesyl transferase using carbon-13 labeling in conjunction with solution-and solid-state NMR. J Am Chem Soc122, 153-7164.
1. Berlin, K., Jain, K.R., Simon, M.D., and Richert, C. A porphyrin embedded in DNA. (1998) J Org Chem , 63, 1527-1535.