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Matthew D. Simon - Publications

Affiliations: 
Molecular Biophysics and Biochemistry Yale University, New Haven, CT 
Area:
Chemical biology; Large non-coding RNAs; Epigenetic regulation; Histone modifications
Website:
http://medicine.yale.edu/mbb/faculty/matthew_simon.profile
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49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Boddu PC, Gupta AK, Roy R, De La Peña Avalos B, Olazabal-Herrero A, Neuenkirchen N, Zimmer JT, Chandhok NS, King D, Nannya Y, Ogawa S, Lin H, Simon MD, Dray E, Kupfer GM, et al. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Molecular Cell. PMID 38521065 DOI: 10.1016/j.molcel.2024.02.032  0.341
2023 Lu-Culligan WJ, Connor LJ, Xie Y, Ekundayo BE, Rose BT, Machyna M, Pintado-Urbanc AP, Zimmer JT, Vock IW, Bhanu NV, King MC, Garcia BA, Bleichert F, Simon MD. Acetyl-methyllysine marks chromatin at active transcription start sites. Nature. PMID 37731000 DOI: 10.1038/s41586-023-06565-9  0.375
2023 Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, et al. Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Molecular Cell. 83: 2872-2883.e7. PMID 37595555 DOI: 10.1016/j.molcel.2023.07.020  0.654
2023 Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, Ioannes P, Vasilyev N, Lee R, Wang M, Simon M, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, et al. Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Biorxiv : the Preprint Server For Biology. PMID 36993485 DOI: 10.1101/2023.03.17.533220  0.685
2020 Luo Y, Schofield J, Simon MD, Slavoff SA. Global profiling of cellular substrates of human Dcp2. Biochemistry. PMID 32365300 DOI: 10.1021/Acs.Biochem.0C00069  0.451
2020 Machyna M, Kiefer L, Simon MD. Author Correction: Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin. Nature Structural & Molecular Biology. PMID 32203493 DOI: 10.1038/S41594-020-0413-9  0.435
2020 Machyna M, Kiefer L, Simon MD. Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin. Nature Structural & Molecular Biology. 27: 297-304. PMID 32157249 DOI: 10.1038/S41594-020-0390-Z  0.497
2020 Olivero CE, Martínez-Terroba E, Zimmer J, Liao C, Tesfaye E, Hooshdaran N, Schofield JA, Bendor J, Fang D, Simon MD, Zamudio JR, Dimitrova N. p53 Activates the Long Noncoding RNA Pvt1b to Inhibit Myc and Suppress Tumorigenesis. Molecular Cell. PMID 31973890 DOI: 10.1016/J.Molcel.2019.12.014  0.449
2019 Simon MD, Machyna M. Principles and Practices of Hybridization Capture Experiments to Study Long Noncoding RNAs That Act on Chromatin. Cold Spring Harbor Perspectives in Biology. 11. PMID 31676573 DOI: 10.1101/Cshperspect.A032276  0.462
2019 Smith TS, Zoltek MA, Simon MD. Reengineering a tRNA methyltransferase to covalently capture new RNA substrates. Journal of the American Chemical Society. PMID 31626536 DOI: 10.1021/Jacs.9B08529  0.454
2019 Canzio D, Nwakeze CL, Horta A, Rajkumar SM, Coffey EL, Duffy EE, Duffié R, Monahan K, O'Keeffe S, Simon MD, Lomvardas S, Maniatis T. Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice. Cell. PMID 30955885 DOI: 10.1016/J.Cell.2019.03.008  0.516
2019 Kiefer L, Simon MD. Stella's Role in Oocyte DNA Methylation Suggests Additional Activities of DNMT1. Biochemistry. PMID 30920202 DOI: 10.1021/Acs.Biochem.9B00146  0.481
2018 Wang PY, Sexton AN, Culligan WJ, Simon MD. Carbodiimide reagents for the chemical probing of RNA structure in cells. Rna (New York, N.Y.). PMID 30389828 DOI: 10.1261/Rna.067561.118  0.437
2018 Duffy EE, Schofield JA, Simon MD. Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine. Wiley Interdisciplinary Reviews. Rna. e1513. PMID 30370679 DOI: 10.1002/Wrna.1513  0.355
2018 Kiefer L, Schofield JA, Simon MD. Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine. Journal of the American Chemical Society. PMID 30353734 DOI: 10.1021/Jacs.8B08554  0.332
2018 Duffy EE, Canzio D, Maniatis T, Simon MD. Solid phase chemistry to covalently and reversibly capture thiolated RNA. Nucleic Acids Research. PMID 29986098 DOI: 10.1093/Nar/Gky556  0.328
2018 Schofield JA, Duffy EE, Kiefer L, Sullivan MC, Simon MD. TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding. Nature Methods. PMID 29355846 DOI: 10.1038/Nmeth.4582  0.338
2017 Machyna M, Simon MD. Catching RNAs on chromatin using hybridization capture methods. Briefings in Functional Genomics. PMID 29126220 DOI: 10.1093/Bfgp/Elx038  0.393
2017 Sexton AN, Wang PY, Rutenberg-Schoenberg M, Simon MD. Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA. Biochemistry. PMID 28820243 DOI: 10.1021/Acs.Biochem.7B00323  0.347
2016 Duffy EE, Simon MD. Enriching s(4) U-RNA Using Methane Thiosulfonate (MTS) Chemistry. Current Protocols in Chemical Biology. 8: 234-250. PMID 27925666 DOI: 10.1002/Cpch.12  0.324
2016 Sexton AN, Machyna M, Simon MD. Capture Hybridization Analysis of DNA Targets. Methods in Molecular Biology (Clifton, N.J.). 1480: 87-97. PMID 27659977 DOI: 10.1007/978-1-4939-6380-5_8  0.456
2016 Rutenberg-Schoenberg M, Sexton AN, Simon MD. The Properties of Long Noncoding RNAs that Regulate Chromatin. Annual Review of Genomics and Human Genetics. PMID 27147088 DOI: 10.1146/Annurev-Genom-090314-024939  0.41
2016 Simon MD. Insight into lncRNA biology using hybridization capture analyses. Biochimica Et Biophysica Acta. 1859: 121-7. PMID 26381323 DOI: 10.1016/J.Bbagrm.2015.09.004  0.349
2015 Fang R, Moss WN, Rutenberg-Schoenberg M, Simon MD. Probing Xist RNA Structure in Cells Using Targeted Structure-Seq. Plos Genetics. 11: e1005668. PMID 26646615 DOI: 10.1371/Journal.Pgen.1005668  0.36
2015 Duffy EE, Rutenberg-Schoenberg M, Stark CD, Kitchen RR, Gerstein MB, Simon MD. Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry. Molecular Cell. 59: 858-66. PMID 26340425 DOI: 10.1016/J.Molcel.2015.07.023  0.307
2014 West JA, Davis CP, Sunwoo H, Simon MD, Sadreyev RI, Wang PI, Tolstorukov MY, Kingston RE. The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. Molecular Cell. 55: 791-802. PMID 25155612 DOI: 10.1016/J.Molcel.2014.07.012  0.708
2014 Alpatov R, Lesch BJ, Nakamoto-Kinoshita M, Blanco A, Chen S, Stützer A, Armache KJ, Simon MD, Xu C, Ali M, Murn J, Prisic S, Kutateladze TG, Vakoc CR, Min J, et al. A chromatin-dependent role of the fragile X mental retardation protein FMRP in the DNA damage response. Cell. 157: 869-81. PMID 24813610 DOI: 10.1016/J.Cell.2014.03.040  0.605
2013 Simon MD, Pinter SF, Fang R, Sarma K, Rutenberg-Schoenberg M, Bowman SK, Kesner BA, Maier VK, Kingston RE, Lee JT. High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature. 504: 465-9. PMID 24162848 DOI: 10.1038/Nature12719  0.53
2013 Bowman SK, Simon MD, Deaton AM, Tolstorukov M, Borowsky ML, Kingston RE. Multiplexed Illumina sequencing libraries from picogram quantities of DNA. Bmc Genomics. 14: 466. PMID 23837789 DOI: 10.1186/1471-2164-14-466  0.581
2013 Simon MD. Capture hybridization analysis of RNA targets (CHART). Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 21.25.. PMID 23288463 DOI: 10.1002/0471142727.Mb2125S101  0.454
2013 Fang R, Chen F, Dong Z, Hu D, Barbera AJ, Clark EA, Fang J, Yang Y, Mei P, Rutenberg M, Li Z, Zhang Y, Xu Y, Yang H, Wang P, ... Simon MD, et al. LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Molecular Cell. 49: 558-70. PMID 23260659 DOI: 10.1016/J.Molcel.2012.11.019  0.602
2012 Simon MD, Shokat KM. A method to site-specifically incorporate methyl-lysine analogues into recombinant proteins. Methods in Enzymology. 512: 57-69. PMID 22910202 DOI: 10.1016/B978-0-12-391940-3.00003-2  0.587
2011 Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE. The genomic binding sites of a noncoding RNA. Proceedings of the National Academy of Sciences of the United States of America. 108: 20497-502. PMID 22143764 DOI: 10.1073/Pnas.1113536108  0.621
2011 Canzio D, Chang EY, Shankar S, Kuchenbecker KM, Simon MD, Madhani HD, Narlikar GJ, Al-Sady B. Chromodomain-mediated oligomerization of HP1 suggests a nucleosome-bridging mechanism for heterochromatin assembly. Molecular Cell. 41: 67-81. PMID 21211724 DOI: 10.1016/J.Molcel.2010.12.016  0.639
2010 Simon MD. Installation of site-specific methylation into histones using methyl lysine analogs. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 21.18.1-10. PMID 20373501 DOI: 10.1002/0471142727.Mb2118S90  0.451
2009 Shen X, Kim W, Fujiwara Y, Simon MD, Liu Y, Mysliwiec MR, Yuan GC, Lee Y, Orkin SH. Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell. 139: 1303-14. PMID 20064376 DOI: 10.1016/J.Cell.2009.12.003  0.355
2009 Francis NJ, Follmer NE, Simon MD, Aghia G, Butler JD. Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro. Cell. 137: 110-22. PMID 19303136 DOI: 10.1016/J.Cell.2009.02.017  0.716
2009 Hung T, Binda O, Champagne KS, Kuo AJ, Johnson K, Chang HY, Simon MD, Kutateladze TG, Gozani O. ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation. Molecular Cell. 33: 248-56. PMID 19187765 DOI: 10.1016/J.Molcel.2008.12.016  0.412
2009 Li B, Jackson J, Simon MD, Fleharty B, Gogol M, Seidel C, Workman JL, Shilatifard A. Histone H3 lysine 36 dimethylation (H3K36me2) is sufficient to recruit the Rpd3s histone deacetylase complex and to repress spurious transcription. The Journal of Biological Chemistry. 284: 7970-6. PMID 19155214 DOI: 10.1074/Jbc.M808220200  0.609
2008 Lu X, Simon MD, Chodaparambil JV, Hansen JC, Shokat KM, Luger K. The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Nature Structural & Molecular Biology. 15: 1122-4. PMID 18794842 DOI: 10.1038/Nsmb.1489  0.594
2008 Simon MD, Shokat KM. Engineering Control Over Protein Function Using Chemistry: Revealing Biological Specificity by Engineering Protein-Ligand Interactions Chemical Biology: From Small Molecules to Systems Biology and Drug Design, Volume 1-3. 1: 115-139. DOI: 10.1002/9783527619375.ch3a  0.401
2007 de la Cruz CC, Kirmizis A, Simon MD, Isono K, Koseki H, Panning B. The polycomb group protein SUZ12 regulates histone H3 lysine 9 methylation and HP1 alpha distribution. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 15: 299-314. PMID 17406994 DOI: 10.1007/S10577-007-1126-1  0.321
2007 Simon MD, Chu F, Racki LR, de la Cruz CC, Burlingame AL, Panning B, Narlikar GJ, Shokat KM. The site-specific installation of methyl-lysine analogs into recombinant histones. Cell. 128: 1003-12. PMID 17350582 DOI: 10.1016/j.cell.2006.12.041  0.689
2006 Simon MD, Feldman ME, Rauh D, Maris AE, Wemmer DE, Shokat KM. Structure and properties of a re-engineered homeodomain protein-DNA interface. Acs Chemical Biology. 1: 755-60. PMID 17240973 DOI: 10.1021/Cb6003756  0.717
2006 Magarvey NA, Beck ZQ, Simon MD, Feldman ME, Rosivatz E, Pokharel S. Introduction to Our Authors Acs Chemical Biology. 1: 728-729. DOI: 10.1021/Cb600482X  0.551
2004 Sato K, Simon MD, Levin AM, Shokat KM, Weiss GA. Dissecting the Engrailed homeodomain-DNA interaction by phage-displayed shotgun scanning. Chemistry & Biology. 11: 1017-23. PMID 15271360 DOI: 10.1016/J.Chembiol.2004.05.008  0.537
2004 Simon MD, Sato K, Weiss GA, Shokat KM. A phage display selection of engrailed homeodomain mutants and the importance of residue Q50. Nucleic Acids Research. 32: 3623-31. PMID 15247345 DOI: 10.1093/Nar/Gkh690  0.547
2004 Simon MD, Shokat KM. Adaptability at a protein-DNA interface: re-engineering the engrailed homeodomain to recognize an unnatural nucleotide. Journal of the American Chemical Society. 126: 8078-9. PMID 15225024 DOI: 10.1021/Ja048113W  0.543
1998 Berlin K, Jain RK, Simon MD, Richert C. A Porphyrin Embedded in DNA The Journal of Organic Chemistry. 63: 1527-1535. DOI: 10.1021/Jo9718051  0.366
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