My Bibliography

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Link CN, Thalalla Gamage S, Gallimore D, Kopajtich R, Evans C, Nance S, Fox SD, Andresson T, Chari R, Ivanic J, Prokisch H, Meier JL. Protonation-Dependent Sequencing of 5-Formylcytidine in RNA. Biochemistry. 2022 Apr 5;61(7):535-544. doi: 10.1021/acs.biochem.1c00761. Epub 2022 Mar 14. PubMed PMID: 35285626; PubMed Central PMCID: PMC10518769.

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Bartee D, Nance KD, Meier JL. Site-Specific Synthesis of N(4)-Acetylcytidine in RNA Reveals Physiological Duplex Stabilization. J Am Chem Soc. 2022 Mar 2;144(8):3487-3496. doi: 10.1021/jacs.1c11985. Epub 2022 Feb 16. PubMed PMID: 35172571.

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Nance KD, Gamage ST, Alam MM, Yang A, Levy MJ, Link CN, Florens L, Washburn MP, Gu S, Oppenheim JJ, Meier JL. Cytidine acetylation yields a hypoinflammatory synthetic messenger RNA. Cell Chem Biol. 2022 Feb 17;29(2):312-320.e7. doi: 10.1016/j.chembiol.2021.07.003. Epub 2021 Aug 25. PubMed PMID: 35180432; PubMed Central PMCID: PMC10370389.

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Müller S, Ackloo S, Al Chawaf A, Al-Lazikani B, Antolin A, Baell JB, Beck H, Beedie S, Betz UAK, Bezerra GA, Brennan PE, Brown D, Brown PJ, Bullock AN, Carter AJ, Chaikuad A, Chaineau M, Ciulli A, Collins I, Dreher J, Drewry D, Edfeldt K, Edwards AM, Egner U, Frye SV, Fuchs SM, Hall MD, Hartung IV, Hillisch A, Hitchcock SH, Homan E, Kannan N, Kiefer JR, Knapp S, Kostic M, Kubicek S, Leach AR, Lindemann S, Marsden BD, Matsui H, Meier JL, Merk D, Michel M, Morgan MR, Mueller-Fahrnow A, Owen DR, Perry BG, Rosenberg SH, Saikatendu KS, Schapira M, Scholten C, Sharma S, Simeonov A, Sundström M, Superti-Furga G, Todd MH, Tredup C, Vedadi M, von Delft F, Willson TM, Winter GE, Workman P, Arrowsmith CH. Target 2035 - update on the quest for a probe for every protein. RSC Med Chem. 2022 Jan 27;13(1):13-21. doi: 10.1039/d1md00228g. eCollection 2022 Jan 27. PubMed PMID: 35211674; PubMed Central PMCID: PMC8792830.

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Jing Y, Bergholtz SE, Omole A, Kulkarni RA, Zengeya TT, Yoo E, Meier JL. Synthesis and Evaluation of a Stable Isostere of Malonyllysine. Chembiochem. 2022 Jan 5;23(1):e202100491. doi: 10.1002/cbic.202100491. Epub 2021 Nov 5. PubMed PMID: 34652056; PubMed Central PMCID: PMC10262540.

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Jhulki I, Meier JL. Enzymatic Catalysts to Combat COVID-19. ACS Cent Sci. 2021 Dec 22;7(12):1963-1965. doi: 10.1021/acscentsci.1c01356. Epub 2021 Nov 22. PubMed PMID: 34963888; PubMed Central PMCID: PMC8704042.

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Thalalla Gamage S, Meier JL. Activity-based profiling in RNA. Nat Chem Biol. 2021 Nov;17(11):1121-1122. doi: 10.1038/s41589-021-00879-3. PubMed PMID: 34675421.

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Bartee D, Thalalla Gamage S, Link CN, Meier JL. Arrow pushing in RNA modification sequencing. Chem Soc Rev. 2021 Sep 7;50(17):9482-9502. doi: 10.1039/d1cs00214g. Epub 2021 Jul 14. Review. PubMed PMID: 34259263.

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Shrimp JH, Jing Y, Gamage ST, Nelson KM, Han J, Bryson KM, Montgomery DC, Thomas JM, Nance KD, Sharma S, Fox SD, Andressen T, Sinclair WR, Wu H, Allali-Hassani A, Senisterra G, Vedadi M, Lafontaine D, Dahlin JL, Marmorstein R, Walters MA, Meier JL. Remodelin Is a Cryptic Assay Interference Chemotype That Does Not Inhibit NAT10-Dependent Cytidine Acetylation. ACS Med Chem Lett. 2021 Jun 10;12(6):887-892. doi: 10.1021/acsmedchemlett.0c00193. eCollection 2021 Jun 10. PubMed PMID: 34141066; PubMed Central PMCID: PMC8201477.

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Nance KD, Meier JL. Modifications in an Emergency: The Role of N1-Methylpseudouridine in COVID-19 Vaccines. ACS Cent Sci. 2021 May 26;7(5):748-756. doi: 10.1021/acscentsci.1c00197. Epub 2021 Apr 6. Review. PubMed PMID: 34075344; PubMed Central PMCID: PMC8043204.

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Lieberman WK, Jing Y, Meier JL. Chemical control of multidomain acetyltransferase activity. Cell Chem Biol. 2021 Apr 15;28(4):433-435. doi: 10.1016/j.chembiol.2021.03.015. PubMed PMID: 33861955.

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Thalalla Gamage S, Sas-Chen A, Schwartz S, Meier JL. Quantitative nucleotide resolution profiling of RNA cytidine acetylation by ac4C-seq. Nat Protoc. 2021 Apr;16(4):2286-2307. doi: 10.1038/s41596-021-00501-9. Epub 2021 Mar 26. PubMed PMID: 33772246; PubMed Central PMCID: PMC9103714.

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Jing Y, Montano JL, Levy M, Lopez JE, Kung PP, Richardson P, Krajewski K, Florens L, Washburn MP, Meier JL. Harnessing Ionic Selectivity in Acetyltransferase Chemoproteomic Probes. ACS Chem Biol. 2021 Jan 15;16(1):27-34. doi: 10.1021/acschembio.0c00766. Epub 2020 Dec 29. PubMed PMID: 33373188; PubMed Central PMCID: PMC9093059.

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Crooks DR, Maio N, Lang M, Ricketts CJ, Vocke CD, Gurram S, Turan S, Kim YY, Cawthon GM, Sohelian F, De Val N, Pfeiffer RM, Jailwala P, Tandon M, Tran B, Fan TW, Lane AN, Ried T, Wangsa D, Malayeri AA, Merino MJ, Yang Y, Meier JL, Ball MW, Rouault TA, Srinivasan R, Linehan WM. Mitochondrial DNA alterations underlie an irreversible shift to aerobic glycolysis in fumarate hydratase-deficient renal cancer. Sci Signal. 2021 Jan 5;14(664). doi: 10.1126/scisignal.abc4436. PubMed PMID: 33402335; PubMed Central PMCID: PMC8039187.

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Bryson KM, Thalalla-Gamage S, Meier JL. Visualizing RNA Cytidine Acetyltransferase Activity by Northern Blotting. Curr Protoc Chem Biol. 2020 Dec;12(4):e89. doi: 10.1002/cpch.89. PubMed PMID: 33275333.

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Perez M, Bak DW, Bergholtz SE, Crooks DR, Arimilli BS, Yang Y, Weerapana E, Linehan WM, Meier JL. Heterogeneous adaptation of cysteine reactivity to a covalent oncometabolite. J Biol Chem. 2020 Sep 25;295(39):13410-13418. doi: 10.1074/jbc.AC120.014993. Epub 2020 Aug 19. PubMed PMID: 32820045; PubMed Central PMCID: PMC7521642.

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Varner EL, Trefely S, Bartee D, von Krusenstiern E, Izzo L, Bekeova C, O'Connor RS, Seifert EL, Wellen KE, Meier JL, Snyder NW. Quantification of lactoyl-CoA (lactyl-CoA) by liquid chromatography mass spectrometry in mammalian cells and tissues. Open Biol. 2020 Sep;10(9):200187. doi: 10.1098/rsob.200187. Epub 2020 Sep 23. PubMed PMID: 32961073; PubMed Central PMCID: PMC7536085.

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Sas-Chen A, Thomas JM, Matzov D, Taoka M, Nance KD, Nir R, Bryson KM, Shachar R, Liman GLS, Burkhart BW, Gamage ST, Nobe Y, Briney CA, Levy MJ, Fuchs RT, Robb GB, Hartmann J, Sharma S, Lin Q, Florens L, Washburn MP, Isobe T, Santangelo TJ, Shalev-Benami M, Meier JL, Schwartz S. Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping. Nature. 2020 Jul;583(7817):638-643. doi: 10.1038/s41586-020-2418-2. Epub 2020 Jun 17. PubMed PMID: 32555463; PubMed Central PMCID: PMC8130014.

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Kung PP, Bingham P, Burke BJ, Chen Q, Cheng X, Deng YL, Dou D, Feng J, Gallego GM, Gehring MR, Grant SK, Greasley S, Harris AR, Maegley KA, Meier J, Meng X, Montano JL, Morgan BA, Naughton BS, Palde PB, Paul TA, Richardson P, Sakata S, Shaginian A, Sonnenburg WK, Subramanyam C, Timofeevski S, Wan J, Yan W, Stewart AE. Characterization of Specific N-α-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library. ACS Med Chem Lett. 2020 Jun 11;11(6):1175-1184. doi: 10.1021/acsmedchemlett.0c00029. eCollection 2020 Jun 11. PubMed PMID: 32550998; PubMed Central PMCID: PMC7294708.

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Bergholtz SE, Briney CA, Najera SS, Perez M, Linehan WM, Meier JL. An Oncometabolite Isomer Rapidly Induces a Pathophysiological Protein Modification. ACS Chem Biol. 2020 Apr 17;15(4):856-861. doi: 10.1021/acschembio.0c00044. Epub 2020 Apr 6. PubMed PMID: 32250583; PubMed Central PMCID: PMC8453589.

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Levy MJ, Montgomery DC, Sardiu ME, Montano JL, Bergholtz SE, Nance KD, Thorpe AL, Fox SD, Lin Q, Andresson T, Florens L, Washburn MP, Meier JL. A Systems Chemoproteomic Analysis of Acyl-CoA/Protein Interaction Networks. Cell Chem Biol. 2020 Mar 19;27(3):322-333.e5. doi: 10.1016/j.chembiol.2019.11.011. Epub 2019 Dec 10. PubMed PMID: 31836350; PubMed Central PMCID: PMC8237707.

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Kulkarni RA, Montgomery DC, Meier JL. Epigenetic regulation by endogenous metabolite pharmacology. Curr Opin Chem Biol. 2019 Aug;51:30-39. doi: 10.1016/j.cbpa.2019.02.002. Epub 2019 Mar 15. Review. PubMed PMID: 30884380; PubMed Central PMCID: PMC6698396.

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Kulkarni RA, Bak DW, Wei D, Bergholtz SE, Briney CA, Shrimp JH, Alpsoy A, Thorpe AL, Bavari AE, Crooks DR, Levy M, Florens L, Washburn MP, Frizzell N, Dykhuizen EC, Weerapana E, Linehan WM, Meier JL. A chemoproteomic portrait of the oncometabolite fumarate. Nat Chem Biol. 2019 Apr;15(4):391-400. doi: 10.1038/s41589-018-0217-y. Epub 2019 Feb 4. PubMed PMID: 30718813; PubMed Central PMCID: PMC6430658.

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Thomas JM, Batista PJ, Meier JL. Metabolic Regulation of the Epitranscriptome. ACS Chem Biol. 2019 Mar 15;14(3):316-324. doi: 10.1021/acschembio.8b00951. Epub 2019 Feb 1. Review. PubMed PMID: 30653309.

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Briney CA, Najera S, Meier JL. Bioorthogonal oncometabolite ligation. Methods Enzymol. 2019;622:431-448. doi: 10.1016/bs.mie.2019.02.037. Epub 2019 Mar 14. PubMed PMID: 31155064; PubMed Central PMCID: PMC8195447.

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Thomas JM, Bryson KM, Meier JL. Nucleotide resolution sequencing of N4-acetylcytidine in RNA. Methods Enzymol. 2019;621:31-51. doi: 10.1016/bs.mie.2019.02.022. Epub 2019 Mar 12. PubMed PMID: 31128786; PubMed Central PMCID: PMC8194367.

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Parida M, Nilson KA, Li M, Ball CB, Fuchs HA, Lawson CK, Luse DS, Meier JL, Price DH. Nucleotide Resolution Comparison of Transcription of Human Cytomegalovirus and Host Genomes Reveals Universal Use of RNA Polymerase II Elongation Control Driven by Dissimilar Core Promoter Elements. mBio. 2019 Feb 12;10(1). doi: 10.1128/mBio.02047-18. PubMed PMID: 30755505; PubMed Central PMCID: PMC6372792.

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Kulkarni RA, Briney CA, Crooks DR, Bergholtz SE, Mushti C, Lockett SJ, Lane AN, Fan TW, Swenson RE, Marston Linehan W, Meier JL. Photoinducible Oncometabolite Detection. Chembiochem. 2019 Feb 1;20(3):360-365. doi: 10.1002/cbic.201800651. Epub 2018 Dec 13. PubMed PMID: 30358041; PubMed Central PMCID: PMC8141106.

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Arango D, Sturgill D, Alhusaini N, Dillman AA, Sweet TJ, Hanson G, Hosogane M, Sinclair WR, Nanan KK, Mandler MD, Fox SD, Zengeya TT, Andresson T, Meier JL, Coller J, Oberdoerffer S. Acetylation of Cytidine in mRNA Promotes Translation Efficiency. Cell. 2018 Dec 13;175(7):1872-1886.e24. doi: 10.1016/j.cell.2018.10.030. Epub 2018 Nov 15. PubMed PMID: 30449621; PubMed Central PMCID: PMC6295233.

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Bruning U, Morales-Rodriguez F, Kalucka J, Goveia J, Taverna F, Queiroz KCS, Dubois C, Cantelmo AR, Chen R, Loroch S, Timmerman E, Caixeta V, Bloch K, Conradi LC, Treps L, Staes A, Gevaert K, Tee A, Dewerchin M, Semenkovich CF, Impens F, Schilling B, Verdin E, Swinnen JV, Meier JL, Kulkarni RA, Sickmann A, Ghesquière B, Schoonjans L, Li X, Mazzone M, Carmeliet P. Impairment of Angiogenesis by Fatty Acid Synthase Inhibition Involves mTOR Malonylation. Cell Metab. 2018 Dec 4;28(6):866-880.e15. doi: 10.1016/j.cmet.2018.07.019. Epub 2018 Aug 23. PubMed PMID: 30146486; PubMed Central PMCID: PMC8057116.

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Thomas JM, Briney CA, Nance KD, Lopez JE, Thorpe AL, Fox SD, Bortolin-Cavaille ML, Sas-Chen A, Arango D, Oberdoerffer S, Cavaille J, Andresson T, Meier JL. A Chemical Signature for Cytidine Acetylation in RNA. J Am Chem Soc. 2018 Oct 10;140(40):12667-12670. doi: 10.1021/jacs.8b06636. Epub 2018 Sep 25. PubMed PMID: 30252461; PubMed Central PMCID: PMC8054311.

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Cha J, Nani RR, Luciano MP, Kline G, Broch A, Kim K, Namgoong JM, Kulkarni RA, Meier JL, Kim P, Schnermann MJ. A chemically stable fluorescent marker of the ureter. Bioorg Med Chem Lett. 2018 Sep 1;28(16):2741-2745. doi: 10.1016/j.bmcl.2018.02.040. Epub 2018 Feb 24. PubMed PMID: 29510880; PubMed Central PMCID: PMC6437767.

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Shrimp JH, Garlick JM, Tezil T, Sorum AW, Worth AJ, Blair IA, Verdin E, Snyder NW, Meier JL. Defining Metabolic and Nonmetabolic Regulation of Histone Acetylation by NSAID Chemotypes. Mol Pharm. 2018 Mar 5;15(3):729-736. doi: 10.1021/acs.molpharmaceut.7b00943. Epub 2017 Dec 29. PubMed PMID: 29240439; PubMed Central PMCID: PMC6320251.

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Meier JL, Schnermann MJ. Pharmacology by Chemical Biology. Mol Pharm. 2018 Mar 5;15(3):703-704. doi: 10.1021/acs.molpharmaceut.8b00067. PubMed PMID: 29502427; PubMed Central PMCID: PMC6346420.

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Shrimp JH, Grose C, Widmeyer SRT, Thorpe AL, Jadhav A, Meier JL. Chemical Control of a CRISPR-Cas9 Acetyltransferase. ACS Chem Biol. 2018 Feb 16;13(2):455-460. doi: 10.1021/acschembio.7b00883. Epub 2018 Jan 17. PubMed PMID: 29309117; PubMed Central PMCID: PMC6320253.

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Sinclair WR, Shrimp JH, Zengeya TT, Kulkarni RA, Garlick JM, Luecke H, Worth AJ, Blair IA, Snyder NW, Meier JL. Bioorthogonal pro-metabolites for profiling short chain fatty acylation. Chem Sci. 2018 Feb 7;9(5):1236-1241. doi: 10.1039/c7sc00247e. eCollection 2018 Feb 7. PubMed PMID: 29675169; PubMed Central PMCID: PMC5885804.

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Sinclair WR, Arango D, Shrimp JH, Zengeya TT, Thomas JM, Montgomery DC, Fox SD, Andresson T, Oberdoerffer S, Meier JL. Profiling Cytidine Acetylation with Specific Affinity and Reactivity. ACS Chem Biol. 2017 Dec 15;12(12):2922-2926. doi: 10.1021/acschembio.7b00734. Epub 2017 Oct 17. PubMed PMID: 29039931; PubMed Central PMCID: PMC7900898.

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Dahlin JL, Nelson KM, Strasser JM, Barsyte-Lovejoy D, Szewczyk MM, Organ S, Cuellar M, Singh G, Shrimp JH, Nguyen N, Meier JL, Arrowsmith CH, Brown PJ, Baell JB, Walters MA. Assay interference and off-target liabilities of reported histone acetyltransferase inhibitors. Nat Commun. 2017 Nov 15;8(1):1527. doi: 10.1038/s41467-017-01657-3. PubMed PMID: 29142305; PubMed Central PMCID: PMC5688144.

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Carrer A, Parris JLD, Trefely S, Henry RA, Montgomery DC, Torres A, Viola JM, Kuo YM, Blair IA, Meier JL, Andrews AJ, Snyder NW, Wellen KE. Impact of a High-fat Diet on Tissue Acyl-CoA and Histone Acetylation Levels. J Biol Chem. 2017 Feb 24;292(8):3312-3322. doi: 10.1074/jbc.M116.750620. Epub 2017 Jan 11. PubMed PMID: 28077572; PubMed Central PMCID: PMC5336165.

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Kulkarni RA, Worth AJ, Zengeya TT, Shrimp JH, Garlick JM, Roberts AM, Montgomery DC, Sourbier C, Gibbs BK, Mesaros C, Tsai YC, Das S, Chan KC, Zhou M, Andresson T, Weissman AM, Linehan WM, Blair IA, Snyder NW, Meier JL. Discovering Targets of Non-enzymatic Acylation by Thioester Reactivity Profiling. Cell Chem Biol. 2017 Feb 16;24(2):231-242. doi: 10.1016/j.chembiol.2017.01.002. Epub 2017 Feb 2. PubMed PMID: 28163016; PubMed Central PMCID: PMC5864104.

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Zengeya TT, Garlick JM, Kulkarni RA, Miley M, Roberts AM, Yang Y, Crooks DR, Sourbier C, Linehan WM, Meier JL. Co-opting a Bioorthogonal Reaction for Oncometabolite Detection. J Am Chem Soc. 2016 Dec 14;138(49):15813-15816. doi: 10.1021/jacs.6b09706. Epub 2016 Nov 30. PubMed PMID: 27960310; PubMed Central PMCID: PMC6377280.

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Barajas JF, Finzel K, Valentic TR, Shakya G, Gamarra N, Martinez D, Meier JL, Vagstad AL, Newman AG, Townsend CA, Burkart MD, Tsai SC. Structural and Biochemical Analysis of Protein-Protein Interactions Between the Acyl-Carrier Protein and Product Template Domain. Angew Chem Int Ed Engl. 2016 Oct 10;55(42):13005-13009. doi: 10.1002/anie.201605401. PubMed PMID: 27653519; PubMed Central PMCID: PMC5161458.

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Shirakawa K, Wang L, Man N, Maksimoska J, Sorum AW, Lim HW, Lee IS, Shimazu T, Newman JC, Schröder S, Ott M, Marmorstein R, Meier J, Nimer S, Verdin E. Salicylate, diflunisal and their metabolites inhibit CBP/p300 and exhibit anticancer activity. Elife. 2016 May 31;5. doi: 10.7554/eLife.11156. PubMed PMID: 27244239; PubMed Central PMCID: PMC4931907.

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Montgomery DC, Garlick JM, Kulkarni RA, Kennedy S, Allali-Hassani A, Kuo YM, Andrews AJ, Wu H, Vedadi M, Meier JL. Global Profiling of Acetyltransferase Feedback Regulation. J Am Chem Soc. 2016 May 25;138(20):6388-91. doi: 10.1021/jacs.6b03036. Epub 2016 May 17. PubMed PMID: 27149119; PubMed Central PMCID: PMC6320254.

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Sorum AW, Shrimp JH, Roberts AM, Montgomery DC, Tiwari NK, Lal-Nag M, Simeonov A, Jadhav A, Meier JL. Microfluidic Mobility Shift Profiling of Lysine Acetyltransferases Enables Screening and Mechanistic Analysis of Cellular Acetylation Inhibitors. ACS Chem Biol. 2016 Mar 18;11(3):734-41. doi: 10.1021/acschembio.5b00709. Epub 2015 Oct 14. PubMed PMID: 26428393; PubMed Central PMCID: PMC6320249.

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Day CR, Chen H, Coulon A, Meier JL, Larson DR. High-throughput single-molecule screen for small-molecule perturbation of splicing and transcription kinetics. Methods. 2016 Mar 1;96:59-68. doi: 10.1016/j.ymeth.2015.11.025. Epub 2015 Nov 30. PubMed PMID: 26655523; PubMed Central PMCID: PMC4766052.

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Montgomery DC, Meier JL. Mapping Lysine Acetyltransferase-Ligand Interactions by Activity-Based Capture. Methods Enzymol. 2016;574:105-123. doi: 10.1016/bs.mie.2016.01.006. Epub 2016 Feb 16. PubMed PMID: 27423859.

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Shrimp JH, Sorum AW, Garlick JM, Guasch L, Nicklaus MC, Meier JL. Characterizing the Covalent Targets of a Small Molecule Inhibitor of the Lysine Acetyltransferase P300. ACS Med Chem Lett. 2016 Feb 11;7(2):151-5. doi: 10.1021/acsmedchemlett.5b00385. eCollection 2016 Feb 11. PubMed PMID: 26985290; PubMed Central PMCID: PMC4753543.

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Montgomery DC, Sorum AW, Guasch L, Nicklaus MC, Meier JL. Metabolic Regulation of Histone Acetyltransferases by Endogenous Acyl-CoA Cofactors. Chem Biol. 2015 Aug 20;22(8):1030-1039. doi: 10.1016/j.chembiol.2015.06.015. Epub 2015 Jul 16. PubMed PMID: 26190825; PubMed Central PMCID: PMC4546520.

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Zengeya TT, Kulkarni RA, Meier JL. Modular synthesis of cell-permeating 2-ketoglutarate esters. Org Lett. 2015 May 15;17(10):2326-9. doi: 10.1021/acs.orglett.5b00737. Epub 2015 Apr 27. PubMed PMID: 25915096; PubMed Central PMCID: PMC6320255.