*Co-corresponding author; ¹co-first author

[27] Bose R, Saleem I, Mustoe AM. Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states. Cell Chem Biol. 2024 Jan 18;31(1):17-35. doi: 10.1016/j.chembiol.2023.12.010. Epub 2024 Jan 9. PMID: 38199037; PMCID: PMC10842484. (link)

[26] Mitchell D, Cotter J, Saleem I, Mustoe AM. Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS. bioRxiv [Preprint]. 2023 Apr 11:2023.04.10.536308. doi: 10.1101/2023.04.10.536308. PMID: 37090560; PMCID: PMC10120657. (link | pdf)

[25] Mustoe AM, Weidmann CA, Weeks KM. Single-Molecule Correlated Chemical Probing: A Revolution in RNA Structure Analysis. Acc Chem Res. 2023 Apr 4;56(7):763-775 (link | pdf)

[24] J. Kumar, L. Lackey, J.M. Waldern, A. Dey, A.M. Mustoe, K.M. Weeks, D.H. Mathews, A. Laederach. Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. eLife, 2022, 11:e73888 (link | pdf)

[22] C.A. Weidmann, A.M. Mustoe, P.B. Jariwala, J.M. Calabrese, K.M. Weeks. Analysis of RNA–protein networks with RNP-MaP defines functional hubs on RNA. Nature Biotechnol., 2021, 39:347-356 (link | pdf).

[21] R.S. Dhindsa, B.R. Copeland, A.M. Mustoe, D.B. Goldstein. Natural selection shapes codon usage in the human genome. Am. J. Hum. Genet., 2020, 107: 83-95 (link | pdf)

[19] A.M. Mustoe*, M. Corley, A. Laederach, and K.M. Weeks*. mRNA structure regulates translation initiation: A mechanism exploited from bacteria to humans. Biochemistry, 2018, 57: 3537-3539. (link | pdf)

[18] A.M. Mustoe*¹, S. Busan¹, G.M. Rice¹, C.E. Hajdin, B.K. Peterson, V.M. Ruda, N. Kubica, R. Nutiu, J.L. Baryza, and K.M. Weeks*. Pervasive regulatory functions of mRNA structure revealed by high-resolution SHAPE probing. Cell, 2018, 173: 181-195. (link | pdf)

Highlighted in: C&EN, Biocentury Innovations, and Nature Chemical Biology

[17] M. Corley, A. Solem, G. Phillips, L. Lackey, B. Ziehr, H.A. Vincent, A.M. Mustoe, S.B.V. Ramos, K.M. Weeks, N.J. Moorman, and A. Laederach. An RNA structure-mediated, post-transcriptional model of human a-1-antitrypsin expression. Proc. Natl. Acad. Sci. U.S.A., 2017, 114: E10244-E10253. (link | pdf)

[16] M. Daher¹, A.M. Mustoe¹, A. Morriss-Andrews¹, C. L. Brooks III, and N. G. Walter. Tuning RNA folding and function through rational design of junction topology. Nucleic Acids Res., 2017, 45: 9706-9715. (link | pdf)

[15] A. Krokhotin¹, A.M. Mustoe¹, K. M. Weeks, and N. V. Dokholyan. Direct identification of base-paired RNA nucleotides by correlated chemical probing. RNA, 2017, 23: 6-13. (link | pdf)

[14] C. A. Weidman¹, A.M. Mustoe¹, and K. M. Weeks. Direct duplex detection: an emerging tool in the RNA structural analysis toolbox. Trends Biochem. Sci, 2016, 41: 734-736. (link | pdf)

[13] A.M. Mustoe, H. M. Al-Hashimi, C. L. Brooks III. Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme. Nucleic Acids Res., 2016, 44:402-412. (link | pdf)

[12] A.M. Mustoe, X. Liu, P. Lin, H. M. Al-Hashimi, C. A. Fierke, and C. L. Brooks III. Noncanonical secondary structure stabilizes human mitochondrial tRNASer(UCN) by reducing the entropic cost of tertiary folding. J. Amer. Chem. Soc., 2015, 137: 3592–3599. (link | pdf)

[11] A. Dickson, A.M. Mustoe, L. Salmon, and C.L. Brooks III. Efficient in-silico exploration of RNA interhelical conformations using Euler angles and WExplore. Nucleic Acids Res., 2014, 42: 12126- 12137. (link | pdf)

[10] A.M. Mustoe, C.L. Brooks III, and H.M. Al-Hashimi. Topological constraints are major determinants of tRNA tertiary structure and provide basis for tertiary folding cooperativity. Nucleic Acids Res., 2014, 42: 11792-11804. (link | pdf)

[9] L. R. Ganser, A.M. Mustoe, and H. M. Al-Hashimi. An RNA tertiary switch by modifying how helices are tethered. Genome Biol., 2014, 15: 425-428. (link | pdf)

[8] A.M. Mustoe, C. L. Brooks III, and H. M. Al-Hashimi. Hierarchy of RNA functional dynamics. Annu. Rev. Biochem., 2014, 83: 441-466. (link | pdf)

[7] A.M. Mustoe, H. M. Al-Hashimi, and C. L. Brooks III. Coarse-grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges. J. Phys. Chem. B., 2014, 118: 2615–27. (link | pdf)

[6] K. C. Suddala, A. J. Rinaldi, J. Feng, A.M. Mustoe, C. D. Eichhorn, J. A. Liberman, J. E. Wedekind, H. M. Al-Hashimi, C. L. Brooks III, and N. G. Walter. Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Res., 2013, 41: 10462-75. (link | pdf)

[5] A. R. Pah, R. Guimerà, A.M. Mustoe, and L. A. N. Amaral. Use of a global metabolic network to curate organismal metabolic networks. Sci. Rep., 2013, 3: 1695. (link | pdf)

[4] E. A. Dethoff, J. Chugh, A.M. Mustoe, and H. M. Al-Hashimi. Functional complexity and regulation through RNA dynamics. Nature, 2012, 482:322-330. (link | pdf)

[3] A.M. Mustoe, M. H. Bailor, R. Teixeira, C. L. Brooks III, and H. M. Al-Hashimi. New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation. Nucleic Acids Res., 2012, 40: 892-904. (link | pdf)

[2] M. H. Bailor¹, A.M. Mustoe¹, C. L. Brooks III, and H. M. Al-Hashimi. 3D maps of RNA interhelical junctions. Nature Protoc., 2011, 6:1536-45. (link | pdf)

[1] M. H. Bailor, A.M. Mustoe, C. L. Brooks III, and H. M. Al-Hashimi. Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. Curr. Opin. Struct. Biol., 2011, 21:296-305. (link | pdf)