Publications

Peer-Reviewed Publications:

1. • 1. Targeting a pathogenic cryptic exon that drives HLRCC to induce exon skipping.
        Maligireddy SS*, Mandler MD*, Lunger JC, Yuen M, Kulkarni S, Perez AR, Fitzsimmons CM, Crooks DR, Chari R, Linehan WM, Batista PJ. Molecular Therapy Nucleic Acids. Volume 36, Sept. 2025. 

     2. Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma.
        Fitzsimmons CM, Mandler MD, Lunger JC, Chan D, Maligireddy SS, Schmiechen AC, Thalalla Gamage S, Link C, Jenkins LM, Crooks DR, Meier JL, Linehan WM, and Batista PJ. 2024 NAR Cancer. 6(1) 2024 zcae004.

     3. The methyltransferases METTL7A and METTL7B confer resistance to thiol-based histone deacetylase inhibitors in cancer cells.
        Robey RW*, Fitzsimmons CM*, Guiblet WM, Frye WJE, Gonzalez Dalmasy J, Wang L, Huff LM, Ali-Fahmani F, Lipsey CC, Wade HM, Mitchell AV, Maligireddy SS, Jenkins LM, Nikitina T, Zhurkin VB, Piscopio AD, Bates SE, Arda HE, Gottesman MM, Batista PJ. 2024 Molecular Cancer Therapeutics. 23 (4): 464–477.

     4. The modification landscape of P. aeruginosa tRNAs.
        Mandler MD, Maligireddy SS, Guiblet WM, Fitzsimmons CM, McDonald KS, Warrell DL, Batista PJ. 2024. RNA. 30(8) 1025-1040. 

     5. The thiol methyltransferase activity of TMT1A (METTL7A) is conserved across species.
        Gonzalez-Dalmasy J, Fitzsimmons CM, Frye WJ, Perciaccante AJ, Jewell CP, Jenkins LM, Batista PJ, Robey RW, Gottesman MM. 2024. Chem. Biol. Interact. vol. 394, 110989.

     6. Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.
        Bryce-Smith S*, Burri D*, Gazzara MR*, Herrmann CJ*, Danecka W^^, Fitzsimmons CM^^, Wan YK^^, Zhuang F^^, Fansler MM, Fernández JM, Ferret M, Gonzalez-Uriarte A, Haynes S, Herdman C, Kanitz A, Katsantoni M, Marini F, McDonnel E, Nicolet B, Poon C, Rot G, Schärfen L, Wu PJ, Yoon Y, Barash Y, Zavolan M. 2023. RNA. 29: 1839-1855.

     7. Cryptic splice mutation in the fumarate hydratase gene in patients with clinical manifestations of hereditary leiomyomatosis and renal cell cancer (HLRCC). Crooks DR, Cawthon GM, Fitzsimmons CM, Perez, M, Ricketts CJ, Vocke CD, Yang Y, Middleton L, Neilsen D, Schmidt LS, Tandon M, Merino MJ, Ball MW, Meier JL, Batista PJ, Linehan WM. 2023. Human Molecular Genetics, 32(22) 3135–3145.

     8. Dual inhibition of histone deacetylases and the mechanistic target of rapamycin promotes apoptosis in cell line models of uveal melanoma.
        Patel RP, Thomas JR, Curt KM, Fitzsimmons CM, Batista PJ, Bates SE, Gottesman MM, Robey RW. 2021. Investigative Ophthalmology and Visual Sciences. Vol.62, 16.

     9. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs
        Kundert K,  Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes, BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T. Nature Communications. 2019. (10) Article number: 2127

     10. Determinants of tRNA Recognition by the Radical SAM Enzyme RlmN
         Fitzsimmons CM and Fujimori DG. PLoS One. 2016. 11(11): e0167298. 

Reviews, Commentaries, and Opinions:

1. Invest in science, invest in the future
   Fitzsimmons CM. The Sentinel. Published 30 June 2025. 

2. Ten simple rules for acing virtual interviews.
   Chan D* Fitzsimmons CM*#, Mandler MD, Batista PJ#. PLoS Comput Biol 2020. 17(6): e1009057

3. It’s complicated…m6A-dependent regulation of gene expression in cancer.
   Fitzsimmons CM and Batista PJ. BBA Gene Regulatory Mechanisms. 2019. 1862, 3, 382-393.