Publications

Arrakis Publication

“PEARL-seq: A Photoaffinity Platform for the Analysis of Small Molecule-RNA Interactions” Mukherjee, H., Blain, J.C., Vandivier, L.E, Chin, D.N., Friedman, J.E., Liu, F., Maillet, A., Fang, C., Kaplan, J. B., Li, J., Chenoweth, D.M., Christensen, A.B., Petersen, L.K., Vest Hansen, N.J., Barrera, L., Kubica, N., Gnanasambandam Kumaravel, G., Petter, J.C., ACS Chem. Biol. 2020, 15, 9, 2374–2381, published online August 17, 2020.

Key publications by leaders in the RNA field

“Evidence for Ligandable Sites in Structured RNA Throughout the Protein Data Bank” Hewitt, William M., et al., Bioorganic & Medicinal Chemistry, published online April 6, 2019.

“Messenger RNA Structure Regulates Translation Initiation: A Mechanism Exploited from Bacteria to Humans” Weeks, et al., Biochemistry 2018, 57 (26), 3537–3539.

“Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing” Mustoe, et al., Cell 2018, 173, 1-15.

“The Emerging Role of RNA as a Therapeutic Target for Small Molecules” Connelly et al., Cell Chemical Biology 2016, 23, 1077-1090.

“Modulation of the E. coli rpoH Temperature Sensor with Triptycene-Based Small Molecules” Barros et al., Angew. Chem. Int. Ed. 2016, 55, 8258-8261.

“Approaches to Validate and Manipulate RNA Targets with Small Molecules in Cells” Childs-Disney & Disney, Ann. Rev. Pharm. Tox. 2016, 56, 123-140.

“Toward All RNA Structures, Concisely” Weeks, Biopolymers 2016, 103, 138-148.

“SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice” Palacino et al., Nat. Chem. Bio. 2015, 11, 511-517.

“Selective small-molecule inhibition of an RNA structural element” Howe et al., Nature 2015, 526, 672-677.

“Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genome” Eddy, Ann. Rev. Biophys. 2015, 43, 433-456.

“Recognition of Nucleic Acid Junctions Using Triptycene-Based Molecules” Barros & Chenoweth, Angew. Chem. 2014, 126, 13966 –13970.

“Transient RNA Structure Features are Evolutionarily Conserved and can be Computationally Predicted” Zhu et al., Nucleic Acids Res. 2013, 41, 6273-6285.

“Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks” Butcher & Pyle, Acc. Chem. Res. 2011, 44, 1302-1311.

“RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins” Lambert et al., Mol. Cell 2014, 54, 887-900.