Publications
Papers & writing
A list of my research publications and other writings.
Research Papers
Published
Arena: Rapid and Accurate Reconstruction of Full Atomic RNA Structures from Coarse-grained Models
Arena is a C++ program that rebuilds full-atomic RNA structures from coarse-grained models faster and more accurately than prior methods.
Perry, Z. R., Pyle, A. M., & Zhang, C. (2023). Journal of Molecular Biology, 435(18), 168210. doi.org/10.1016/j.jmb.2023.168210 ↗
RSCanner: rapid assessment and visualization of RNA structure content
RSCanner is a tool for assessing RNA secondary structure content across long transcripts using probing data or in silico predictions.
Mahadeshwar, G., Tavares, R. C. A., Wan, H., Perry, Z. R., & Pyle, A. M. (2023). Bioinformatics, 39(3), btad111. doi.org/10.1093/bioinformatics/btad111 ↗
Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor
Characterization of ligand-induced allostery in the lac repressor, including computational analysis of water molecules in the binding pocket.
Glasgow, A., Hobbs, H. T., Perry, Z. R., Wells, M. L., Marqusee, S., & Kortemme, T. (2023). Nature Communications, 14(1), 1179. doi.org/10.1038/s41467-023-36798-1 ↗
Under Revision/Preprints
Conserved structural features of the lncRNA HOTAIR in breast cancer cells
Modeling of the in cellulo SHAPE-MaP structure of HOTAIR, with a roadmap of structural features, molecular interaction sites, and candidate modification sites. A bioinformatics analysis across 174 primates reveals a conserved structural module in Domain 3.
Perry, Z. R., Beeram, A., Lee, L., Pyle, A. M. (2026). BioRxiv. doi.org/10.64898/2026.05.18.725451 ↗ · under revision at RNA
Sequence alignment of the primate lineage reveals evolutionary divergence and conserved secondary structural motifs in noncoding RNAs
Discovery and alignment of noncoding RNA sequences across 190 unannotated primate genomes. The primate alignments can be used to detect covariation in the lncRNA SChLAP1.
Beeram, A., Perry, Z. R., Pyle, A. M. (2026). BioRxiv. doi.org/10.64898/2026.05.18.725462 ↗ · under revision at RNA
The long noncoding RNA Malat1 contains an internal ribosome entry site mediating micropeptide translation
Evidence that the lncRNA Malat1 harbors an ORF for a small micropeptide, including a secondary structure of the putative IRES from in cellulo fbDMS-MaP.
Xiao, W., Hann, T., Perry, Z. R., Pandey, V., Cheng, J., Wohlschlegel, J., Pyle, A. M., Black, D. (2026). BioRxiv. doi.org/10.64898/2026.02.11.705401 ↗ · under revision at Science Advances
Discovery of a Well-Folded Protein Interaction Hub Within the Human Long Non-Coding RNA NORAD
Identification of a structural module in NORAD that may serve as a platform for protein binding.
Kumar, A., Wan, H., Perry, Z. R., Patel, S., Tavares, R., Pyle, A. M. (2023). BioRxiv. doi.org/10.1101/2023.08.07.552337 ↗
Other Writing
Thesis: Computational and Experimental Investigations of Noncoding RNA Structures
Ph.D. Dissertation, Yale University, Dept. of Molecular Biophysics & Biochemistry — May 2026 · Read thesis (PDF) ↗
Essay: Spinning Creation
A personal essay on protein folding, beauty, and faith. et Spiritus — MIT's Journal of Christian Thought, Issue 6, Spring 2020 · Read essay (PDF) ↗