Matthew F. Allan, Ph.D.

Thesis Title: Investigating and Reprogramming RNA Folding with Molecular Probes

Publications While at MIT:

1. Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells.

Lan TCT, Allan MF, Malsick LE, Woo JZ, Zhu C, Zhang F, Khandwala S, Nyeo SSY, Sun Y, Guo JU, Bathe M, Näär A, Griffiths A, Rouskin S.Nat Commun. 2022 Mar 2;13(1):1128. doi: 10.1038/s41467-022-28603-2.PMID: 35236847 Free PMC article.

2. Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA.

Allan MF, Aruda J, Plung JS, Grote SL, des Taillades YJM, de Lajarte AA, Bathe M, Rouskin S.Res Sq [Preprint]. 2024 Aug 7:rs.3.rs-4814547. doi: 10.21203/rs.3.rs-4814547/v1.PMID: 39149495 Free PMC article. Preprint.

3. 3D RNA-scaffolded wireframe origami.

Parsons MF, Allan MF, Li S, Shepherd TR, Ratanalert S, Zhang K, Pullen KM, Chiu W, Rouskin S, Bathe M.Nat Commun. 2023 Jan 24;14(1):382. doi: 10.1038/s41467-023-36156-1.PMID: 36693871 Free PMC article.

4. RNA levers and switches controlling viral gene expression.

Allan MF, Brivanlou A, Rouskin S.Trends Biochem Sci. 2023 Apr;48(4):391-406. doi: 10.1016/j.tibs.2022.12.002. Epub 2023 Jan 27.PMID: 36710231 Review.