Our lab is interested in alternative RNA structures and the myriad of roles they have in both viral and human biology. In particular, we study how RNA folding informs alternative splicing and how mis-folding can lead to disease. Our goal is to understand gene expression regulation in physiology and disease through the lens of RNA.
SEISMIC-RNA: SEISMIC-RNA is software for solving RNA structures (including alternative structures formed by one sequence) in high throughput from mutational profiling experiments (e.g. DMS-MaPseq and SHAPE-MaP) and expectation-maximization clustering. Check out our preprint on bioRxiv!
SEISMICgraph A tool for visualizing results from SEISMIC-RNA.
eFold: Our RNA structure prediction tool. Preprint here: link.
eFold data: The whole data processing pipeline from the source to the model. Uses RouskinHF to push and pull to HuggingFace.
eFold figures: The code for the figures from the eFold paper.
RouskinHF: This repo is a Python wrapper around HuggingFace API to pull/push data from the RouskinLab HF organization.
RNAstructure This repo is a Python wrapper around RNAstructure software from the David Mathews lab.
