98 citations · 204 across the 8 of their papers we have counts for
8 papers
Protein language model rescue mutations highlight variant effects and structure in clinically relevant genes
Onuralp Soylemez, Pablo Cordero
Despite being self-supervised, protein language models have shown remarkable performance in fundamental biological tasks such as predicting impact of genetic variation on protein s…
Correcting a SHAPE-directed RNA structure by a mutate-map-rescue approach
Siqi Tian, Pablo Cordero, Wipapat Kladwang +1
The three-dimensional conformations of non-coding RNAs underpin their biochemical functions but have largely eluded experimental characterization. Here, we report that integrating…
HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis
Hanjoo Kim, Pablo Cordero, Rhiju Das +1
To facilitate the analysis of large-scale high-throughput capillary electrophoresis data, we previously proposed a suite of efficient analysis software named HiTRACE (High Throughp…
A mutate-and-map protocol for inferring base pairs in structured RNA
Pablo Cordero, Wipapat Kladwang, Christopher C. VanLang +1
Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resoluti…
Quantitative DMS mapping for automated RNA secondary structure inference
Pablo Cordero, Wipapat Kladwang, Christopher C. VanLang +1
For decades, dimethyl sulfate (DMS) mapping has informed manual modeling of RNA structure in vitro and in vivo. Here, we incorporate DMS data into automated secondary structure inf…
The Stanford RNA Mapping Database for sharing and visualizing RNA structure mapping experiments
Pablo Cordero, Julius Lucks, Rhiju Das
We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA s…