San Jewell

Generative modeling for RNA splicing predictions and design

This paper introduces TrASPr+BOS, a generative AI model for predicting and designing RNA to achieve tissue-specific splicing outcomes, showing improved performance over existing methods.

G4mer: An RNA language model for transcriptome-wide identification of G-quadruplexes and disease variants from population-scale genetic data

G4mer identifies G-quadruplexes and disease variants from population-scale genetic data, improving accuracy and highlighting sequence features affecting rG4 formation.

A Deep Dive into Statistical Modeling of RNA Splicing QTLs Reveals New Variants that Explain Neurodegenerative Disease

The paper improves sQTL modeling by incorporating alternative splicing representation and introduces MAJIQTL, finding new sQTLs linked to Alzheimer's disease.

MAJIQ-CLIN: A novel tool for the identification of Mendelian disease-causing variants from RNA-Seq data

MAJIQ-CLIN improves the detection of Mendelian disease-causing variants from RNA-Seq by addressing splicing aberrations, showing better accuracy and efficiency than existing tools.

Machine learning-optimized targeted detection of alternative splicing

This paper introduces LSV-seq, a targeted RNA-seq method optimized with machine learning to detect alternative splicing with high sensitivity and low sequencing depth.

Contrasting and Combining Transcriptome Complexity Captured by Short and Long RNA Sequencing Reads

The paper compares short and long read RNA sequencing technologies, finds they detect different transcriptome features, and introduces software to combine their results for improved analysis.

MAJIQ V3 offers improvements in accuracy, performance, and usability for splicing analysis from RNA sequencing

RNA splicing analysis using heterogeneous and large RNA-seq datasets

The paper introduces MAJIQ v2, a tool for analyzing RNA splicing in large and heterogeneous RNA-seq datasets, showing improved performance over existing methods and applying it to brain subregion-specific splicing analysis.