Colin N. Dewey

The paper identifies an exitron in UBQLN2 that generates an alternatively spliced isoform with distinct properties linked to ALS.

Vimentin-driven maturation of col1a1a-positive fibroblasts after larval zebrafish burn parallels fin development, but prolonged neutrophil presence delays fibroblast maturation and organized collagen regrowth.

IsoBayes infers protein isoform presence and abundance using Bayesian methods integrating proteomics and transcriptomics data, showing good sensitivity and specificity in simulations and real datasets.

The paper develops CRSP, a pipeline for RNA-seq analysis in species without a sequenced genome or reference transcripts, and applies it to generate a comprehensive Nile grass rat transcriptomic atlas.

CellO is a machine learning tool for hierarchically classifying human cell types using the Cell Ontology, achieving competitive performance with a comprehensive training dataset and interpretable models.

PRAM improves transcript discovery from RNA-seq data by combining datasets in a single step, outperforming two-step methods and identifying new transcripts in human and mouse data.

MetaSRA normalizes SRA sample metadata using a schema inspired by ENCODE, enabling better analysis of biological relationships across diverse samples.