Christopher Wilks

The paper introduces REPAC, a framework for analyzing alternative polyadenylation from RNA-sequencing data, showing it identifies APA changes in B cell activation and is faster than existing methods.

recount3 provides uniformly processed RNA-seq data and tools for querying and analyzing large-scale human and mouse expression and splicing data.

Megadepth efficiently quantifies coverage in BigWig and BAM files, outperforming existing tools in speed and memory usage.

LongTron evaluates long-read spliced alignment accuracy by simulating errors, training a classifier, and comparing results across platforms and datasets.

The paper presents FC-R2, an expanded transcriptome atlas of over 109,000 genes, including lncRNAs, and demonstrates its utility in analyzing gene expression across normal and diseased human samples.

ASCOT identifies key regulators of neuronal subtype-specific splicing by analyzing public RNA-Seq data and demonstrating the role of PTBP1, MSI1, and PCBP2 in rod photoreceptor splicing.

The paper improves thread scaling in read aligners on multi-core processors by addressing architectural challenges and implementing changes in Bowtie, Bowtie 2, and HISAT.

Snaptron provides a search engine for querying and visualizing splicing patterns across 70,000 human RNA-seq samples and 146 million splice junctions.

The paper introduces derfinder, a tool for RNA-seq analysis that identifies differentially expressed regions at single base resolution without relying on gene annotations, showing it works well with incomplete annotations and large datasets.

Rail-dbGaP enables secure analysis of dbGaP-protected RNA-seq data in the cloud using Amazon Elastic MapReduce, with a spliced aligner tool and protocol for compliance with NIH guidelines.