Charles E. Grant

Label-free quantification in the Crux toolkit

The paper introduces a label-free quantification feature in the Crux toolkit, demonstrating improved efficiency and accuracy compared to existing methods.

Fast and memory efficient searching of large-scale mass spectrometry data using Tide

The paper improves the Tide search engine to handle large-scale mass spectrometry data efficiently, achieving faster speeds and lower memory usage than previous versions.

The Crux toolkit for analysis of bottom-up tandem mass spectrometry proteomics data

The paper summarizes recent developments in the Crux toolkit for analyzing bottom-up proteomics data, including speedups, new features, and tools.

XSTREME: Comprehensive motif analysis of biological sequence datasets

XSTREME couples MEME and STREME de novo discovery with SEA known-motif enrichment, ranking motifs by enrichment anywhere in sequences, unlike center-focused MEME-ChIP; illustrated on Gata1 Cut&Run.

SEA: Simple Enrichment Analysis of motifs

Motif enrichment scored with a held-out threshold and a single test per motif yields p-values close to uniform under the null, where AME and CentriMo come out conservative.

T-Gene: Improved target gene prediction

T-Gene predicts target genes of transcription factors by combining histone modification correlation and genomic distance, achieving high positive predictive value.

MoMo: Discovery of statistically significant post-translational modification motifs

MoMo provides a method to assign statistical confidence to PTM motifs, showing improved accuracy over motif-x and offering a web server and software tool.

MoMo: Discovery of post-translational modification motifs

MoMo identifies post-translational modification motifs from mass spectrometry data using re-implemented algorithms and provides web-accessible results.