Amanda J. Clare

StORF-Reporter identifies missing genes in prokaryotic genomes by detecting Stop-ORFs in unannotated regions, expanding gene collections across multiple species.

FrameRate predicts coding frames from unassembled metagenomic reads using machine learning, bypassing assembly and capturing functional profiles efficiently.

The paper evaluates ORF prediction tools and finds their performance varies greatly by organism, with no single tool being most accurate across all genomes.

The paper formalizes and addresses the computational complexity of haplotyping microbial communities using metagenomic data and provides open-source tools for the task.

This paper introduces a method to recover gene haplotypes from metagenomes and shows it accurately identifies mutation rate differences between core and accessory gene families in rumen microbiomes.

GiraFFe Browse provides a lightweight, user-friendly tool for viewing GFF and FASTA data, available as open-source software.

This paper introduces a probabilistic method to recover haplotypes from metagenomic data, achieving 100% accuracy in recovering cryptic gene isoforms from HIV-1 strain mix data.