Aaron O’Brien

The paper evaluates learned fungal ITS embeddings against correctly configured alignment and finds alignment performs better in open-world settings due to evaluation choices.

MycoAI ITS classifiers trail alignment, SINTAX and HiTaC on full-length ITS and drop to 28.3% and 18.5% seen-genus family accuracy on ITS2, as predictions track flanking regions.

The paper introduces a calibrated novelty flag for fungal ITS metabarcoding that provides a user-chosen error rate for declaring sequences novel, evaluated across multiple datasets and scores.

SSUplex is a tool for extracting and sorting small-subunit rRNA reads by origin, improving accuracy in environmental DNA metabarcoding.

EMITS improves fungal ITS abundance estimation using expectation-maximization, outperforming naive counting and EMU in resolving closely related species and reducing errors.

ITSxRust improves ITS region extraction from long-read amplicon sequencing by increasing accuracy and speed, with additional recovery of partial sequences.

PEPhub is a database and web interface for sharing, editing, and validating biological sample metadata, enabling fast semantic search and interoperability.