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Author

Michael Goneos

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#artificial intelligence Preprint Oct 2026

Evaluating and improving AI agents for sequencing protocol understanding

LibStructBench is introduced, a document-grounded benchmark for reconstructing sequencing-library structures and molecular workflows and shows that frontier agents often produce approximately correct reconstructions but remain unreliable at exact reconstruction, particularly in molecular-state representation and workfl...

Chi-Lam Poon, Michael Goneos, Zezheng Song et al. · 0 citations
Open access Oct 2026

Modulator Resolves Transcript-, Allele-, and Condition-associated RNA Modification Differences from Direct RNA Sequencing

Nanopore direct-RNA sequencing (DRS) reports RNA modifications on single molecules, but there is no comprehensive algorithm for processing, aligning, and differentiating base modifications across reads that are often 5′-truncated. Here we present Modulator, which assigns every read, truncated or not, to a “fragmentform...

Theodore M. Nelson, Michael Goneos, Caroline J. Aufgebauer et al. · 0 citations

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