Author

Daniel Berman

Johns Hopkins University Applied Physics LaboratoryORCID 0000-0002-9176-7535Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Bioinformatics· 2 Synthetic Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:benchmarking· 2 Approach:deep learning· 2 Research Focus:gene regulatory network inference· 2 Research Focus:variant effect prediction· 2 Organism:bacteria (other)· 1 Research Focus:differential expression· 1 Assay:DNA methylation· 1 Research Focus:drug response / drug discovery· 1

Frequent Co-Authors

Jeremy D. RatcliffiD· 2 shared Stanley TaiD· 2 shared Arturo CasadevalliD· 1 shared Brian B. Merritt· 1 shared Brian MerrittiD· 1 shared Daniel F. Q. SmithiD· 1 shared Daniel JimeneziD· 1 shared Daniel Jimenez· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersBioinformatics

Jeremy D. RatcliffORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

MicrobeRT: A Framework and Suite of Fine-tuned Language Models for Genomic Sequences

Vijay Narayan, Brian Merritt, Sanjeevani Choudhery, Daniel Jimenez, Stanley Ta, Daniel S Berman, Jeremy Ratcliff, Molly E Gallagher

MicrobeRT is a framework of fine-tuned language models for metagenomic analysis, achieving strong performance in taxonomic classification, antibiotic resistance detection, and pathogenicity assessment.

bioRxiv · Nov 4, 2026 · PreprintBioinformatics

Fung-AI: An AI/ML-driven pipeline for antifungal peptide discovery

Daniel Berman, Elizabeth A. Lewis, Tom D. Curtis, Olivia N. Tiburzi, Daniel F. Q. Smith, Arturo Casadevall, Laura J. Dunphy

The paper presents a generative AI pipeline for discovering antifungal peptides, identifying five with activity against fungal pathogens and low cytotoxicity.

PLoS Computational Biology · Jun 15, 2026Peer-reviewedSynthetic Biology

Evaluating the Effectiveness of Parameter-Efficient Fine-Tuning in Genomic Classification Tasks

Daniel Berman, Daniel Jimenez, Stanley Ta, Brian B. Merritt, Jeremy D. Ratcliff, Vijay Narayan

This study evaluates parameter-efficient fine-tuning in genomic classification and finds it underperforms compared to full and partial fine-tuning methods.

bioRxiv · Aug 21, 2025 · PreprintBioinformatics