Author

Brian B. Merritt

Johns Hopkins University Applied Physics Laboratory

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 4 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Assay:metagenomics· 2 Research Focus:software / tool· 2 Approach:statistical model· 2 Research Focus:variant calling· 2 Assay:whole-genome sequencing· 2 Assay:CRISPR screen· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Jeremy D. RatcliffiD· 3 shared Peter ThieleniD· 2 shared Stanley TaiD· 2 shared Abhi Srikanth· 1 shared Angeline AguinaldoiD· 1 shared Brant W. CheeiD· 1 shared Christopher E. BradburneiD· 1 shared Daniel BermaniD· 1 shared

Activity by Year

2019-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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3 shared papersBioinformatics

Jeremy D. RatcliffORCID

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Author profile →

5 papers

Recent·Most cited

TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection

Brian B. Merritt, Jeremy D. Ratcliff, Stanley Ta, Gunars Osis, Matthew R. Mauldin, Peter Thielen

TaxTriage is a metagenomic analysis pipeline that detects putative pathogens in sequencing data using read classification, mapping, and de novo assembly, with comparable performance to cloud-based tools.

Bioinformatics · Mar 31, 2026Peer-reviewedBioinformatics

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

Improved Resolution of Highly Pathogenic Avian Influenza Virus Haemagglutinin Cleavage Site Using Oxford Nanopore R10 Sequencing Chemistry

Jeremy D. Ratcliff, Brian B. Merritt, Hannah Gooden, Jurre Y. Siegers, Abhi Srikanth, Sokhoun Yann, Sonita Kol, Sarath Sin, Songha Tok, Erik A. Karlsson, Peter Thielen

This study compares Oxford Nanopore R9.4.1 and R10.4.1 sequencing chemistries for resolving the hemagglutinin cleavage site in avian influenza viruses, finding improved accuracy with R10.4.1.

bioRxiv · Sep 30, 2023 · PreprintGenomics

The META tool optimizes metagenomic analyses across sequencing platforms and classifiers.

Robert A. Player, Angeline Aguinaldo, Brian B. Merritt, Lisa N. Maszkiewicz, Oluwaferanmi E. Adeyemo, Ellen R. Forsyth, Kathleen J. Verratti, Brant W. Chee, Sarah L. Grady, Christopher E. Bradburne

The META tool generates simulated metagenomic data to evaluate and compare sequencing platforms and classifiers across different use cases.

Frontiers in Bioinformatics · Jan 6, 2023Peer-reviewedBioinformatics

GRIBCG: A software for selection of sgRNAs in the design of balancer chromosomes

Brian B. Merritt, Lily S. Cheung

GRIBCG is a tool for designing balancer chromosomes using CRISPR/Cas9, selecting sgRNAs that efficiently cut chromosomes while minimizing off-target effects across six model organisms.

BMC Bioinformatics · Mar 12, 2019Peer-reviewedBioinformatics