Featuring Briana Benton
Show Notes:
In this episode, David Yarmosh and Briana Benton revisit the origins and evolution of the ATCC Genome Portal, tracing its journey from an ambitious research concept in 2017 to a groundbreaking resource for high-quality, traceable genomic data. Benton shares how early internal research proposals—including her push for long-read sequencing and Dr. Marco Riojas’ vision for sequencing ATCC’s collection—laid the foundation for the portal. Their work, along with challenges in microbiome research where public genome assemblies failed to match known inputs, underscored the need for a reliable genomic resource. Launched in 2019 with just 250 genomes and basic sequencing tools, the portal has since expanded to over 5,500 genomes, backed by automation, a larger team, and advanced sequencing capabilities. The portal is continually evolving and now includes data from bacteriology, virology, mycology, and protistology collections, all accessible via a secure REST-API. Looking ahead, ATCC plans to enhance the portal with methylation data, expanded annotations, and additional QC-related metadata, striving to create a comprehensive “digital twin” of each organism to reinforce scientific reproducibility and informed decision-making.
Guest:
Briana Benton, BS
Technical Manager, ATCC
Briana Benton is a Program Manager for ATCC’s Sequencing and Bioinformatics department. Her current focus is on the ATCC Genome Portal and expanding the collection of published reference genomes. Briana previously worked on the development of mock microbial communities for microbiome research and synthetic molecular standards for molecular diagnostics assays. Prior to joining ATCC, she developed molecular diagnostic assays for the Henry M. Jackson Foundation.
Host:
David Yarmosh, MS
Lead Bioinformatician, ATCC
David Yarmosh is a lead bioinformatician in ATCC’s Sequencing and Bioinformatics Center. He’s a graduate of New York University’s Tandon School of Engineering. He has been working in large data aggregation and analysis since 2013 and microbial genomics with a focus on biosurveillance R&D efforts since 2016. David has led international training exercises in Peru and Senegal, sharing metagenomic analytical capabilities. His interests include genomics database construction, metadata collection, drug resistance mechanisms, bioinformatics standards, and machine learning. Since joining ATCC in 2020, David has worked extensively in SARS-CoV-2 classification, epidemiology, and genomics evaluation, including enhanced and uniform variant reporting. He has contributed more broadly to genomics reporting and analytical standardization and he has helped develop the podcast Behind the Biology, which he now hosts.
