Research project
Evaluating AI agents for pathogen genomic surveillance
How accurately and reproducibly can supervised AI agents analyze sequencing data to support pathogen cluster detection and variant surveillance?
Clinical specimens, wastewater, and environmental sampling provide different contexts for interpreting a genomic signal. Sampling context, genome quality, and epidemiologic evidence all shape what a result can support.
October 12, 2026
First meeting
Project introduction, surveillance context, and evaluation design.
Reading
Start here
Public-health foundations, a clinical example, and an AI evaluation study.
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Armstrong, MacCannell, et al. · NEJM · 2019
Pathogen Genomics in Public Health
A foundation for understanding how genomic evidence informs public-health surveillance.
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Jansen, Tegomoh, et al. · MMWR · 2021
An early Omicron cluster in Nebraska
A clinical surveillance example that brings genomic and epidemiologic evidence together.
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Bhasin et al. · arXiv · 2026 preprint
BioSecBench-Surveillance
A study of how to evaluate AI agents on pathogen genomic surveillance tasks.
Reference
Tools, data, and guidance
Use the documentation to understand what each resource provides and where its limits lie.
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Nextstrain
A framework for genomic epidemiology and visualization.
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Nextclade
Sequence quality assessment, alignment, and clade assignment.
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Pango lineage designation
SARS-CoV-2 lineage naming and designation.
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Pangolin
Software for assigning Pango lineages to SARS-CoV-2 sequences.
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NCBI Sequence Read Archive
A public archive of sequencing data and associated metadata.
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GenBank
An overview of the public nucleotide sequence database.
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NCBI Pathogen Detection
Background and frequently asked questions about the surveillance resource.
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GISAID
Data access requires registration and adherence to the applicable access agreement.
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WHO genomic surveillance strategy
The public-health context for strengthening genomic surveillance.
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CDC wastewater data methods
How wastewater surveillance data are collected and interpreted.
Slide image credits
- Nextstrain global SARS-CoV-2 view: screenshot, Nextstrain team. CC BY 4.0.
- BioSecBench-Surveillance, Bhasin et al. (2026 preprint): Figure 2, extracted from the published PDF; scientific content unchanged. CC BY 4.0.
- Nebraska Omicron phylogenetic tree: figure from Jansen, Tegomoh, et al., MMWR (2021).