IGVFagent
A local, auditable AI agent for discovering, retrieving, and analyzing data from the IGVF Portal, Catalog, Knowledge Graph, ENCODE, FAVOR, and related public resources.
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Software
Open and consortium-facing software for variant annotation, rare-variant association testing, pathway integration, and protein interaction analysis.
Portfolio
Scientific software with research impact
These tools support auditable AI agents, variant annotation, rare-variant association testing, pathway integration, and protein interaction analysis.
FAVOR
Functional Annotation of Variants Online Resource, including FAVOR 2.0, FAVORannotator, and FAVOR-GPT for genome-wide variant annotation, search, batch analysis, and interpretation.
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STAAR
Annotation-informed rare-variant association testing for whole-genome sequencing studies.
Open resource
STAARpipeline
A scalable pipeline for coding, noncoding, gene-centric, and region-based rare-variant association analysis.
Open resource
WGSagent
An autonomous AI agent for end-to-end whole-genome sequencing analysis, coordinating QC, ancestry and relatedness modeling, annotation, rare-variant testing, meta-analysis, cell-type-aware interpretation, eGASS storage, and human review.
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cellSTAAR
Single-cell-informed rare-variant association testing for noncoding regions, integrating functional data to improve power in whole-genome sequencing studies.
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IntPath
Integrated pathway gene relationship database for model organisms and important pathogens.
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PPI prediction tools
Computational prediction and evaluation of intra-species and host-pathogen protein-protein interactions.
Learn morePrinciples
What the tools are built to do
For a job-market page, software is framed as a research contribution rather than a side project.
Scale
Handle whole-genome sequencing data, large cohorts, consortium meta-analysis, and annotation resources that exceed ordinary desktop workflows.
Interpretability
Use auditable agent loops, functional annotation, visualization, and searchable resources so variant-level results become biologically meaningful.
Reusability
Package methods as tools, portals, and reproducible workflows that collaborators can adopt in real studies.