Basic science of human genome informatics
Human genomics is at an inflection point. Long-read sequencing is becoming cost-competitive with short-read technologies, and new informatic tools now make telomere-to-telomere genome assembly broadly accessible. The next challenge is organizational: how to represent many high-quality genomes in a way that supports analysis, comparison, and discovery. Graph-based genome representations offer clear advantages by naturally capturing alternative alleles and complex variation.
At the same time, the vast existing collections of genomes and exomes can be reused to represent more human diversity and to rigorously evaluate methods at scale. This multi-platform, multi-omic landscape creates opportunities to build new reference resources, analytical tools, and novel biological insights.
Representative publication
- Benchmarking long-read genome sequence alignment tools for human genomics applications. PeerJ (2023).https://doi.org/10.7717/peerj.16515
Translational science of informatic technologies
Emerging informatic technologies are rapidly entering research and clinical workflows, yet robust evidence of their performance often lags behind adoption. The lab focuses on establishing clear benchmarks to demonstrate non-inferiority—and where possible, superiority—of new genome reference materials and analytic approaches relative to established standards.
Beyond genomics, we apply these translational principles to conversational AI. Chatbots now play a growing role in digital health and biomedical research, but many systems remain opaque and difficult to audit. Our work emphasizes ethically grounded, versioned, and auditable chatbot systems for informed consent and other high-stakes decision contexts.
Representative publications and resources
- Using a chat-based informed consent tool in large-scale genomic research. JAMIA (2024).https://doi.org/10.1093/jamia/ocad217
- Documentation for our current, graph-based chatbot: https://github.com/UCI-ICTS/mia
Empirical and conceptual bioethics
Genomics and bioinformatics continually raise ethical questions that are both practical and conceptual. Lab members are supported to explore bioethical issues emerging directly from their technical work, while applying empirical approaches ranging from quantitative analysis to clinical trial design to study the ethics–technology interface.
Our approach embeds ethical reflection throughout scientific workflows, from data governance and consent to data sharing and system design. This integration allows us to generate evidence about how ethics can be operationalized in rapidly evolving fields.
Representative publications
- Overcoming challenges associated with broad sharing of human genomic data. Nature Genetics (2025). https://doi.org/10.1038/s41588-024-02049-2
- Ethics choices during the Human Genome Project reflected their policy world, not ours. Cell Genomics (2025). https://doi.org/10.1016/j.xgen.2025.100497