We develop methods to annotate, index and analyze large unstructured datasets for enabling use cases of the learning health system. Our research group is part of the Center for Biomedical Informatics Research at Stanford and the National Center for Biomedical Ontology. Press coverage of our work can be found in Forbes, GigaOM, Science News, EHR Intelligence and the Stanford Medicine magazine. We combine machine learning, text-mining, and prior knowledge in medical ontologies to discover hidden trends, build risk models, and drive comparative effectiveness studies to enable data-driven medicine.
We have shown that using unstructured data, it is possible to monitor for adverse drug events, learn drug-drug interactions, identify off-label drug usage, generate practice-based evidence for difficult-to-test clinical hypotheses, identify new medical insights, and generate phenotypic fingerprints as well as build predictive models. We have efforts around combining multiple information sources for drug safety surveillance, which were recently the focus of a commentary titled Advancing the Science of Pharmacovigilance. We have also shown that it is possible to use automated annotations and multiple biomedical ontologies to go beyond just Gene Ontology annotations for enrichment analysis using disease ontologies in order to understand the “gene lists” from analysis of high-throughput data.
Learning Health System examples:
Data mining for drug safety:
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Postdoc position | Data Science Fellow
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