Title:  Making data-driven hypotheses for novel metabolic gene functions

Abstract:  Identifying the key functions of human genes is a major biomedical research goal. While some genes are well-studied, most human genes we know little about. New tools in data science -- a combination of computer programming, math & statistics, and topical expertise -- combined with the rapid adoption of open science and data sharing allow scientists to access publicly available datasets and interrogate these data before performing any experiments. We present here a new research tool called data-driven hypothesis (DDH) for predicting pathways and functions for thousands of genes across the human genome. Importantly, this method integrates gene essentiality, gene expression, and literature mining to identify candidate molecular functions or pathways of known and unknown genes. Beyond single gene queries, DDH can uniquely handle queries of defined gene ontology pathways or custom gene lists containing multiple genes. The DDH project holds tremendous promise to generate hypotheses, data, and knowledge in order to provide a deep understanding of the dynamic properties of mammalian genes. We present this tool via an intuitive online interface, which will provide the scientific community a platform to query and prioritize experimental hypotheses to test in the lab.

Bio:  Matthew Hirschey is associate professor at Duke University in the Departments of Medicine, Division of Endocrinology, Metabolism and Nutrition and Pharmacology & Cancer Biology, and is a faculty member of the Duke Molecular Physiology Institute. He is also the Director of the Center for Computational Thinking, a University-wide initiative to enhance computational thinking across all disciplines of study.

He obtained a Bachelor’s of Science at the University of Vermont and a Ph.D. in Chemistry and Biochemistry at the University of California, Santa Barbara with Alison Butler, where he combined inorganic semiconductor research with microbiology, exploring new applications in biomaterials research. He was a post-doctoral research fellow with Eric Verdin at the Gladstone Institutes at the University of California in San Francisco, where he studied the function of acetylation and deacetylation by the enzyme SIRT3 in the mitochondria.

At Duke since 2011, Dr. Hirschey studies how cells integrate nutrient sensing and metabolism. He is particularly interested in how metabolites and chemical modifications control metabolism. Metabolic regulation is important for several physiological states and disease processes, including diabetes, cardiovascular disease, cancer, and the aging process.