Dr. Joseph Bundy

Dr. Joseph Bundy (Joe) holds a Ph.D. in Biomedical Sciences from Florida State University and has a background in bioinformatics and computational toxicology. Joe has extensive experience analyzing ‘omics’ data from a variety of model systems including mouse, zebrafish, and human cancer cell lines. He received extensive training as a post-doc in the Center for Computational Toxicology and Exposure at the U.S. EPA where he developed bioinformatic approaches for interpreting High Throughput Transcriptomics datasets. Joe is continuing to develop computational methods to support interpretation of data generated by New Approach Methodologies at Vindhya Data Science.

Dr. Bundy’s fellowship project focuses on enhancing the adoption of New Approach Methodologies (NAMs) for measuring chemical bioactivity. The proposed project will develop computational tools and datasets to support the use of high throughput transcriptomics (HTTr) to evaluate environmental chemicals of concern. The project has two components: the first is to develop computational methods for estimating chemical potency from publicly available HTTr chemical screening data generated by EPA and other stakeholders.  These methods will be bundled into a publicly available R package and will integrate signature scoring with concentration response analysis to estimate transcriptomic points of departure from large datasets.  The second component of the proposed project is a peer reviewed manuscript describing a HTTr screen of reference chemicals conducted in a human cell line model system. This screen contains well-studied chemicals that perturb specific molecular targets and is essential for developing bioinformatic methods for elucidating mechanism(s) of action of understudied chemicals. These two projects aim to reduce reliance on repeat dose chronic animal studies by facilitating adoption of high throughput transcriptomics for chemical bioactivity evaluation.