Atul Deshpande, MS, PhD

Atul Deshpande, PhD, is an Assistant Professor in the Departments of Oncology at the Johns Hopkins University School of Medicine. His research program bridges high-dimensional biological measurements and mechanistic understanding by developing bioinformatics methods and computational frameworks that calibrate models to multi-scale tissue data with quantified uncertainty. The lab builds bioinformatics tools for spatial biology and applies them to spatial and single-cell data from clinical and simulated biological data. The lab develops open source software for spatial biology which quantify tissue architecture and identify molecular interactions in the cellular microenvironment.

Dr. Deshpande applies these tools directly to clinical cancer specimens. His work includes the spatial characterization of metastatic PDAC by imaging mass cytometry, and, with the Popel laboratory, proof-of-concept for calibrating spatial agent-based (quantitative systems pharmacology) models to clinical specimens — showing that calibrated models reproduce observed tissue architectures and that the derived spatial metrics predict patient survival. He collaborates closely with investigators across Johns Hopkins, including Popel (BME), Phillip (BME), Stein-O’Brien (Neuroscience), and Ho (Oncology) groups, and serves as the Johns Hopkins representative to the Break Through Cancer consortium, coordinating multi-institutional spatial-analysis efforts in PDAC. Dr. Deshpande is also a member of the Department of Biomedical Engineering and the Data Science and AI Institute. 

Research Interests: Computational biology; machine learning and statistical inference for biomedical data; data assimilation, model calibration, and uncertainty quantification; multi-scale modeling of biological systems.

Assistant Professor, Sidney Kimmel Comprehensive Cancer Center

Member, Data Science and AI Institute

Assistant Professor, Department of Electrical and Computer Engineering 

Member, Department of Biomedical Engineering