I'm a data scientist currently specializing in developing open-source tools for computational biology.
- SpaceCat: (Core Developer) A computational pipeline that automatically extracts a spatial catalog of 100s of distinct features from single cell data to enable easy downstream quantification. SpaceCat features have been normalized, correlation filtered, and pre-processed for quick integration with any statistical model.
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ark-analysis: (Maintainer) A package for performing spatial analysis on highly multiplexed imaging microscopy data, adapting machine learning techniques for automated biological analysis. Provides researchers with a powerful suite of tools (via user-friendly jupyter notebooks) to analyze their millions of cells automatically and efficiently.
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toffy (Maintainer): A package for extracting and preprocessing image data generated from the commercial MIBIScope platform. Provides researchers with an easy interface to efficiently perform channel compensation, background subtraction, and batch correction without requiring users to have prior coding skills.
- Breast cancer
- Temporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition 📓 Paper 🧵 Twitter thread
- QUICHE reveals structural definitions of anti-tumor responses in triple negative breast cancer 📓 Paper 🧵 Twitter thread
- Temporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition 📓 Paper 🧵 Twitter thread
- Methods
- Automated classification of cellular expression in multiplexed imaging data with Nimbus 📓 Paper 🧵 Twitter thread
