Research
My research centers around engineering new tools for studying biology. I have designed new tools for studying biological systems at length scales ranging from individual molecules to whole tissues.
You can find a full list of my papers and patents on my Google Scholar profile.
Image processing
Open source image processing software I have contributed to:
- napari: python-based, GPU-accelerated n-dimensional image viewer for annotating images and exploring analysis results that integrates with modern deep learning algorithms and big data tools.
- starfish: a scaleable pipeline for image-based transcriptomics
- dotblotr: image processing pipeline for . See our paper to learn how dotblotr was used to study the antibody response to SARS-CoV-2.
- insta: a tool for using crowd-sourced annotations to calibrate and validate in situ transcriptomics image processing pipelines. See our preprint here.
In Situ Transcriptomics
At the Chan Zuckerberg Biohub, I led the development of the in situ transcriptomics platform . Towards this, I built hardware and software tools to reproducibly automate in situ transcriptomics assays and contributing to open sources software projects such as starfish, napari, and imagingDB.
Microfluidic tools for single-cell analysis
Protein localization and post translational modifications are key to understanding cell state, yet remain difficult to measure with single cell resolution. To meet this need, as a graduate student in the Herr Lab, I developed microfluidic tools for single cell protein analysis. Leveraging the favorable mass transport scaling of microfluidic length scales, we extended the sensitivity of traditional protein assays. In particular, we developed tools for measuring the subcellular localization of proteins from single cells and for highly-selective measurement of protein isoforms from single cells.
Selected publications
Microfabrication of functional hydrogels
To extend the capabilities of microfluidic devices for biological assays, I developed fabrication methods that add new functions to hydrogels.
Selected publications
Computational biomechanics
To elucidate the mechanisms through which soft tissues (e.g., articular cartilage) transduce mechanical signals into microstructual and biochemical changes, we integrated experimental systems and computional models to study how mechanical properties change in response to mechanical stimulus.
Selected publications