Our lab combines high-throughput/high-content single-cell experiments with machine learning to obtain a systems biology view of how environmental cues and signaling pathways are integrated to generate in vivo tissue architecture and function, using the gut epithelia of mouse and human as model systems.


We adopted inDrop single-cell RNA-seq, an open microfluidic system that enables oil-emulsion-based encapsulation of single cell in droplets. Transcriptome data from thousands of cells, thousands of unique molecular identifiers per cell, and a high cell recovery rate, can be obtained from a relatively low read count per cell.

We use multiplex imaging via iterative staining, along with cloud-based image segmentation, to decipher the spatial interactions between epithelial and immune cells in Inflammatory Bowel Disease, with a special focus on the multi-system influence of TNF inflammatory signaling.


We develop novel algorithmic approaches, such as p-Creode, to reveal biological insights hidden in large single-cell datasets. The term creode was coined by C.H. Waddington, combining the Greek words for "necessary" and "path" to describe the cell state transitional trajectories that define cell fate specification. p-Creode aims to identify consensus routes from relatively noisy single-cell data. Conceptually, p-Creode determines the geometric shape of a collection of dense data points (i.e., a data cloud) in order to reveal the underlying structure of transitional routes.
dissect We apply DISSECT to mass cytometry, which has the capacity to query rare cells in hundreds of thousands of cells, to link signaling states to rare epithelial phenotypes. For example, this technique is being used to interrogate the malignant properties of colorectal cancer stem cells.

From a translational perspective, our approaches, when applied to FFPE archival tissues, can be combined with Vanderbilt BioVU/Pathlink data to obtain a comprehensive, single-cell view of patient samples.

gut on a chip

We are also interested in novel ways by which signal transduction pathways are regulated. We are currently investigating the effects of mechanotransudction on autophagy using a microfluidics platform, and how microbial and nutrient sensing pathways regulate cell specification.