Research Papers

Spatial genomic sequencing-based approaches are limited by the complexities of associating DNA barcodes with spatial coordinates. To overcome these challenges, we developed SCOPE (Spatial reConstruction via Oligonucleotide Proximity Encoding), an optics-free method inspired by DNA microscopy. We demonstrate SCOPE's capabilities by reconstructing a color Snellen eye chart for visual acuity.

A new framework for the use of single cell sequencing as tool for whole organism phenotyping. We sequenced cells from individual zebrafish allowing us to estimate the variance in cell type abundance organism-wide and to detect perturbation-dependent deviance in cell type composition.

Single-cell RNA sequencing can provide information about cellular relationships based on shared transcriptomes, but most methods lose spatial information. Sci-Space, developed by Srivatsan et. al. uses a set of gridded barcodes to mark the spatial positions to cells in a tissue prior to single cell sequencing.

First proof-of-concept experiment for showing that single cell sequencing can be used as a high content phenotyping modality to ascertain the effects of a library of chemicals on cancer cell lines. This assay can be used to interpret the biochemical properties (e.g. EC50 or affinity) with a transcriptome-wide readout.