I am currently a Simons Postdoctoral Fellow in the laboratory of Feng Zhang at the Broad Institute and the Department of Brain and Cognitive Sciences at MIT. I received my PhD at MIT in Sebastian Seung's lab and I completed my undergraduate education at Stanford University.
My scientific interests include genome engineering, functional genomic screening, autism genetics, and the regulation of RNA editing in neurons.
functional genomics with CRISPR-Cas9
One of the most exciting aspects of developing new genome engineering technologies is that they can have broad applications in biology and medicine. Recently, I and another postdoc in the Zhang Lab developed a Genome-scale CRISPR Knock-Out (GeCKO) library. Taking advantage of the easy programmability of CRISPR, GeCKO enables pooled functional genomics screens to interrogate loss-of-function mutations in a massively parallel fashion. When compared to shRNA knock-down, individual CRISPR reagents are much more consistent in their ability to target and knock-out (not knock-down) genes, resulting in a greater number of validated hits from the screen. With GeCKO, we have conducted genome-scale positive and negative selection screens using human cancer cells and human pluripotent stem cells. Through our work, we have been able to discover and validate several new loss-of-function mutations that confer resistance to vemurafenib, a FDA-approved BRAF-inhibitor commonly prescribed for malignant melanoma. For more information, please visit the GeCKO website.
genome engineering toolbox with TALEs
We are now able to sequence entire genomes easily and cheaply. But what about our ability to write DNA? How can we make targeted changes to genomes? Genome engineering has immense potential to transform genomics, bioengineering, and medicine. Currently, I use modular programmable DNA binding proteins to test the causal role of putative genetic disease variants in human cells and to rescue animal models of disease in vivo. My goal is to expand the available tools for genome engineering while applying these technologies to understand and treat neurological diseases. For more information, please visit TALEffectors.com.
activity-dependent RNA editing in neurons
There is a growing number of newly identified A-to-I RNA editing sites in the genome. We previously screened all known coding, non-synonymous editing sites in the rat genome to see how neural activity can influence RNA editing.
long-term time-lapse imaging of growing cortical axons
What can the movements of axon growth cones tell us about how nervous systems are wired up? Applying stochastic modeling techniques to time-series of growth cone positions, we find that axons have distinct stereotyped behaviors during early outgrowth. Our goal is to use these models of "cellular behavior" to discover the underlying biophysical mechanisms in the axon growth cone. On the experimental side, we have developed an integrated software-hardware platform and primary neuron prep for long-term (weeks) unattended time-lapse microscopy of genetically labeled axons and dendrites in culture.
microfluidics for diffusable growth factor gradients
How can we create target-derived, diffusible (vs. substrate-bound, see inkjet project below) chemotropic signals to neurons in vitro? We developed a simple microfluidic system to use for time-lapse imaging of axon outgrowth from rat dorsal root ganglia neurons. The microfluidic chamber was designed to produce a linear gradient of a neurotrophic factor for guiding growing axons.
inkjet-based substrate micropatterning
For precise micropatterning of substrate-bound neural adhesion and guidance molecules, we developed a custom inkjet printer and flexible surface chemistry. We have created viable, healthy cultures of primary hippocampal neurons and glia that adhere to specific patterns for weeks in vitro. An example of a patterned culture is shown in the image to the left: Each letter contains an isolated micronetwork of tens of neurons.