Current position: Benaroya Research Institute
Graduate student Bioengineering 2012-2017
Current position: Ultivue, Inc.
Graduate student Electrical Engineering 2010-2015
Current position: Microsoft Research
Xi Sherry Chen
Graduate student Electrical Engineering 2010-2014
Current position: postdoctoral research, Zhang lab, Rice University
Current position: Cancer Research UK
Lab technician 2012-2013
Current position: Graduate student Bioengineering, Rice University
Current position: Research scientist, Kraemer lab, UW medicine
Computing Innovation postdoctoral fellow 2009-2011
Current position: Assistant professor Electrical Engineering, UT Austin
Graduate student Electrical Engineering, 2009-2010
Friends and collaborators
We are working with David Baker, James Carothers, Eric Klavins, Suzie Pun, Jesse Zlatan and all the other awesome people in the UW Center for Synthetic Biology. With Eric, we are working on synthetic morphogenesis in yeast. With David, we are collaborating on applying and developing methods for characterizing protein-protein interactions.
Karin Strauss, Luis Ceze and our lab first collaborated on a novel architecture for DNA computing. More recently, they (and the MISL team) have been leading the charge on scaling up DNA storage and random access retrieval.
Jay Shendure at UW Genome Sciences helped us get started with RNA-seq and we've been collaborating on massively parallel reporter assays for splicing and more ever since. With Stanley Fields and his group (also at Genome Sciences) we have been collaborating on learning the grammar governing cis-regulation in yeast 5'UTRs using similar high-throughput methods.
We are working with Sreeram Kannan and Su-In Lee on developing novel computational tools for analyzing single-cell RNA-seq data.
I was a postdoc in Erik Winfree's lab where I also started working with David Soloveichik. Our first paper was about digital logic circuits made only from DNA. Since I left Caltech, David, Erik and I have been working on the theory and experimental implementation of DNA-based chemical reaction networks.
David Yu Zhang and I have been working on molecular classifiers and SNP detections also going back to our time in the Winfree lab.
My group has a long-standing collaboration with Andrew Phillips, Neil Dachau and Luca Cardelli at Microsoft Research in Cambridge. We experimentally built and modeled DNA CRNs. More recently, we demonstrated that spatial organization can be used as a design principle to make DNA circuits faster and more modular.
Christoph Zechner from Mustafa Kammash's lab was visiting for a couple of weeks in 2015. The experiments he did at the UW found their way into a nice paper. Christoph is now a group leader at the Max Planck institute and in 2016-2017 I was on a sabbatical at ETH visiting Mustafa and Martin Fussenegger.
We have yet to write a paper together but I've had so many great conversation with Michael Elowitz. The Roger Federer of science was my co-supervisor and occasional tennis partner at Caltech.
We are part of the NSF funded Molecular Programming Project.