To effectively address our questions, we often work with other laboratories. Our key collaborators are:
We work closely with the Black lab on specific questions of the X-inactivation problem.
Together with the Guttman lab, we examined how Xist RNA spreads across the X chromosome. Employing the powerful RAP-seq technology, developed in Mitch’s lab, we found that Xist initially localizes to sites on the X chromosome that are in close spatial proximity to the Xist transcription locus, suggesting that Xist exploits the three-dimensional conformation of the X-chromosome to spread across the X (see manuscript). We continue to work closely with the Guttman lab on many of our Xist-related questions. We also have bi-monthly joined lab meetings alternating between UCLA and Caltech.
The Elowitz Lab is interested in how genetic circuits enable individual cells to make decisions, oscillate, and communicate with one another. They are experts in single cell expression analysis, time-lapse imaging, and mathematical modeling. Together with the Elowitz lab, we are attempting to reveal the specific sequences of dynamic events that occur in individual cells as they reprogram to pluripotency. Kathrin also serves on the thesis committee of several graduate students in the Elowitz lab.
Right from the beginning our lab collaborated extensively with the Lowry lab. Starting out, we demonstrated that the Yamanaka approach can also be applied to human cells, establishing some of the first human iPSC lines (see manuscript). Subsequently, we derived disease specific human iPSC lines and began to study Rett Syndrome using these lines. We continue to closely interact, share a NIH program project grant, and are starting to look at chromatin processes in neural differentiation together.
The Kosuri lab develops and leverages new technologies in DNA synthesis, DNA sequencing, and genome engineering to study gene regulation and develop new synthetic biology products. Together, we are using these technologies to address the regulation of cell identity, genome organization, reprogramming, and X-inactivation.
The Clark lab uses mouse model and pluripotent stem cells to understand the epigenetic reprogramming in the germ line. We work together on the regulation of X-inactivation in early human development.
The Pellegrini lab develops new computational approaches to interpret genomics data and integrate various kinds of data generated by high-throughput sequencing. We have been working together for a long time to analyze Plath lab genomics data, and Matteo Pellegrini and Kathrin also co-mentor graduate students.
The focus of the Ernst lab is on developing and applying machine learning methods for the analysis of high-throughput experimental data to address problems in epigenomics and gene regulation. We are working very closely with the Ernst laboratory to define the epigenomics roadmap to pluripotency during reprogramming.
We share a NIH program project grant with the Zaret, Smale, and Lowry labs. Currently, we are comparing the mouse and human reprogramming processes with the Zaret lab. The Smale lab is supporting us in our reprogramming and X-inactivation studies.