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We study large multinucleate cells such as fungi, muscle and placenta to understand how cells are organized in time and space.  Using quantitative live cell microscopy, biochemical reconstitution and computational approaches we examine how the physical properties of molecules generate spatial patterning of cytosol and scaling of cytoskeleton scaffolds in the cell cycle.

My group develops and deploys computational tools to predict physiological function and dysfunction. We are interested in a range of applications in medicine and biology, but our primary focus is the cardiovascular system. My group is actively developing fluid-structure interaction (FSI) models of the heart, arteries, and veins, and of cardiovascular medical devices, including bioprosthetic heart valves, ventricular assist devices, and inferior vena cava filters. We are also validating these models using in vitro and in vivo approaches. We also model cardiac electrophysiology and electro-mechanical coupling, with a focus on atrial fibrillation (AF), and aim to develop mechanistically detailed descriptions of thrombosis in AF. This work is carried out in collaboration with clinicians, engineers, computer and computational scientists, and mathematical scientists in academia, industry, and regulatory agencies.

We focus on a variety of design goals including the creation of novel protein-protein interactions, protein structures, vaccine antigens and light activatable protein switches. Central to all of our projects is the Rosetta program for protein modeling. In collaboration with developers from a variety of universities, we are continually adding new features to Rosetta as well as testing it on new problems.

The Yun Li group develops statistical methods and computational tools for modern genetic, genomic, and epigenomic data. We do both method development and real data applications. The actual projects in the lab vary from year to year because I am motivated by real data problems, and genomics is arguably (few people argue with me though) THE most fascinating field with new types and huge amount of data generated at a pace more than what we can currently deal with. For current projects, please see:

One of the most amazing discoveries of recent years has been the profound role of RNA in regulating all areas of biology. Further, the functions of many RNA molecules require that an RNA fold back on itself to create intricately and complexly folded structures. Until recently, however, we had little idea of the broad contributions of RNA structure and function because there simply did not exist rigorous methods for understanding RNA molecules in cells and viruses. The vision of our laboratory is therefore, first, to invent novel chemical microscopes that reveal quantitative structure and function interrelationships for RNA and, second, to apply these RNA technologies to broadly important problems in biology. Mentoring and research in the lab are highly interdisciplinary. Students learn to integrate ideas and concepts spanning chemical and computational biology, and technology development, and extending to practical applications in virology, understanding biological processes in cells, and discovery of small molecule ligands targeted against medically important RNAs. Each student has a distinct project which they drive to an impactful conclusion, but do so as part of the lab team which, collectively, has shown an amazing ability to solve big problems in RNA biology. The overarching goal of mentoring in the lab is to prepare students for long-term leadership roles in science.