Princeton: Center for Quantitative Biology

Amy Caudy , Ph.D. (Lewis-Sigler Fellow) studies the function and replication of mitochondria. Using genetic approaches in yeast and mammalian cell culture, she plans to clarify the relationship between mitochondrial function and cell growth. While oxidative phosphorylation is dispensable in some types of cells, an intact mitochondrial compartment is essential for cell survival. A major focus is the development of biochemical approaches to identify functional protein complexes and to validate the predictions made by genetic experiments.

Michael M. Desai , Ph.D. (Lewis-Sigler Theory Fellow) works on evolutionary dynamics, particularly in the presence of positive selection. He is studying the diversity maintained by adapting asexual populations, the effects of sex, and ways of drawing inferences from sequence data about the selective forces acting on linked sites. His primary focus is t

Maitreya Dunham , Ph.D. (Lewis-Sigler Fellow) and her group combine experimental evolution with genomic analysis to study the structure and function of genetic networks in yeast. By comparing "evolved" strains to their ancestral founders, they can study the adaptations selected in nutrient-limited chemostat growth. Growth phenotypes, cell morphology, global gene expression, and DNA copy number all change during the course of chemostat evolution. Genetic dissection of the small number of mutations responsible for these many changes should allow them to recognize the rate limiting steps and control points regulating the cells' response to long-term, narrow selection.

Matthias Kaschube , Ph.D. (Lewis-Sigler Theory Fellow) is interested in how structured collective behavior emerges in biological systems, in particular how these remarkable phenomena arise from the properties and interactions of microscopic individual components. In the mammalian cortex, he studies the formation of neural circuits underlying selective responses of neurons to visual stimuli. In Drosophila embryos, he investigates cell shape changes and the intercellular interactions involved in the coordinated collective cell movement during ventral furrow gastrulation. His aim is to characterize biological systems with quantitative precision and to develop mathematical descriptions that capture the essence of these observed phenomena.

Ethan Perlstein , Ph.D. (Lewis-Sigler Fellow) introduces small molecules, including therapeutic drugs, into simple model organisms like the budding yeast Saccharomyces cerevisiae, and studies the impact on their physiology, thereby revealing evolutionarily conserved aspects of human diseases (e.g., schizophrenia and diabetes). More specifically, using genomic and chemical-screening technologies, he assesses effects of genetic variation, both natural and engineered, on the complex physiological responses of yeast cells to therapeutic drugs, in order (1) to discern the mechanism of action of these drugs on yeast, and, (2) to translate that insight to mammalian disease models. More generally, his methodology enables a comprehensive study of the evolution of complex traits.

William S. Ryu , Ph.D. (Lewis-Sigler Fellow) studies Caenorhabditis elegans behavior and movement. He is developing new techniques to quantify and classify worm behavior using novel computer automated or assisted behavior assays, with the hope that combining high resolution behavioral data with traditional genetic and neuronal analysis will provide understanding how these behaviors are biologically implemented at a more detailed level. Some of the behaviors studied in the lab are thermotaxis, chemotaxis, social clustering, and movement through complex 2D environments.

Eva-Maria Schoetz , Ph.D. (Lewis-Sigler Fellow) studies generic physical mechanisms that play a role for cell movements and tissue formation during embryogenesis and regeneration. Cell movements and tissue flow constitute a beautiful problem of bridging scales: On the microscopic scale, cells are expressing particular genes which determine their identities and also their fate. These molecular determinants then lead to the macroscopic phenomena of cell movements and tissue arrangements, for which one needs a continuum description in terms of active fluids. A complete coarse graining, however, is not possible, since the number of cells is fairly small. Thus, a characterization of both mesoscopic (individual cell motion) and macroscopic (flow) properties is required for a full description. In my group, we want to address both scales experimentally by 3D and 4D fluorescent light microscopy and image analysis, laser ablation, application of external magnetic and electric fields, microrheology and whole tissue rheology. Experimental systems include zebrafish embryos and planaria.