Center for Computational Biology Seminar: Dr. Robert Murphy, Professor and Head of Computational Biology and Professor of Biological Sciences, Biomedical Engineering and Machine Learning, Carnegie Mellon University

Seminar | September 6 | 4-5 p.m. | 125 Li Ka Shing Center

 Center for Computational Biology

Title: Integrating Information from Diverse Microscope Images: Learning and Using Generative Models of Cell Organization

Abstract: Systems biology efforts require accurate, cell-type specific information about the shape and distributions of subcellular structures and the distributions of proteins and other macromolecules in order to be able to capture and simulate cellular spatiotemporal dynamics. We have developed tools to build generative models of cell organization directly from microscope images of many cells. Our open source system, CellOrganizer (http://CellOrganizer.org), contains components that can build probabilistic generative models of cell, nuclear and organelle shape, and organelle, microtubule and protein distribution. Critically, these models can be created from images of different proteins and organelles and then combined to create synthetic cells having many more components than can be imaged together. The models also capture heterogeneity within cell populations, and can capture dependence of the pattern of one structure upon others. The parameters of these models are as a highly interpretable basis for analyzing perturbations (e.g., induced by drug addition), and generative models of cell organization can also be used as a basis for cell simulations to identify mechanisms underlying cell behavior. Lastly, we have recently developed approaches to identify potential causal relationships between different protein locations, for example, learning that a change in location of one protein in one cell region is always followed by a change in location of a different protein at a different time.

 Light refreshments will be provided at reception from 3:30-4:00m, 125 LKS foyer.

 ccbadmin@berkeley.edu