Plenary Session 3 – Computational Methods

9/1 8:00 - 10:30, Memorial Auditorium

Plenary Session 3.1

Adam P. Arkin

University of California, Berkeley.

Plenary Session 3.2

Toward a Whole-Cell Model of Mycoplasma genitalium

Markus W. Covert

Stanford University.

Plenary Session 3.3

Understanding Gene Regulation: From Networks to Mechanisms

Daphne Koller

Stanford University.

Gene expression is regulated by a complex network that involves multiple layers. The activity of this network is modified by multiple internal and external perturbations. This talk describes computational methods that utilize high-throughput data and statistical models to understand these processes. I will show how gene expression data from a population of genetically diverse individuals can be used to uncover genetic mechanisms that cause phenotypic diversity. We demonstrate the applicability of these methods to tasks ranging from understanding basic regulatory mechanisms (such as chromatin modification or mRNA degradation) to to elucidating mechanisms involved in human disease.

Plenary Session 3.4

Imaging Bioinformatics

Gene Myers

Janelia Farm Research Campus, Howard Hughes Medical Institute.

Arguably the most significant contribution of the human genome project is that we can now build a recombinant construct of every gene and every promotor in C. elegans (worm), D. melanogaster (fly), M. musculus (mouse), and H. sapiens (human). These include fluorescent proteins and other markers that can be induced at controlled time points via a change in temperature, light, or chemistry. Combined with tremendous advances in light and electron microscopy in recent years, I believe we are now poised to visualize the meso-scale of the cell, and the development small organs (e.g. a fly's brain) and organisms (e.g. the worm) at the resolution of individual cells. These advances will require new imaging and data-mining methods for what I call “imaging bioinformatics”.

Toward this end, my group is working on a number of imaging projects along these lines. These include (a) studies of development and gene expression in worms and flies, (b) the biophysics of mitosis, and (c) the construction of a detailed reconstruction of a fly's brain. We describe preliminary results and extrapolate on what we hope to be able to infer from such data.