School of Informatics

School of Informatics

Whole Genome Sequencing and Imaging-Based Systems Biology

By Gene Myers

Gene Myers

We give a two-part talk on our past and current work on computational problems in molecular biology at a level accessible to a general scientific audience.

In the first part we give an overview of the whole-genome shotgun sequencing method with paired end-reads that we developed and used to sequence Drosophila (2000), Human (2001) and Mouse (2001), in quick succession. Because the finishing phase of genome assembly is an order of magnitude more expensive then the shotgun phase, most genomes being sequenced today will never be finished. This makes the goal of building better whole genome assemblers more important than ever. A string graph concept developed by us (2005) portends near perfect assembly and has provided the core idea for new advances. We present the history and ideas in brief.

The second part of the talk focuses on our new work on the development of algorithms and software for the automatic interpretation of images produced by light and electron microscopy of stained samples with a particular emphasis on building 3D and 4D "atlases" of brains, developing organisms, and cellular processes. Specific project include (a) the in vivo monitoring of mitotic processes in a developing C. elegans embryo (with T. Hyman, MPI-CBG, Dresden), (b) the in situ observation of C. elegans' cells in stages L1 through adult to decode their transcriptional and functional states (with S. Kim, Stanford), (c) the detailed neuro-anatomy of an entire fly brain including all synaptic connections via a hybrid approach combining EM and light-microscopy (with colleagues at Janelia), and (d) mapping the developmental trajectory of the fly brain via the visual analysis of MARCM clones and promotor fusions (with V. Hartenstein, UCLA, G. Rubin, J. Simpson, and J. Truman, JFRC).

Whole Genome Sequencing and Imaging-Based Systems Biology Wednesday 11 June 2008, 4.00pm