Interpreting the Cancer Genome through Physical and Functional Models of the Cancer Cell

Friday, February 28, 2020 -
2:00pm to 3:00pm
The FUNG Auditorium
Trey Ideker

Professor of Medicine

University of California, San Diego

Interpreting the Cancer Genome through Physical and Functional Models of the Cancer Cell

Abstract: 

Recently we and other laboratories have launched the Cancer Cell Map Initiative (ccmi.org) and have been building momentum. The goal of the CCMI is to produce a complete map of the gene and protein wiring diagram of a cancer cell. We and others believe this map, currently missing, will be a critical component of any future system to decode a patient's cancer genome. I will describe efforts along several lines: 1. Coalition building. We have made notable progress in building a coalition of institutions to generate the data, as well as to develop the computational methodology required to build and use the maps. 2. Development of technology for mapping gene-gene interactions rapidly using the CRISPR system. 3. Causal network maps connecting DNA mutations (somatic and germline, coding and noncoding) to the cancer events they induce downstream. 4. Development of software and database technology to visualize and store cancer cell maps. 5. A machine learning system for integrating the above data to create multi-scale models of cancer cells. In a recent paper by Ma et al., we have shown how a hierarchical map of cell structure can be embedded with a deep neural network, so that the model is able to accurately simulate the effect of mutations in genotype on the cellular phenotype.

Bio: 

Dr. Trey Ideker is a Professor of Medicine at UC San Diego. He is the Director of the National Resource for Network Biology, the Cancer Cell Map Initiative and the Psychiatric Cell Map Initiative. He is a pioneer in using genome-scale measurements to construct network models of cellular processes and disease.