Interpreting the cancer genome through physical and functional models of the cancer cell

Trey Ideker.jpg

Trey Ideker

Director & Founding Chair of Systems Biology,
Max Planck Institute for Molecular Cell Biology and Genetics

Monday, October 7, 2019
Room 1202, EBU-3B

Faculty Host
Vineet Bafna



Recently we and other laboratories have launched the Cancer Cell Map Initiative ( 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.


Dr. 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.