Workshop

This workshop is co-sponsored by the Lawrence Berkeley National Laboratory and SRI International. The focus will be on the application of mathematical and computational tools to understand the properties of cancer and other biological systems. It is recognized that many biological processes cannot be understood by studying individual components. Instead, it is the interactions between these components that define the properties of the system. The past thirty years has seen the identification of dozens of processes and hundreds of genes or proteins that become disregulated during cancer development. While certain types of cancers share common properties, each cancer is a unique genetic disease where mutations in many components and pathways interact. A systems based approach has the greatest chance of determining the system malfunctions that cause each individual's disease and of identifying effective treatments. This workshop is designed to encourage and support the mathematical community's involvement in the effort to study cancer using system approaches. Conference presenters will include mathematicians and computer scientists presently involved in systems approaches to cancer and more general fields of biology. These presenters will cover general approaches to systems biology including analysis of genome scale data as well as statistical, continuous, and hybrid methods for pathway modeling. The workshop will also provide tutorials covering the use of tools and methods in systems biology as well as on the fundamental biological processes involved in cancer. In addition, the workshop will provide travel support for students and postdocs from the mathematical sciences to foster interest in this field. From a biological perspective, the workshop will capitalize on work being performed by Investigators at LBNL, SRI, and UCSF who study the signaling networks associated with breast cancer. The LBNL/SRI/UCSF program uses two main tools: SRI's Pathway Logic system is used to model the mechanisms that lead to the development of cancer. A panel of 50 breast cancer cell lines is used to represent the biological variation found in disease. The program is developing high throughput assays to characterize these cell lines and examine how they respond to manipulations of key genes. Assays include mRNA expression profiling, measurements of protein abundance, and phenotypic responses using high content screening microscopy. Data and models from this program will be shared at this workshop (prior to publication) for examination and analysis by the participants. It is hoped that participants become engaged in these problems for the long term and that the LBNL led effort will continue to provide data and models for analysis in the future. LBNL even intends to allow its experimental infrastructure to be used to test hypotheses generated by meeting participants in future years. Schedule Download schedule and abstracts (PDF file format). Wednesday, May 3 8:45 – 9:00 Welcome by MSRI Three statistics tutorials 9:00 – 9:40 Jane Fridlyand (Epidemiology & Biostatistics, UCSF): "Analysis of gene expression and CGH microarray data" 9:40 – 10:10 Keith Baggerly (Biostatistics, M D Anderson Cancer Center): "Analysis of reverse-phase protein lysate arrays" 10:10 –10:30 Frances Tong (Statistics, UCB): "Normalization of Western blots" 10:30 – 11:00 Tea Break 11:00 – 12:00 Joe Gray (Life Sciences, LBNL): “Predicting response to pathway targeted cancer therapies; an ICBP systems opportunity” 12:00 –1:30 Lunch 1:30 – 2:30 Claire Tomlin (Aeronautics & Astronautics, Stanford University): "Using the adjoint method for parameter identification of large scale protein regulatory networks. Application to planar cell polarity in Drosophila" 2:30 – 3:30 Rich Neve (Life Sciences, LBNL): "The ICBP data set; an EPHA2 example" 3:30 – 4:00 Tea Break 4:00 – 5:00 Claire Tomlin (Aeronautics & Astronautics, Stanford University): "Hybrid system models for protein regulatory networks - Models and analysis methods. Application to Notch Delta signaling" Thursday, May 4 8:30 – 9:30 Carolyn Talcott (Computer Science, SRI International): "Pathway Logic Models" 9:15 – 10:00 Paraic Kenny (Life Sciences, LBNL): "3D models of normal and malignant breast epithelial cells" 10:00 – 10:45 Michael Korn (Cancer Center USCF): “Systems-based analyses of response to targeted therapies in cancer cells” 10:45 – 11:15 Tea Break 11:15 – 12:15 Paul Spellman (LifeSciences, LBNL): "Pathway modelling" 12:15 – 1:45 Lunch 1:45 – 2:30 Mary Helen Barcellos-Hoff (Life Sciences, LBNL): "Integrative Radiation Biology" 2:30 – 3:30 Mike West (Statistics & Decision Sciences, Duke University): "Data, Models and Computation in the Duke NCI Integrative Cancer Biology Program" 3:30 – 4:00 Tea Break 4:00 – 5:00 Bud Mishra (Computer Science, NYU): “Inheritance of Loss: Computational Systems Biology for Cancer” Friday, May 5 8:30 – 9:15 Damir Sudar (Life Sciences, LBNL): "Computational bioimaging and informatics, I" 9:15 – 10:00 Bahram Parvin (Life Sciences, LBNL): "Computational bioimaging and informatics, II" 10:00 – 10:45 Larry Lok (Molecular Sciences Institute, Berkeley): "Optimal binning strategies" 10:45 – 11:15 Tea Break 11:15 – 12:15 Trey Ideker (Bioengineering UCSD): "Protein network comparative genomics" 12:15 – 1:30 Lunch 1:30 – 2:30 Jasmine Zhou (Molecular and Computational Biology USC): "Identifying cancer genetic network signature from integrative microarray analysis" 2:30 – 3:30 Ben Raphael (Computer Science UCSD): "Analysis of large-scale alterations in tumor genomes" 3:30 – 4:00 Tea Break 4:00 – 5:00 Steve Ethier (Karmanos Cancer Institute) & Greg Dewey (Keck Graduate Institute): "Network Analysis of Gene Expression Kinetics in Human Breast Cancer Cells"