Mathematical Sciences Research Institute - Mathematical Systems Biology of Cancer II

This workshop is co-sponsored by the Lawrence Berkeley National Laboratory and SRI International.

We will again focus 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 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.

Previous participants are strongly encouraged to attend again, and should notify the conference organizers if they have work that utilizes data from the Integrative Cancer Biology Program that may be of general interest.

A block of rooms has been reserved at the Rose Garden Inn. Reservations may be made by calling 1-800-992-9005 OR directly on their website. Click on "Groups" on the bottom of the page and enter the appropriate group code CGMSBC (this code is not case sensitive) into box labeled: "I am an Attendee" - this will open up a window showing all of the group information. You will proceed from there.
The cut-off date for reservations is October 1, 2007.

Schedule
Wednesday October 24, 2007
08:45AM - 09:00AM	Welcome by MSRI
08:45AM - 05:00PM	TUTORIALS
09:00AM - 09:45AM	Elizabeth Purdom	Introduction to Exon Arrays (See Abstract)
09:45AM - 10:30AM	Sach Mukherjee	Monte Carlo Methods For Learning Biological Networks (See Abstract)
11:00AM - 12:00PM	William Chen	Issues in Modeling Signal Transduction and Other Reaction Networks with ODEs
12:00PM - 01:30AM	Lunch
01:30PM - 02:15PM	Li Lang	The Applications of Differential Equation Based Nonlinear Regression in Pharmacokinetics and Metabolomics
02:15PM - 03:00PM	Serban Nacu	Searching for differentially expressed pathways in microarray data (See Abstract)
03:00PM - 03:30PM	Tea break
03:30PM - 04:15PM	Ben Raphael	Analyzing Structural Rearrangements in Cancer Genomes (See Abstract)
04:15PM - 05:00PM	Susan Holmes	New in situ data for the analysis of interactions between cancer and the immune system in auxillary lymph nodes (See Abstract)
05:00PM - 06:00PM	Reception
Thursday October 25, 2007
09:00AM - 05:00PM	INVITED SPEAKER PRESENTATIONS
09:00AM - 10:00AM	Suzanne Gaudet	Analysis of the regulators of caspase activation by death receptor ligands (See Abstract)
10:00AM - 10:30AM	Coffee break
10:30AM - 11:30AM	Neil Hayes	Genomic Classification of Lung Cancer for Clinical Use (See Abstract)
11:30AM - 12:30PM	Lingchong You	A Bistable Rb/E2F Switch: A Model for Mammalian Cell Cycle Entry (See Abstract)
12:30PM - 01:30PM	Lunch
01:30PM - 02:30PM	Garry Nolan	Inference engines for primary cell signaling using patient samples
02:30PM - 03:30PM	Khuloud Jaqaman	Stochastic models of yeast kinetochore-microtubule interactions (See Abstract)
03:30PM - 04:00PM	Tea break
04:00PM - 05:00PM	Alan Perelson	Modeling viral infections MSRI Biology Colloquium Lecture Series
Friday October 26, 2007
09:00AM - 05:00PM	DATA ANALYSIS PRESENTATIONS
09:00AM - 09:45AM	Introduction to ICBP data
09:45AM - 10:30AM	Mark Robinson	A Comparison of Affymetrix Gene Expression Arrays (See Abstract)
10:30AM - 11:00AM	Coffee break
11:00AM - 11:45AM	Elizabeth Purdom	Detection of Alternative Splicing with Exon Arrays
12:00PM - 01:30PM	Lunch
01:30PM - 02:15PM	Dustin Potter	The Analysis of Differential Methylation Hybridization Data (See Abstract)
02:15PM - 03:00PM	Keith Baggerly	Cell Lines, Microarrays, Drugs and Disease: Trying to Predict Response to Chemotherapy (See Abstract)
03:00PM - 03:30PM	Tea break
03:30PM - 04:15PM	Ben Raphael	Derivation and Consequences of Rearranged Cancer Genomes (See Abstract)
04:15PM - 05:00PM	Adam Olshen	Segmentation of Array CGH Data with Application to Allele Specific Copy Number, Clonality, and Copy Number Variation (See Abstract)

For more information:
Questions about this workshop should be sent either by email to

436@msri.org

or by regular mail to:

Mathematical Systems Biology of Cancer II Mathematical Sciences Research Institute 17 Gauss Way, Berkeley, CA 94720-5070. USA

The Institute is committed to the principles of Equal Opportunity and Affirmative Action.

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Mathematical Systems Biology of Cancer II

Schedule

Wednesday October 24, 2007

Thursday October 25, 2007

Friday October 26, 2007