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Mathematical Systems Biology of Cancer II October 24, 2007 - October 26, 2007
Registration Deadline: October 26, 2007 over 15 years ago
To apply for Funding you must register by: July 24, 2007 almost 16 years ago
Parent Program: --
Organizers Joe Gray, Elizabeth Purdom, Terry Speed and Paul Spellman.

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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.
Keywords and Mathematics Subject Classification (MSC)
Primary Mathematics Subject Classification No Primary AMS MSC
Secondary Mathematics Subject Classification No Secondary AMS MSC
Funding & Logistics Show All Collapse

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To apply for funding, you must register by the funding application deadline displayed above.

Students, recent Ph.D.'s, women, and members of underrepresented minorities are particularly encouraged to apply. Funding awards are typically made 6 weeks before the workshop begins. Requests received after the funding deadline are considered only if additional funds become available.

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MSRI does not hire an outside company to make hotel reservations for our workshop participants, or share the names and email addresses of our participants with an outside party. If you are contacted by a business that claims to represent MSRI and offers to book a hotel room for you, it is likely a scam. Please do not accept their services.

MSRI has preferred rates at the Hotel Shattuck Plaza, depending on room availability. Guests can call the hotel's main line at 510-845-7300 and ask for the MSRI- Mathematical Science Research Institute discount. To book online visit this page (the MSRI rate will automatically be applied).

MSRI has preferred rates at the Graduate Berkeley, depending on room availability. Reservations may be made by calling 510-845-8981. When making reservations, guests must request the MSRI preferred rate. Enter in the Promo Code MSRI123 (this code is not case sensitive).

MSRI has preferred rates at the Berkeley Lab Guest House, depending on room availability. Reservations may be made by calling 510-495-8000 or directly on their website. Select "Affiliated with the Space Sciences Lab, Lawrence Hall of Science or MSRI." When prompted for your UC Contact/Host, please list Chris Marshall (coord@msri.org).

MSRI has a preferred rates at Easton Hall and Gibbs Hall, depending on room availability. Guests can call the Reservations line at 510-204-0732 and ask for the MSRI- Mathematical Science Research Inst. rate. To book online visit this page, select "Request a Reservation" choose the dates you would like to stay and enter the code MSRI (this code is not case sensitive).

Additional lodging options may be found on our short term housing page.

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