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Workshop

Mathematical Systems Biology of Cancer May 03, 2006 - May 05, 2006
Registration Deadline: April 24, 2006 over 8 years ago
To apply for Funding you must register by: February 03, 2006 almost 9 years ago
Organizers Dick Karp, Bahram Parvin, Terry Speed, Paul Spellman, Carolyn Talcott, Wing Wong
Speaker(s)

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Description

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:

  1. SRI's Pathway Logic system is used to model the mechanisms that lead to the development of cancer.
  2. 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"


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 has preferred rates at the Rose Garden Inn, depending on room availability. Reservations may be made by calling 1-800-992-9005 OR directly on their website. Click on Corporate at the bottom of the screen and when prompted enter code MATH (this code is not case sensitive). By using this code a new calendar will appear and will show the MSRI rate on all room types available.

MSRI has preferred rates at the Hotel Durant. Reservations may be made by calling 1-800-238-7268. When making reservations, guests must request the MSRI preferred rate. If you are making your reservations on line, please go to this link and enter the promo/corporate code 123MSRI. Our preferred rate is $139 per night for a Deluxe Queen/King, based on availability.

MSRI has preferred rates of $149 - $189 plus tax at the Hotel Shattuck Plaza, depending on room availability. Guests can either call the hotel's main line at 510-845-7300 and ask for the MSRI- Mathematical Science Research Inst. discount; or go to www.hotelshattuckplaza.com and click Book Now. Once on the reservation page, click “Promo/Corporate Code“ and input the code: msri.

MSRI has preferred rates of $110 - $140 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 “I am an individual traveler affiliated with MSRI”.

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

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Schedule
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May 03, 2006
Wednesday
09:00 AM - 09:40 AM
  Analysis of gene expression and CGH
Jane Fridlyand
09:40 AM - 10:10 AM
  Analysis of reverse-phase protein
Keith Baggerly
10:10 AM - 10:30 AM
  Normalization of Western blots"
Frances Tong
11:00 AM - 12:00 PM
  Predicting response to pathway targeted cancer therapies;
Joe Gray (Lawrence Berkeley Laboratory)
01:30 PM - 02:30 PM
  Hybrid system models for protein
Claire Tomlin
02:30 PM - 03:30 PM
  The ICBP data set; an EPHA2 example
Rich Neve
04:00 PM - 05:00 PM
  Using the adjoint method for
Claire Tomlin
May 04, 2006
Thursday
08:30 AM - 09:30 AM
  Pathway Modelling
Paul Spellman (Lawrence Berkeley Laboratory)
09:15 AM - 10:00 AM
  3D models of normal and malignant breast epithelial cells
Paraic Kenny
11:15 AM - 12:15 PM
  Pathway Logic Models"
Carolyn Talcott (SRI International)
01:45 PM - 02:30 PM
  Integrative Radiation Biology
Mary-Helen Barcellos-Hoff
04:00 PM - 05:00 PM
  Inheritance of Loss: Computational Systems Biology for Cancer
Bud Mishra
May 05, 2006
Friday
08:30 AM - 09:15 AM
  Computational bioimaging and informatics, I
Damir Sudar
09:15 AM - 10:00 AM
  Computational bioimaging and informatics, II
Bahram Parvin
10:00 AM - 10:45 AM
  Optimal binning strategies"
Larry Lok
11:15 AM - 12:15 PM
  Protein network comparative genomics
Trey Ideker
01:30 PM - 02:30 PM
  Identifying cancer genetic network signature from integrative microarray analysis
Jasmine Zhou
02:30 PM - 03:30 PM
  Analysis of large-scale alterations in tumor genomes
Ben Raphael
04:00 PM - 05:00 PM
  Network Analysis of Gene Expression Kinetics in Human Breast Cancer Cells
Steve Ethier