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ICBP Centers
Case Western Reserve University
University Hospital of Cleveland
Principal Investigator: Timothy Kinsella, M.D.
Website: http://www.case.edu/med/icbp/
Summary
Description of Center: DNA repair and its relation to drugs: a clinical perspective. Case ICBP is working towards unraveling the role of DNA repair pathways in the processing of clinically important nucleotide analogs. Case ICBP center is serving to create a set of DNA repair models which can be used in combination with other centers to facilitate the understanding of cancer therapeutics at higher levels of organization.
Dana Farber Cancer Institute
Principal Investigator: Todd Golub, M.D.
Website: http://www.broad.mit.edu/cancer/collaborations/icbp/
Summary
The Dana-Farber Cancer Institute and the Broad Institute of MIT and Harvard ICBP center focuses on creating predictive models for cancer defined in terms of cellular modules (such as pathways). We will focus specifically on the kinases, which are arguably the most critical modules in establishing and maintaining cancer cell survival. More specifically, we propose to create computational models able to predict kinase activity in a biological sample (cell line or tumor). Focusing initially on each of the approximately 100 tyrosine kinases, the predictive models will consist of ‘cellular signatures’ (distinctive sets of co-expressed genes) that can accurately predict:
Duke University
Principal Investigator: Joseph Nevins, Ph.D.
Website: http://icbp.genome.duke.edu/
Summary
The Duke Integrative Cancer Biology Program is focused on the development of data and computational tools that will substantially advance our understanding of critical cell signaling pathways. We are focusing primarily on the Rb-E2F pathway with additional interest in the intersection with Ras, Myc and p53. The activity of these pathways is critical to the control of normal cell proliferation, and many aspects of their deregulation is crucial to the development of human cancer. The Duke ICBP is developing an integrated approach to analysis of genomic-scale measures of gene expression, incorporating protein interaction analysis together with DNA sequence predictions, whose interpretation will underlie advances towards a comprehensive understanding of the complex regulatory network comprised of these fundamental pathways that contribute to human cancer.
E. O. Lawrence Berkeley National Laboratory
Principal Investigator: Joe W. Gray, Ph.D.
Website: http://icbp.lbl.gov/index.htm
Summary
The goal of the Integrative Cancer Biology Program (ICBP) Award entitled "Systems based predictions of responses to cancer therapy" is to develop experimental and computational strategies to predict individual responses to therapies targeted along the Raf-MEK-ERK signaling pathway. The overall thrust of this program is the integration of experimental and computational approaches towards the understanding of cancer biology using both 2D and 3D cell culture models. While experimental data are supported by cell-based assays and expression data, in silico models leverage deterministic and probabilistic techniques to support the integrative cancer biology program.
Massachusetts General Hospital
Principal Investigator: Thomas Deisboeck, M.D.
Website: http://www.cvit.org
Summary
CViT is building the first web-based community dedicated to computational and mathematical cancer modeling and the IT infrastructure to support it, including a digital model repository. CViT's long term goal is the design and development of a module-based tool-kit for cancer research.
Guided by a complex systems approach, the resulting Virtual Tumor will integrate multiple levels of information about cancer, including molecular, cellular, tissue, organ, and patient clinical data.
Both CViT platform and Virtual Tumor tool set will allow mathematicians and clinicians to interact online to make testable predictions with the goal of improving the prevention, diagnosis, prognosis, and therapy of cancer.
Massachusetts Institute of Technology (MIT)
Principal Investigator: Doug Lauffenburger, Ph.D.
Website: http://web.mit.edu/icbp/
Summary
The research in the MIT Integrative Cancer Biology Program is organized into three projects, each involving scientists working at different levels of analysis - cancer biology, cell biology and computational modeling. The members of each project interact closely to integrate these different approaches to understand the underlying molecular and cellular processes that govern each process and to develop testable models to drive future understanding, analysis, and intervention into those processes and their malfunctions in cancer.
The focus of the MIT Integrative Cancer Biology Program is to advance the state of the art in cancer biology beyond the analysis of data to the construction of quantitative, predictive and testable, computational and mathematical models based on that data.
The MIT ICBP center complements those of other efforts within the ICBP program and the larger NCI through its focus on three thrust areas that cover three key processes involved in cancer progression (i) mitogenic signaling networks, (ii) DNA repair, and (iii) migration signaling networks. The MIT ICBP center also has a strong emphasis on producing the next generation of young investigators trained in interdisciplinary investigations of cancer.
The Ohio State University
Principal Investigator: Tim H-M Huang, Ph.D.
Websites: http://icbp.med.ohio-state.edu/
http://mbi.osu.edu/
http://bioinformatics.med.ohio-state.edu/
Summary
Our Center assembles an integrated team of scientists to uncover how the epigenome interacts with the genome in the genesis and the progression of human cancers, at both the global level and the single gene level, to provide opportunities for personalized medicine in cancer prevention and recurrence.
The OSU-ICBP Center uses cutting-edge microarray technologies coupling with novel bioinformatics and computational approaches to unravel the role of epigenetic alternations in human cancers and their microenvironment in the dysregulated cellular and molecular functions observed in this disease.
The OSU-ICBP team systematically amasses information on the cancer epigenome and provides informatics tools to the ICBP and the cancer community to integrate this new body of information with global genomic data to shed light on the complex nature of cancer biology.
Stanford University School of Medicine
Principal Investigator: Sylvia Plevritis, Ph.D.
Website: http://icbp.stanford.edu
Summary
Stanford ICBP aims to foster collaborations in computational cancer biology between researchers from disciplines as diverse as oncology, statistics, aeronautics, computer sciences, and others.
Stanford is a major clinical center for lymphoma, and one of our major aims is to understand the mechanisms driving the transformation of follicular lymphoma to the more aggressive diffuse large B-cell lymphoma. We also work closely with oncologists studying transgenic mouse models of cancer.
Vanderbilt University Medical Center
Principal Investigator: Vito Quaranta, M.D.
Website: http://www.vanderbilt.edu/VICBC
Summary
Cancer is a multifactorial disease too complex for intuitive understanding. Its outcome is the result of a complex interplay between conflicting factors, which are specific to different cancers, and different patients. Thus, cancer is particularly suited for integrative approaches, such as mathematical modeling. The Vanderbilt Integrative Cancer Biology Center (VICBC) fuses several disciplines (BioMathematics, Cancer Biology, Training, Bioengineering and Cancer Imaging) in the quest to develop mathematical models of Cancer Invasion that should enable a rational approach for accurate diagnostic staging and therapeutic targeting of cancer. Our focus is on the parameterization of the Mathematical Models of Cancer (i.e., hybrid discrete continuous) at the cellular, multicellular and organ biological scales. This approach fits well with that of other ICBP Centers that focus on molecular and subcellular scales.
University Hospital of Cleveland
Principal Investigator: Timothy Kinsella, M.D.
Website: http://www.case.edu/med/icbp/
Summary
Description of Center: DNA repair and its relation to drugs: a clinical perspective. Case ICBP is working towards unraveling the role of DNA repair pathways in the processing of clinically important nucleotide analogs. Case ICBP center is serving to create a set of DNA repair models which can be used in combination with other centers to facilitate the understanding of cancer therapeutics at higher levels of organization.
Dana Farber Cancer Institute
Principal Investigator: Todd Golub, M.D.
Website: http://www.broad.mit.edu/cancer/collaborations/icbp/
Summary
The Dana-Farber Cancer Institute and the Broad Institute of MIT and Harvard ICBP center focuses on creating predictive models for cancer defined in terms of cellular modules (such as pathways). We will focus specifically on the kinases, which are arguably the most critical modules in establishing and maintaining cancer cell survival. More specifically, we propose to create computational models able to predict kinase activity in a biological sample (cell line or tumor). Focusing initially on each of the approximately 100 tyrosine kinases, the predictive models will consist of ‘cellular signatures’ (distinctive sets of co-expressed genes) that can accurately predict:
- whether a given kinase pathway is activated in the sample;
- whether a given kinase pathway is essential for viability; and
- whether a given chemical or drug modulates the kinase pathway.
Duke University
Principal Investigator: Joseph Nevins, Ph.D.
Website: http://icbp.genome.duke.edu/
Summary
The Duke Integrative Cancer Biology Program is focused on the development of data and computational tools that will substantially advance our understanding of critical cell signaling pathways. We are focusing primarily on the Rb-E2F pathway with additional interest in the intersection with Ras, Myc and p53. The activity of these pathways is critical to the control of normal cell proliferation, and many aspects of their deregulation is crucial to the development of human cancer. The Duke ICBP is developing an integrated approach to analysis of genomic-scale measures of gene expression, incorporating protein interaction analysis together with DNA sequence predictions, whose interpretation will underlie advances towards a comprehensive understanding of the complex regulatory network comprised of these fundamental pathways that contribute to human cancer.
E. O. Lawrence Berkeley National Laboratory
Principal Investigator: Joe W. Gray, Ph.D.
Website: http://icbp.lbl.gov/index.htm
Summary
The goal of the Integrative Cancer Biology Program (ICBP) Award entitled "Systems based predictions of responses to cancer therapy" is to develop experimental and computational strategies to predict individual responses to therapies targeted along the Raf-MEK-ERK signaling pathway. The overall thrust of this program is the integration of experimental and computational approaches towards the understanding of cancer biology using both 2D and 3D cell culture models. While experimental data are supported by cell-based assays and expression data, in silico models leverage deterministic and probabilistic techniques to support the integrative cancer biology program.
Massachusetts General Hospital
Principal Investigator: Thomas Deisboeck, M.D.
Website: http://www.cvit.org
Summary
CViT is building the first web-based community dedicated to computational and mathematical cancer modeling and the IT infrastructure to support it, including a digital model repository. CViT's long term goal is the design and development of a module-based tool-kit for cancer research.
Guided by a complex systems approach, the resulting Virtual Tumor will integrate multiple levels of information about cancer, including molecular, cellular, tissue, organ, and patient clinical data.
Both CViT platform and Virtual Tumor tool set will allow mathematicians and clinicians to interact online to make testable predictions with the goal of improving the prevention, diagnosis, prognosis, and therapy of cancer.
Massachusetts Institute of Technology (MIT)
Principal Investigator: Doug Lauffenburger, Ph.D.
Website: http://web.mit.edu/icbp/
Summary
The research in the MIT Integrative Cancer Biology Program is organized into three projects, each involving scientists working at different levels of analysis - cancer biology, cell biology and computational modeling. The members of each project interact closely to integrate these different approaches to understand the underlying molecular and cellular processes that govern each process and to develop testable models to drive future understanding, analysis, and intervention into those processes and their malfunctions in cancer.
The focus of the MIT Integrative Cancer Biology Program is to advance the state of the art in cancer biology beyond the analysis of data to the construction of quantitative, predictive and testable, computational and mathematical models based on that data.
The MIT ICBP center complements those of other efforts within the ICBP program and the larger NCI through its focus on three thrust areas that cover three key processes involved in cancer progression (i) mitogenic signaling networks, (ii) DNA repair, and (iii) migration signaling networks. The MIT ICBP center also has a strong emphasis on producing the next generation of young investigators trained in interdisciplinary investigations of cancer.
The Ohio State University
Principal Investigator: Tim H-M Huang, Ph.D.
Websites: http://icbp.med.ohio-state.edu/
http://mbi.osu.edu/
http://bioinformatics.med.ohio-state.edu/
Summary
Our Center assembles an integrated team of scientists to uncover how the epigenome interacts with the genome in the genesis and the progression of human cancers, at both the global level and the single gene level, to provide opportunities for personalized medicine in cancer prevention and recurrence.
The OSU-ICBP Center uses cutting-edge microarray technologies coupling with novel bioinformatics and computational approaches to unravel the role of epigenetic alternations in human cancers and their microenvironment in the dysregulated cellular and molecular functions observed in this disease.
The OSU-ICBP team systematically amasses information on the cancer epigenome and provides informatics tools to the ICBP and the cancer community to integrate this new body of information with global genomic data to shed light on the complex nature of cancer biology.
Stanford University School of Medicine
Principal Investigator: Sylvia Plevritis, Ph.D.
Website: http://icbp.stanford.edu
Summary
Stanford ICBP aims to foster collaborations in computational cancer biology between researchers from disciplines as diverse as oncology, statistics, aeronautics, computer sciences, and others.
Stanford is a major clinical center for lymphoma, and one of our major aims is to understand the mechanisms driving the transformation of follicular lymphoma to the more aggressive diffuse large B-cell lymphoma. We also work closely with oncologists studying transgenic mouse models of cancer.
Vanderbilt University Medical Center
Principal Investigator: Vito Quaranta, M.D.
Website: http://www.vanderbilt.edu/VICBC
Summary
Cancer is a multifactorial disease too complex for intuitive understanding. Its outcome is the result of a complex interplay between conflicting factors, which are specific to different cancers, and different patients. Thus, cancer is particularly suited for integrative approaches, such as mathematical modeling. The Vanderbilt Integrative Cancer Biology Center (VICBC) fuses several disciplines (BioMathematics, Cancer Biology, Training, Bioengineering and Cancer Imaging) in the quest to develop mathematical models of Cancer Invasion that should enable a rational approach for accurate diagnostic staging and therapeutic targeting of cancer. Our focus is on the parameterization of the Mathematical Models of Cancer (i.e., hybrid discrete continuous) at the cellular, multicellular and organ biological scales. This approach fits well with that of other ICBP Centers that focus on molecular and subcellular scales.
last modified
2007-04-11 13:53
