The emerging complexity of molecular interactions in the cell calls for a new level
of sophistication in the design of genome-wide computational approaches:
NIH Grant Will Establish Nation’s Biomedical Computing Infrastructure
ADDRESSING THE CRITICAL NEED FOR NEW WAYS TO ANALYZE THE enormous amounts of data being generated by genomics and proteomics, Columbia University has established a National Center for Biomedical Computing with an $18.5 million, five-year grant from the National Institutes of Health.
The new center, the National Center for Multi-Scale Analysis of Genetic and Cellular Networks (MAGNet), is part of a network of seven centers created by the NIH to begin developing the computational and scientific infrastructure as well as software and data management tools needed to leverage the vast core data generated in part by the Human Genome Project.
This grant is part of the NIH Roadmap for Medical Research. Of $235 million in grants for new and continuing Roadmap projects in 2005, Columbia has been awarded a combined total of nearly $50 million. Earlier in 2005, Columbia received $25 million from the Protein Structure Initiative, another component of the NIH Roadmap. In June 2005, $9 million was awarded to James Rothman, Ph.D., director of the Judith P. Sulzberger, M.D. Columbia Genome Center and the Clyde and Helen Wu Professor of Physiology, for his work with the Molecular Libraries Screening Centers Network of the NIH Roadmap.
"These NIH Roadmap grants establish Columbia as one of the nation’s major centers for computational biology and bioinformatics,” says David Hirsh, Ph.D., executive vice president for research at Columbia University. “Biomedical research is moving away from small experiments on individual genes or proteins to the simultaneous analysis of tens of thousands of genes and proteins and entire systems inside cells.”
"Computational biology, a new field of science, has the potential to revolutionize biology and the translation of biology into medicine,” says MAGNet Director Andrea Califano, Ph.D., professor of biomedical informatics and chief of bioinformatics in the Department of Biomedical Informatics. “The goal of the National Center for Biomedical Computing is to make it easier for the wider scientific community to exploit the power of computers to address fundamental biological and biomedical challenges.”
Among the seven centers, MAGNet has the unique goal of creating computational methods and tools to help solve one of the biggest challenges in biology: understanding how all the genes and proteins inside cells work together to implement specific biological processes.
“With approximately 20,000 genes in the human genome, there are trillions of possible interactions among genes and proteins within a cell. Exploring each one in the laboratory would take a very long time, even with current high throughput methods,” says Dr. Califano.
“Instead, we plan to use computers and new methods of systems biology to predict which proteins are interacting with each other and with DNA and how these interactions change in disease. Eventually, this will have a major impact on how we understand a variety of human diseases, including cancer.”
MAGNet will be housed on the Columbia University Medical Center campus in the newly established Center for Computational Biology and Bioinformatics (C2B2). C2B2 researchers play a central role in MAGnet, as well as the Protein Structure Initiative of the NIH Roadmap.
“I expect that a close synergy will evolve between the computational tools being developed in MAGnet and the analysis of the three-dimensional structure of the proteins that will be determined in the context of the Protein Structure Initiative, since C2B2 researchers will be engaged in both activities,” says C2B2 director and MAGNet co-director Barry Honig, Ph.D., professor of biochemistry and molecular biophysics and Howard Hughes Medical Institute investigator. “We also hope that C2B2 will enhance Columbia’s leadership position in this important new scientific area.”
C2B2 is an interdepartmental center that works toward catalyzing research between biology and the computational and physical sciences. It supports active research programs in such areas as computational biophysics and structural biology, the modeling of regulatory, signaling and metabolic networks, pattern recognition, machine learning, and functional genomics. The center also offers access to a range of software tools.
C2B2 is located at the medical center, but faculty members are based on both the medical and Morningside campuses of Columbia University. Center faculty have appointments in a broad range of departments, including biochemistry, biomedical informatics, biological sciences, chemistry, computer science, applied mathematics and applied physics, electrical engineering, and the Center for Computational Learning Systems.
C2B2 and MAGNet capitalize on significant investments made by AMDeC, a not-for-profit consortium of 35 New York medical schools, academic health centers, and research institutions, to build bioinformatics resources for New York state researchers. AMDeC’s Bioinformatics Core is housed within C2B2. MAGnet also leverages the interactions with two other AMDeC initiatives: the Microarray Research Center and the New York Cancer Project.
News in Brief
Columbia University Medical Center hopes to double the number of families participating in a landmark study of genetics and Alzheimer’s disease with a new $10 million, five-year grant from the National Institute on Aging. More than 500 families affected by Alzheimer’s disease currently participate in the study, and bringing the number of participating families to 1,000 will accelerate the efforts to locate the genes involved in late-onset Alzheimer’s, the most common form of the disease. The new grant continues the nationwide Alzheimer’s Disease Genetics Study, led by a Genetics Coordinating Core at Columbia University in partnership with the National Cell Repository for Alzheimer’s Disease at Indiana University. The study has already overseen the collection of 2,600 samples from 519 families, and the new grant will include follow-up and genotyping for these families. Six Alzheimer’s Disease Centers (Columbia University, Indiana University, Mayo Clinic, University of Washington, Washington University, and the University of Texas at Southwestern Medical Center at Dallas) will form a consortium with the genetics core at Columbia to coordinate follow up of families already participating in the study and to reach out to the public to recruit additional families for the research. “Many steps in the development of Alzheimer’s disease remain unknown, and the discovery of genes involved in the process will bring us critically important insights,” says the project director, Richard Mayeux, M.D., M.Sc., the Gertrude H. Sergievsky Professor of Neurology, Psychiatry, and Epidemiology at Columbia, director of the Gertrude H. Sergievsky Center and co-director of the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain. “Identifying the genes and then their function should be directly useful in the development of drugs to treat or possibly prevent the disease altogether.” Study investigators encourage families in which two or more siblings have AD or severe memory loss to consider participating in this research effort. Families can call 1-800-526-2839 or e-mail email@example.com. The study is also described at the NCRAD website at www.ncrad.org. A search is under way for a successor to RICHARD KESSIN, PH.D., who stepped down Nov. 1, 2005, after five years as associate dean of graduate students. Dr. Kessin oversaw the studies of more than 350 Graduate School of Arts and Sciences Ph.D. students in the basic sciences doctoral program. The search continues for a new executive vice president for Columbia University Medical Center and dean for P&S. The search committee has interviewed several candidates. Columbia President Lee Bollinger held town hall meetings in November 2005 to brief the medical center community and seek input from faculty, staff, and students at P&S, the School of Nursing, the School of Dental and Oral Surgery, and the Mailman School of Public Health. Members of the search committee also participated in the discussions. Gerald Fischbach, executive vice president and dean since February 2001 intends to leave the post no later than June 2006.
Glenda Garvey Teaching Academy Director, Gender Dean Named
THE FIRST DIRECTOR OF THE NEW GLENDA GARVEY TEACHING Academy and the first dean for gender equity, new positions that will help secure the future of education at the medical center and faculty development at P&S, have
been appointed by Gerald D. Fischbach, executive vice president and dean.
Thomas Garrett, M.D., professor of clinical medicine since 1996, has been named director of the Glenda Garvey Teaching Academy. Jeanine D’Armiento, M.D., Ph.D., assistant professor of medicine, has been appointed the new associate dean for gender equity and career development.
Dr. Garrett will guide and coordinate the activities of the first 12 fellows appointed to the academy in September and work with the founding members to expand the vision of the academy as it grows. He joined the faculty in 1979 but spent time at Columbia earlier as an intern, resident, and visiting clinical fellow. Other than fellowships at Memorial Sloan-Kettering Cancer Center and two years on the Cornell faculty, Dr. Garrett has been at Columbia since graduating from medical school at Queen’s University in Canada in 1971.
Dr. Garrett is course director for Pathophysiology I and II, an intensive course that runs through the entire second year of the P&S curriculum. He also directs the oncology section in the pathophysiology course and is a preceptor in the third-year clerkship in medicine.
He is a diplomate of the American Board of Internal Medicine and of Medical Oncology, a fellow of the American College of Physicians, and a member of the American Society for Clinical Oncology and the American Association for the Advancement of Science.
He has received many awards for teaching since 1990, including Teacher of the Year, the Charles W. Bohmfalk Award for Distinguished Contributions to Teaching in the Pre-Clinical Years, and the Gender Equity in Teaching Award. Besides teaching medical students, he has instructed house staff and fellows in medical oncology. He is a member of the P&S Curriculum Committee, the Department of Medicine Executive Committee, and he served on the Executive Committee of the Faculty of Medicine Faculty Council from 2002-2005.
The Glenda Garvey Teaching Academy, named for the late Glenda Garvey’69, a long-time faculty member, is unique in that it embraces the School of Nursing, the Mailman School of Public Health, the College of Dental Medicine, and the uptown component of the Graduate School of Arts and Sciences, as well as P&S. “We share common principles of education, and there is significant overlap in our goals,” says Dr. Fischbach. “Together we provide a remarkably diverse range of experiences.”
The new dean for gender equity position was created on the advice of the Task Force on Women Faculty, which was formed to identify issues facing women faculty at P&S. Dr. D’Armiento, who was a member of the task force, will guide the implementation of the task force recommendations and be responsible for fostering a climate of support and development for all P&S faculty.
Dr. D’Armiento has been a researcher, physician, and mentor at P&S since 1992. She is a diplomate of the American Board of Internal Medicine and of Pulmonary Medicine. Since 2004 she has served on the American Heart Association’s Women’s Leadership Committee and is vice president this year. She has also served on the Clinical Trials Grant Review Committee, the Executive Committee of Faculty Council, and currently is a member of the Faculty Council.
Dr. D’Armiento is a faculty member in the Department of Medicine’s molecular medicine and pulmonary medicine divisions. She received her M.D. and Ph.D. degrees from the University of Medicine and Dentistry of New Jersey and completed her residency in internal medicine at New York-Presbyterian. In 1996 she was granted a Burroughs Wellcome Career Award, designed to bolster the careers of the most promising up and coming scientists. Her research focuses on the pathogenesis of emphysema and airway injury. In particular, her laboratory is investigating the molecular consequences of acute and chronic smoke exposure.
Dr. D’Armiento also specializes in the treatment of a rare lung disease, lymphagiomyomatosis (LAM), and directs the Center for LAM and Rare Lung Diseases in Women.
“I know Dr. D’Armiento will be a valuable asset to all faculty at P&S in the coming years as we move forward with the recommendations of the task force,” says Dr. Fischbach. The task force recommendations can be reviewed online at www.cumc.columbia.edu/dept/ps/facultycouncil/docs/TaskForceonWomenFacultyFinalReport02_24_05.doc