NIH Common Fund programs are large-scale projects designed to collect cutting-edge biomedical research data from human cells, tissues, and patients to rapidly advance biomedical research.
The Common Fund Data Ecosystem (CFDE) program was created by the NIH to enhance the findability, accessibility, interoperability, and reusability of data generated by NIH Common Fund programs, thereby ensuring adherence to the FAIR guiding principles for scientific data.
This ensures that researchers can efficiently explore NIH Common Fund-produced datasets to facilitate new biomedical discoveries and will enable researchers to search across Common Fund-produced datasets to ask complex scientific and clinical questions to catalyze new biomedical discoveries.
Building on the successes of the pilot phase of the CFDE program, and with a five-year investment of $17 million, the NIH has established two new centers: the CFDE Data Resource Center and the CFDE Knowledge Center. Investigators from Icahn Mount Sinai and the University of California San Diego were selected to lead the CFDE Data Resource Center, and investigators from the Broad Institute of MIT and Harvard were awarded the CFDE Knowledge Center.
“By integrating data from various omics technologies and by making these datasets readily available for analysis and visualization with artificial intelligence and machine learning, many discoveries can emerge,” says the Contact Principal Investigator of the CFDE Data Resource Center, Avi Ma’ayan, PhD, Director of the Mount Sinai Center for Bioinformatics and Professor of Pharmacological Sciences, and Artificial Intelligence and Human Health. “We are delighted that the NIH has recognized our past contributions to the CFDE, the library of integrated cellular-based signatures (LINCS), and the illuminating the druggable genome (IDG) Common Fund programs and trusts us to lead this new effort.”
“This is a unique opportunity to enable a biomedical researcher to make innovative discoveries through full utilization of the data that has emerged from the large investments the National Institutes of Health have made under the aegis of the NIH Common Fund,” said Principal Investigator of the CFDE Data Resource Center, Shankar Subramaniam, PhD. Subramaniam, the Joan and Irwin Endowed Chair of Bioengineering and Systems Biology is a Distinguished Professor of Bioengineering, Bioinformatics & Systems Biology, Computer Science & Engineering, Cellular & Molecular Medicine, and Nanoengineering at UC San Diego. Subramaniam has a longstanding record of establishing NIH-funded national data infrastructures. He is currently the PI of the NIH Common Fund Metabolomics Project.
Currently, most Common Fund datasets are dispersed across distinct data portals, resulting in underutilization due to the absence of standardized community practices and shared data processing protocols. By enabling seamless discovery of datasets across the Common Fund data, uniformly processing the data, and better combining data from different programs, the investigators anticipate the emergence of synergistic discoveries.
By working with the Common Fund data coordination centers, the Data Resource Center and Knowledge Center are expected to produce highly valuable computational resources for the entire field of biomedical research.
"As one example, by integrating exercise-induced gene expression changes from the Common Fund MoTRPAC program, tissue expression data from the GTEx Common Fund program, and drug response data from the LINCS Common Fund program, we can discover new drug candidates and potential treatment targets for muscular dystrophies,” says Dr. Ma’ayan.
Dr. Ma’ayan and Dr. Subramaniam will lead the Data Resource Center. The Knowledge Center award will be led by Jason Flannick, PhD, Assistant Professor of Pediatrics at Harvard Medical School and the Division of Genetics and Genomics at Boston Children’s Hospital, and an Associate Member of the Broad Institute, along with Dr. Noel Burtt, Director of the Diabetes Research & Knowledge Portals Program at the Broad Institute and Dr. Kyle Gaulton, Associate Professor in Pediatrics at the University of California San Diego.
In the past 10 years, Dr. Ma’ayan served as a Principal Investigator of the Common Fund data coordination centers: LINCS and IDG programs, and Dr. Subramaniam serves as the Principal Investigator of the Common Fund Metabolomics program. Building on this experience, the research teams work will involve:
Establishing a Data Resource Portal to enable user-friendly queries of Common Fund data sets Developing the CFDE Portal for the ecosystem, housing information and links to related resources, trainings, and events Assisting Common Fund programs in standardizing how metadata, data, and digital resources are handled in the ecosystem, and liaising with other relevant NIH efforts “The NIH Common Fund programs produce flagship cutting-edge and transformative resources for the entire biomedical research community. This new award solidifies the central role Mount Sinai is playing in the revolution of biomedical research into a data-driven and AI-driven enterprise which is expected to significantly improve patient health and lifespan in the coming two decades,” says Eric J. Nestler, MD, PhD, Nash Family Professor of Neuroscience, Director of The Friedman Brain Institute, and Dean for Academic Affairs of Icahn Mount Sinai, and Chief Scientific Officer of the Mount Sinai Health System.
The work is being supported by the NIH Office of the Director (award number OT2OD036435).
The Mount Sinai Center for Bioinformatics is developing algorithms, web-based software tools, and databases, and collaborating with wet-bench experimental laboratories at Mount Sinai. Customized original data analysis software developed by the Center is currently used by thousands of biomedical researchers worldwide daily. The Center conducts courses, workshops, tutorials, and seminars, including an acclaimed Summer Undergraduate Research Program in Biomedical Big Data Science.
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About the Icahn School of Medicine at Mount Sinai
The Icahn School of Medicine at Mount Sinai is internationally renowned for its outstanding research, educational, and clinical care programs. It is the sole academic partner for the eight- member hospitals* of the Mount Sinai Health System, one of the largest academic health systems in the United States, providing care to a large and diverse patient population.
Ranked 14th nationwide in National Institutes of Health (NIH) funding and among the 99th percentile in research dollars per investigator according to the Association of American Medical Colleges, Icahn Mount Sinai has a talented, productive, and successful faculty. More than 3,000 full-time scientists, educators, and clinicians work within and across 44 academic departments and 36 multidisciplinary institutes, a structure that facilitates tremendous collaboration and synergy. Our emphasis on translational research and therapeutics is evident in such diverse areas as genomics/big data, virology, neuroscience, cardiology, geriatrics, as well as gastrointestinal and liver diseases.
Icahn Mount Sinai offers highly competitive MD, PhD, and Master’s degree programs, with current enrollment of approximately 1,300 students. It has the largest graduate medical education program in the country, with more than 2,000 clinical residents and fellows training throughout the Health System. In addition, more than 550 postdoctoral research fellows are in training within the Health System.
A culture of innovation and discovery permeates every Icahn Mount Sinai program. Mount Sinai’s technology transfer office, one of the largest in the country, partners with faculty and trainees to pursue optimal commercialization of intellectual property to ensure that Mount Sinai discoveries and innovations translate into healthcare products and services that benefit the public.
Icahn Mount Sinai’s commitment to breakthrough science and clinical care is enhanced by academic affiliations that supplement and complement the School’s programs.
Through the Mount Sinai Innovation Partners (MSIP), the Health System facilitates the real-world application and commercialization of medical breakthroughs made at Mount Sinai. Additionally, MSIP develops research partnerships with industry leaders such as Merck & Co., AstraZeneca, Novo Nordisk, and others.
The Icahn School of Medicine at Mount Sinai is located in New York City on the border between the Upper East Side and East Harlem, and classroom teaching takes place on a campus facing Central Park. Icahn Mount Sinai’s location offers many opportunities to interact with and care for diverse communities. Learning extends well beyond the borders of our physical campus, to the eight hospitals of the Mount Sinai Health System, our academic affiliates, and globally.
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* Mount Sinai Health System member hospitals: The Mount Sinai Hospital; Mount Sinai Beth Israel; Mount Sinai Brooklyn; Mount Sinai Morningside; Mount Sinai Queens; Mount Sinai South Nassau; Mount Sinai West; and New York Eye and Ear Infirmary of Mount Sinai.
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