Mount Sinai genomics team partners with Chan Zuckerberg Initiative to bring big data solutions to the data-rich world of biology
The research team will develop software tools allowing efficient and interactive exploratory data analysis of unprecedented amounts of single-cell data
Uri Laserson, PhD, Assistant Professor in the Department of Genetics and Genomics Sciences at the Icahn School of Medicine at Mount Sinai, and collaborators have been awarded one of 85 grants announced today from the Chan Zuckerberg Initiative DAF (CZI), an advised fund of Silicon Valley Community Foundation. The CZI grants totaling $15 million over one year are dedicated to research projects aimed at building tools and technologies to support the goals of Human Cell Atlas, a global effort to map every type of cell in the human body as a resource for medical research. Dr. Laserson’s team will be collaborating on the project with the research group of Anthony Joseph, PhD, at the University of California, Berkeley.
“I am thrilled to welcome this distinguished group of grantees to the CZI family, and I am excited about how they will support the ambitious Human Cell Atlas effort,” said Priscilla Chan, MD, co-founder of the Chan Zuckerberg Initiative. “Working together and with our team of scientists and engineers, these partners will create new ways for scientists to use information about healthy and diseased cells. Their efforts will help to accelerate progress toward our goal of curing, preventing, or managing all diseases by the end of the century.”
Because the Human Cell Atlas project will generate a large variety of molecular and imaging data across a wide range of modalities and spatial scales, Dr. Laserson’s team plans to develop software to help scientists analyze these massive amounts of data in a way that allows interactive, scalable exploratory analysis – eliminating much of the laborious and complicated processes that scientists currently must perform to gain insights from their data and providing a platform where they can quickly react to and interact with data. Their proposal is built on the principles of distributed computing, where enormous data sets are loaded into memory across a cluster of computers, massively decreasing processing time.
After studying mathematics at MIT and genomics at Harvard, Dr. Laserson worked for a Silicon Valley start-up that developed open-source technology for data analysis with an interest in how the tools being used at places like Google and Facebook could be applied to problems in biology. Dr. Laserson says this is the “right place, and the right time,” to bring Silicon Valley thinking into the lab.
“Essentially what we’re trying to do is apply tools that are commonly used in the Valley for processing enormous datasets to allow researchers to scale up their capabilities to handle the large amounts of data we’ll soon see coming out of projects like the Human Cell Atlas,” said Dr. Laserson. “In the past 15 years, there’s been a huge proliferation of open-source software tools that handle a lot of common big data problems. But in the case of data management, the ideas from industry haven’t really made it over the fence to the academic labs.”
When scientists analyze large data sets today, they often have to conceive of clever ways just to handle the data itself. If it’s too large to be handled by one computer, it may need to be manually broken up into smaller pieces and processed separately. Steps such as these are not only complicated, time-consuming, and disruptive to scientific exploration; they’re also a major cause of error. “If what I’m trying to do as the scientist is think about the data and develop hypotheses about the data, I want to do it interactively, without waiting minutes or hours for computations to finish, and without worrying about the data plumbing. Every time I have an idea for a figure, I want it to render instantaneously” said Dr. Laserson. “This CZI-funded project aims to provide a platform where we could put all of the single-cell data in one place in the cloud and when a researcher needs to do an analysis, they can connect to our platform and say, ‘I want this data, filtered this way, displayed that way,’ and have it served up to them very quickly.”
Participants in CZI’s Human Cell Atlas funding will collaborate with each other to accelerate progress, facilitate communications, and maximize open dissemination of the resulting tools. All software developed will be licensed with a permissive, open-source license so anyone can use it freely, including commercial entities.
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About the Icahn School of Medicine at Mount Sinai
The Icahn School of Medicine at Mount Sinai is an international leader in medical and scientific training, biomedical research, and patient care. It is the medical school for the Mount Sinai Health System, which includes seven hospital campuses, and has more than 5,000 faculty and nearly 2,000 students, residents and fellows. The School is made up of 36 multidisciplinary research, educational, and clinical institutes and 33 academic departments. It ranks 13th among U.S. medical schools for NIH funding and 2nd in research dollars per principal investigator among U.S. medical schools by the Association of American Medical Colleges (AAMC). The School was named 4th among “World’s Most Innovative Companies in Data Science” by Fast Company magazine in 2016. For more information, visit http://icahn.mssm.edu
About the Chan Zuckerberg Initiative
The Chan Zuckerberg Initiative was launched in December 2015 by Mark Zuckerberg, founder and CEO of Facebook, and Priscilla Chan, a pediatrician and founder and CEO of The Primary School in East Palo Alto. The Chan Zuckerberg Initiative is a new kind of philanthropy that seeks to engineer change at scale. By pairing world-class engineering with grant-making, impact investing, policy, and advocacy work, CZI hopes to build a future for everyone. Initial areas of focus include supporting science through basic biomedical research and education through personalized learning. CZI is also exploring ways to address barriers to justice and opportunity - from criminal justice reform, to expanded access, to economic opportunity and affordable housing.
About the Mount Sinai Health System
Mount Sinai Health System is one of the largest academic medical systems in the New York metro area, with more than 43,000 employees working across eight hospitals, over 400 outpatient practices, nearly 300 labs, a school of nursing, and a leading school of medicine and graduate education. Mount Sinai advances health for all people, everywhere, by taking on the most complex health care challenges of our time — discovering and applying new scientific learning and knowledge; developing safer, more effective treatments; educating the next generation of medical leaders and innovators; and supporting local communities by delivering high-quality care to all who need it.
Through the integration of its hospitals, labs, and schools, Mount Sinai offers comprehensive health care solutions from birth through geriatrics, leveraging innovative approaches such as artificial intelligence and informatics while keeping patients’ medical and emotional needs at the center of all treatment. The Health System includes approximately 7,300 primary and specialty care physicians; 13 joint-venture outpatient surgery centers throughout the five boroughs of New York City, Westchester, Long Island, and Florida; and more than 30 affiliated community health centers. We are consistently ranked by U.S. News & World Report's Best Hospitals, receiving high "Honor Roll" status, and are highly ranked: No. 1 in Geriatrics and top 20 in Cardiology/Heart Surgery, Diabetes/Endocrinology, Gastroenterology/GI Surgery, Neurology/Neurosurgery, Orthopedics, Pulmonology/Lung Surgery, Rehabilitation, and Urology. New York Eye and Ear Infirmary of Mount Sinai is ranked No. 12 in Ophthalmology. U.S. News & World Report’s “Best Children’s Hospitals” ranks Mount Sinai Kravis Children's Hospital among the country’s best in several pediatric specialties.
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