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Department of Biomedical Informatics and Data Science

The University of Alabama at Birmingham (UAB) has been awarded a U54 grant from the National Institutes of Health (NIH) and their initiative, the Common Fund Data Ecosystem (CFDE). The grant, $9.5 million over five years, will be in collaboration with the University of Colorado (CU) and the University of California, Los Angeles (UCLA). The U54 grant aims to modernize data sharing, integration, and innovation across the biomedical research community, while enhancing interoperability and accessibility of NIH-funded data repositories.

Led by the director of the Systems Research AI Pharmacology Center (SPARC)Systems Research AI Pharmacology Center (SPARC) and contact principal investigator Jake Chen, Ph.D., and his team at UAB, UCLA, and CU, the Collaborative Network for Nurturing Ecosystems of Common Fund Team Science (CONNECT) Integration and Coordination Center (ICC) will serve as the cornerstone of this effort. Chen will collaborate with CU Department of Biomedical Informatics chair Casey Greene, Ph.D., and professor Sean Davis, M.D., Ph.D., as well as UCLA professor of Physiology, Medicine/Cardiology and Biomedical Informatics Peipei Ping, Ph.D., and professor Wei Wang, Ph.D.

As the lead institution for this grant, UAB will oversee project management, strategic planning, and coordination, while partners will contribute their expertise in evaluation, effectiveness, and sustainability.

The initiative is part of the CFDE's vision to create a cohesive framework for seamless access to biomedical data, develop standards and tools for integrating diverse data types and sources, and leverage advanced technologies to elevate data analytics and research applications.

“The awarding of the U54 by the Common Fund Data Ecosystem is significant recognition of the qualifications and hard work by Jake, his collaborators, and the UAB Heersink School of Medicine, and acknowledges their leadership in biomedical informatics and data science,” said James Cimino, M.D., distinguished professor of Medicine and chair of the UAB Department of Biomedical Informatics and Data Science.

The CFDE has championed numerous data-generation consortiums, investing over $1 billion to a dozen consortiums over the last decade, including UAB’s prior involvement with Bridge2ai, including LINCS, GTEx, and 4D Genomics. The NIH Common Fund allocates up to five percent of its budget to perform major projects across NIH institutions.

In the first phase of the creation of the CFDE online discovery portal, the goal was to “help make Common Fund data sets FAIR (Findable, Accessible, Interoperable, and Reusable) and to enable researchers to search across Common Fund data sets to ask scientific and clinical questions from a single access point.”

The second phase of the online discovery portal will allow CFDE to enable comprehensive use of Common Fund Data in accelerating discovery, and will now be structured around five centers: the Data Resource Center (DRC), the Knowledge Center (KC), the Cloud Workspace Implementation Center (CWIC), the Center for Training, and the Integration and Coordination Center.

“The leadership of this new award for the NIH-led Common Fund Data Ecosystem (CFDE) is a tribute to the growth of informatics and data science at UAB Heersink School of Medicine and to Dr. Jake Chen’s deep expertise in this area, said Robert Kimberly, M.D., director of the Center for Clinical and Translational Science at UAB.

DRC is working to establish a portal that will allow users to probe and use outside digital resources from programs across the Common Fund. Common Fund programs will establish a knowledge network through the KC, and support cloud computing activities in select cloud workspaces within the CWIC. Within the Center for Training, researchers will be provided the opportunity to engage with CFDE tools and resources, regardless of experience level.

“The reach and impact of Dr. Chen’s team and the new Department of Biomedical Informatics and Data Science will continue to grow as we advance innovative research and develop the future of data-driven medicine, beginning with this collaboration with UCLA and the University of Colorado,” Kimberly said.

The Integration and Coordination Center (ICC) within the CFDE will now oversee the efforts of assimilating CFDE-related activities between the CFDE Centers and Common Fund data coordinating centers, while also conducting evaluation activities.

“The CONNECTS ICC symbolizes a significant leap in our ambition to transform biomedical research through data-driven innovation,” Chen said. “Our multidisciplinary team is dedicated to aligning missions, goals, and strategies to catalyze transformative discoveries within the CFDE."


The administrative core, led by UAB, will employ an Agile project management system and tools such as U-BRITE to enhance collaboration among CFDE entities. The evaluation core, led by the University of Colorado, will develop evaluation metrics and innovative approaches for continuous quality improvement. The sustainability core, under the guidance of UCLA, will focus on the long-term preservation and accessibility of Common Fund program data.

The long-term goals of the new center are to develop and implement standards and tools that promote the integration of disparate data types and sources while also creating a collaborative infrastructure that encourages cross-disciplinary partnerships.

The collaborative endeavor for this grant will support 13 current NIH Common Fund programs, providing various perspectives and expertise to navigate the intricacies of managing and integrating diverse types of biomedical data.

Some of the programs involved include the Library of Integrated Network-based Cellular Signatures (LINCS), which aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes, 4D Nucleome (4DN), which explores the three-dimensional organization of the nucleus over time, and the Human BioMolecular Atlas Program (HuBMAP), which charts the human body at a cellular resolution to transform the understanding of anatomy and pathology.

Programs such as the Genotype-Tissue Expression (GTEx) and the Molecular Transducers of Physical Activity Consortium (MoTrPAC) represent a concerted effort of the CFDE to foster a data-sharing culture that accelerates discovery and enhances the utility of biomedical data.

Through research initiatives such as the Acute to Chronic Pain Signatures (A2CPS) and the Stimulating Peripheral Activity to Relieve Conditions (SPARC), the ICC looks to broaden its impact by steering future Common Fund programs towards a new horizon in biomedical research.

“I look forward to the collaboration of our department and Jake’s center, as well as UCLA and the University of Colorado to shape the future of data-driven medicine. I want to extend my sincere appreciation to all who have contributed to this success and look forward to leveraging this opportunity to further advance transformative research initiatives at UAB,” Cimino said.

With this collaborative effort, the profile of UAB within biomedical data science and future data-driven medicine will be significantly raised on a national stage.