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Sean Davis, MD, PhD

CU Cancer Center Informatics Leader Part of $5.2 Million NIH Grant for Cancer Genomics Research Tool 

A collaboration between the CU Cancer Center and City University of New York, the Bioconductor ecosystem allows cancer researchers to analyze and comprehend biological big data. 

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Written by Greg Glasgow on July 2, 2024

Sean Davis, MD, PhD, associate director of informatics and data science at the University of Colorado Cancer Center, is part of a team that recently received a $5.2 million grant renewal from the National Institutes of Health (NIH) to continue funding cancer genomics research. 

Led by Davis and Levi Waldron, PhD, at the City University of New York, the project aims to enhance and expand the Bioconductor ecosystem, a cornerstone resource for statistical analysis and data management in cancer genomics research. Bioconductor gives researchers advanced tools and resources for analyzing and understanding cancer genomics data, potentially accelerating discoveries that could improve cancer diagnostics and treatments. 

The grant will fund collaborative efforts among the City University of New York, the Harvard T.H. Chan School of Public Health, the CU School of Medicine, and the University of Padova in Italy. 

Access and analysis 

Bioconductor has been funded by the National Cancer Institute’s (NCI’s) Information Technology for Cancer Research (ITCR) program for the past 10 years as an open-source project focused on the analysis and comprehension of ’omics data.  

The Bioconductor ecosystem has two primary categories of user, Davis says — software developers who develop tools for specific functions within Bioconductor, and end users who employ those tools for their research.  

“End users comprise everyone from biologists and bioinformaticians to data scientists and even high school students,” Davis says. While it is challenging to estimate an exact number of users, he says, Bioconductor is downloaded over 400,000 times per year. 

Addressing challenges 

The latest NCI renewal grant will fund years 11-15 of the Bioconductor project. Davis and Waldron plan to use the funding to address evolving challenges in cancer genomics, particularly in the realm of multimodal experiments and spatial transcriptomics. 

“Many biology projects these days are multimodal, meaning that we're simultaneously measuring multiple aspects of a cell or a system,” Davis says. “We want to understand how those measurements relate to each other, including spatial relationships.” 

Sharing knowledge 

Other goals for the renewal grant include transitioning to a federated, language-agnostic data-sharing system; creating curated and integrated data repositories; and developing comprehensive user training programs, including advanced cloud-based learning platforms. 

“Bioconductor is about encoding knowledge in software, enhancing reproducibility and reusability of that software, and allowing interoperability across an entire ecosystem of state-of-the-art algorithms and tools,” Davis says. “Thousands of cancer researchers already rely on Bioconductor, and this award offers new opportunities for adding new capabilities to Bioconductor, attracting new users through outreach and education, and advancing research capabilities for the cancer research community.”