UC Santa Cruz researcher wins grant to develop standards for describing “cell trajectories” found in single-cell RNA sequencing datasets

The Chan Zuckerberg Initiative (CZI) has announced funding for three new projects at the UC Santa Cruz Genomics Institute to support the Human Cell Atlas, a global effort to map every type of cell in the healthy human body as a resource for studies of health and disease. The UCSC projects are among 85 to receive new grants from CZI totaling $15 million over one year.

In addition to the three new projects, researchers at the Genomics Institute have been collaborating with partners in the United States and Europe to build the Data Coordination Platform for the Human Cell Atlas. The new projects are focused on developing open computational tools, algorithms, visualizations, and benchmark datasets to enable researchers around the globe to work with the large variety of molecular and imaging data being generated by the effort.

In one of the projects Joshua Stuart, Baskin Professor of Biomolecular Engineering, will use CZI funding to develop a unified classification of cellular processes. His team will develop standards for describing “cell trajectories” found in single-cell RNA sequencing datasets. RNA sequencing (RNA-Seq) is used to study changes in gene expression over time by analyzing the RNA transcripts copied from active genes. Studying RNA-Seq data at the single-cell level promises new insights into cellular processes. Stuart’s project includes developing methods to align cell trajectories, and tools to search known and novel cell differentiation transitions. Using these tools with Human Cell Atlas data will enable detailed comparisons of intermediate cell states within and across a variety of cellular processes.

Over the course of the next year, the grantees will work together and share progress to coordinate efforts and maximize the usability of these tools. Working with CZI’s science and software engineering teams, they will work to bring these tools to the broader scientific community and, where appropriate, link them to the Human Cell Atlas Data Coordination Platform.

The Human Cell Atlas is an international effort to create a shared, open reference atlas of all cells in the healthy human body as a resource for studies of both health and disease. The effort has been spearheaded by Aviv Regev at the Broad Institute of MIT and Harvard and Sarah Teichmann at the Wellcome Trust Sanger Institute, co-chairs of the HCA Organizing Committee.

CZI is supporting the project in several ways—through funding to develop the Data Coordination Platform to facilitate open sharing of data produced for the HCA efforts, and through funding for 38 pilot projects to build new technologies, best practices, and data analysis techniques for the Human Cell Atlas. Recommended funding for the 85 new projects is the latest support CZI is providing toward this effort.

Source – UC Santa Cruz

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