Ocean Genomics Granted $235,000 in Funding from the Chan Zuckerberg Initiative

PITTSBURGH, Pa. — Ocean Genomics, a biotechnology software company spun out of Carnegie Mellon University, has received $235,000 in funding from the Chan Zuckerberg Initiative (CZI) to expand the reach of open-source tools for fast and accurate gene expression analysis.

Gene expression analysis compares the RNA expression levels of multiple genes in samples under various conditions. Such analyses can provide insight into variations in gene expression between healthy and diseased samples, and enable the discovery and validation of multidimensional biomarkers for disease.

The CZI award will allow Ocean Genomics to improve the open-source projects called Salmon (bulk RNA-seq) and Alevin (single-cell RNA-seq) by expanding the types of input that Salmon and Alevin can support and the types of data processing they can handle. Salmon and Alevin were originally created by two of Ocean Genomics’ co-founders.

“Salmon and Alevin are easy, fast, and accurate methods to extract transcript- and gene-level expression quantification from RNA-seq samples. This award will make these tools even easier to use by supporting additional input formats and additional single-cell protocols.”
– Carl Kingsford, Ph.D., Co-founder, CEO at Ocean Genomics.

Specifically, the award will support directly reading genomically aligned BAM files and NIH SRA files, two formats in which RNA-seq data is often stored, while keeping Salmon and Alevin’s well-known speed. It will also add support for highly multiplexed single-cell protocols such as Sci-seq, support for the QIAseq UPX 3′ protocol, and protocols with variable-length barcodes and UMIs to the software’s single-cell analysis module, Alevin, which is among the fastest and most accurate ways to process many types of single-cell protocols to produce expression estimates. This work will make that speed and accuracy available to more types of single-cell experiments, and improve the tools available to researchers worldwide.

The award will also fund creation of additional tutorials and documentation so a broader population can use the advanced features of Salmon and Alevin and help to strengthen the community of users and code contributions around the projects.
“We’re very excited to be able to work with the Chan-Zuckerberg Initiative through their Essential Open-Source Software program. CZI has demonstrated a strong commitment to support open-source tools in science, and we at Ocean Genomics are proud to participate in this effort.”
– Rob Patro, Ph.D., Co-founder, CTO at Ocean Genomics.

Ocean Genomics is dedicated to expanding the reach of accurate gene expression analysis. This award will bolster their efforts to continue to support and improve the open-source tools available to researchers worldwide.

About Ocean Genomics

Ocean Genomics’s AI-driven transcriptome analysis platform and expert services empower discovery and translational research. The company was founded by authors and inventors of several leading new-generation transcriptome analysis applications used by tens of thousands of researchers world-wide with over 1,500 citations. Ocean Genomics works to democratize transcriptome analysis and expand the usefulness of gene expression analysis by offering additional software, support, integration, and services around these tools by leveraging their larger and more comprehensive transcriptomics analysis framework.

About the Chan Zuckerberg Initiative

Founded by Dr. Priscilla Chan and Mark Zuckerberg in 2015, the Chan Zuckerberg Initiative (CZI) is a new kind of philanthropy that’s leveraging technology to help solve some of the world’s toughest challenges — from eradicating disease, to improving education, to reforming the criminal justice system. Across three core Initiative focus areas of Science, Education, and Justice & Opportunity, we’re pairing engineering with grant-making, impact investing, and policy and advocacy work to help build an inclusive, just and healthy future for everyone. For more information, please visit www.chanzuckerberg.com.