Rummagene and Rummageo: Automated Mining of Gene Sets from PubMed Central (PMC) and the Gene Expression Omnibus (GEO)

January 24, 2024 11:00 a.m. - 12:00 p.m. ET

In this seminar, you’ll learn about Rummagene and Rummageo, two web-based tools developed by researchers in the Ma’ayan Lab, Icahn School of Medicine, at Mount Sinai in New York.

Dr. Avi Ma’ayan will show how you can use these tools to access hundreds of thousands of gene sets. You’ll learn about:

  • Rummagene: A tool that lets you access human and mouse gene sets from the supporting materials in PubMed Central (PMC). To date, researchers have used this application to scan 5,670,312 PMC articles, uncovering 126,390 publications with 667,029 gene sets.
  • Rummageo: A tool that gives you access to gene sets from human and mouse RNA-sequencing studies in the Gene Expression Omnibus (GEO) database. Rummageo currently contains 135,264 human and 158,062 mouse gene sets from 23,395 GEO studies.

Don’t miss this opportunity to learn from Dr. Ma’ayan. His lab focuses on developing web-based bioinformatics software tools and databases to help us better understand important cellular events, such as cell differentiation, growth, and death, and how these processes link to gene expression (i.e., to identify networks, pathways, and possible targets for therapy). To date, more than 3 million people have used these bioinformatics tools.

To view upcoming speakers or recordings of past presentations, visit the CBIIT Data Science Seminar Series webpage.

The Data Science Seminar Series presents talks from innovators in the cancer research and informatics communities both within and outside of NCI.

Avi Ma’ayan, Ph.D.

Dr. Ma’ayan is the director of the Mount Sinai Center for Bioinformatics and a professor in the Department of Pharmacological Sciences.

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