Friday, Jun 28, 2024

• Illuminating the Druggable Genome (IDG) Overview and Highlights

  Jeremy Yang, Ph.D

  Research Associate Professor, UNM SoM, DoIM, TI Division

  Anna Waller, Ph.D.

  Scientist & Project Manager, UNM SoM, Dept of Pathology

  Jayme Holmes

  Sr Engineer & Lead Developer, UNM SoM, DoIM, TI Division

  Timothy Sheils

  Sr Engineer & Project Manager, NIH NCATS

Friday, May 31, 2024

• Improved Methods to Query the LINCS L1000 Data

  Avi Ma'ayan, PhD

  LINCS Data Coordination Center and the CFDE Data Resource Center

  Summary

  The Library of Integrated Network-Based Cellular Signatures (LINCS) was an NIH Common Fund program that was established to catalog how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and gene expression signatures. The presentation will cover LINCS datasets, tools, and a newly developed method to query the LINCS L1000 data for better prioritization of drugs, small molecules and single gene perturbations.
  
  Relevant resources that will be discussed:
  Rummagene: https://rummagene.com/
  SigCom LINCS: https://maayanlab.cloud/sigcom-lincs/
  Playbook Workflow Builder: https://playbook-workflow-builder.cloud/

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• Automatic Mining of Human and Mouse Gene Sets from GEO

  Giacomo Marino

  LINCS Data Coordination Center and the CFDE Data Resource Center

  Summary

  RummaGEO is a web server application that enables gene expression signature search against thousands of human and mouse RNA-seq studies deposited into GEO. To enable such a search engine, an offline automatic process was established to identify the experimental conditions from uniformly aligned GEO studies available from ARCHS4. Once conditions are identified, differential expression signatures are computed to extract gene sets from these signatures. In total, RummaGEO currently contains 135,264 human and 158,062 mouse gene sets from 23,395 GEO studies. Overall, RummaGEO provides an unprecedented resource for the biomedical research community enabling hypothesis generation for many future studies.
  
  Relevant resources that will be discussed:
  RummaGEO: https://rummageo.com/
  ARCHS4: https://maayanlab.cloud/archs4/

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Friday, Apr 26, 2024

• Overview of the Common Fund Data Ecosystem

  George Papanicolaou, PhD

  NIH, CFDE Program Leader

  Christy Kano, PhD

  NIH, CFDE Program Officer

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• Metabolomics Workbench/National Metabolomics Data Repository

  Shankar Subramaniam, PhD and Mano Maurya, PhD

  Metabolomics Workbench DCC and CFDE Data Resource Center

  WATCH VIDEO ON YOUTUBE

• CFDE and the Biomedical Research Community

  Noël Burtt and Kyle Gaulton, PhD

  CFDE Knowledge Center

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