The Bonney Lab

Spencer Lab Collaboration at Washington University

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Spencer Lab Collaboration at Washington University

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About the Spencer Lab

The David Spencer Lab at Washington University in St. Louis focuses on translational cancer genomics, with particular emphasis on hematologic malignancies like Acute Myeloid Leukemia (AML). The lab integrates computational approaches with experimental validation to understand disease mechanisms and identify novel therapeutic targets.

Key research areas include:

  • Epigenetic dysregulation in cancer
  • Clonal evolution and heterogeneity in leukemia
  • Integration of multi-omics data for precision medicine
  • Development of computational tools for cancer genomics

Collaboration Focus

As of September 2024, I’ve joined the Spencer Lab as a Bioinformatics Research Assistant, establishing a collaboration to further develop the EpiBench platform. The key goals of this collaboration include:

  1. Adaptation of EpiBench for cancer-specific applications

    • Creating specialized modules for detecting cancer-specific epigenetic patterns
    • Developing models for tumor heterogeneity and evolution

  2. Integration with Spencer Lab datasets

    • Leveraging unique patient cohorts available at WashU
    • Incorporating multi-modal data from WashU clinical samples

  3. Tool development for clinical applications

    • Creating interpretable visualizations for clinicians
    • Developing prediction models relevant to treatment decisions

Current Projects

The initial focus of our collaboration is on:

  1. AML Methylation Profiling

    • Analyzing whole-genome bisulfite sequencing data from AML patients
    • Correlating methylation patterns with clinical outcomes

  2. Enhancer Activity Prediction

    • Developing models to predict enhancer activity from histone modification data
    • Identifying cancer-specific enhancer patterns

  3. Clonal Heterogeneity Analysis

    • Methods for decomposing bulk sequencing data into clonal populations
    • Tracking epigenetic changes during disease progression

Resources

The Spencer Lab provides significant resources that enhance the EpiBench project:

  • Access to Washington University Research Computing Cluster
  • Extensive patient sample collections with long-term follow-up
  • Integration with the WashU cancer genomics ecosystem
  • Experimental validation capabilities

Team Members

Spencer Lab Collaborators

  • Dr. David Spencer - Principal Investigator
  • [Additional lab members to be added]

Bonney Lab Contribution

  • Andrew Bonney - Bioinformatics Research Assistant
  • [Future team members]

Meeting Schedule

  • Biweekly project coordination meetings
  • Monthly research progress presentations
  • Quarterly strategic planning sessions

Notes

[This section will be filled with ongoing notes about the collaboration]

This document will be updated regularly as the collaboration progresses. For more information about the EpiBench project, see the Introduction to EpiBench.

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