Future Research Ideas
This is a collection of potential research directions that I’m considering exploring in the future. These are preliminary thoughts that need further development.
Epigenetics & Genomics
- Developing improved methods for integrating DNA methylation and histone modification data
- Exploring the role of 3D chromatin structure in epigenetic regulation
- Comparative analysis of epigenetic patterns across different cell types and disease states
- Investigating the dynamics of epigenetic changes during cellular differentiation
Machine Learning Applications
- Applying transfer learning to improve prediction accuracy across different cell types
- Developing interpretable deep learning models for genomic data
- Exploring reinforcement learning for optimizing experimental design in epigenetics
- Benchmarking different neural network architectures for epigenetic pattern prediction
Bioinformatics Tool Development
- Creating interactive visualization tools for multi-modal epigenetic data
- Developing scalable pipelines for processing large-scale genomic datasets
- Building user-friendly interfaces for complex bioinformatics analyses
- Improving reproducibility in computational biology workflows
Questions to Explore
- How can we better integrate prior biological knowledge into machine learning models?
- What are the most effective ways to visualize complex relationships in epigenetic data?
- How can we address batch effects and technical variability in epigenetic datasets?
- What are the ethical considerations in developing AI tools for genomic medicine?
Resources to Investigate
- Recent advances in single-cell epigenomics technologies
- Benchmark datasets for evaluating epigenetic prediction models
- State-of-the-art methods for multi-modal data integration
- Emerging standards for reproducible bioinformatics research
This note contains preliminary research ideas that will be refined and developed over time. Suggestions and collaborations are welcome.