Bioinformatics PhD working with Vineet Bafna at UC San Diego. We study extrachromosomal DNA and genomic focal amplifications - developing methods to detect and reconstruct them using a variety of different technologies.
Some stuff I work on
The following tools are available on Github.
1. Detecting and reconstructing focal amplifications:
- AmpliconArchitect: Detect and analyze focal amplifications with NGS data. Originally developed by Viraj Deshpande - I am a maintainer of this codebase.
- AmpliconReconstructor: Reconstruct focal amplifications using NGS and optical mapping data.
- AmpliconClassifier: Classify AA outputs to detect ecDNA, BFB, etc.
- PrepareAA: A quickstart wrapper for AA + other upstream/downstream analysis utilities.
2. Alignment of optical maps:
- FaNDOM: Fast, open-source aligner for Bionano optical map data (co-developer).
- SegAligner: Sensitive alignment of small reference genome segments to optical map contigs (part of AmpliconReconstructor).
3. Visualization of focal amplifications:
- CycleViz: Visualize focal amplifications detected by AmpliconArchitect and AmpliconReconstructor.
4. Simulation projects:
- ReactionDiffusionSimulator: Simulating and visualizing Turing patterns.
- ecSimulator: For simulating focal amplifications from the ground up.
jluebeck[ at] ucsd.edu.