Assistant Project Scientist working in Vineet Bafna’s group 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. I also lead the AmpliconSuite GitHub organization and manage the development of AmpliconRepository.org.

Tools I built or maintain

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.
• AmpliconSuite-pipeline: 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 ecDNA genome structures from the ground up.

Contact

jluebeck[ at] ucsd.edu.