I’m a recently-minted bioinformatics PhD working with Vineet Bafna at UC San Diego. We study genomic focal amplifications and develop methods to detect and reconstruct them using a variety of different technologies. Specifically, I study circular extrachromosomal DNA and breakage-fusion-bridges to understand their structures and the consequences of these amplifications in cancer.

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. 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:


jluebeck[ at] ucsd.edu.