Open source

Software

Open-source tools I build and maintain for genomics — from DNA language models to splice-site prediction, genome annotation, and pangenome indexing. Build what you need, use what you build.

Research software

Shorkie
Apache 2.0
Yeast RNA-Seq coverage predictor powered by a fungal DNA language model.
Code Paper Blog
OpenSpliceAI
GPLv3
Efficient, modular splice-site prediction framework — easy to retrain on non-human species.
Code Docs Paper Poster Blog
LiftOn
GPLv3
Genome-annotation lift-over tool that combines DNA and protein alignments.
Code Docs Paper Blog
Splam
MIT
Deep-learning splice-site predictor that improves spliced alignments.
Code Docs Paper Poster Blog
Wheeler Graph Toolkit
MIT
Tools and algorithms for recognizing, visualizing, and generating Wheeler graphs.
Code Paper Poster Blog
sangeranalyseR
MIT
R/Bioconductor package for simple, interactive Sanger-sequencing analysis.
Code Docs Paper Poster Blog

Side projects

A few games I built for fun — browser games you can play right here, plus some older Unity WebGL games.

Genome Jumper
Endless browser jumper — procedural platforms, nucleotide boosts, and mutation enemies
Play
Proofreader
First-person browser shooter — a Canvas-2D raycast maze, mutation enemies, and nucleotide pickups
Play
Dino Run
Browser runner - jump / duck / tap / swipe, with a genomic riff
Play
Snake
Browser game — arrow keys / WASD / swipe, with a genomic twist
Play
Tetris
Browser game — keyboard / touch, modern SRS with hold & ghost
Play
Jetpack Joyride
Browser side-scroller — hold to fly, dodge mutagens, collect A/C/G/T bases
Play
Biobaby
Unity WebGL game
Play
Flappy Penguin
Unity WebGL game
Play
Tank Fire
Unity WebGL game
Play