I'm Michael, a computational biologist. This means that I'm using computers and code to analyze biological data, often in collaboration with experimental scientists. I'm working on how cancer cells overcome their growth limitations and how we can use that to help patients. Here you can find some of the work I did, and more general purpose tools I wrote for anyone to use. Please reach out if you want to collaborate!
This is what I do for research 👨🔬 (full list 🔗)
| article | code | |
|---|---|---|
| Developed a reliable method for estimating cell signaling pathways from gene expression |   |
github  bioc 📦 |
| Showed how gene coexpression networks often reflect cell mixtures instead of regulation |  |
github |
| Found a way how cancer cells can tolerate abnormal DNA content (aneuploidy, chromosomal instability) and potential treatments, in collaboration with experimental scientists |    |
transposon cgas_ko ToxicGenes |
| Working on estimating DNA copy number of single-cell RNA sequencing | coming soon |
Here are some of my open source contributions 👨💻 (full list 🔗)
| status | code | ||
|---|---|---|---|
| clustermq | R package for efficient high performance computing  |
  |
github cran 📦 testing ⚙️ |
| narray | R package for simplifying array operations |
  |
github cran 📦 |
| ebits | R bioinformatics toolkit incubator and data API |  |
ebits data |
| Software build scripts for the ArchLinux User Repository 🔗 and as Gentoo overlay 🔗 |  |
pkgbuilds overlay |