Computational biology · genomics · creative coding
Enrique M
Toledo
Scientist working at the intersection of genomics, computational biology and target discovery, with one foot in creative coding.
01 — About
Cells, genomes and the code in between.
Interests
- Cellular and molecular biology, genomics and biomedicine
- Data science: finding patterns in complex biological datasets
- Creative coding: seeing what computational tools can do
Work
- Cellular and molecular biology, mostly neurobiology, developmental neurobiology and cardio-metabolism across tissues.
- Genomics, first at the bench, then on the computational side.
- Academia, then early research in pharma.
- Still in academic collaborations: papers, internships, rotations, supervision… et al.
02 — Projects
Tools, hardware and things that solved a problem once.
R package · CRAN
PubMatrixR
Pairwise literature searches on PubMed and PMC. Returns co-occurrence matrices for genes, diseases and pathways.
Python · PyPI
PubMatrixPython
The Python port. Two lists of terms in, a pandas DataFrame of PubMed counts out, with parallel queries and an on-disk cache.
R package · Zenodo
MSigDF
The Molecular Signatures Database as a tidy tibble, kept current with MSigDB 2025.1, for enrichment and pathway analysis.
R + Rust
emeansR
e-means in R: a mini-batch replacement for k-means with a multi-threaded Rust core. You supply the data, k and an epoch budget.
Docker · web
linXiv-web
A self-hosted PDF paper library: tags, projects and reading lists, with in-browser reading and annotation. Optional AI and an MCP server.
ESP32 · firmware
ESP32 DuckDNS Client
A standalone dynamic DNS client on a microcontroller that keeps a DuckDNS domain pointed at home. Why? Because I can.
Raspberry Pi · HACS
NTP & GPS Home Bridge
NTP and GPS monitoring on a Raspberry Pi, exposed as an API for Home Assistant.
Add-on repository · amd64 + aarch64
HA Add-ons Playground
They used to live in a repo each. Now they sit in one place: BentoPDF, Manyfold with its own PostgreSQL and Redis, Nginx Proxy Manager with a static server, Obsidian LiveSync on CouchDB (plain, SSL or with NPM), and Stirling-PDF in ultra-lite, full and fat (about 4 GB, so pick accordingly).
Three.js · web
STL Shaper
Real-time deformation of STL models: noise, sine waves and pixelation in layers, then export the mesh.
R · ggplot2
XKCD ggplot2 theme
Hand-drawn XKCD-style plots, with jittered lines, segments, circles and stick figures as geoms.
OpenSCAD · 3D print
Parametric designs
Parametric OpenSCAD models for 3D printing, Gridfinity trays included.
Python · Zigbee
ZHA mesh graph export
Exports ZHA devices and their neighbour edges to CSV. Applications: none. But you get to nerd out over your mesh in igraph, Cytoscape or Gephi.
Shell · cross-platform
Ollama history cleaner
Clears only Ollama's chat history and logs, with an optional backup first. Models and settings stay.
Swift · Bash · Zenodo
Blind rename
Renames image files for blind manual quantification, to keep bias out. From the ImageJ/Fiji days.
03 — Papers
Selected publications.
AI/ML with genomics, computational biology and target discovery. The full list is on Google Scholar.
04 — Connect