Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"

openpilot is an operating system for robotics. Currently, it upgrades the driver assistance system on 300+ supported cars.

A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. All in a modern, AI-native editor.

GenoVi, an automated customizable circular genome visualizer for bacteria and archaea

Protein function prediction in bacteria using genomic context

Synteny-aware gene function prediction for bacteria using protein embeddings

Scalene: a high-performance, high-precision CPU, GPU, and memory profiler for Python with AI-powered optimization proposals

A high-performance, zero-overhead, extensible Python compiler with built-in NumPy support

RPA primer and CRISPR-Cas12a guide RNA design for diagnostics

Organism-specific interpretation of AMR genotypes

Metadata template for genomic surveillance of bacterial pathogens for vaccine and AMR purposes

Drop in a screenshot and convert it to clean code (HTML/Tailwind/React/Vue)

A Generative Pre-Trained Transformer Package for Pangenomes

Biological foundation modeling from molecular to genome scale

Auxiliary Common Lisp Utilities for Generative Art

A repo to evaluate various LLM's chess playing abilities.

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Distribute and run LLMs with a single file.

Successful Job Applications and Grants

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

The most used Rust library for date and time handling.

Python programs for processing GFF3 files

tree visualization for tree + annotation data

Snakemake workflow management system and CLI generation tool