hi, I'm
I'm a bioinformatician who reads genomes to understand how tuberculosis and SARS-CoV-2 evolve, spread and adapt to their hosts. I also build open-source tools, and I draw.
PhD candidate at the PathoGenOmics Lab, I2SysBio (CSIC and University of Valencia), in Valencia, Spain.
nowWriting up my PhD thesis, Evolutionary genomics of pathogen diversity in Mycobacterium tuberculosis and SARS-CoV-2.
Tuberculosis and COVID-19 look like different problems, but their genomic data share a trap: much of what we can conclude is decided before any hypothesis is tested, by the reference genome we map to in tuberculosis and by which samples get sequenced in SARS-CoV-2. My work tries to measure those biases and build methods that hold up despite them.
The M. tuberculosis complex is split into lineages that differ in where they circulate and which hosts they infect. I build tools that type lineages and resistance the same way across surveillance programmes, and I study how the match between strain and host changes the way macrophages respond to infection.
From the first pandemic wave in Spain to Omicron, I have followed spike mutations that arise again and again and tested whether they matter. Lately I compare wastewater with clinical sequencing: hospital wastewater caught KP.3 about three months before routine clinical surveillance did.
I write fast, low-memory command-line tools, mostly in Rust, and reproducible Nextflow and Snakemake pipelines. Six of them are on Bioconda, downloaded about 7,000 times so far, and one R package is on CRAN.
I also illustrate: graphical abstracts, outreach pieces for the institute and the logo at the top of this page. A clear figure is often what makes a genomics result travel beyond the people who already work on it.
swipe along the chromosome →
drag a helix to spin it, click a node for details, or a strand name to isolate it
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When I am not at the terminal I build mechanical keyboards and 3D print things. Everything on this desk does something: press it, or type in the console under it.
press the lamp, the mug, the printer, the jar, the coconut or a microbe, and type help in the console
Email is the quickest way to reach me. Write if you want to talk about tuberculosis or SARS-CoV-2 genomics, use one of my tools, or need a scientific illustration.
paula.ruiz.rodriguez@csic.esPathoGenOmics Lab
I2SysBio (CSIC and University of Valencia)
Valencia, Spain
