Research Software Engineer and computational biologist in the Department of Infection Biology at the London School of Hygiene & Tropical Medicine, where I lead code development for AMRnet. I build open platforms that turn pathogen genome data into antimicrobial resistance surveillance that public health bodies can act on.
I trained as a computer scientist before becoming a genomicist — a BSc in Computer Science, an MSc in Genetics and Molecular Biology, then a PhD in microbial genomics at the University of São Paulo. That order is why the things I build are architected to stay up, rather than to survive one grant cycle.
Adviser on data visualisation to the World Health Organization, on health policy to the UK House of Lords, and on genomic surveillance to Brazil's Ministry of Health.
louisecerdeira.com · ORCID 0000-0002-4495-2615 · Google Scholar · LinkedIn
Also publishes as Louise Teixeira Cerdeira.
AMRnet — Genome-derived AMR surveillance for WHO priority pathogens: national prevalence estimates, interactive dashboard, public API. I led the design and development and am first author of the platform paper in Nucleic Acids Research.
TyphiNET — Genomic surveillance dashboard for Salmonella Typhi, translating typhoid genomics into evidence public health teams can use without needing bioinformatics. I developed the software; co-coordinated with Zoe Dyson and Kat Holt. Paper in Genome Medicine (2025).
OneBR — Brazil's first One Health resistance-integrated genomic database, spanning human, animal and environmental sources. Co-creator; led the bioinformatics infrastructure and web architecture.
| Repository | What it does |
|---|---|
| dragon | Cloud-native aligner for surveillance-scale microbial genomics. Rust. |
| CNVRock | AMR gene copy-number variation using variational autoencoders. |
| PlasmidNet | Interactive exploration of plasmid sequences. |
| Pipa | Integrated microbial genomic analysis across Illumina, Nanopore and PacBio. |
| infectonet | Global viral genomic surveillance across 50+ pathogens. |
| Spyder | Automated data acquisition from Pathogen Watch via REST API. |
| BraSeqTB | Brazilian pipeline for AMR detection in M. tuberculosis. |
I am one of the five code developers of Kleborate, the community-standard genotyping framework for Klebsiella pneumoniae, and a co-author on Trycycler, for long-read bacterial genome assembly.
Cerdeira L, Dyson Z, Sharma V, Maranga M, Foster-Nyarko E, Carey M, Holt K (2025). AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance. Nucleic Acids Research. 10.1093/nar/gkaf1101
Lam MMC, et al. (2021). A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nature Communications. (1,161 citations)
Wick RR, et al. (2021). Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biology. (573 citations)
Marinotti O, et al. including Cerdeira L (2013). The genome of Anopheles darlingi, the main neotropical malaria vector. Nucleic Acids Research.
155 peer-reviewed papers · 5,589 citations · h-index 34 (Google Scholar, July 2026)
Making genomic surveillance work without a compute cluster. Much of what I build now targets low-cost, GPU-accelerated and embedded systems, so that sequencing analysis becomes viable in low- and middle-income settings rather than only where the hardware budget already exists. The energy cost of that computation is a design constraint, not an afterthought.
Research across Brazil, the UK, Australia, the USA, Argentina, Peru, Chile and sub-Saharan Africa, funded by the Bill & Melinda Gates Foundation, NIAID, Wellcome, CNPq, FAPESP and CAPES.
Working mainly in Python, Rust, C++, TypeScript and Nextflow.
Open to collaboration on AMR genomic surveillance, research software sustainability, and bioinformatics capacity building in Latin America.