About
I’m Badran Elshenawy, a computational biologist at the University of Oxford. I spend most of my time convincing several hundred thousand cells to tell me what they’re doing.
What I work on Link to heading
I’m a Senior Computational Postdoctoral Research Scientist in the Pathania Group at the Ludwig Institute for Cancer Research, Oxford. The group studies brain tumours, and my work focuses on paediatric high-grade glioma. I use single-cell and spatial transcriptomics to understand H3K27M-mutant diffuse midline glioma: which cell states the tumour occupies, how it borrows from normal development, and how the microenvironment is organised around it. I also support the group’s glioblastoma programme.
The other half of the job is infrastructure. I look after the group’s computational setup: reproducible R and Python pipelines, HPC environments, analysis standards, and the mentoring that makes them stick.
How I got here Link to heading
I started in the wet lab with an MSci in Pharmacology at Bristol, and realised I preferred the data. My DPhil at Oxford studied hypoxic heterogeneity in triple-negative breast cancer using bulk and single-cell RNA-seq. After that I used 10x Xenium spatial transcriptomics to study chronic hepatitis B in the human liver, including measuring how badly dissociation-based single-cell atlases underrepresent hepatocytes. It turns out that when you dissolve a tissue, you lose most of the organ.
Why this blog exists Link to heading
Most biologists are one clear explanation away from running their own analysis. This blog is my attempt at those explanations: what a tool actually does, where its assumptions hide, and how to use it on real data.
It has grown into series on single-cell and bulk RNA-seq, spatial data, R and the move to Python, reproducibility, AI-assisted research with Claude Code, and the command-line tools I use every day. I have opinions and I try to be clear about them, including when the old tool is still the right one.
Elsewhere Link to heading
I maintain BadranSeq, an R package for publication-ready single-cell figures, along with other open-source tools and guides on GitHub. I teach when I can: I designed a single-cell course for Nile University and have taught at the Wellcome Sanger Institute. I’m also a marimo Ambassador and an AI Ambassador for Oxford’s AI Competency Centre.