Computational Biologist · Cancer Gene Regulation · 3D Genomics · Cancer WGS & ecDNA · Single-Cell · Computational Methods
Postdoctoral researcher in the Department of Oncology-Pathology at Karolinska Institutet, Stockholm. I study how distal regulatory elements control cancer genes such as MYC, integrating GRO-seq, ATAC-seq, CUT&RUN, 4C-seq and RNA-seq, and I analyse single-nucleus RNA-seq cohorts and patient-tumour whole genomes for focal amplifications and ecDNA.
- 🔬 Now: MYC/CTCF enhancer regulation (co-author, under revision at Nucleic Acids Research) · a 17-donor clinical snRNA-seq cohort · cancer WGS / ecDNA
- 🧮 PhD work: two original, peer-reviewed gene-prioritisation algorithms, released here as tested, citable software
- 📄 Output: 8 peer-reviewed articles + 3 preprints. See the full list
- 🤝 Open to: computational biology / bioinformatics scientist roles and collaborations
| Method | Paper | Code | Software DOI |
|---|---|---|---|
| Chaos game + 2D multifractal cross-correlation for alignment-free gene prioritisation | Theory in Biosciences 2024 · doi | cgr-mfxdfa-gene-prioritization |  |
| Moment-of-inertia tensor protein descriptors for gene prioritisation | Proteins 2022 · doi | moment-of-inertia-tensor-gene-prioritization |  |
| Project | What it does | Stack |
|---|---|---|
| ecDNA-WGS-circdna | Version-pinned, config-driven wrapper around nf-core/circdna for detecting ecDNA from whole-genome sequencing (AmpliconArchitect + Circle-Map branches) | Nextflow · nf-core · AmpliconSuite |
| scRNA-seq-reproducible | Deterministic Scanpy/scverse pipeline from a GEO accession or 10x file to QC, clusters and marker genes | Python · Scanpy · scverse |
| efficiency-corrected-rt-qpcr | Pfaffl-style amplification-efficiency correction for RT-qPCR, with a live report | R · Excel |
Code is MIT-licensed; the methods and pipelines are tested with GitHub Actions.
Assays: GRO-seq · ATAC-seq · CUT&RUN · ChIP-seq · 4C-seq · RNA-seq · sc/snRNA-seq · WGS
📫 arjun.ins@gmail.com · Stockholm, Sweden