computational biology · transcriptomics · genomics · pipeline engineering
MSc Biotechnology, Istanbul Technical University · Research Assistant, Istanbul Yeni Yüzyıl University
I work on transcriptomics, functional genomics, and single-cell analysis. My day-to-day covers bulk RNA-seq and microarray analysis, differential expression (DESeq2, limma), functional enrichment (GO, KEGG, g:Profiler), and protein–protein interaction networks (STRING), together with single-cell and single-nucleus RNA-seq (sc/snRNA-seq) run on HPC systems, including work on Huntington's disease model organisms. A recurring theme is non-model organisms (crops, fungi, and yeast), such as Fusarium graminearum in wheat and barley, that lack ready-made Bioconductor annotation, so I spend most of my time building reproducible, portable pipelines in R and Python.
| Languages |
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| Bulk RNA-seq |
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| Single-cell |
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| Genomics |
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| Resources |
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| Reproducibility |
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BulkSeq Studio — a cross-platform, no-code desktop app for reproducible bulk RNA-seq and microarray analysis: STAR / HISAT2 / Salmon alignment, DESeq2 / limma, GO / KEGG / g:Profiler enrichment, and STRING interaction networks, with first-class support for crops and fungi that lack a Bioconductor OrgDb.
Arf — a local-first second brain for
scientists and coders: plain-Markdown notes with [[wikilinks]], LaTeX and
syntax-highlighted code, a knowledge graph, and on-device embeddings (MiniLM,
in the browser) that surface related but unlinked notes. Runs as a web app, an
installable PWA, and native desktop builds for Windows, macOS, and Linux.
Open Arf.
Beyond code, I write essays, in Turkish and English, at tunabirgun.com.