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3 followers · 45 following
  • United Kingdom

Achievements

Achievement: Pair ExtraordinaireAchievement: Pull Sharkx2Achievement: YOLO

Achievements

Achievement: Pair ExtraordinaireAchievement: Pull Sharkx2Achievement: YOLO

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Ekin-Kahraman/README.md

Ekin Kahraman

I build pipelines that find things in genomics data — then build systems that act on what they find.

What I've found

1,773 genes change expression during SARS-CoV-2 infection. 12 do so differently in men vs women. Nobody had tested for that interaction in the original study.

Which cells are responsible? A PyTorch neural network trained on tissue-matched single-cell data decomposes 484 bulk samples into 14 airway cell types. Basal stem cells are depleted. Goblet cells expand. Immune cells infiltrate. 10 cell types significantly changed (r = 0.954). First tissue-matched deconvolution of this dataset.

5 immune cell types in 2,604 PBMCs — subclustered T cells to split CD4⁺/CD8⁺ that standard resolution misses.

What I've built

Nextflow RNA-seq pipeline — FASTQ to DE results in 7 containerised steps. Docker, Singularity, CI.

SafetyNett — AI safety netting for NHS GPs. 39 conditions. Built in 2.5 hours. Live.

Contributor to scanpy, muon, PyDESeq2 (scverse ecosystem).

Molecular Biology & Genetics, UEA. Volunteer in the Grieshop Lab (evolutionary genetics).

ekinkhrmn@outlook.com

Pinned Loading

  1. bulk-rnaseq-differential-expression bulk-rnaseq-differential-expression Public

    Reproducible bulk RNA-seq pipeline for SARS-CoV-2 host response in R (DESeq2, pathway enrichment, viral load and sex-interaction analyses). Zenodo DOI.

    R 1

  2. covid-airway-deconvolution covid-airway-deconvolution Public

    Neural network deconvolution of 484 COVID-19 nasopharyngeal samples into 14 airway cell types. PyTorch, tissue-matched scRNA-seq reference. Validation r = 0.954.

    Python

  3. single-cell-rnaseq-immune-profiling single-cell-rnaseq-immune-profiling Public

    End-to-end single-cell RNA-seq immune cell profiling pipeline in Python (scanpy, PBMC 3k)

    Python

  4. rnaseq-nextflow-pipeline rnaseq-nextflow-pipeline Public

    Bulk RNA-seq Nextflow pipeline: FastQC, fastp, HISAT2, featureCounts, DESeq2, MultiQC. Dockerised, tested, reproducible.

    Nextflow

  5. safetynett safetynett Public

    AI-powered clinical safety netting for NHS primary care. Red flag detection, automated patient follow-up, GP escalation.

    TypeScript 1 1