Bioinformatician · Data Scientist · Pipeline Developer · Comparative Genomics · Deep Learning
Multi-omics × AI building reproducible pipelines across genomics, glycomics, and deep learning. Excited about the moment omics layers start talking to each other through unified computational models.
Pipeline & Infrastructure
AI / ML
Analysis & Visualization
Genomics ▓▓▓▓▓▓▓▓▓▓
Proteomics ▓▓▓▓▓▓▓▓▓░
Transcriptomics ▓▓▓▓▓▓▓░░░
AI / ML ▓▓▓▓▓▓▓▓░░
Glycomics ▓▓▓▓▓░░░░░
| Project | What it does | Stack | Output |
|---|---|---|---|
| GenoDiplo | End-to-end genome assembly & annotation pipeline · Nanopore → structural annotation → functional annotation → repeat masking · reproduced on 2 independent genomes |  |
Scientific Data 2024 |
| CompareDiplo | Comparative genomics pipeline for diplomonads · protein family clustering (OrthoFinder) · functional annotation (InterProScan · EggNOG-mapper · KEGG) · traces evolutionary divergence between free-living & parasitic species |    |
manuscript in preparation |
| Deep-Bio | Deep learning on 4 biological datasets — anuran acoustics · thyroid diagnostics · protein localization · HIV cleavage sites · FFNN & LSTM · 78%→95% accuracy |  |
M.Sc. Thesis 2018 |
| Bioinformatics-Bootcamp | Full curriculum: Python · NGS · Snakemake workflows · comparative genomics · functional annotation · visualisation | |
50+ graduates |
Between Data Dreams · private repo · in development
A gamified bioinformatics learning platform built around the life stages of Hexamita inflata — the free-living diplomonad at the centre of my PhD. The learner's journey mirrors the organism: Past (Marsfield School) → Present (Digital Campus) → Future (Between Institute). Real science. Real data. The goal: become a free-living scientist.
| Area | Why |
|---|---|
| Spatial transcriptomics | Gene expression mapped to tissue coordinates |
| Single-cell multi-omics | scRNA-seq · scATAC-seq · CITE-seq at cell-type resolution |
| Biological foundation models | ESM · Evo · Nucleotide Transformer |
| Multimodal AI integration | Merging omics layers with clinical data |
| Drug target discovery | Multi-omics pipelines for target ID & biomarker stratification |
Nature Communications · Dec 2025 · GlyContact analyzes glycan 3D structures at scale
Thomès · Joeres · Akdeniz · Bojar
Scientific Data · Aug 2024 · Expanded genome of Hexamita inflata, a free-living diplomonad
Akdeniz et al.
Scientific Data · Sep 2022 · Chromosome-scale reference genome of Spironucleus salmonicida
Xu · Jiménez-González · Akdeniz et al.