Computational Biologist | Bioinformatics Specialist | Microbial & Clinical Genomics
🧬 PhD Candidate in Biology
🏥 R&D Bioinformatics Researcher – NGS & Genomic Data Analysis
🌍 Based in Türkiye
✉️ Contact: efedalli@outlook.com
I work at the intersection of biology, genomics, and computation, focusing on
reproducible bioinformatics pipelines, microbial comparative genomics, and
NGS-based clinical and research applications.
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NGS bioinformatics pipelines
- WGS / WES / RNA-seq / smallRNA
- Variant calling (SNV, CNV, SV)
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Clinical & translational bioinformatics
- Rare disease genomics
- RNA aberrant expression & splicing (MAE / FRASER / DROP)
- Fusion detection & functional annotation
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Antimicrobial & functional genomics
- Small ORF discovery (smORFs)
- Antimicrobial peptide (AMP) prediction & in silico characterization
- Structure modeling & peptide–protein dockin
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Microbial genomics & systematics
- Novel species discovery (ANI / AAI / dDDH / phylogenomics)
- Comparative genomics & pangenome analysis
- Thermophilic bacteria (Anoxybacillus, Bacillota, extremophiles)
- Genome assembly & annotation: Unicycler, SPAdes, Prokka, Bakta, KEGG
- Comparative genomics: Bactopia, Panaroo, PIRATE, OrthoFinder
- Taxonomy & phylogenomics: GTDB-Tk, TYGS, IQ-TREE, iTOL
- AMP discovery: Macrel, AMPEP, AMP-Scanner, AntiBP, SignalP
- Variant analysis: GATK, BCFTools, freebayes, Snippy
- Metagenomics: Kraken2, Kaiju, QIIME2
- Conda / Mamba environments
- HPC & Slurm-based workflows
- Reproducible & scalable pipeline design
- Multi-omics integration
- Workflow optimization for large-scale datasets
