I am a Bioinformatics Researcher specializing in Metagenomics and Metabolomics analysis. My research focuses on developing and applying computational methods to understand complex biological systems through the analysis of microbial communities and metabolic pathways. I am particularly interested in genome scaffolding, biosynthetic gene cluster analysis, and multi-omics data integration.

• 🔬 Metagenomics: Microbial community analysis and taxonomic profiling
• 🧬 Genome Scaffolding: Development and application of tools like Medusa, Multi-CSAR, and Ragout
• 📊 Metabolomics: Metabolite identification and pathway analysis
• ⚙️ Workflow Development: Snakemake and Nextflow pipeline optimization
• 🤖 Machine Learning: Application of ML methods in bioinformatics

🔗 IAMPGutMB Genome assembly and scaffolding analysis of gut microbiome data

🧬 Scaffolding Tools Medusa, Multi-CSAR, Ragout implementation and optimization

🧪 Metabolomics Seminar Reproducibility case studies in metabolomics bioinformatics

🔬 Biosynthetic Gene Clusters Analysis of specialized metabolite biosynthetic diversity

🖼️ Turkish Image Captioning Multimodal AI for Turkish language image description

🧠 ML in Bioinformatics Machine learning applications in omics data analysis

📄 Academic Portfolio Personal website showcasing research, publications, and professional experience

• Microbial community analysis and taxonomic profiling
• 16S rRNA and shotgun metagenomics data processing
• Functional metagenomics and pathway analysis
• Multi-omics data integration

• Medusa: Multi-reference genome scaffolding
• Multi-CSAR: Comparative scaffolding with rearrangements
• Ragout: Reference-assisted genome assembly
• De novo assembly optimization and quality assessment

• Metabolite identification and quantification
• Pathway analysis and enrichment studies
• Integration with genomic and transcriptomic data
• Statistical analysis of metabolic profiles

• Snakemake: Reproducible bioinformatics workflows
• Nextflow: Scalable pipeline development
• Containerization with Docker
• High-performance computing optimization

I am actively seeking collaborations in:

• Genome scaffolding algorithm development
• Multi-omics data integration
• Microbial community analysis
• Bioinformatics tool development
• Reproducible research workflows

• Metagenomics data analysis workflows
• Metabolomics data processing and interpretation
• Bioinformatics pipeline development
• Statistical analysis of omics data
• R and Python for bioinformatics
• Snakemake and Nextflow workflow optimization