Bioinformatics Scientist with hands-on experience in NGS data analysis, spanning genomics and transcriptomics. Currently working remotely as a bioinformatics data analyst, where I translate raw sequencing data into reproducible, interpretable results. I have a habit of picking up public datasets and playing around until I find something the original study missed; most of the projects here started exactly that way.
Genomics
- WGS & WES analysis: preprocessing, alignment, variant calling (GATK Best Practices)
- Targeted exome sequencing; germline variant filtering & clinical annotation
- Reference genome alignment (BWA-MEM), post-alignment processing (samtools, Picard)
Transcriptomics
- Bulk RNA-seq: differential gene expression, non-coding RNA analysis
- Single-cell RNA-seq (10x Genomics, Seurat): clustering, cell-type annotation, marker identification
- In progress: Spatial transcriptomics
Pipeline & Software
- Languages: R, Python, Bash
- Tools: GATK, FastQC, Fastp, BWA, samtools, bcftools, DESeq2, Seurat
- In progress: Nextflow pipeline development
Wet Lab
- DNA/RNA extraction
- PCR
- Gel electrophoresis
- Library QC
| Repository | Description | Stack |
|---|---|---|
| targeted-exome-seq-analysis | End-to-end germline variant calling pipeline on cancer predisposition genes | Bash, GATK |
| scRNA_seq_Analysis_Mouse_Brain | scRNA-seq analysis of E18 mouse brain; identified 7 neural cell populations | R, Seurat |
| Differential_Expression_Analysis_PTC | DEG analysis of papillary thyroid carcinoma (GEO: GSE224356) | R, DESeq2 |
| Isoform_Switch_Analysis_HCC | Analyzing isoform switches in Hürthle cell carcinoma, using Salmon & IsoformSwitchAnalyzeR (GEO: GSE228870) | Bash, R |
- Spatial transcriptomics analysis
- Nextflow pipeline development