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munaberhe/README.md

Hi, I'm Muna

I'm an MSc Bioinformatics student at Queen Mary University of London. My thesis involves building a full multi-omics pipeline for rare disease genomics, covering everything from raw sequencing data through to differential expression, methylation analysis, and pathway enrichment.

I'm most interested in the engineering side of bioinformatics — building pipelines that are reproducible, well-documented, and actually run on real HPC infrastructure.

What I work with

Languages: Python, R, bash
Pipeline tools: Snakemake, SLURM, conda, Singularity
Sequencing: bulk RNA-seq, bisulfite sequencing, paired-end Illumina
R / Bioconductor: DESeq2, DMRcaller, clusterProfiler, GenomicRanges, BSseq
Python: pandas, scikit-learn, matplotlib, scanpy
Other: Git, GitHub Actions CI, HPC (Apocrita/QMUL)

What I'm working on

Currently building a multi-omics pipeline on an HPC cluster — STAR and Bismark alignment on hg38, differential expression with DESeq2, differential methylation with DMRcaller, and GO/KEGG enrichment with clusterProfiler. Everything managed with Snakemake and validated with GitHub Actions CI.

Outside of the thesis I've built smaller projects around single-cell label transfer, variant pathogenicity classification, and phenotype-disease matching.

Interests

Rare disease genomics, epigenomics, pipeline infrastructure, and translational applications in pharma. Long term I want to work on the engineering and infrastructure side — building tools that make large-scale genomic analysis reproducible and scalable.

Pinned Loading

  1. scRNA_label_transfer_benchmark scRNA_label_transfer_benchmark Public

    Benchmarking kNN, RandomForest and Scanpy ingest for cell type label transfer on PBMC single-cell RNA-seq data.

    Python

  2. phenotype_disease_matching phenotype_disease_matching Public

    Toy benchmark of BM25, TF-IDF and an LLM baseline for phenotype–disease matching, supporting an MSc project on LLMs for genomic diagnosis.

    Python

  3. rnaseq_deseq2_pathway rnaseq_deseq2_pathway Public

    DESeq2 and clusterProfiler pipeline for differential expression and GO enrichment on the airway RNA-seq dataset.

    R

  4. variant_pathogenicity_classifier variant_pathogenicity_classifier Public

    ClinVar-style toy project that trains and evaluates a RandomForest classifier to predict variant pathogenicity from gene, consequence, impact, PolyPhen-like score, and allele frequency.

    Python

  5. exomiser_llm_benchmark exomiser_llm_benchmark Public

    Experimental benchmark for rare disease prioritisation tools, contrasting algorithmic (Exomiser-like) and LLM-based approaches.

    Python

  6. Afolab62/Directed-Evolution-Portal Afolab62/Directed-Evolution-Portal Public

    Final Project Submission - BIO727P - Bioinformatics Software Development Group Project - 2025/26 Ventura -- Muna Berhe, Olaoluwa Afolabi, Virginia La Spina, Leora Tejal Mouli, Jasmee Navaratnarajah

    Python 1