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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 WGBS methylation pipeline on an HPC cluster — Bismark alignment on hg38, differential methylation calling with DMRcaller across a four-contrast pairwise design, GO/KEGG enrichment with clusterProfiler, and permutation-based enhancer and regional enrichment testing with regioneR. Managed with Slurm array jobs.

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. sma_epigenomics_pipeline sma_epigenomics_pipeline Public

    Genome-wide analysis of DNA methylation and transcriptional changes induced by combined ASO and valproic acid treatment in spinal muscular atrophy cell models.

    R 1

  2. 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

  3. 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

  4. 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

  5. rnaseq_deseq2_pathway rnaseq_deseq2_pathway Public

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

    R

  6. exomiser_llm_benchmark exomiser_llm_benchmark Public

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

    Python