M.Sc. Bioinformatics — Saarland University
Coursework: epigenetics & epigenomics, single-cell bioinformatics, machine learning, neural networks, genomic data analysis & NGS, microbiome data analysis, computational drug design.
Abdullah Hanif
Bioinformatics Master’s student, Saarland University
Saarbrücken, Germany
I am a Master’s student in Bioinformatics at Saarland University, currently working on my thesis: a genomic language model that predicts antibiotic resistance directly from bacterial DNA, built with an industry partner. Before switching into bioinformatics I spent three years as a backend developer, which is probably why I care as much about whether a pipeline actually runs end-to-end as I do about the model behind it. I’m currently looking for part-time or Hiwi opportunities in bioinformatics, genomics, or machine learning alongside my thesis.
Education
M.Sc. Applied Data Science & Analytics — SRH University Heidelberg
B.Sc. Computer Science — Herat University
Experience
Master’s Thesis Researcher — Genomic Language Model for AMR Prediction
My thesis is on predicting antimicrobial resistance from genotype data, instead of running a lab test to see which antibiotics a bacterial strain resists, the goal is to predict it from its genome. I’m building a transformer-based model for this with DATABIOMIX, co-supervised by their CEO and by a professor at Saarland University, working from curated resistance data benchmarked against real lab results.
Genomic Language Model — pipeline diagram
Project Lead & Bioinformatician — PhageMatch
I led a 4-person team building a model to predict which phages (viruses that infect bacteria) would work against which bacterial strains, useful for phage therapy as an alternative to antibiotics. We used graph neural networks and self-supervised learning to make the most of limited labeled data, and I built the Snakemake pipeline that took raw data through to evaluation. We placed 3rd at Startup Weekend Saarbrücken 2024.
PhageMatch — pipeline diagram
Research Assistant, Data Science & Public Health Analysis
I worked on predictive models for infertility risk and disease patterns (TB, hepatitis, polio), using public health data to help identify where healthcare resources were most needed.
Backend Developer & Data Analyst
I built backend systems and REST APIs in Python/Django for an e-commerce platform, and helped migrate it from a multi-page to single-page architecture. I also pulled sales and product insights out of SQL data using Redash and did the database design work.
Web Developer
I built StockOCR, an internal inventory tool that used Tesseract OCR to read serial numbers and MAC addresses straight off equipment photos, plus the check-in/check-out workflow around it.
Projects
AutomateHire
An ML pipeline I built using K-means clustering and logistic regression to automate candidate profiling for a recruitment scenario, with asynchronous data pulled from GitHub and Stack Overflow and real-time feedback via code-evaluation checks.
Technical deep-dives
Pipeline diagrams for the two projects above, in more architectural detail.
Genomic Language Model — pipeline diagram
PhageMatch — pipeline diagram
Skills
Programming
Python, SQL, R, Bash
Machine Learning
PyTorch, scikit-learn, NumPy, Pandas, transformers, graph neural networks, self-supervised learning, statistical modeling
Genomics & Epigenomics
DNA methylation analysis (WGBS/RRBS, Bismark), ChIP-seq/ATAC-seq (MACS2), differential expression (DESeq2/edgeR), RNA-seq analysis, single-cell analysis (Scanpy, Seurat), multi-omics integration (MOFA, WNN)
Structural Bioinformatics
ColabFold, Foldseek, Prokka, HHblits/HHsearch, Sourmash
Bioinformatics Tools
Biopython, Bioconductor, Snakemake, NGS pipelines
Tools
Git, Docker, Django, Linux
Contact
I’m open to part-time or Hiwi opportunities in bioinformatics, genomics, or machine learning alongside my thesis, and to conversations about genomic ML, AMR, or phage therapy.