Muhammad U.
Research Assistant
Experience
Oct 2024 - Jul 2025
10 monthsResearch Assistant
Saarland University
- Applied AI-driven CADD methodologies for biosynthetic pathway optimization and molecule screening.
- Integrated synthetic biology with computational chemistry workflows for rapid in-silico experimentation.
- Automated ML pipelines using Python, PyTorch, and Scikit-learn on Linux, improving model testing and reproducibility.
Jun 2024 - Present
1 year 6 monthsMachine Learning & Bioinformatics Engineer
Myria Biosciences
- Processed and analyzed 1,000+ genomic and proteomic samples, reducing pipeline runtime by 35% using workflow managers and HPC clusters.
- Benchmarked variant calling pipelines, improving SNP detection sensitivity by 8% vs reference datasets.
- Built ETL workflows (Python, Pandas, SQL) to manage 50 GB/week multi-omics data with <2% error rate, enabling efficient data onboarding.
- Engineered a Neo4j knowledge graph with 10,000+ biological entities, improving R&D query speed by 50%.
- Delivered 30+ interactive dashboards and reproducible reports, accelerating research decisions across 3 clinical programs.
- Developed and containerized reproducible NGS and ML pipelines using Docker, Git, CI/CD, increasing workflow reliability and automation.
Jun 2024 - Dec 2024
7 monthsData Scientist in Drug Bioinformatics
Helmholtz Institute (HIPS)
- Analyzed and integrated NGS and LC-MS/MS proteomics datasets, contributing to the discovery of 15 novel biosynthetic gene clusters.
- Developed ML models increasing expression efficiency prediction accuracy by 22%.
- Applied graph-based data science for pathway discovery; 3 computational predictions validated experimentally.
- Built Snakemake pipelines with version control, saving 40+ hours/month of manual processing time.
- Delivered reproducible bioinformatics pipelines now used by multiple research groups for genomic and biochemical analysis.
Dec 2022 - Sep 2024
1 year 10 monthsResearch Assistant
KIST Europe
- Supported sequencing-driven synthetic biology projects, validating 100+ molecular cloning experiments.
- Led student training and workflow standardization, reducing onboarding time by 30%.
- Executed and analyzed ELISA, cloning workflows, and phage–host interaction studies to support bacteriophage engineering.
- Performed sequencing-based validation for construct integrity and experimental reliability.
Summary
Bioinformatician and DevOps-oriented Machine Learning Engineer with experience delivering scalable solutions across genomics, transcriptomics, and proteomics.
Skilled in reproducible NGS/ML pipeline development, workflow automation, and CI/CD-driven deployment across Linux and HPC environments.
Strong background in Python, R, and C++, with expertise in multi-omics data integration, ETL workflows, knowledge graphs (Neo4j), and developing dashboards and data products for research and clinical decision support.
Languages
Urdu
NativeEnglish
AdvancedGerman
ElementaryEducation
Oct 2022 - Present
Saarland University
Bioinformatics · Saarbrücken, Germany
Oct 2018 - Aug 2022
UET Lahore
Biomedical Engineering · Lahore, Pakistan · 3.721/4.0
Certifications & licenses
ETL And ELT In Python
(Short course)
Neo4j Certified Professional
GraphAcademy
Neo4j Graph Data Science Certification
GraphAcademy
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