Muhammad U.

Research Assistant

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Saarbrücken, Germany

Experience

Oct 2024 - Jul 2025
10 months

Research 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 7 months

Machine 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 months

Data 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 months

Research 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.

Skills

  • Ngs & Bioinformatics: Wgs, Wes, Rna-seq (Bulk & Single-cell), Methylome, Variant Calling, Annotation, Bioconductor
  • Ml & Data Science: Scikit-learn, Pytorch, Pca/umap/t-sne, Clustering, Random Forest, Svm, Xgboost, Shap, Gnnexplainer, Graph Ml
  • Devops & Infrastructure: Docker, Git, Bash, Linux Server Management, Ci/cd, Workflow Automation, Cloud Deployment
  • Pipelines & Tools: Snakemake, Nextflow (Fundamentals), Biopython, Pandas, Numpy, Jupyter, Flask
  • Data Engineering & Databases: Sql, Etl/elt, Api Pipelines, Neo4j Knowledge Graphs, Data Modeling
  • Visualization: Plotly, R Shiny, Jupyter Dashboards, Rmarkdown, Interactive Reporting

Languages

English
Advanced
German
Intermediate

Education

Oct 2022 - Present

Saarland University

M.Sc. Bioinformatics · Bioinformatics · Saarbrücken, Germany

Oct 2018 - Aug 2022

UET Lahore

B.Sc. Biomedical Engineering · Biomedical Engineering · Lahore, Pakistan · GPA: 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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