Muhammad Usman-Research Assistant
Check rate
Experience
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.
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.
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.
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.
Industry experience
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Experienced in Biotechnology and Pharmaceutical.
Business area experience
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Experienced in Research and Development, Business Intelligence, Information Technology, and Quality Assurance.
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
Education
Saarland University
M.Sc. Bioinformatics · Bioinformatics · Saarbrücken, Germany
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
Statistics
Experience
Expertise
Qualifications
Profile
Frequently asked questions
Have questions? Find more information here.
Muhammad is based in Saarbrücken, Germany.
Muhammad speaks the following languages: English (Advanced), German (Intermediate).
Muhammad has at least 4 years of experience. During this time, Muhammad has worked in at least 3 different roles and for 4 different companies. The average length of individual experience is 1 year and 11 months. Note that Muhammad may not have shared all experience and actually has more experience.
Based on recent experience, Muhammad would be well-suited for roles such as: Research Assistant, Machine Learning & Bioinformatics Engineer, Data Scientist in Drug Bioinformatics.
Muhammad's most recent position is Research Assistant at Saarland University.
In recent years, Muhammad has worked for Saarland University, Myria Biosciences, Helmholtz Institute (HIPS), and KIST Europe.
Muhammad is most experienced in industries like Biotechnology and Pharmaceutical.
Muhammad is most experienced in business areas like Research and Development, Business Intelligence, and Information Technology. Muhammad also has some experience in Quality Assurance.
Muhammad holds a Master in Bioinformatics from Saarland University and a Bachelor in Biomedical Engineering from UET Lahore.
Muhammad has 3 certificates. These include: ETL And ELT In Python, Neo4j Certified Professional, and Neo4j Graph Data Science Certification.
The availability of Muhammad needs to be confirmed.
Daily rate distribution
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Average rates for similar positions
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The average daily rate is the mean of all daily rates from recent contracts of comparable freelancers on our platform.
The median daily rate is the middle value of all daily rates — half of comparable freelancers charge less, half charge more. Unlike the average, it is barely affected by outliers.
Calculated based on our freelancers’ daily rates as of 7 Sep 2026. Actual rates may vary depending on seniority level, experience, skill specialization, project complexity, and engagement length.
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