Muhammad Usman - Research Assistant

Q: Where is Muhammad based?

Muhammad is based in Saarbrücken, Germany .

Q: What languages does Muhammad speak?

Muhammad speaks the following languages: English (Advanced), German (Intermediate) .

Q: How many years of experience does Muhammad have?

Muhammad has at least 3 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 10 months . Note that Muhammad may not have shared all experience and actually has more experience.

Q: What roles would Muhammad be best suited for?

Based on recent experience, Muhammad would be well-suited for roles such as: Research Assistant, Machine Learning & Bioinformatics Engineer, Data Scientist in Drug Bioinformatics .

Q: What is Muhammad's latest experience?

Muhammad's most recent position is Research Assistant at Saarland University .

Q: What companies has Muhammad worked for in recent years?

In recent years, Muhammad has worked for Saarland University , Myria Biosciences , Helmholtz Institute (HIPS) , and KIST Europe .

Q: Which industries is Muhammad most experienced in?

Muhammad is most experienced in industries like Biotechnology and Pharmaceutical .

Q: Which business areas is Muhammad most experienced in?

Muhammad is most experienced in business areas like Research and Development (R&D) , Quality Assurance (QA) , and Business Intelligence . Muhammad also has some experience in Information Technology (IT) .

Q: What is Muhammad's education?

Muhammad holds a Master in Bioinformatics from Saarland University and a Bachelor in Biomedical Engineering from UET Lahore .

Q: Does Muhammad have any certificates?

Muhammad has 3 certificates . These include: ETL And ELT In Python , Neo4j Certified Professional , and Neo4j Graph Data Science Certification .

Recommended expert

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 9 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.

Industries Experience

See where this freelancer has spent most of their professional time. Longer bars indicate deeper hands-on experience, while shorter ones reflect targeted or project-based work.

Experienced in Biotechnology (3 years) and Pharmaceutical (0.5 years).

Biotechnology

Pharmaceutical

Business Areas Experience

The graph below provides a cumulative view of the freelancer's experience across multiple business areas, calculated from completed and active engagements. It highlights the areas where the freelancer has most frequently contributed to planning, execution, and delivery of business outcomes.

Experienced in Research and Development (3 years), Quality Assurance (2 years), Business Intelligence (1.5 years), and Information Technology (1.5 years).

Research and Development

Quality Assurance

Business Intelligence

Information Technology

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

Profile

Created

November 2025

Need a freelancer? Find your match in seconds.

Try FRATCH GPT

Frequently asked questions

Do you have questions? Here you can find further information.

Where is Muhammad based?

Muhammad is based in Saarbrücken, Germany.

What languages does Muhammad speak?

Muhammad speaks the following languages: English (Advanced), German (Intermediate).

How many years of experience does Muhammad have?

Muhammad has at least 3 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 10 months. Note that Muhammad may not have shared all experience and actually has more experience.

What roles would Muhammad be best suited for?

Based on recent experience, Muhammad would be well-suited for roles such as: Research Assistant, Machine Learning & Bioinformatics Engineer, Data Scientist in Drug Bioinformatics.

What is Muhammad's latest experience?

Muhammad's most recent position is Research Assistant at Saarland University.

What companies has Muhammad worked for in recent years?

In recent years, Muhammad has worked for Saarland University, Myria Biosciences, Helmholtz Institute (HIPS), and KIST Europe.

Which industries is Muhammad most experienced in?

Muhammad is most experienced in industries like Biotechnology and Pharmaceutical.

Which business areas is Muhammad most experienced in?

Muhammad is most experienced in business areas like Research and Development (R&D), Quality Assurance (QA), and Business Intelligence. Muhammad also has some experience in Information Technology (IT).

What is Muhammad's education?

Muhammad holds a Master in Bioinformatics from Saarland University and a Bachelor in Biomedical Engineering from UET Lahore.

Does Muhammad have any certificates?

Muhammad has 3 certificates. These include: ETL And ELT In Python, Neo4j Certified Professional, and Neo4j Graph Data Science Certification.

What is the availability of Muhammad?

Muhammad is immediately available for suitable projects.

What is the rate of Muhammad?

Muhammad's rate depends on the specific project requirements. Please use the Meet button on the profile to schedule a meeting and discuss the details.