CV
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Freek van Hemert, Ph.D. Link to heading
Entrepreneur with a Ph.D. in Biophysics and 12+ years in industrial research. | Project Leader in a large Academic Hospital | Advocate for an open software development culture. | Expertise in Software Development and Data Analysis in Genomics and Digital Pathology. | Adept at bridging communication between medical professionals and computer scientists.
https://www.linkedin.com/in/fvanhemert/
Experience Link to heading
Owner, Qodon (’s Gravenmoer), 2022-current Link to heading
Project Leader, ErasmusMC, 2024-Current Link to heading
Developed and proposed a strategic plan to streamline high-performance computing (HPC) and bioinformatics support, addressing infrastructure and expertise gaps to elevate research efficiency.
- Led analysis of HPC infrastructure across ErasmusMC, mapping computational resources across 16 departments
- Developed strategic plan for a bioinformatics and HPC support facility, including governance and funding models
- Conducted benchmark analysis at UMC Groningen, WUR (Wageningen), UMC Utrecht, RadboudUMC and Leiden UMC to establish best practices for bioinformatics and HPC support
- Quantified missed funding opportunities due to infrastructure gaps, building business case for institutional investment
- Created proposal for Bioinformatics Coordinator amd HPC Product Owner roles to implement recommendations and establish support function
Bioinformatician/Linux sysadmin, DCDC Tx (Vught), 2022-current Link to heading
Established and managed comprehensive IT infrastructure, bioinformatics workflows, and data analysis systems for NGS research.
- Set up IT infrastucture for Next Generation Sequencing (NGS) bioinformatics, hardware to software
- Implemented NGS data processing pipelines on Snellius (the Dutch Tier 1 supercomputer)
- Set up software development environments and workflows using Git (GitHub)
- Processed and analyzed public and company owned NGS datasets
- Implemented data management and backup strategies
- Set up a collaborative office suite (Microsoft 365)
Senior Scientist, Philips research (Eindhoven), 2018-2023 Link to heading
Led development of a lasting NGS analysis framework while fostering open collaboration through education, quality control implementation, and international engagement in oncology research.
- Lead a small team that developed an NGS data analysis framework increasing effectiveness of NGS data analysis based projects, this codebase is still used in Philips and in 2 spin-outs
- Developed a Quality Control module for RNAseq by deeply understanding the NGS process from sample to data and by maintaining very close collaborations between the lab and bioinformatics teams
- Worked on establishing an open and pleasant software development culture, increasing collaboration in genomics within Philips
- Researched HL7 FHIR and its implementation in a Philips Genomics related platform
- Studied Circulating Tumor cells in pan-European collaborations
- Deployed and Experimented with GA4GH NGS data processing tools like WES, (possibly) the future of cloud based Genomics data processing
- Reported on many international oncology related conferences (i.e. ELCC and similar)
- Increased collaboration by educating colleagues on open software development practices
- Developed and presented a course: Programming for Biologists, bring your own data
Development engineer Life Science, TMC (Eindhoven), 2010-2018 Link to heading
- Improving immunofluorescence assays for Breast Cancer stratification by equipping a whole slide digital pathology scanner with a high multiplex filter
- Improving breast cancer digital pathology assays by developing image and data analysis software
- Developing lab-on-a-chip and organ-on-a-chip rapid prototyping technologies for better staining assays and more realistic drug testing modalities
Languages Link to heading
- Dutch: Mother tongue
- English: Proficient, published and presented in English on many occasions
Courses Link to heading
- PECB ISO/IEC 27001 Foundation (Implementing and Managing an Information Security Management System)
- Microsoft Azure Fundamentals (Vijfhart)Microsoft Azure Fundamentals (Vijfhart) AZ-900AZ-900
- Change management, YEARTH Management Development Program
- Marketing for Software Architects
- EACR-OECI Joint Training Course: Molecular Pathology Approach to CancerEACR-OECI Joint Training Course: Molecular Pathology Approach to Cancer
- Updates on Liquid Biopsy for Advanced NSCLC: A Consensus Statement from the IASLCUpdates on Liquid Biopsy for Advanced NSCLC: A Consensus Statement from the IASLC
- ESMO webinar applications - Liquid biopsies in lung cancer
- Global Data Protection and Privacy: Respecting a person’s Privacy
- How to Write a Competitive Proposal for Framework 7
- Django Web Development (SpiralTrain)
- Introduction to programming in Python
- Numerical Python
- Leading Projects
- GMP for laboratoria
Education Link to heading
Ph.D. project, Leiden University, 2005-2009 Link to heading
“Characterization of the molecular movements of individual GPCRs and G proteins responsible for Dictyostelium discoideum chemotaxis” (link to full thesis)
- Understand the movement of proteins in cell membranes in relation to directed cell movement using advanced microscopic setups and matlab based data analysis
Master of Science (M.Sc., Cum Laude) Molecular and Cellular Biology, Leiden University, 2003-2005 Link to heading
Bachelor of Applied Science (B.Sc.), Biochemistry, Hogeschool Rotterdam, 1999-2003 Link to heading
Professional Development Link to heading
Health-RI conference 2024 ‘Trusting Forward’ | European Lung Cancer Congress 2022 | ESMO webinar applications - liquid biopsy lung cancer 2022 | Updates on Liquid Biopsy for Advanced NSCLC: A Consensus Statement from the IASLC 2022 | EACR Cancer Genomics 2019 | Genomic Medicine Nordic 2018 | Leading Projects | Numerical Python | Information Security Fundamentals and Concepts | Introduction to Ethics, ICBE (Philips Ethics Committee) processes and Regulations for Research | General Business Principles EACR-OECI Joint Training Course: Molecular Pathology Approach to Cancer 2012 | GMP for Laboratories | How to write a competitive proposal for Framework 7 | Global Data Protection and Privacy: Respecting a person’s Privacy | Lorenz Workshop on Circulating Tumor Cells 2010 | Biophysical Society meeting 2008