CV

Freek van Hemert, Ph.D. Link to heading

Experienced Bioinformatician with a Ph.D. in Biophysics and 12+ years in industrial research. | 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

Helped a startup set up their IT infrastucture and get started doing effective NGS bioinformatics, hardware to software
Set up software development environments and workflows using Git (GitHub)
Set up compute infrastructure and implemented NGS data analysis tools
Analyzed public and company owned NGS datasets
Implemented data management and backup strategies
Set up a collaborative office suite (MS365) for client
To be PECB Certified ISO/IEC 27001 Foundation (Implementing and Managing an Information Security Management System)

Senior Scientist, Philips research (Eindhoven), 2018-2023 Link to heading

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
Studied Circulating Tumor cells by collaborating in pan-European projects
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

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

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