Dr. Wim Cuypers | Curriculum Vitae

Bioinformatics Researcher

ORCID: https://orcid.org/0000-0002-1895-3526

Email: wim.cuypers@uantwerpen.be

About

I am a multidisciplinary researcher with expertise in microbial genomics, bridging wet-lab and bioinformatics approaches. I have contributed to impactful studies on antimicrobial resistance (AMR), including publications in Nature Communications and mBio. My work spans research, teaching, and capacity strengthening, with experience in developing courses such as a microbial genomics program in Ethiopia.

As part of the ISCB Student Council executive team, I advocate for equitable bioinformatics education and global collaboration. Currently, I focus on leveraging Nanopore sequencing for wastewater-based epidemiology to study bacterial AMR and viruses. My goal is to advance interdisciplinary research that empowers local scientists and addresses global health challenges.

Education

  • Doctor of Science, University of Antwerp & Institute of Tropical Medicine Antwerp (2018–2023)
    • Thesis: Genomic adaptation of Salmonella to antimicrobials and the human host.
    • Supervisors: Prof. Kris Laukens and Prof. Sandra Van Puyvelde.
  • Master in Biology: Cell & Systems Biology, University of Antwerp (2015–2017)
    • Graduated with Great Distinction.
  • Bachelor in Biology, University of Antwerp (2012–2015)

Professional experience

  • Postdoctoral Researcher, Computational Biology – Nanopore sequencing, Adrem Data Lab, University of Antwerp (2022–Present)
  • PhD Fellow, Bioinformatics and Microbiology, University of Antwerp (2018–2021)
    • Research Foundation Flanders (FWO) Grant 1S40018N.

Key projects

  • Awarded a personal postdoc grant from Flanders innovation and entrepreneurship (VLAIO) to collaborate with Prof. Kris Laukens, Prof. Peter Delputte, and Aquafin on optimizing nanopore sequencing for wastewater-based epidemiology. (Started November 2024). 
  • Leading the development of SquiDBase, a database designed to store raw nanopore data, enabling advanced algorithm development for nanopore sequencing. To facilitate data upload, I developed a NextFlow pipeline (SquiDPipe). 
  • For my PhD (defended in 2023) I specialised in microbial genomics and transcriptomics analyses. This led to the Salmonella Concord paper published in Nature Communications, and an R package to study gene co-expression in Salmonella. 

Skills

  • Programming: R, Bash, Python.
  • Bioinformatics: DNA and nanopore sequencing, computational biology, bacterial genomics.
  • Microbiology and Molecular Biology: Cultivating bacteria, AST (disk diffusion & Sensititre), high-molecular-weight DNA extractions, library prep, Nanopore sequencing.

  • Web skills: Content management, theme customization, module/plugin configuration and site building with Drupal and WordPress.

  • Project management & collaboration: Knowledge management, project tracking, collaboration, team communication and management. Tools: Notion, Slack, Basecamp.

  • Languages: Native Dutch speaker, fluent in English, proficient in French.

Publications

A selection of my key publications:

  • Cuypers WL et al. (2023). A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia. Nature Communications. 14(1), 3517. 
  • Cuypers WL et al. (2024). Selective whole-genome sequencing of Plasmodium parasites directly from blood samples by nanopore adaptive sampling. mBio. 15:e01967-23.
  • Cuypers WL et al. (2018). Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing. Microbial genomics. 4(7):e000195.

Contributions as co-author:

  • Van Puyvelde S. et al. (2023). A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan Africa. Nature Communications. 14(1):6392.
  • de Vrij N. et al. (2024). A preliminary indication that HLA-A*03:01 may be associated with visceral leishmaniasis development in people living with HIV in Ethiopia. PLoS Negl Trop Dis. 30;18(9):e0012000.

  • Rutanga J-P et al. (2023). Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58. PLOS Neglected Tropical Diseases. 17(6):e0011285

Google Scholar: https://scholar.google.be/citations?user=hBcM9w8AAAAJ&hl=en

Community engagement & leadership

  • Secretary, International Society for Computational Biology Student Council (ISCB-SC) (2025–...). 
  • Active member of the ELIXIR Wastewater Surveillance Working Group (2024 - ...).
  • Vice Chair, ISCB-SC (2023–2024). Before my role as vice-chair, I have led the Web Team of this organisation together with Spencer Krieger. Almost every year I attend either ISMB or ECCB, and assist with the organisation of the preceding student symposia. 
  • Co-developed and taught a two-week bioinformatics course in Ethiopia (October 2024). Materials can be found here. Also check out this website article from our colleagues from AHRI about our training. We have applied for follow-up funding to continue bioinformatics capacity strengthening in Ethiopia. 
  • Co-organizer, Nanopore Research Day Antwerp (September 2024). We welcomed 105 participants in Antwerp and will organise an even larger version of this event. 
  • Led the organisation of two international symposia (SCS2020 & ESCS2024). An article of our SCS2020 journey can be found here. 
  • Co-organiser of the BIOMINA Lunch Talks at the University of Antwerp (2018 - 2019). 

Teaching & mentoring

Supervised several Master’s students in thesis projects and internships:

  • Kristof Van Den Neucker (MSc Biomedical Sciences)
  • Laura Valgaeren (MSc Biochemistry)
  • Thijs Vanbruggen (MSc Biochemistry)
  • Quinten Van Looy (MSc Biochemistry)
  • Peter Kirby (MSc Computer Science)
  • Myra Nasser (MSc Biomedical Sciences)
  • Pavei Amin (MSc Biomedical Sciences)

Scientific outreach

  • My PhD research was featured in Belgian national news: VRT News.
  • Finalist in the 2024 Tahko SkiLift Pitch, presenting a Nanopore sequencing commercialization idea for the food industry.
  • Organized science outreach activities, including bioinformatics workshops using LEGO and interactive sessions at the Nerdland Festival.

Presentations (coming soon!)