Dr. Wim Cuypers | Curriculum Vitae

Bioinformatics Researcher

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

Academic email: wim.cuypers@uantwerpen.be

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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

  • Senior Researcher, Microbial genomics, Laboratory of Medical Microbiology, University of Antwerp (2026–present).
  • Postdoctoral Researcher, Bioinformatics – Nanopore sequencing - Wastewater metagenomics, Adrem Data Lab, University of Antwerp (2022–2026).
  • PhD Fellow, Bioinformatics and Microbiology, Insitute of Tropical Medicine Antwerp and 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 also 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.

International research and collaboration

  • Research stay at Institut Pasteur, Paris, December 2018: Three-week research stay in Prof. François-Xavier Weill’s group, focused on collecting Salmonella Concord isolates and exchanging expertise.
  • International collaboration on Salmonella Concord: helped bring together a consortium and coordinate isolate collection for the study published in Nature Communications. Specify the countries or institutions involved and your precise role.
  • ELIXIR Wastewater Surveillance Working Group (2024–present): contribute to international collaboration on wastewater sequencing, bioinformatics and surveillance.
  • International bioinformatics training in Ethiopia (2024 and 2026): co-developed and taught introductory and advanced courses with local and international partners.

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. (2026). SquiDBase: a community resource of raw nanopore data from microbes. NAR Genomics and Bioinformatics, 8(1), lqaf213. https://doi.org/10.1093/nargab/lqaf213
  • 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. https://doi.org/10.1038/s41467-023-39123-0
  • Cuypers WL, et al. (2024). Selective whole-genome sequencing of Plasmodium parasites directly from blood samples by nanopore adaptive sampling. mBio, 15, e01967-23. https://doi.org/10.1128/mbio.01967-23
  • Cuypers WL, et al. (2018). Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing. Microbial Genomics, 4(7), e000195. https://doi.org/10.1099/mgen.0.000195

Contributions as co-author:

  • De Smedt M, Cuypers WL, Hudda NU, Delputte P. (2026). Sequencing the wastewater virome: Current strategies and bioinformatic pitfalls. iScience, 29(10), 117596. https://doi.org/10.1016/j.isci.2026.117596
  • Psomopoulos F, O’Cathail C, Anastasiadou N, et al. (2025). Toward a unified approach: considerations for bioinformatic and sequencing activities and data in wastewater surveillance of biologic public health threats. Open Research Europe, 5, 267. https://doi.org/10.12688/openreseurope.20934.1
  • 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

  • Organising committee member, Nanopore Day Flanders. The event welcomed 150 participants.
  • Active member, ELIXIR Wastewater Surveillance Working Group (2024–present).
  • Co-developed and taught an eight-day advanced bioinformatics course in Addis Ababa, Ethiopia (March 2026), with colleagues from AHRI, ITM and the University of Antwerp. I helped select participants, develop the course materials, plan the programme and deliver the training (the website and materials can be found here).
  • Secretary, International Society for Computational Biology Student Council (ISCB-SC) (2025–2026).
  • 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 introductory 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.
  • Co-organizer, Nanopore Research Day Antwerp (September 2024). The event welcomed 105 participants.
  • I regularly serve as a peer reviewer for journals in my field. A non-exhaustive record of my reviewing activities is available on my ORCID profile.
  • 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 and mentoring

I currently co-supervise two PhD candidates:

  • 2025–present — Marie De Smedt
  • 2024–present — Laura Raes

I have also supervised students during MSc and BSc thesis projects and internships:

  • 2026–present — Mit Vanbruggen (MSc Bioinformatics, thesis)
  • 2026 — Jens Nackaerts (BSc Biomedical Laboratory Technology, internship)
  • 2026 — Aagash Krishnan (BSc Biomedical Laboratory Technology, internship)
  • 2026 — Sien De Koster (BaNaBa Bioinformatics, internship)
  • 2025 — Myra Nasser (MSc Biomedical Sciences, thesis)
  • 2025 — Pavei Amin (MSc Biomedical Sciences, thesis)
  • 2023 — Peter Kirby (MSc Computer Science, internship)
  • 2023 — Yassine Akrim (MSc Computer Science, internship)
  • 2022 — Quinten Van Looy (MSc Biochemistry, thesis)
  • 2021 — Thijs Vanbruggen (MSc Biochemistry, thesis)
  • 2020 — Kristof Van Den Neucker (MSc Biomedical Sciences, thesis)
  • 2019 — Laura Valgaeren (MSc Biochemistry, internship)

From 2018 to 2025, I contributed to courses and practical classes taught by Prof. Kris Laukens. My work included developing and teaching practical exercises, marking exams, and delivering an annual computational biology lecture on phylogenetics and nanopore sequencing.

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.

Selected conference presentations

Oral presentations

  • SquiDBase: A FAIR resource of microbial squiggle data. Nanopore Research Day. Antwerp, Belgium, 2024.
  • A leap forward in revolutionizing infectious disease surveillance with nanopore sequencing. BIOMINA Research Day. Antwerp, Belgium, 2023.
  • Comparative genomics of Salmonella Concord from the Horn of Africa reveals genomic signatures related to high resistance and virulence. European Student Council Symposium, ISCB Student Council. Athens, Greece, 8 September 2018.
  • Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing. Systems Biology Seminar, Institute of Tropical Medicine Antwerp. Antwerp, Belgium, March 2018.

Poster presentations

  • Monitoring pathogens and AMR in wastewater using nanopore sequencing. London Calling. London, United Kingdom, 2026.
  • Monitoring pathogens and AMR in wastewater using nanopore sequencing. ESCMID, 2025.
  • SquiDBase: A centralized community resource of microbial paired squiggle–sequence data. London Calling. London, United Kingdom, 2024.
  • Transcriptional rewiring in Salmonella Typhimurium from sub-Saharan Africa. ISMB 2024. Montreal, Canada, 2024.
  • Posters on the ISCB Student Council. ECCB 2024. Finland, 2024.
  • Exploring the potential of adaptive sampling for Plasmodium WGS from blood samples. London Calling. London, United Kingdom, 2023.
  • Transcriptional rewiring in Salmonella Typhimurium from sub-Saharan Africa. ISMB/ECCB 2023. Lyon, France, 2023.
  • Exploring the potential of adaptive sampling for Plasmodium WGS from blood samples. Nanopore Community Meeting. New York, United States, 2022.
  • Transcriptional rewiring via promoter sequences in Salmonella. ISMB/ECCB 2019. Basel, Switzerland, 25–30 July 2019.
  • Comparative genomic analysis of Salmonella Concord from the Horn of Africa reveals signatures related to high resistance and invasive infections. 11th International Conference on Typhoid and Other Invasive Salmonelloses. Hanoi, Vietnam, 26–28 March 2019.
  • Comparative genomics of Salmonella Concord from the Horn of Africa reveals genomic signatures related to high resistance and virulence. European Conference on Computational Biology (ECCB). Athens, Greece, 8–12 September 2018.
  • Comparative genomics of Salmonella Concord, a resistant and virulent Salmonella serotype in the Horn of Africa. SMRT Leiden. Leiden, Netherlands, 12–13 June 2018.
  • First genome of Salmonella Concord, a highly resistant and virulent Salmonella serotype in the Horn of Africa. Bioinformatics Student Symposium. Antwerp, Belgium, 22 May 2018.