CV

Education

PhD in Bioinformatics, Wageningen University, 2020-2025
MSc in Plant Biotechnology, Wageningen University, 2018-2020
BSc in Plant Sciences, Wageningen University, 2015-2018

Experience

2025-present: Postdoctoral researcher
- Wageningen University
  - Laboratory of Plant Physiology
  - Biosystematics Group
- Supervisors: Charlotte Gommers & Marian Bemer
2020-2025: PhD candidate
- Wageningen University
  - Bioinformatics Group
- Promotor: Dick de Ridder
- Co-promotors: Eric Schranz & Sandra Smit
- Daily supervisor: Sandra Smit
2018-2020: MSc Internship
- GeneTwister
- Supervisor: Peter van Dam

Skills (not limited to the below)

Programming
- Bash
- Java
- Snakemake
- Python
- R
Research
- Genomics
- Pangenomics
- Comparative genomics
- Transcriptomics

Publications

MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment

van Workum, D.J.M., Dey, K.K., Kozik, A. Lavelle, D.O., de Ridder, D., Schranz, M.E., Michelmore, R.W., Smit, S. (2026). MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment. NAR Genomics and Bioinformatics, 8(1), lqag008.

High-Quality Plant Genomes for and through Pangenomics

Papastolopoulou, C., Yang, Z., van Workum, F.J.M., Wijfjes, R.Y., Smit, S. High-Quality Plant Genomes for and through Pangenomics. In: Genome Assembly. Methods in Molecular Biology, vol 2955. Humana, New York, NY.

Multipla: Multiscale Pangenomic Locus Analysis

van den Brandt, A., Ståhlbom, E., van Workum, F.J.M., van de Wetering, H., Lundström, C., Smit, S. and Vilanova, A. (2025), Multipla: Multiscale Pangenomic Locus Analysis. Computer Graphics Forum, e70147.

Lactuca super-pangenome reduces bias towards reference genes in lettuce research

van Workum, D.J.M., Mehrem, S.L., Snoek, B.L., Alderkamp, M.C., Lapin, D., Mulder, F.F., ... & Smit, S. (2024). Lactuca super-pangenome reduces bias towards reference genes in lettuce research. BMC Plant Biology, 24(1), 1019.

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Xiong, W.*, van Workum, D.J.M.*, Berke, L., Bakker, L.V., Schijlen, E., Becker, F.F., ... & Schranz, M.E. (2023). Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding. G3: Genes, Genomes, Genetics, 13(11), jkad204.

PanVA: Variant Analysis within Pangenomes

van den Brandt, A., Jonkheer, E.M., van Workum, D.J.M., van de Wetering, H., Smit, S., & Vilanova, A. (2023). Panva: Pangenomic variant analysis. IEEE Transactions on Visualization and Computer Graphics.

The genome of Lactuca saligna, a wild relative of lettuce, provides insight into non-host resistance to the downy mildew Bremia lactucae

Xiong, W., Berke, L., Michelmore, R., van Workum, D.J.M., Becker, F.F., Schijlen, E., ... & Schranz, M.E. (2023). The genome of Lactuca saligna, a wild relative of lettuce, provides insight into non‐host resistance to the downy mildew Bremia lactucae. The Plant Journal, 115(1), 108-126.

Genetic mechanisms underlying increased microalgal thermotolerance, maximal growth rate, and yield on light following adaptive laboratory evolution

Barten, R., van Workum, D.J.M., de Bakker, E., Risse, J., Kleisman, M., Navalho, S., ... & Barbosa, M.J. (2022). Genetic mechanisms underlying increased microalgal thermotolerance, maximal growth rate, and yield on light following adaptive laboratory evolution. BMC biology, 20(1), 242.

PanTools v3: functional annotation, classification and phylogenomics

Jonkheer, E.M., van Workum, D.J.M., Sheikhizadeh Anari, S., Brankovics, B., de Haan, J.R., Berke, L., ... & Smit, S. (2022).PanTools v3: functional annotation, classification and phylogenomics. Bioinformatics, 38(18), 4403-4405.

Dirk-Jan M. van Workum

CV