Sitemap
A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
Future Blog Post
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Blog Post number 4
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
publications
PanTools v3: functional annotation, classification and phylogenomics
Published in Bioinformatics, 2022
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.
Direct Link
Genetic mechanisms underlying increased microalgal thermotolerance, maximal growth rate, and yield on light following adaptive laboratory evolution
Published in BMC Biology, 2022
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.
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The genome of Lactuca saligna, a wild relative of lettuce, provides insight into non-host resistance to the downy mildew Bremia lactucae
Published in The Plant Journal, 2023
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.
Direct Link
PanVA: Variant Analysis within Pangenomes
Published in IEEE, 2023
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.
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Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding
Published in G3 Genes|Genomes|Genetics, 2023
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.
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Lactuca super-pangenome reduces bias towards reference genes in lettuce research
Published in BMC Plant Biology, 2024
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.
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Multipla: Multiscale Pangenomic Locus Analysis
Published in Computer Graphics Forum, 2025
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.
Direct Link
High-Quality Plant Genomes for and through Pangenomics
Published in Genome Assembly. Humana, New York, NY., 2025
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.
Direct Link
MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment
Published in NAR Genomics and Bioinformatics, 2026
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.
Direct Link
software
MoGAAAP Permalink
During my PhD (2020-2025) I have developed the workflow MoGAAAP (Modular Genome Assembly, Annotation and Quality Assessment Pipeline), written in Snakemake. This pipeline is designed to automate the assembly, annotation and QA of sets of genomes with the aim of constructing population-level pangenomes. It is modular, so that it can also be used for e.g. the annotation and QA of an already existing assembly.
PanTools Permalink
For my PhD (2020-2025) I have developed several major features for PanTools as well as general code improvements. I was involved in designing new features for versions 3 and 4, and I have been one of the maintainers of version 4. Some of the major features I have worked on include: (1) Implementation of integrating PAV and VCF data into a pangenome graph for gene analysis. (2) Implementation of a region of interest analysis in pangenomic context. (3) Update of PanTools to Java 21 and neo4j 5.