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.
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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.
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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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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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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.
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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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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.
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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.
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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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