de Groot, DH., Morillo Leonardo, SX., Pachkov, M., van Nimwegen, E. (2026). Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data. Nat Biotechnol.
Julou, T., Gervais, T., de Groot, D., van Nimwegen, E. (2025). Growth rate controls the sensitivity of gene regulatory circuits. Sci Adv. 11(17):eadu9279
de Groot, DH., Tjalma, AJ., Bruggeman, FJ., van Nimwegen, E. (2023). Effective bet-hedging through growth rate dependent stability. Proc Natl Acad Sci U S A. 120(8):e2211091120
Buchner, B., Clement, TJ., de Groot, DH., Zanghellini, J. (2023). ecmtool: fast and memory-efficient enumeration of elementary conversion modes. Bioinformatics. 39(3)
Clement, TJ., Baalhuis, EB., Teusink, B (...) Planqué, R., de Groot, DH. (2021). Unlocking Elementary Conversion Modes: ecmtool Unveils All Capabilities of Metabolic Networks. Patterns (N Y). 2(1):100177
Schulte, CCM., Borah, K., Wheatley, RM (...) Papachristodoulou, A., Poole, PS. (2021). Metabolic control of nitrogen fixation in rhizobium-legume symbioses. Sci Adv. 7(31)
van Pelt-KleinJan, E., de Groot, DH., Teusink, B. (2021). Understanding FBA Solutions under Multiple Nutrient Limitations. Metabolites. 11(5)
van Tatenhove-Pel, RJ., de Groot, DH., Bisseswar, AS., Teusink, B., Bachmann, H. (2021). Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth. ISME J. 15(10):3050-3061
de Groot, DH., Lischke, J., Muolo, R (...) Bruggeman, FJ., Teusink, B. (2020). The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints. Cell Mol Life Sci. 77(3):441-453
de Groot, DH., Hulshof, J., Teusink, B., Bruggeman, FJ., Planqué, R. (2020). Elementary Growth Modes provide a molecular description of cellular self-fabrication. PLoS Comput Biol. 16(1):e1007559
Botman, D., de Groot, DH., Schmidt, P., Goedhart, J., Teusink, B. (2019). In vivo characterisation of fluorescent proteins in budding yeast. Sci Rep. 9(1):2234
de Groot, DH., van Boxtel, C., Planqué, R., Bruggeman, FJ., Teusink, B. (2019). The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates. PLoS Comput Biol. 15(3):e1006858
