IPH-TRIM3D-PCLake: A three-dimensional complex dynamic model for subtropical aquatic ecosystems. - Carlos R. Fragoso Jr.; Egbert H. van Nes; Jan H. Janse; David da Motta Marques (Environ. Model. Softw., 2009)

Early Warnings for Catastrophic Shifts in Ecosystems: Comparison between Spatial and Temporal Indicators. - Raul Donangelo; Hugo Fort; Vasilis Dakos; Marten Scheffer; Egbert H. van Nes (Int. J. Bifurc. Chaos, 2010)

Potential effects of climate change and eutrophication on a large subtropical shallow lake. - Carlos R. Fragoso Jr.; David M. L. Motta Marques; Tiago Finkler Ferreira; Jan H. Janse; Egbert H. van Nes (Environ. Model. Softw., 2011)

Serving many at once: How a database approach can create unity in dynamical ecosystem modelling. - Wolf M. Mooij; Robert J. Brederveld; Jeroen J. M. de Klein; Don L. DeAngelis; Andrea S. Downing; Michiel Faber; Daan J. Gerla; Matthew R. Hipsey; Jochem 't Hoen; Jan H. Janse; Annette B. G. Janssen; Michel Jeuken; et al. (Environ. Model. Softw., 2014)

Climbing Escher's stairs: A way to approximate stability landscapes in multidimensional systems. - Pablo Rodríguez-Sánchez; Egbert H. van Nes; Marten Scheffer (PLoS Comput. Biol., 2020)

Species abundance correlations carry limited information about microbial network interactions. - Susanne Pinto; Elisa Benincà; Egbert H. van Nes; Marten Scheffer; Johannes A. Bogaards (PLoS Comput. Biol., 2022)