Spontaneous Branching in a Polyp Oriented Model of Stony Coral Growth. - Roeland Merks; Alfons G. Hoekstra; Jaap A. Kaandorp; Peter M. A. Sloot (International Conference on Computational Science (1), 2002)

A Problem Solving Environment for Modelling Stony Coral Morphogenesis. - Roeland Merks; Alfons G. Hoekstra; Jaap A. Kaandorp; Peter M. A. Sloot (International Conference on Computational Science, 2003)

Cell-Oriented Modeling of In Vitro Capillary Development. - Roeland Merks; Stuart A. Newman; James A. Glazier (ACRI, 2004)

Problem-Solving Environments for Biological Morphogenesis. - Roeland Merks; Alfons G. Hoekstra; Jaap A. Kaandorp; Peter M. A. Sloot; Paulien Hogeweg (Comput. Sci. Eng., 2006)

From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development. - Trevor M. Cickovski; Kedar Aras; Maciej Swat; Roeland Merks; Tilmann Glimm; H. George E. Hentschel; Mark S. Alber; James A. Glazier; Stuart A. Newman; Jesús A. Izaguirre (Comput. Sci. Eng., 2007)

Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth. - Roeland Merks; Erica D. Perryn; Abbas Shirinifard; James A. Glazier (PLoS Comput. Biol., 2008)

A Web-based Repository of Reproducible Simulation Experiments for Systems Biology. - Michael A. Guravage; Roeland Merks (SIMULTECH, 2011)

Redox balance is key to explaining full vs. partial switching to low-yield metabolism. - Milan van Hoek; Roeland Merks (BMC Syst. Biol., 2012)

The Next Boom of Big Data in Biology: Multicellular Datasets. - Roeland Merks (ERCIM News, 2014)

Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro. - René F. M. van Oers; Elisabeth G. Rens; Danielle J. LaValley; Cynthia A. Reinhart-King; Roeland M. H. Merks (PLoS Comput. Biol., 2014)

A global sensitivity analysis approach for morphogenesis models. - Sonja E. M. Boas; María I. Navarro Jimenez; Roeland M. H. Merks; Joke G. Blom (BMC Syst. Biol., 2015)

Tip cell overtaking occurs as a side effect of sprouting in computational models of angiogenesis. - Sonja E. M. Boas; Roeland M. H. Merks (BMC Syst. Biol., 2015)

Tackling Big Data in the Life Sciences - Introduction to the Special Theme. - Roeland Merks; Marie-France Sagot (ERCIM News, 2016)

Modelling the Growth of Blood Vessels in Health and Disease. - Elisabeth G. Rens; Sonja E. M. Boas; Roeland M. H. Merks (ERCIM News, 2016)

Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism. - Milan J. A. van Hoek; Roeland M. H. Merks (BMC Syst. Biol., 2017)

Blood vessel tortuosity selects against evolution of aggressive tumor cells in confined tissue environments: A modeling approach. - András Szabó; Roeland M. H. Merks (PLoS Comput. Biol., 2017)

A local uPAR-plasmin-TGFβ1 positive feedback loop in a qualitative computational model of angiogenic sprouting explains the in vitro effect of fibrinogen variants. - Sonja E. M. Boas; Joao Carvalho 001; Marloes van den Broek; Ester M. Weijers; Marie-José Goumans; Pieter Koolwijk; Roeland M. H. Merks (PLoS Comput. Biol., 2018)

Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics. - Leonie van Steijn; Inge M. N. Wortel; Clément Sire; Loïc Dupré; Guy Theraulaz; Roeland M. H. Merks (PLoS Comput. Biol., 2022)

A new model of Notch signalling: Control of Notch receptor cis-inhibition via Notch ligand dimers. - Daipeng Chen; Zary Forghany; Xinxin Liu; Haijiang Wang; Roeland M. H. Merks; David A. Baker (PLoS Comput. Biol., 2023)

The shapes of elongating gastruloids are consistent with convergent extension driven by a combination of active cell crawling and differential adhesion. - Martijn A. de Jong; Esmée Adegeest; Noémie M. L. P. Bérenger-Currias; Maria Mircea; Roeland M. H. Merks; Stefan Semrau (PLoS Comput. Biol., 2024)

A model of Notch signalling control of angiogenesis: Evidence of a role for Notch ligand heterodimerization. - Daipeng Chen; Xinxin Liu; Haijiang Wang; Roeland M. H. Merks; David A. Baker (PLoS Comput. Biol., 2025)