(M, R) Systems and RAF Sets - Common Ideas, Tools and Projections. - Juan-Carlos Letelier; Sebastián Jaramillo; Ricardo Honorato-Zimmer; Ulises Pereira; Diego Contreras; Bryan Reynaert; Valentina C. Hernandez; Jorge Soto Andrade; María Luz Cárdenas; Athel Cornish-Bowden (ALIFE, 2010)

Rigid Geometric Constraints for Kappa Models. - Vincent Danos; Ricardo Honorato-Zimmer; Sebastián Jaramillo-Riveri; Sandro Stucki (SASB, 2012)

Coarse-graining the Dynamics of Ideal Branched Polymers. - Vincent Danos; Ricardo Honorato-Zimmer; Sebastián Jaramillo-Riveri; Sandro Stucki (SASB, 2012)

Reversible Sesqui-Pushout Rewriting. - Vincent Danos; Tobias Heindel; Ricardo Honorato-Zimmer; Sandro Stucki (ICGT, 2014)

Approximations for Stochastic Graph Rewriting. - Vincent Danos; Tobias Heindel; Ricardo Honorato-Zimmer; Sandro Stucki (ICFEM, 2014)

Mean Quantitative Coverability in Stochastic Graph Transformation Systems. - Tobias Heindel; Vincent Danos; Ricardo Honorato-Zimmer; Sandro Stucki (Electron. Commun. Eur. Assoc. Softw. Sci. Technol., 2014)

Moment Semantics for Reversible Rule-Based Systems. - Vincent Danos; Tobias Heindel; Ricardo Honorato-Zimmer; Sandro Stucki (RC, 2015)

Thermodynamic graph-rewriting. - Vincent Danos; Russ Harmer; Ricardo Honorato-Zimmer (Log. Methods Comput. Sci., 2015)

Emergent Communities in Socio-cognitive Networks. - Vincent Danos; Ricardo Honorato-Zimmer (FAS*W@SASO/ICCAC, 2016)

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. - Goksel Misirli; Matteo Cavaliere; William Waites; Matthew R. Pocock; Curtis Madsen; Owen Gilfellon; Ricardo Honorato-Zimmer; Paolo Zuliani; Vincent Danos; Anil Wipat (Bioinform., 2016)

Annotations for Rule-Based Models. - Matteo Cavaliere; Vincent Danos; Ricardo Honorato-Zimmer; William Waites (CoRR, 2018)

Chromar, a Rule-based Language of Parameterised Objects. - Ricardo Honorato-Zimmer; Andrew J. Millar; Gordon D. Plotkin; Argyris Zardilis (SASB, 2018)

Chromar, a language of parameterised agents. - Ricardo Honorato-Zimmer; Andrew J. Millar; Gordon D. Plotkin; Argyris Zardilis (Theor. Comput. Sci., 2019)

Rate Equations for Graphs. - Vincent Danos; Tobias Heindel; Ricardo Honorato-Zimmer; Sandro Stucki (CMSB, 2020)