Beyond Digital Naturalism. - Walter Fontana; Günter P. Wagner; Leo W. Buss (Artif. Life, 1994)

Complexity. - Walter Fontana; Susan Ballati (Complex., 1999)

Logic and Systems Biology. - Walter Fontana (LICS, 2005)

Scalable Simulation of Cellular Signaling Networks. - Vincent Danos; Jérôme Feret; Walter Fontana; Jean Krivine (APLAS, 2007)

Rule-Based Modelling of Cellular Signalling. - Vincent Danos; Jérôme Feret; Walter Fontana; Russell Harmer; Jean Krivine (CONCUR, 2007)

Rule-Based Modelling, Symmetries, Refinements. - Vincent Danos; Jérôme Feret; Walter Fontana; Russell Harmer; Jean Krivine (FMSB, 2008)

Investigation of a Biological Repair Scheme. - Vincent Danos; Jérôme Feret; Walter Fontana; Russell Harmer; Jean Krivine (Workshop on Membrane Computing, 2008)

Systems biology, models, and concurrency. - Walter Fontana (POPL, 2008)

Abstract Interpretation of Cellular Signalling Networks. - Vincent Danos; Jérôme Feret; Walter Fontana; Jean Krivine (VMCAI, 2008)

Sizing Up Allometric Scaling Theory. - Van M. Savage; Eric J. Deeds; Walter Fontana (PLoS Comput. Biol., 2008)

Internal coarse-graining of molecular systems. - Jérôme Feret; Vincent Danos; Jean Krivine; Russ Harmer; Walter Fontana (Proc. Natl. Acad. Sci. USA, 2009)

Rule-Based Modelling and Model Perturbation. - Vincent Danos; Jérôme Feret; Walter Fontana; Russell Harmer; Jean Krivine (Trans. Comp. Sys. Biology, 2009)

Abstracting the Differential Semantics of Rule-Based Models: Exact and Automated Model Reduction. - Vincent Danos; Jérôme Feret; Walter Fontana; Russell Harmer; Jean Krivine (LICS, 2010)

Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models. - Vincent Danos; Jérôme Feret; Walter Fontana; Russell Harmer; Jonathan Hayman; Jean Krivine; Christopher D. Thompson-Walsh; Glynn Winskel (FSTTCS, 2012)

A knowledge representation meta-model for rule-based modelling of signalling networks. - Adrien Basso-Blandin; Walter Fontana; Russ Harmer (DCM, 2015)

A Trace Query Language for Rule-Based Models. - Jonathan Laurent; Héctor F. Medina-Abarca; Pierre Boutillier; Jean Yang; Walter Fontana (CMSB, 2018)

Counterfactual Resimulation for Causal Analysis of Rule-Based Models. - Jonathan Laurent; Jean Yang; Walter Fontana (IJCAI, 2018)

The Kappa platform for rule-based modeling. - Pierre Boutillier; Mutaamba Maasha; Xing Li; Héctor F. Medina-Abarca; Jean Krivine; Jérôme Feret; Ioana Cristescu; Angus G. Forbes; Walter Fontana (Bioinform., 2018)

Interactions between Causal Structures in Graph Rewriting Systems. - Ioana Cristescu; Walter Fontana; Jean Krivine (CREST@ETAPS, 2018)

Dynamic Influence Networks for Rule-Based Models. - Angus Graeme Forbes; Andrew Burks; Kristine Lee; Xing Li; Pierre Boutillier; Jean Krivine; Walter Fontana (IEEE Trans. Vis. Comput. Graph., 2018)

RuleVis: Constructing Patterns and Rules for Rule-Based Models. - David Abramov; Jasmine Otto; Mahika Dubey; Cassia Artanegara; Pierre Boutillier; Walter Fontana; Angus G. Forbes (IEEE VIS (Short Papers), 2019)

Graph transformation for enzymatic mechanisms. - Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Walter Fontana; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (Bioinform., 2021)

Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry. - Nikolai Nøjgaard; Walter Fontana; Marc Hellmuth; Daniel Merkle (J. Comput. Biol., 2021)

Characterizing Catalytic Mechanisms with Overlay Graphs. - Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Walter Fontana; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (CoRR, 2022)

Probabilistic Inference with Polymerizing Biochemical Circuits. - Yarden Katz; Walter Fontana (Entropy, 2022)

Representing Catalytic Mechanisms with Rule Composition. - Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Walter Fontana; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (J. Chem. Inf. Model., 2022)

Automated Inference of Graph Transformation Rules. - Jakob L. Andersen; Akbar Davoodi; Rolf Fagerberg; Christoph Flamm; Walter Fontana; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (CoRR, 2024)