Y. Katz, M. Springer, and W. Fontana. Working Paper. “Embodying probabilistic inference in biochemical circuits”.

N. Nøjgaard, W. Fontana, M. Hellmuth, and D. Merkle. In Press. “Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry.” Journal of Computational Biology (accepted).

J. L. Andersen, R. Fagerberg, C. Flamm, W. Fontana, J. Kolčák, C. V. F. P. Laurent, D. Merkle, and N. Nøjgaard. Forthcoming. “Graph Transformation for Enzymatic Mechanisms.” Bioinformatics (conditionally accepted).

Robert J. H. Ross and Walter Fontana. Forthcoming. “Balancing conservative and disruptive growth in the voter model.” J. Stat. Phys. (accepted).

W. Fontana. 9/16/2020. Du calcul au vivant : le défi d’une science de l’organisation (Leçons inaugurales du Collège de France. no 291). Paris: Collège de France | Fayard ISBN: 978-2-213-71683-1. Publisher's Version

A. Ortiz-Muñoz, H. F. Medina-Abarca, and W. Fontana. 2020. “Combinatorial protein-protein interactions on a polymerizing scaffold.” Proc. Natl. Acad. Sci. USA 117 (6), Pp. 2930-2937. Publisher's Version

R. J. H. Ross and W. Fontana. 2019. “Modeling random walkers on growing random networks.” Physica A, 526, 121117.

R. J. H. Ross, C. Strandkvist, and W. Fontana. 2019. “Compressibility of random walker trajectories on growing networks.” Physics Letters A, 383, Pp. 2028-2032.

R. J. H. Ross, C. Strandkvist, and W. Fontana. 2019. “A random walker’s view of networks whose growth it shapes.” Physical Review E, 99, 062306.

J. Laurent, H. F. Medina-Abarca, P. Boutillier, J. Yang, and W. Fontana. 2018. “A Trace Query Language for Rule-based Models.” Computational Methods in Systems Biology (CMSB), Lecture Notes in Bioinformatics, 11095, Pp. 220-237.

J. Laurent, J. Yang, and W. Fontana. 2018. “Counterfactual Resimulation for Causal Analysis of Rule-Based Models.” Intl. Joint Conference on Artificial Intelligence (IJCAI), Pp. 1882-1890.

P. Boutillier, M. Maasha, X. Li, H. F. Medina-Abarca, J. Krivine, J. Feret, I. Cristescu, A. G. Forbes, and W. Fontana. 2018. “The Kappa platform for rule-based modeling.” Bioinformatics, 34, 13, Pp. i583–i592. Publisher's Version

I. Cristescu, W. Fontana, and J. Krivine. 2018. “Interactions between causal structures in graph rewriting systems.” Third International Workshop on Formal reasoning about Causation, Responsibility, and Explanations in Science and Technology [CREST] 2018 286, Pp. 65-78. Electronic Proceedings in Theoretical Computer Science.

A. G. Forbes, A. Burks, K. Lee, X. Li, P. Boutillier, J. Krivine, and W. Fontana. 2018. “Dynamic Influence Networks for Rule-Based Models.” IEEE Transactions on Visualization and Computer Graphics, 24, 1, Pp. 184-194.

J. Apfeld and W. Fontana. 2018. “Age-Dependence and Aging-Dependence: Neuronal Loss and Lifespan in a C. elegans Model of Parkinson’s Disease.” Biology, 7, 1.

A. Basso-Blandin, W. Fontana, and R. Harmer. 2016. “A knowledge representation meta-model for rule-based modelling of signalling networks.” Electronic Proceedings in Theoretical Computer Science (DCM 2015), 204, Pp. 47-59.

N. Stroustrup, W. E. Anthony, Z. M. Nash, V. Gowda, A. Gomez, I. F. López-Moyado, J. Apfeld*, and W. Fontana*. 2016. “The temporal scaling of C. elegans ageing.” Nature, 530, Pp. 103-107.

C. Romero-Aristizabal, D. S. Marks, W. Fontana*, and J. Apfeld*. 2014. “Regulated spatial organization and sensitivity of cytosolic protein oxidation in Caenorhabditis elegans.” Nature Communications, 5, 5020, Pp. 1–13.

D. A. Fernandes de Abreu, A. Caballero, P. Fardel, N. Stroustrup, Zhunan C., K. Lee, W. D. Keyes, Z. M. Nash, I. F. López-Moyado, F. Vaggi, Astrid C., M. Regenass, A. Neagu, I. Ostojic, C. Liu, Y. Cho, D. Sifoglu, Y. Shen, W. Fontana, Hang L., A. Csikasz-Nagy, C. T. Murphy, A. Antebi, E. Blanc, J. Apfeld, Y. Zhang, Joy A., and Q. Ch'ng. 2014. “An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology.” PLoS Genetics, 10, 3, Pp. e1004225.

N. Stroustrup, B. E. Ulmschneider, Z. M. Nash, I. F. López-Moyado, J. Apfeld, and W. Fontana. 2013. “The Caenorhabditis elegans Lifespan Machine.” Nature Methods, 10, Pp. 665–670.