Papers and manuscripts

Papers marked with ◑ indicate computer science literature with alphabetical author order.

◑ J. L. Andersen, A. Davoodi, R. Fagerberg, C. Flamm, W. Fontana, J. Kolčák, C. V. F. P. Laurent, D. Merkle and N. Nøjgaard
Automated Inference of Graph Transformation Rules
arXiv:2404.02692 (2024)

A. Ershova, D. Minev, F. E. Corea-Dilbert, D. Yu, J. Deng, W. Fontana and W. M. Shih
Enzyme-Free Exponential Amplification via Growth and Scission of Crisscross Ribbons from Single-Stranded DNA Components
J. Am. Chem. Soc., 146, 1, 218-227 (2024)

W. Fontana
The shadow of a mechanism
[A commentary to C. H. Waddington’s 1942 paper “Canalization of development and the inheritance of acquired characters”.]
Foundational Papers in Complexity Science, Vol. 1 (1922-1962), D. C. Krakauer (ed.), pp. 71–87, The SFI Press (2024)

P. Honegger and W. Fontana
The Wheels of Chemistry
[Translation of the 1971 paper by Otto Rössler on “A System–Theoretic Model of Biogenesis (Ein systemtheoretisches Modell zur Biogenese)” with margin notes and a commentary.]
Foundational Papers in Complexity Science, Vol. 2 (1962-1973), D. C. Krakauer (ed.), pp. 1085–1103, The SFI Press (2024)

W. Fontana
Informatique et sciences numériques, Résumé des cours et travaux
Annuaire du Collège de France 2019-2020. 120, 41-51 (2023) [OpenEdition]

◑ J. L. Andersen, R. Fagerberg, C. Flamm, W. Fontana, J. Kolčák, C. V. F. P. Laurent, D. Merkle and N. Nøjgaard
Representing catalytic mechanisms with rule composition
J. Chem. Inf. Model. 62, 5513−5524 (2022)

Y. Katz and W. Fontana
Probabilistic Inference With Polymerizing Biochemical Circuits
Entropy 2022, 24, 629 (2022)

◑ J. L. Andersen, R. Fagerberg, C. Flamm, W. Fontana, J. Kolčák, C. V. F. P. Laurent, D. Merkle and N. Nøjgaard
Graph Transformation for Enzymatic Mechanisms
Bioinformatics, 37, i392-i400 (2021)

N. Nøjgaard, W. Fontana, M. Hellmuth and D. Merkle
Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry
Journal of Computational Biology, 28 (7), 701-715 (2021)

R. J. H. Ross and W. Fontana
Balancing conservative and disruptive growth in the voter model
J. Stat. Phys., 183:15 (2021)

W. Fontana
Du calcul au vivant : le défi d'une science de l'organisation (French and English)
Leçons inaugurales du Collège de France. no 291. Collège de France | Fayard. ISBN: 978-2-213-71683-1 (2020)
[English only: From computation to life: The challenge of a science of organization]

A. Ortiz-Muñoz*, H. F. Medina-Abarca* and W. Fontana
Combinatorial protein-protein interactions on a polymerizing scaffold
Proc. Natl. Acad. Sci. USA, 117 (6), 2930–2937 (2020)

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

R. J. H. Ross, C. Strandkvist and W. Fontana
Random walker’s view of networks whose growth it shapes
Phys Rev E, 99, 062306 (2019)

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

D. Abramov, J. Otto, M. Dubey, C. Artanegara, P. Boutillier, W. Fontana and A. G. Forbes
RuleVis: Constructing Patterns and Rules for Rule-Based Models
IEEE VIS (Short Papers), 191-195 (2019)

J. Laurent, J. Yang and W. Fontana
Counterfactual Resimulation for Causal Analysis of Rule-Based Models
Intl. Joint Conference on Artificial Intelligence (IJCAI-18), 1882-1890 (2018)

P. Boutillier, M. Maasha, X. Li, H. F. Medina-Abarca, J. Krivine, J. Feret, I. Cristescu, A. G. Forbes and W. Fontana
The Kappa platform for rule-based modeling
Bioinformatics, 34/13, i583–i592 (2018)

J. Laurent, H. F. Medina-Abarca, P. Boutillier, J. Yang and W. Fontana
A Trace Query Language for Rule-based Models
In: Computational Methods in Systems Biology (CMSB 2018), M. Češka and D. Šafránek (Eds.), Lecture Notes in Bioinformatics, 11095, 220-237 (2018)

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

A. G. Forbes, A. Burks, K. Lee, X. Li, P. Boutillier, J. Krivine and W. Fontana
Dynamic Influence Networks for Rule-Based Models
IEEE Transactions on Visualization and Computer Graphics, 24(1), 184-194 (2018)
[DIN visualization web site] [video]

◑ I. Cristescu, W. Fontana and J. Krivine
Interactions between causal structures in graph rewriting systems
In: Third International Workshop on Formal reasoning about Causation, Responsibility, and Explanations in Science and Technology (CREST 2018), B. Finkbeiner and S. Kleinberg (Eds.), Electronic Proceedings in Theoretical Computer Science, 286, 65-78 (2018) [paper including appendices]

J. Laurent , J. Yang and W. Fontana
Causal analysis of rule-based models by counterfactual reasoning
Abstract, 8th International Workshop on Static Analysis for Systems Biology (SASB 2017), August 29, 2017; New York, NY.

N. Stroustrup, W. E. Anthony, Z. M. Nash, V. Gowda, A. Gomez, I. F. López-Moyado, J. Apfeld* and W. Fontana*
The temporal scaling of C. elegans ageing
Nature, 530, 103-107 (2016) doi:10.1038/nature16550
[paper | supplement | article+supplement | lifespan machine]
- News & Views by Zach Pincus, "A stretch in time", Nature, 530, 37-38 (2016)

◑ A. Basso-Blandin, W. Fontana and R. Harmer
A knowledge representation meta-model for rule-based modelling of signalling networks
In: Developments in Computational Models (DCM 2015), C. A. Munoz and J. A. Perez (Eds.), Electronic Proceedings in Theoretical Computer Science, 204, 47-59 (2016) [preproceedings version]

C. Romero, D. S. Marks, W. Fontana* and J. Apfeld*
Regulated spatial organization and sensitivity of cytosolic protein oxidation in C. elegans
Nature Communications, 5.5020 (2014)
[paper | supplement]

D. A. Fernandes de Abreu, A. Caballero, P. Fardel, N. Stroustrup, Z. Chen, K.-H. Lee, W. D. Keyes, Z. M. Nash, I. F. López-Moyado, F. Vaggi, A. Cornils, M. Regenass, A. Neagu, I. Ostojic, C. Liu, Y. Cho, D. Sifoglu, Y. Shen, W. Fontana, H. Lu, A. Csikasz-Nagy, C. Murphy, A. Antebi, E. Blanc, J. Apfeld, Y. Zhang, J. Alcedo and Q.-L. Ch'ng
An Insulin-to-Insulin Regulatory Network Orchestrates Phenotypic Specificity in Development and Physiology
PLOS Genetics, 10 (3), e1004225 (2014)
[paper]

N. Stroustrup, B. E. Ulmschneider, Z. M. Nash, I. F. López Moyado, J. Apfeld and W. Fontana
The C. elegans Lifespan Machine
Nature Methods, 10, 665-670 (2013) doi:10.1038/nmeth.2475
[paper | supplement | combined] Supplementary video

M. Rowland, W. Fontana and E. J. Deeds
Crosstalk and competition in signaling networks [with supplement]
Biophysical Journal, 103(11), 2389–-2398 (2012)
- New & Notable feature by Robert G. Endres, "Signaling Crosstalk: New Insights Require New Vocabulary", Biophys. J., 103(11), 2241-2242 (2012)
- Included in the Biophysical Journal's "Best of 2012" supplement.

◑ V. Danos, J. Feret, W. Fontana, R. Harmer, J. Hayman, J. Krivine, C. Thompson-Walsh and G. Winskel
Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models
In: Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012), D. D'Souza, T. Kavitha and J. Radhakrishnan (Eds.), Leibniz International Proceedings in Informatics, 18, 276-288 (2012)

E. J. Deeds, J. Krivine, J. Feret, V. Danos and W. Fontana
Combinatorial complexity and compositional drift in protein interaction networks
PLoS ONE 7(3): e32032 (2012)
[paper with supplement]

E. J. Deeds, J. A. Bachman and W. Fontana
Optimizing ring assembly reveals the strength of weak interactions
Proc. Natl. Acad. Sci. USA, 109(7), 2348-2353 (2012)

E. Smith, S. Krishnamurthy, W. Fontana and D. C. Krakauer
Non-equilibrium phase transitions in biomolecular signal transduction
Phys. Rev. E, 84:051917 (2011)

D. C. Krakauer, J. P. Collins, D. Erwin, J. C. Flack, W. Fontana, M. D. Laubichler, S. J. Prohaska, G. B. West and P. F. Stadler
The Challenges and Scope of Theoretical Biology
J. Theor. Biol., 276, 269-276 (2011)

R. Harmer, V. Danos, J. Feret, J. Krivine and W. Fontana
Intrinsic Information Carriers in Combinatorial Dynamical Systems
Chaos, 20, 037108 (2010)

◑ V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine
Abstracting the differential semantics of rule-based models: exact and automated model reduction
In: Proceedings of the 25th Annual IEEE Symposium on Logic in Computer Science (LICS). J-P Jouannaud (Ed.), pp. 362--381 (2010). IEEE Computer Society Press

T. Kolokotrones, V. M. Savage, E. J. Deeds and W. Fontana
Curvature in Metabolic Scaling
Nature, 464:753-756 (2010)
[paper | paper+supplement]
- News & Views feature by Craig R. White, "There is no single p", Nature, 464:691 (2010)
- Commentary by Niall MacKay, J. Theor. Biol., 280, 194-196 (2011) [pdf]
E. J. Deeds, V. M. Savage and W. Fontana, Reply to MacKay, J. Theor. Biol., 280, 197–198 (2011) [pdf]

S. E. Hulme, S. S. Shevkoplyas, A. P. McGuigan, J. Apfeld, W. Fontana and G. M. Whitesides
Lifespan-on-a-Chip: microfluidic chambers for performing lifelong observation of C. elegans
Lab on a Chip, 10:589-597 (2010)

◑ V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine
Rule-based Modelling and Model Perturbation
In: Priami C., Back R. J., Petre I. (Eds.) Transactions on Computational Systems Biology XI. Lecture Notes in Computer Science, 5750, 116-137 (2009)

◑ V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine
Investigation of a biological repair scheme
In: Workshop on Membrane Computing 9, D. Corne et al. (Eds.), Lecture Notes in Computer Science, 5391, 1-12 (2009)

J. Feret, V. Danos, J. Krivine, R. Harmer and W. Fontana
Internal coarse-graining of molecular systems
Proc. Natl. Acad. Sci. USA, 106, 6453-6458 (2009)
[paper with supplement]

V. M. Savage, E. J. Deeds and W. Fontana
Sizing up allometric scaling theory
PLoS Comput Biol 4(9): e1000171 (2008)
[paper with supplement]

◑ V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine
Rule-based modeling, symmetries, refinements
In: Formal Methods in Systems Biology (FMSB 2008), J. Fisher (Ed.), Lecture Notes in Bioinformatics, 5054:103-122 (2008)

◑ V. Danos, J. Feret, W. Fontana and J. Krivine
"Abstract interpretation of cellular signalling networks"
In: VMCAI 2008, F. Logozzo et al. (Eds.), Lecture Notes in Computer Science, 4905, 83-–97 (2008)

W. Fontana
Systems biology, models, and concurrency
In: Proceedings of the 35th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages (POPL 2008), invited talk, [extended abstract] [slides]

S. E. Hulme, S. S. Shevkoplyas, J. Apfeld, W. Fontana and G. M. Whitesides
A Microfabricated Array of Clamps for Immobilizing and Imaging C. elegans
Lab on a Chip, 7, 1515-1523 (2007)

◑ V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine
Rule-Based Modeling of Cellular Signaling
In: CONCUR 2007, L. Caires and V. T. Vasconcelos (Eds.), Lecture Notes in Computer Science, 4703, 17-41 (2007)

S. Krishnamurthy, E. Smith, D. Krakauer and W. Fontana
The stochastic behavior of a molecular switching circuit with feedback
Biology Direct, 2:13 (31 May 2007)

◑ V. Danos, J. Feret, W. Fontana and J. Krivine
"Scalable simulation of cellular signalling networks"
In: APLAS 2007, Z. Shao (Ed.), Lecture Notes in Computer Science 4807, 139–-157 (2007)

W. Fontana
“The topology of the possible”
In: Understanding Change - Models, Methodologies and Metaphors. A. Wimmer and R. Kössler (Eds.) Palgrave Macmillan (2006)
[manuscript with color figures]

W. Fontana
[Perspective:] "Pulling Strings"
Science, 314, 1552-1553 (2006)

W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka and W. Fontana
"Rules for Modeling Signal-Transduction Systems"
Science STKE, Vol. 2006, Issue 344, pp. re6, 18 July 2006
[paper]

M. D. Laubichler, G. B. Müller, W. Fontana, and G. P. Wagner
Sacrificing dialogue for politics?
Science, 309, 1324 (2005)

L. W. Ancel and W. Fontana
Evolutionary lock-in and the origin of modularity in RNA structure
In: Modularity - Understanding the development and evolution of complex natural systems. W. Callebaut and D. Rasskin-Gutman (Eds.), pp. 129-141 (2005) Cambridge, MA: MIT Press.

J. Lobo, J. Miller, and W. Fontana
Neutrality in Technological Landscapes
SFI Working Paper, unpublished manuscript (2004)

W. Fontana, J. Karkanias, L. G. Meredith, and M. Radestock
Lab-to-lab connectivity and semantics in the life sciences
Position Paper for the W3C workshop on "Semantic Web for Life Sciences". 27-28 October 2004, pp. 1–4. Cambridge, MA.

J. A. G. M. de Visser, J. Hermisson, G. Wagner, L. Ancel Meyers, H. Bagheri-Chaichian, J. L. Blanchard, L. Chao, J. M. Cheverud, S. F. Elena, W. Fontana, G. Gibson, T. F. Hansen, D. Krakauer, R. C. Lewontin, C. Ofria, S. H. Rice, G. von Dassow, A. Wagner, and M. C. Whitlock
Perspective: Evolution and detection of genetic robustness
Evolution, 57, 9, 1959-1972 (2003)

N. Fedoroff and W. Fontana
Genetic networks. Small numbers of big molecules
Science, 297, 1129–1131 (2002)

W. Fontana
Modelling 'evo-devo' with RNA
BioEssays, 24, 1164–1177 (2002)

B. M. Stadler, P. F. Stadler, G. P. Wagner, and W. Fontana
The topology of the possible: formal spaces underlying patterns of evolutionary change
Journal of Theoretical Biology, 213, 2, 241–274 (2001)

L Ancel and W. Fontana
Plasticity, evolvability, and modularity in RNA
Journal of Experimental Zoology (Mol. Dev. Evol.), 288, 242-283 (2000)

C. Flamm, W. Fontana, I. L. Hofacker, and P. Schuster
RNA folding at elementary step resolution
RNA, 6, 325–338 (2000)

W. Fontana and S. Ballati
Complexity
Complexity, 4, 14-16 (1999)

P. Schuster and W. Fontana
Chance and necessity in evolution: lessons from RNA
Physica D (Nonlinear Phenomena), 133, 427–452 (1999)

S. Wuchty, W. Fontana, and I. Hofacker
Complete suboptimal folding of RNA and the stability of secondary structures
Biopolymers, 49, 145-165 (1999)

W. Fontana and P. Schuster
Continuity in evolution: On the nature of transitions
Science, 280, 1451–1455 (1998)

W. Fontana
Keine Information ohne Evolution
Ethik- und Sozialwissenschaften, 9, 198–200 (1998)

W. Fontana and P. Schuster
Shaping space: The possible and the attainable in RNA genotype-phenotype mapping
Journal of Theoretical Biology, 194, 491–515 (1998)

D. Heiss-Czedik and W. Fontana
Evolution of lambda-expressions through Genetic Programming
unpublished manuscript (1997)

M. A. Huynen, P. F. Stadler, and W. Fontana
Smoothness within ruggedness: The role of neutrality in adaptation
Proc. Natl. Acad. Sci. USA, 93, 397–401 (1996)

W. Fontana and L. W. Buss.
The barrier of objects: From dynamical systems to bounded organizations
In: Boundaries and Barriers. J. Casti and A. Karlqvist (Eds.), 56–116, Reading MA: Addison-Wesley (1996)
[A summary was reprinted as: “On organization” in The future of science has begun: Approaches to Artificial Life and Artificial Intelligence. Fondazione Carlo Erba, volume 4, 23–40 (1996)]

W. Fontana, G. P. Wagner, and L. W. Buss
Beyond digital naturalism
Artificial Life, 1 (2) 211–227 (1994)
[Reprinted in: Artificial Life - An Overview. Chris Langton (Ed.), pp. 211–227, MIT Press, Cambridge, MA, 1995]

I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, and P. Schuster
Fast folding and comparison of RNA secondary structures
Monatshefte für Chemie / Chemical Monthly, 125, 167–188 (1994)

P. Schuster, W. Fontana, P. F. Stadler, and I. L. Hofacker
From sequences to shapes and back: a case study in RNA secondary structures
Proceedings of The Royal Society (London) B, 255, 279–284 (1994)

W. Fontana
Molekulare Semantik: Evolution zwischen Variation und Konstruktion
In: Evolution - Entwicklung und Organisation in der Natur. V. Braitenberg and I. Hosp (Eds.), pp. 69–106. rororo-science (1 9706 5), 1994
[Reprinted in: Origenes de la vida. En el centenario de Aleksandr Ivanovich Oparin. F. Moran, J. Pereto and A. Moreno (Eds.), pp. 269–302, Editorial Complutense, 1995]

M. Tacker, W. Fontana, P. F. Stadler, and P. Schuster
Statistics of RNA melting kinetics
European Biophysics Journal, 23, 29–38 (1994)

W. Fontana and L. W. Buss
What would be conserved if "the tape were played twice"?
Proc. Natl. Acad. Sci. USA, 91, 757–761 (1994)
[Reprinted in: Complexity: Metaphors, Models, and Reality. George A. Cowan, David Pines, and David Meltzer (eds.), pp. 223–244, Addison-Wesley, Reading, MA, 1994]

W. Fontana and L. W. Buss
``The arrival of the fittest'': Toward a theory of biological organization
Bulletin of Mathematical Biology, 56, 1–64 (1994)

P. F. Stadler, W. Fontana, and J. H. Miller
Random catalytic reaction networks
Physica D (Nonlinear Phenomena), 63, 378–392 (1993)

W. Fontana, P. F. Stadler, E. Bornberg-Bauer, T. Griesmacher, I. Hofacker, M. Tacker, P. Tarazona, E. Weinberger, and P. Schuster
RNA folding and combinatory landscapes
Physical Review E, 47, 2083–2099 (1993)

W. Fontana, D. Konings, P. F. Stadler, and P. Schuster
Statistics of RNA secondary structures
Biopolymers, 33, 1389-1404 (1993)

W. Fontana
Algorithmic chemistry
In: Artificial life II. C.G.Langton et al. (Eds.), pp. 159–209. Addison-Wesley (1991)

R. J. Bagley, J. D. Farmer, and W. Fontana
Evolution of a Metabolism
In: Artificial Life II. C.G.Langton et al. (Eds.), pp. 141–158. Addison-Wesley (1991)

W. Fontana, T. Griesmacher, W. Schnabl, P. F. Stadler, and P. Schuster
Statistics of landscapes based on free energies, replication and degradation rate constants of RNA secondary structures
Monatshefte für Chemie / Chemical Monthly, 122, 795–819 (1991)

W. Fontana
Functional self-organization in complex systems
In: 1990 Lectures in Complex Systems. SFI Studies in the Sciences of Complexity. L. Nadel and D. Stein (Eds.), pp. 407-426. Reading, MA: Addison-Wesley (1991)
[Reprinted in: Pattern Formation in the Physical and Biological Sciences. H. F. Nijhout, L. Nadel, and D. Stein (Eds.), pp. 43–63, Addison-Wesley, Reading, MA, 1997]

W. Fontana, W. Schnabl, and P. Schuster
Physical aspects of evolutionary optimization and adaptation
Physical Review A, 40, 3301–3321 (1989)

W. Fontana and P Schuster
A computer model of evolutionary optimization
Biophysical Chemistry, 26, 123–147 (1987)