Lab-yrinths

You may find additional publications by current and former lab members on their respective homepages.
Papers marked withindicate computer science literature with traditional alphabetical author order.
 

W. Fontana
Du calcul au vivant : le défi d'une science de l'organisation
Leçons inaugurales du Collège de France. no 291. Collège de France | Fayard. ISBN: 978-2-213-71683-1 (2020)
[English version: 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
"A 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)

Y. Katz, M. Springer and W. Fontana
Embodying probabilistic inference in biochemical circuits
arXiv:1806.10161
 (2018)

J. Laurent, J. Yang and W. Fontana
Counterfactual Resimulation for Causal Analysis of Rule-Based Models
Intl. Joint Conference on Artificial Intelligence (IJCAI), 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
[article | supplement | lifespan machine]
    - News & Views by Zach Pincus, "A stretch in time", Nature, 530, 37-38 (2016)
    - HMS News

◑ 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)
[article | supplement]
    - Harvard News

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)
[article]

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
[article | supplement | combined] Supplementary video
    - More info at www.lifespanmachine.org
   

M. Rowland, W. Fontana and E. J. Deeds
"Crosstalk and competition in signaling networks"
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)
[article | supplement | combined]

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)
[article+supplement | 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"
Formal Methods in Systems Biology 2008, Lecture Notes in Bioinformatics, 5054:103-122 (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
"Abstract interpretation of cellular signalling networks"
in: VMCAI 2008, F. Logozzo et al. (Eds.), Lecture Notes in Computer Science, 4905:83-–97 (2008)

◑ 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]