You may find publications by members before they joined the lab on their respective homepages.
Papers marked with ◑ indicate computer science literature with traditional alphabetical author order


M. Rowland, W. Fontana and E. J. Deeds
"Crosstalk and competition in signaling networks"
submitted (2012)

◑ V. Danos, J. Feret, W. Fontana, R. Harmer, J. Hayman, J. Krivine, C. Thompson-Walsh and G. Winskel
"Graphs, rewriting and causality in rule-based models"
submitted (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)

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)
Supplementary Information
    - 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"
Transactions on Computational Systems Biology, 11:116-137 (2009)

◑ V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine
"Investigation of a biological repair scheme"
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)
[main | supplement | combined] doi:10.1073/pnas.0809908106
HMS Focus commentary.

V. M. Savage, E. J. Deeds and W. Fontana
"Sizing up allometric scaling theory"
PLoS Comput Biol 4(9): e1000171 (2008)
[main | supplement | combined] doi:10.1371/journal.pcbi.1000171

◑ 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"
Principles of Programming Languages 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"
Concurrency Theory 2007, 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"
Verification, Model Checking, and Abstract Interpretation 2008, Lecture Notes in Computer Science, 4905:83–97 (2008)

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

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 [Abstract]