Systems Biology at Harvard Medical School

Home | People | Research | Publications | Contact | Internal
Home | Contact | Faculty
Home | HMS |
subglobal4 link | subglobal4 link | subglobal4 link | subglobal4 link | subglobal4 link | subglobal4 link | subglobal4 link
subglobal5 link | subglobal5 link | subglobal5 link | subglobal5 link | subglobal5 link | subglobal5 link | subglobal5 link
subglobal6 link | subglobal6 link | subglobal6 link | subglobal6 link | subglobal6 link | subglobal6 link | subglobal6 link
subglobal7 link | subglobal7 link | subglobal7 link | subglobal7 link | subglobal7 link | subglobal7 link | subglobal7 link
subglobal8 link | subglobal8 link | subglobal8 link | subglobal8 link | subglobal8 link | subglobal8 link | subglobal8 link

Fontana Laboratory


  Publications


   

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



N. Stroustrup, W. E. Anthony, Z. M. Nash, V. Gowda, A. Gomez, I. F. López-Moyado, J Apfeld* and W Fontana* ( *co-last authors )
"The temporal scaling of C. elegans ageing"
Nature, 320, 103-107 (2016) doi:10.1038/nature16550
[supplement | lifespan machine]
    - News & Views by Zach Pincus, "A stretch in time", Nature, 530, 37-38 (2016)
    - STAT     - 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), Cesar A. Munoz and Jorge A. Perez (Eds.) 16-26 (2015)
[EPTCS version | preproceedings version]


C. Romero, D. S. Marks, W. Fontana* and J. Apfeld* ( *co-last authors )
"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)


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
    - Harvard News


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)


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]