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Items: 43

1.

The Kappa platform for rule-based modeling.

Boutillier P, Maasha M, Li X, Medina-Abarca HF, Krivine J, Feret J, Cristescu I, Forbes AG, Fontana W.

Bioinformatics. 2018 Jul 1;34(13):i583-i592. doi: 10.1093/bioinformatics/bty272.

2.

Age-Dependence and Aging-Dependence: Neuronal Loss and Lifespan in a C. elegans Model of Parkinson's Disease.

Apfeld J, Fontana W.

Biology (Basel). 2017 Dec 23;7(1). pii: E1. doi: 10.3390/biology7010001.

3.

Dynamic Influence Networks for Rule-Based Models.

Forbes AG, Burks A, Lee K, Li X, Boutillier P, Krivine J, Fontana W.

IEEE Trans Vis Comput Graph. 2018 Jan;24(1):184-194. doi: 10.1109/TVCG.2017.2745280. Epub 2017 Aug 29.

PMID:
28866584
4.

The temporal scaling of Caenorhabditis elegans ageing.

Stroustrup N, Anthony WE, Nash ZM, Gowda V, Gomez A, López-Moyado IF, Apfeld J, Fontana W.

Nature. 2016 Feb 4;530(7588):103-7. doi: 10.1038/nature16550. Epub 2016 Jan 27.

5.

Regulated spatial organization and sensitivity of cytosolic protein oxidation in Caenorhabditis elegans.

Romero-Aristizabal C, Marks DS, Fontana W, Apfeld J.

Nat Commun. 2014 Sep 29;5:5020. doi: 10.1038/ncomms6020.

6.

An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology.

Fernandes de Abreu DA, Caballero A, Fardel P, Stroustrup N, Chen Z, Lee K, Keyes WD, Nash ZM, López-Moyado IF, Vaggi F, Cornils A, Regenass M, Neagu A, Ostojic I, Liu C, Cho Y, Sifoglu D, Shen Y, Fontana W, Lu H, Csikasz-Nagy A, Murphy CT, Antebi A, Blanc E, Apfeld J, Zhang Y, Alcedo J, Ch'ng Q.

PLoS Genet. 2014 Mar 27;10(3):e1004225. doi: 10.1371/journal.pgen.1004225. eCollection 2014 Mar.

7.

The Caenorhabditis elegans Lifespan Machine.

Stroustrup N, Ulmschneider BE, Nash ZM, López-Moyado IF, Apfeld J, Fontana W.

Nat Methods. 2013 Jul;10(7):665-70. doi: 10.1038/nmeth.2475. Epub 2013 May 12.

8.

Crosstalk and competition in signaling networks.

Rowland MA, Fontana W, Deeds EJ.

Biophys J. 2012 Dec 5;103(11):2389-98. doi: 10.1016/j.bpj.2012.10.006.

9.

Combinatorial complexity and compositional drift in protein interaction networks.

Deeds EJ, Krivine J, Feret J, Danos V, Fontana W.

PLoS One. 2012;7(3):e32032. doi: 10.1371/journal.pone.0032032. Epub 2012 Mar 8.

10.

Optimizing ring assembly reveals the strength of weak interactions.

Deeds EJ, Bachman JA, Fontana W.

Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2348-53. doi: 10.1073/pnas.1113095109. Epub 2012 Jan 30.

11.

Nonequilibrium phase transitions in biomolecular signal transduction.

Smith E, Krishnamurthy S, Fontana W, Krakauer D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Nov;84(5 Pt 1):051917. Epub 2011 Nov 23.

PMID:
22181454
12.

Curvature in metabolic scaling: a reply to MacKay.

Deeds EJ, Savage V, Fontana W.

J Theor Biol. 2011 Jul 7;280(1):197-8. doi: 10.1016/j.jtbi.2011.03.036. Epub 2011 Apr 9. No abstract available.

PMID:
21497609
13.

The challenges and scope of theoretical biology.

Krakauer DC, Collins JP, Erwin D, Flack JC, Fontana W, Laubichler MD, Prohaska SJ, West GB, Stadler PF.

J Theor Biol. 2011 May 7;276(1):269-76. doi: 10.1016/j.jtbi.2011.01.051. Epub 2011 Feb 15.

PMID:
21315730
14.

Intrinsic information carriers in combinatorial dynamical systems.

Harmer R, Danos V, Feret J, Krivine J, Fontana W.

Chaos. 2010 Sep;20(3):037108. doi: 10.1063/1.3491100.

PMID:
20887074
15.

Curvature in metabolic scaling.

Kolokotrones T, Van Savage, Deeds EJ, Fontana W.

Nature. 2010 Apr 1;464(7289):753-6. doi: 10.1038/nature08920.

PMID:
20360740
16.

Lifespan-on-a-chip: microfluidic chambers for performing lifelong observation of C. elegans.

Hulme SE, Shevkoplyas SS, McGuigan AP, Apfeld J, Fontana W, Whitesides GM.

Lab Chip. 2010 Mar 7;10(5):589-97. doi: 10.1039/b919265d. Epub 2009 Dec 18.

17.

Internal coarse-graining of molecular systems.

Feret J, Danos V, Krivine J, Harmer R, Fontana W.

Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6453-8. doi: 10.1073/pnas.0809908106. Epub 2009 Apr 3.

18.

Sizing up allometric scaling theory.

Savage VM, Deeds EJ, Fontana W.

PLoS Comput Biol. 2008 Sep 12;4(9):e1000171. doi: 10.1371/journal.pcbi.1000171.

19.

A microfabricated array of clamps for immobilizing and imaging C. elegans.

Hulme SE, Shevkoplyas SS, Apfeld J, Fontana W, Whitesides GM.

Lab Chip. 2007 Nov;7(11):1515-23. Epub 2007 Aug 16.

PMID:
17960280
20.

The stochastic behavior of a molecular switching circuit with feedback.

Krishnamurthy S, Smith E, Krakauer D, Fontana W.

Biol Direct. 2007 May 31;2:13.

21.

Chemistry. Pulling strings.

Fontana W.

Science. 2006 Dec 8;314(5805):1552-3. No abstract available.

PMID:
17158311
22.

Rules for modeling signal-transduction systems.

Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W.

Sci STKE. 2006 Jul 18;2006(344):re6. Review.

PMID:
16849649
23.

Sacrificing dialogue for politics?

Laubichler MD, Müller GB, Fontana W, Wagner GP.

Science. 2005 Aug 26;309(5739):1324. No abstract available.

PMID:
16123284
24.

Perspective: Evolution and detection of genetic robustness.

de Visser JA, Hermisson J, Wagner GP, Ancel Meyers L, Bagheri-Chaichian H, Blanchard JL, Chao L, Cheverud JM, Elena SF, Fontana W, Gibson G, Hansen TF, Krakauer D, Lewontin RC, Ofria C, Rice SH, von Dassow G, Wagner A, Whitlock MC.

Evolution. 2003 Sep;57(9):1959-72. Review.

PMID:
14575319
25.

Modelling 'evo-devo' with RNA.

Fontana W.

Bioessays. 2002 Dec;24(12):1164-77. Review.

PMID:
12447981
26.

Genetic networks. Small numbers of big molecules.

Fedoroff N, Fontana W.

Science. 2002 Aug 16;297(5584):1129-31. No abstract available.

PMID:
12183614
27.

The topology of the possible: formal spaces underlying patterns of evolutionary change.

Stadler BM, Stadler PF, Wagner GP, Fontana W.

J Theor Biol. 2001 Nov 21;213(2):241-74.

PMID:
11894994
28.

Plasticity, evolvability, and modularity in RNA.

Ancel LW, Fontana W.

J Exp Zool. 2000 Oct 15;288(3):242-83.

PMID:
11069142
29.

RNA folding at elementary step resolution.

Flamm C, Fontana W, Hofacker IL, Schuster P.

RNA. 2000 Mar;6(3):325-38.

30.

Complete suboptimal folding of RNA and the stability of secondary structures.

Wuchty S, Fontana W, Hofacker IL, Schuster P.

Biopolymers. 1999 Feb;49(2):145-65.

PMID:
10070264
31.

Shaping space: the possible and the attainable in RNA genotype-phenotype mapping.

Fontana W, Schuster P.

J Theor Biol. 1998 Oct 21;194(4):491-515.

PMID:
9790826
32.

Continuity in evolution: on the nature of transitions.

Fontana W, Schuster P.

Science. 1998 May 29;280(5368):1451-5.

33.

Smoothness within ruggedness: the role of neutrality in adaptation.

Huynen MA, Stadler PF, Fontana W.

Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):397-401.

34.

From sequences to shapes and back: a case study in RNA secondary structures.

Schuster P, Fontana W, Stadler PF, Hofacker IL.

Proc Biol Sci. 1994 Mar 22;255(1344):279-84.

PMID:
7517565
35.

What would be conserved if "the tape were played twice"?

Fontana W, Buss LW.

Proc Natl Acad Sci U S A. 1994 Jan 18;91(2):757-61.

36.

Statistics of RNA melting kinetics.

Tacker M, Fontana W, Stadler PF, Schuster P.

Eur Biophys J. 1994;23(1):29-38.

PMID:
7515805
37.

Statistics of RNA secondary structures.

Fontana W, Konings DA, Stadler PF, Schuster P.

Biopolymers. 1993 Sep;33(9):1389-404.

PMID:
7691201
38.

RNA folding and combinatory landscapes.

Fontana W, Stadler PF, Bornberg-Bauer EG, Griesmacher T, Hofacker IL, Tacker M, Tarazona P, Weinberger ED, Schuster P.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993 Mar;47(3):2083-2099. No abstract available.

PMID:
9960229
39.

Erratum: Physical aspects of evolutionary optimization and adaptation

Fontana W, Schnabl W, Schuster P.

Phys Rev A. 1990 Jun 15;41(12):7074. No abstract available.

PMID:
9903133
40.

Physical aspects of evolutionary optimization and adaptation.

Fontana W, Schnabl W, Schuster P.

Phys Rev A Gen Phys. 1989 Sep 15;40(6):3301-3321. No abstract available.

PMID:
9902537
41.

A computer model of evolutionary optimization.

Fontana W, Schuster P.

Biophys Chem. 1987 May 9;26(2-3):123-47.

PMID:
3607225
42.

An automatic, solid-state direct readout for the Buchler-Cotlove chloridometer.

Zettner A, Fontana WC.

Clin Chem. 1972 Mar;18(3):285-9. No abstract available.

43.

Factors needed for prevention of child abuse and neglect.

Fontana WJ.

Pediatrics. 1970 Aug;46(2):318-9. No abstract available.

PMID:
5432167

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