Biology Reference
In-Depth Information
[21] Albert R, Othmer HG. The topology of the regulatory interactions
predicts the expression pattern of the segment polarity genes in
Drosophila melanogaster. J Theor Biol 2003;223:1 e 18.
[22] Sanchez L, Thieffry D. Segmenting the fly embryo: a logical
analysis of the pair-rule cross-regulatory module. J Theor Biol
2003;224:517 e 37.
[23] Ghysen A, Thomas R. The formation of
[40] Chaves M, Sontag ED, Albert R. Structure and timescale analysis
in genetic regulatory networks. SystBiol (Stevenage) 2006;153:
154 e 67.
[41] Albert I, Thakar J, Li S, Zhang R, Albert R. Boolean network
simulations for life scientists. Source Code Biol Med 2008;3:16.
[42] Klamt S, Saez-Rodriguez J, Gilles ED. Structural and functional
analysis of cellular networks with CellNetAnalyzer. BMC Syst
Biol 2007;1:2.
[43] Gonzalez AG, Naldi A, SĀ“nchez L, Thieffry D, Chaouiya C. GIN-
sim: a software suite for the qualitative modeling, simulation and
analysis of regulatory networks. Biosystems 2006;84:91 e 100.
[44] Mussel C, Hopfensitz M, Kestler HA. BoolNet d an R package for
generation, reconstruction and analysis of Boolean networks.
Bioinformatics 2010;26:1378 e 80.
[45] Waddington CH. Canalization of development and the inheritance
of acquired characters. Nature 1942;150:563 e 5.
[46] Waddington CH. Epigenetics and evolution. Symp Soc Exp Biol
1953;7:186 e 99.
[47] Tyson J, Novak B. Regulation of the eukaryotic cell cycle:
molecular antagonism, hysteresis, and irreversible transitions.
J Theor Biol 2001;210:249 e 63.
[48] Huang AC, Hu L, Kauffman SA, Zhang W, Shmulevich I. Using
cell fate attractors to uncover transcriptional regulation of HL60
neutrophil differentiation. BMC Syst Biol 2009;3:20.
[49] Shen-Orr S, Milo R, Mangan S, Alon U. Network motifs in the
transcriptional regulation network of Escherichia coli. Nature
Genetics 2002;31:64 e 8.
[50] Thomas R, D'Ari R. Biological Feedback. 1 st
sense organs
in
Drosophila: a logical approach. Bioessays 2003;25:802 e 7.
[24] Gonzalez A, Chaouiya C, Thieffry D. Logical modelling of the role
of the Hh pathway in the patterning of the Drosophila wing disc.
Bioinformatics 2008;24:i234 e 40.
[25] Diaz J, Alvarez-Buylla ER. A model of the ethylene signaling
pathway and its gene response in Arabidopsis thaliana:
pathway cross-talk and noise-filtering properties. Chaos 2006;
16:023112.
[26] Naldi A, Carneiro J, Chaouiya C, Thieffry D. Diversity and plas-
ticity of Th cell types predicted from regulatory network model-
ling. PLoS Comput Biol 2010;6:e1000912.
[27] Naldi A, Berenguier D, Faure A, Lopez F, Thieffry D, Chaouiya C.
Logical modelling of regulatory networks with GINsim 2.3. Bio-
systems 2009;97:134 e 9.
[28] Mendoza L. A network model for the control and differentiation
process in Th cells. Biosystems 2006;84:101 e 14.
[29] Voit EO. Computational Analysis of Biochemical Systems d A
Practical Guide for Biochemists and Molecular Biologists. Cam-
bridge: Cambridge University Press; 2000.
[30] Wang R, Albert R. Elementary signaling modes predict the
essentiality of signal transduction network components. BMC Syst
Biol 2011;5:44.
[31] Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R,
Lauffenburger DA, Klamt S, et al. Discrete logic modeling as
a means to link protein signaling networks with functional analysis
of mammalian signal transduction. Molecular Systems Biol 2009;
5:331.
[32] Wingender E, Dietze P, Karas H, Knuppel R. Transfac: a database
on transcription factors and their DNA binding sites. Nucleic Acids
Res 1996;24:238 e 41.
[33] Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and
genomes. Nucleic Acids Res 2000;28:27 e 30.
[34] Albert R, DasGupta B, Dondi R, Kachalo S, Sontag E,
Zelikovsky A, et al. A novel method for signal transduction
network inference from indirect experimental evidence. J Comput
Biol 2007;14:927 e 49.
[35] Kachalo S, Zhang R, Sontag E, Albert R, DasGupta B. NET-
SYNTHESIS: a software for synthesis, inference and simplification
of signal transduction networks. Bioinformatics 2008;24:293 e 5.
[36] Kauffman S. Origins of order: self-organization and selection in
evolution. New York: Oxford Univ Press; 1993.
[37] Papin JA, Hunter T, Palsson BO, Subramanian S. Reconstruction of
cellular signalling networks and analysis of their properties. Nat
Rev Mol Cell Biol 2005;6:99 e 111.
[38] Harvey I, Bossomaier T. Time out of joint: Attractors in asynchro-
nous random Boolean networks. In: Husbands P, Harvey I, editors.
Proceedings of the Fourth European Conference on Artificial Life
(ECAL97). Cambridge, MA: MIT Press; 1997. p. 67 e 75.
[39] Chaves M, Albert R, Sontag ED. Robustness and fragility of
Boolean models for genetic regulatory networks. J Theor Biol
2005;235:431 e 49.
ed. Florida: CRC
Press; 1990.
[51] Shinar G, Milo R, MR M, Alon U. Input output robustness in
simple bacterial signaling systems. Proc Natl Acad Sci USA
2007;104:19931 e 5.
[52] Tyson JJ, Borisuk MT, Chen K, Novak B. Analysis of complex
dynamics in cell cycle regulation. In: Bower JM, Bolouri H,
editors. Computational Modeling of Genetic and Biochemical
Networks. Cambridge, MA: MIT Press; 2000. p. 287 e 305.
[53] Bhalla US, Iyengar R. Robustness of the bistable behavior of
a biological signaling feedback loop. Chaos 2001;11:221 e 6.
[54] Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK,
Klamt S. The Logic of EGFR/ErbB Signaling: Theoretical Prop-
erties and Analysis of High-Throughput Data. PLoS Comput Biol
2009;5:e1000438.
[55] von Dassow G, Meir E, Munro EM, Odell GM. The segment
polarity network is a robust developmental module. Nature
2000;406:188 e 92.
[56] Alon U, Surette MG, Barkai N, Leibler S. Robustness in bacterial
chemotaxis. Nature 1999;397:168 e 71.
[57] Eldar A, Dorfman R, Weiss D, Ashe H, Shilo BZ, Barkai N.
Robustness of
the BMP morphogen gradient
in Drosophila
embryonic patterning. Nature 2002;419:304 e 8.
[58] Csete M, Doyle J. Bow ties, metabolism and disease. Trends
Biotechnol 2004;22:446 e 50.
[59] Conant GC, Wagner A. Duplicate genes and robustness to transient
gene knock-downs in Caenorhabditis elegans. Proc R Soc Lond B
Biol Sci 2004;271:89 e 96.
[60] Campbell C, Yang S, Albert R, Shea K. A network model for
plant e pollinator
community
assembly.
PNAS
2011;108:
197 e 202.
Search WWH ::




Custom Search