- Samaga R, Saez-Rodriguez J, Alexopoulos
LG et al (2009) The logic of EGFR/ErbB
signaling: theoretical properties and analysis
of high-throughput data. PLoS Comput Biol
5:e1000438 - Schlatter R, Philippi N, Wangorsch G et al
(2012) Integration of Boolean models exem-
plified on hepatocyte signal transduction.
Brief Bioinform 13:365–376 - Bornholdt S (2005) Less is more in modeling
large genetic networks. Science 310:449–451 - Saez-Rodriguez J, Simeoni L, Lindquist JA
et al (2007) A logical model provides insights
into T cell receptor signaling. PLoS Comput
Biol 3:e163 - Schlatter R, Schmich K, Avalos Vizcarra I et al
(2009) ON/OFF and beyond—a boolean
model of apoptosis. PLoS Comput Biol 5:
e1000595 - Saadatpour A, Wang R-S, Liao A et al (2011)
Dynamical and structural analysis of a T cell
survival network identifies novel candidate
therapeutic targets for large granular lympho-
cyte leukemia. PLoS Comput Biol 7:
e1002267 - Chowdhury S, Pradhan RN, Sarkar RR
(2013) Structural and logical analysis of a
comprehensive Hedgehog signaling pathway
to identify alternative drug targets for glioma,
colon and pancreatic cancer. PLoS One 8:
e69132 - Assmann SM, Albert R (2009) Discrete
dynamic modeling with asynchronous update,
or how to model complex systems in the
absence of quantitative information. Methods
Mol Biol (Clifton, NJ) 553:207–225 - Kauffman SA (1969) Metabolic stability and
epigenesis in randomly constructed genetic
nets. J Theor Biol 22:437–467 - Terfve C, Cokelaer T, Henriques D et al
(2012) CellNOptR: a flexible toolkit to train
protein signaling networks to data using mul-
tiple logic formalisms. BMC Syst Biol 6:133 - Helikar T, Kowal B, McClenathan S et al
(2012) The cell collective: toward an open
and collaborative approach to systems biol-
ogy. BMC Syst Biol 6:96 - Klamt S, Saez-Rodriguez J, Gilles ED (2007)
Structural and functional analysis of cellular
networks with CellNetAnalyzer. BMC Syst
Biol 1:2 - Chaouiya C, Naldi A, Thieffry D (2012) Log-
ical modelling of gene regulatory networks
with GINsim. Methods Mol Biol (Clifton,
NJ) 804:463–479 - M€ussel C, Hopfensitz M, Kestler HA (2010)
BoolNet—an R package for generation,
reconstruction and analysis of Boolean net-
works. Bioinformatics (Oxford)
26:1378–1380
- Albert I, Thakar J, Li S et al (2008) Boolean
network simulations for life scientists. Source
Code Biol Med 3:16 - Zheng J, Zhang D, Przytycki PF et al (2010)
SimBoolNet—a cytoscape plugin for dynamic
simulation of signaling networks. Bioinfor-
matics (Oxford) 26:141–142 - Di Cara A, Garg A, De Micheli G et al (2007)
Dynamic simulation of regulatory networks
using SQUAD. BMC Bioinformatics. 8:462 - Hinkelmann F, Brandon M, Guang B et al
(2011) ADAM: analysis of discrete models of
biological systems using computer algebra.
BMC Bioinformatics 12:295 - Swat M, Kel A, Herzel H (2004) Bifurcation
analysis of the regulatory modules of the
mammalian G1/S transition. Bioinformatics
(Oxford) 20:1506–1511 - Saal LH, Johansson P, Holm K et al (2007)
Poor prognosis in carcinoma is associated
with a gene expression signature of aberrant
PTEN tumor suppressor pathway activity.
Proc Natl Acad Sci U S A 104:7564–7569 - P€utzer BM, Engelmann D (2013) E2F1 apo-
ptosis counterattacked: evil strikes back.
Trends Mol Med 19:89–98 - Polager S, Ginsberg D (2009) p53 and E2f:
partners in life and death, Nature Reviews.
Cancer 9:738–748 - Mirschel S, Steinmetz K, Rempel M et al
(2009) ProMoT: modular modeling for sys-
tems biology. Bioinformatics 25:687–689 - Hennessy BT, Smith DL, Ram PTet al (2005)
Exploiting the PI3K/AKT pathway for cancer
drug discovery. Nat Rev Drug Discov
4:988–1004 - Hallstrom TC, Mori S, Nevins JR (2008) An
E2F1-dependent gene expression program
that determines the balance between prolifer-
ation and cell death. Cancer Cell 13:11–22 - Khan FM, Schmitz U, Nikolov S et al (2014)
Hybrid modeling of the crosstalk between
signaling and transcriptional networks using
ordinary differential equations and multi-
valued logic. Biochim Biophys Acta
1844:289–298 - Ramachandran S, Liu P, Young AN et al
(2005) Loss of HOXC6 expression induces
apoptosis in prostate cancer cells. Oncogene
24:188–198 - Alfieri R, Bartocci E, Merelli E et al (2011)
Modeling the cell cycle: from deterministic
models to hybrid systems. Biosystems
105:34–40
274 Faiz M. Khan et al.