Untangling the wires: A strategy to trace functional interactions in signaling and gene networks

By David Angeli, J. Ferrell, Eduardo Sontag. Proceedings of the National Academy of Sciences of the United States of America, 2002

1,245 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2c5bdebfafe34ab22c712f7f0a323869c0857185

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

In Molecular Biology

Citations in the corpus

Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades (2004, methodology): “…illustrates potential multiple steady states for a MAPK pathway in the absence of any imposed feedback regulation (the kinetic model used for simulations is similar to models reported previously; Huang and Ferrell, 1996; Kholodenko et al., 2002).”
Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods (2009, methodology): “…et al., 2005; Anastassiou, 2007), Bayesian networks (Friedman, 2004; Ferrazzi et al., 2007; Mukherjee and Speed, 2008), and methods based on dynamical models (de la Fuente et al., 2002; Kholodenko et al., 2002; Gardner et al., 2003; Brazhnik, 2005; Perkins et al., 2006; Marbach et al., 2009).”
Monotone Chemical Reaction Networks (2007, methodology): “We refer to [4, 3, 5, 6, 8, 9] for further developments and applications of this theory, including examples from molecular biology, ecology and chemical reaction networks.”
Control of multistability (2014, background): “Nevertheless, it is generally accepted that two paradigmatic gene-regulatory networks in bacteria, the phage switch and the lac operon (at least when induced by non-metabolizable inducers), do show bistability [34,54,55].”
Network resilience (2020, background): “In this process, the bistable switch mechanism is prevalent in directing two mutually exclusive cell fates [279, 287, 333, 306, 321].”
Encoding and Decoding Cellular Information through Signaling Dynamics (2013, positive): “In a similar vein, Modular Response Analysis (Kholodenko et al., 2002), a method for extracting the strength and topology of dynamical subnetworks, is used to identify structural differences between NGF- and EGF-induced MAPK network topology (Santos et al.”
Data Based Identification and Prediction of Nonlinear and Complex Dynamical Systems (2016, methodology): “The problem of extracting local response from global response to perturbation was first addressed using a modular response analysis (MRA) [367].”
Control Principles of Complex Networks (2015, methodology): “An important exception is the Modular Response Analysis method (Kholodenko et al., 2002; Sontag, 2008), which is a special driving-response approach, and guarantees to recover the interaction matrix using steady-state data collected from sufficiently many perturbation experiments.”
A methodology for the structural and functional analysis of signaling and regulatory networks (2006, background): “Bayesian networks) rely on acyclic networks where feedbacks are not allowed, one of the most important features of signaling and regulatory networks are their feedback loops [3,5,18,21,35-38].”
Translation-invariant monotone systems, and a global convergence result for enzymatic futile cycles ☆ (2008, background): “An excellent discussion can be found in [22], which also points out that futile cycles play a central role in signaling processes ranging from GTPase cycles [7] and mitogen-activated protein cascades [9,18] to glucose mobilization [17], actin treadmilling [4], bacterial two-component systems and pho”
Sensitivity analysis approaches applied to systems biology models. (2011, background): “In contrast, the local coefﬁcients stand for the individual functional entity that is ‘isolated’ from the system [32, 33].”