Identification of a topological characteristic responsible for the biological robustness of regulatory networks
… parameter to describe the structural or topological property of a biological control network. …
The first is the guard cell abscisic acid signaling network in plants (ABA). It was first …
The first is the guard cell abscisic acid signaling network in plants (ABA). It was first …
Network analyses in systems pharmacology
SI Berger, R Iyengar - Bioinformatics, 2009 - academic.oup.com
… While without detailed kinetic information a true rate limiting step can not be identified, this
analysis suggests that network topology alone is … Hypothesis generation in signaling networks …
analysis suggests that network topology alone is … Hypothesis generation in signaling networks …
Untangling the wires: a strategy to trace functional interactions in signaling and gene networks
BN Kholodenko, A Kiyatkin… - Proceedings of the …, 2002 - National Acad Sciences
… that demonstrates how the topology and strength of network connections can be retrieved …
signaling network that involves growth factor and stress-activated pathways. For gene networks…
signaling network that involves growth factor and stress-activated pathways. For gene networks…
High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals
… is just another topology of the reaction-diffusion network that we analyzed for the extended
… IP-signaling and IP (Figure 5a). We used RDNets to identify possible signaling networks that …
… IP-signaling and IP (Figure 5a). We used RDNets to identify possible signaling networks that …
Wrestling with pleiotropy: genomic and topological analysis of the yeast gene expression network
DE Featherstone, K Broadie - Bioessays, 2002 - Wiley Online Library
… Using principles of scale-free network topology, we propose that fragmenting the gene
expression network via `genome-engineering' may be a viable and practical approach to isolating …
expression network via `genome-engineering' may be a viable and practical approach to isolating …
A comparative study of topology-based pathway enrichment analysis methods
… In the current comparative study, we examine nine popular topology-based pathway analysis
methods that investigate different null hypotheses. Methods considered in this review have …
methods that investigate different null hypotheses. Methods considered in this review have …
Dirac signal processing of higher-order topological signals
… This operator has recently been shown to be key to treat dynamics of topological signals of
different dimensions on networks, simplicial and cell complexes [23–25, 50], To illustrate the …
different dimensions on networks, simplicial and cell complexes [23–25, 50], To illustrate the …
Analysis of ubiquitin signaling and chain topology cross-talk
… This review aims to provide an overview of ubiquitin chain topology and associated signaling
pathways and discusses the MS-based proteomic methodologies used to determine such …
pathways and discusses the MS-based proteomic methodologies used to determine such …
Modular analysis of biological networks
HM Kaltenbach, J Stelling - Advances in systems biology, 2012 - Springer
… on topology alone work reasonably well for PPI networks, but the input–output dynamics
needs to be taken into consideration when modularizing metabolic or signaling networks with …
needs to be taken into consideration when modularizing metabolic or signaling networks with …
PTPϵ has a critical role in signaling transduction pathways and phosphoprotein network topology in red cells
L De Franceschi, A Biondani, F Carta, F Turrini… - …, 2008 - Wiley Online Library
… Using the signaling network computational analysis of the Tyr-phosphoproteomic data,
we identified seven topological clusters. We studied cluster 1 containing Fyn, SFK, and Syk …
we identified seven topological clusters. We studied cluster 1 containing Fyn, SFK, and Syk …