Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks

R Samaga, S Klamt - Cell communication and signaling, 2013 - Springer
A central goal of systems biology is the construction of predictive models of bio-molecular
networks. Cellular networks of moderate size have been modeled successfully in a …

Discrete dynamic modeling of cellular signaling networks

R Albert, RS Wang - Methods in enzymology, 2009 - Elsevier
Understanding signal transduction in cellular systems is a central issue in systems biology.
Numerous experiments from different laboratories generate an abundance of individual …

Cooperative development of logical modelling standards and tools with CoLoMoTo

A Naldi, PT Monteiro, C Müssel… - …, 2015 - academic.oup.com
The identification of large regulatory and signalling networks involved in the control of
crucial cellular processes calls for proper modelling approaches. Indeed, models can help …

Logic-based models in systems biology: a predictive and parameter-free network analysis method

ML Wynn, N Consul, SD Merajver… - Integrative biology, 2012 - academic.oup.com
Highly complex molecular networks, which play fundamental roles in almost all cellular
processes, are known to be dysregulated in a number of diseases, most notably in cancer …

Computational approaches for modeling regulatory cellular networks

NJ Eungdamrong, R Iyengar - Trends in Cell Biology, 2004 - cell.com
Cellular components interact with each other to form networks that process information and
evoke biological responses. A deep understanding of the behavior of these networks …

A methodology for the structural and functional analysis of signaling and regulatory networks

S Klamt, J Saez-Rodriguez, JA Lindquist, L Simeoni… - BMC …, 2006 - Springer
Background Structural analysis of cellular interaction networks contributes to a deeper
understanding of network-wide interdependencies, causal relationships, and basic …

Logic-based models for the analysis of cell signaling networks

MK Morris, J Saez-Rodriguez, PK Sorger… - Biochemistry, 2010 - ACS Publications
Computational models are increasingly used to analyze the operation of complex
biochemical networks, including those involved in cell signaling networks. Here we review …

The use of machine learning to discover regulatory networks controlling biological systems

R Erbe, J Gore, K Gemmill, DA Gaykalova, EJ Fertig - Molecular cell, 2022 - cell.com
Biological systems are composed of a vast web of multiscale molecular interactors and
interactions. High-throughput technologies, both bulk and single cell, now allow for …

Computational modeling of mammalian signaling networks

JJ Hughey, TK Lee, MW Covert - … Reviews: Systems Biology …, 2010 - Wiley Online Library
One of the most exciting developments in signal transduction research has been the
proliferation of studies in which a biological discovery was initiated by computational …

Systems-level insights into cellular regulation: inferring, analysing, and modelling intracellular networks

C Christensen, J Thakar, R Albert - IET systems biology, 2007 - IET
Genes and gene products interact on several levels, forming transcriptional regulatory-,
protein interaction-, metabolic-and signal transduction networks. Genetic, biochemical and …