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 …
networks. Cellular networks of moderate size have been modeled successfully in a …
Discrete dynamic modeling of cellular signaling networks
Understanding signal transduction in cellular systems is a central issue in systems biology.
Numerous experiments from different laboratories generate an abundance of individual …
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 …
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
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 …
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 …
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 …
understanding of network-wide interdependencies, causal relationships, and basic …
Logic-based models for the analysis of cell signaling networks
Computational models are increasingly used to analyze the operation of complex
biochemical networks, including those involved in cell signaling networks. Here we review …
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 …
interactions. High-throughput technologies, both bulk and single cell, now allow for …
Computational modeling of mammalian signaling networks
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 …
proliferation of studies in which a biological discovery was initiated by computational …
Systems-level insights into cellular regulation: inferring, analysing, and modelling intracellular networks
Genes and gene products interact on several levels, forming transcriptional regulatory-,
protein interaction-, metabolic-and signal transduction networks. Genetic, biochemical and …
protein interaction-, metabolic-and signal transduction networks. Genetic, biochemical and …