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Table representation of search results timeline featuring number of search results per year.

Year Number of Results
1992 2
1993 1
1994 6
1996 2
1997 2
1998 1
1999 5
2000 7
2001 3
2002 14
2003 29
2004 88
2005 123
2006 145
2007 147
2008 127
2009 107
2010 93
2011 85
2012 84
2013 83
2014 94
2015 94
2016 88
2017 84
2018 64
2019 58
2020 50
2021 60
2022 34
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1,605 results
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Computational methodologies for modelling, analysis and simulation of signalling networks.
Gilbert D, Fuss H, Gu X, Orton R, Robinson S, Vyshemirsky V, Kurth MJ, Downes CS, Dubitzky W. Gilbert D, et al. Brief Bioinform. 2006 Dec;7(4):339-53. doi: 10.1093/bib/bbl043. Epub 2006 Nov 20. Brief Bioinform. 2006. PMID: 17116646 Review.
This article is a critical review of computational techniques used to model, analyse and simulate signalling networks. We propose a conceptual framework, and discuss the role of signalling networks in three major areas: signal
This article is a critical review of computational techniques used to model, analyse and simulate signalling
A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks.
Ali Al-Radhawi M, Angeli D, Sontag ED. Ali Al-Radhawi M, et al. PLoS Comput Biol. 2020 Feb 24;16(2):e1007681. doi: 10.1371/journal.pcbi.1007681. eCollection 2020 Feb. PLoS Comput Biol. 2020. PMID: 32092050 Free PMC article.
The problem is then reduced to that of finding a common Lyapunov function for this set of extremals. Based on this characterization, a computational package, Lyapunov-Enabled Analysis of Reaction Networks (LEARN), is provided that constructs such functions or …
The problem is then reduced to that of finding a common Lyapunov function for this set of extremals. Based on this characterization, a co
Conceptual and computational framework for logical modelling of biological networks deregulated in diseases.
Montagud A, Traynard P, Martignetti L, Bonnet E, Barillot E, Zinovyev A, Calzone L. Montagud A, et al. Brief Bioinform. 2019 Jul 19;20(4):1238-1249. doi: 10.1093/bib/bbx163. Brief Bioinform. 2019. PMID: 29237040
We present a pipeline of computational tools that performs a series of analyses to explore a logical model's properties. ...We start by analysing the structure of the interaction network constructed from the literature or existing databases. Next, we s …
We present a pipeline of computational tools that performs a series of analyses to explore a logical model's properties …
Methodologies for the modeling and simulation of biochemical networks, illustrated for signal transduction pathways: a primer.
ElKalaawy N, Wassal A. ElKalaawy N, et al. Biosystems. 2015 Mar;129:1-18. doi: 10.1016/j.biosystems.2015.01.008. Epub 2015 Jan 28. Biosystems. 2015. PMID: 25637875 Review.
Signal transduction pathways (STPs) constitute a class of biochemical networks that receive, process, and respond to stimuli from the environment, as well as stimuli that are internal to the organism. ...This primer presents the methodologies used for
Signal transduction pathways (STPs) constitute a class of biochemical networks that receive, process, and respond to st
Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments.
van Riel NA. van Riel NA. Brief Bioinform. 2006 Dec;7(4):364-74. doi: 10.1093/bib/bbl040. Epub 2006 Nov 14. Brief Bioinform. 2006. PMID: 17107967 Review.
Systems biology applies quantitative, mechanistic modelling to study genetic networks, signal transduction pathways and metabolic networks. ...It is shown how these methods can be applied in the design of model-based experiments wh …
Systems biology applies quantitative, mechanistic modelling to study genetic networks, signal transduction pathw …
Reconstruction of cellular signalling networks and analysis of their properties.
Papin JA, Hunter T, Palsson BO, Subramaniam S. Papin JA, et al. Nat Rev Mol Cell Biol. 2005 Feb;6(2):99-111. doi: 10.1038/nrm1570. Nat Rev Mol Cell Biol. 2005. PMID: 15654321 Review.
The study of cellular signalling over the past 20 years and the advent of high-throughput technologies are enabling the reconstruction of large-scale signalling networks. After careful reconstruction of signalling networks, their properties must …
The study of cellular signalling over the past 20 years and the advent of high-throughput technologies are enabling the reconstructio …
Cerebral cartography and connectomics.
Sporns O. Sporns O. Philos Trans R Soc Lond B Biol Sci. 2015 May 19;370(1668):20140173. doi: 10.1098/rstb.2014.0173. Philos Trans R Soc Lond B Biol Sci. 2015. PMID: 25823870 Free PMC article. Review.
Principal challenges concern the temporal dynamics of functional brain connectivity, the definition of areal parcellations and their hierarchical organization into large-scale networks, the extension of whole-brain connectivity to cellular-scale networks, and the ma …
Principal challenges concern the temporal dynamics of functional brain connectivity, the definition of areal parcellations and their hierarc …
Experimental and computational tools for analysis of signaling networks in primary cells.
Schoof EM, Linding R. Schoof EM, et al. Curr Protoc Immunol. 2014 Feb 4;104:11.11.1-11.11.23. doi: 10.1002/0471142735.im1111s104. Curr Protoc Immunol. 2014. PMID: 24510617
Cellular information processing in signaling networks forms the basis of responses to environmental stimuli. ...Determining which kinases phosphorylate specific phospho sites poses a challenge; this information is critical when trying to elucidate key proteins invol …
Cellular information processing in signaling networks forms the basis of responses to environmental stimuli. ...Determining wh …
Recipes for Analysis of Molecular Networks Using the Data2Dynamics Modeling Environment.
Steiert B, Kreutz C, Raue A, Timmer J. Steiert B, et al. Methods Mol Biol. 2019;1945:341-362. doi: 10.1007/978-1-4939-9102-0_16. Methods Mol Biol. 2019. PMID: 30945255
Mechanistic models of biomolecular processes are established research tools that enable to quantitatively investigate dynamic features of biological processes such as signal transduction cascades. ...In order to calibrate these mechanistic models, the …
Mechanistic models of biomolecular processes are established research tools that enable to quantitatively investigate dynamic feature …
Integrated inference and analysis of regulatory networks from multi-level measurements.
Poultney CS, Greenfield A, Bonneau R. Poultney CS, et al. Methods Cell Biol. 2012;110:19-56. doi: 10.1016/B978-0-12-388403-9.00002-3. Methods Cell Biol. 2012. PMID: 22482944 Free PMC article. Review.
Regulatory network inference is the process of inferring these networks, traditionally from microarray data but increasingly incorporating other measurement types such as proteomics, ChIP-seq, metabolomics, and mass cytometry. We discuss existing techniques for n
Regulatory network inference is the process of inferring these networks, traditionally from microarray data but increasingly i …
1,605 results