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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 84
2012 84
2013 83
2014 94
2015 94
2016 88
2017 84
2018 64
2019 56
2020 33
2021 3
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1,504 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
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
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 …
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 …
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 …
Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways.
Hua F, Hautaniemi S, Yokoo R, Lauffenburger DA. Hua F, et al. J R Soc Interface. 2006 Aug 22;3(9):515-26. doi: 10.1098/rsif.2005.0109. J R Soc Interface. 2006. PMID: 16849248 Free PMC article.
Mathematical models of highly interconnected and multivariate signalling networks provide useful tools to understand these complex systems. ...We used an ordinary differential equation based model for the Fas apoptotic pathway as an example. The first …
Mathematical models of highly interconnected and multivariate signalling networks provide useful tools to understand th …
VANTED: a system for advanced data analysis and visualization in the context of biological networks.
Junker BH, Klukas C, Schreiber F. Junker BH, et al. BMC Bioinformatics. 2006 Mar 6;7:109. doi: 10.1186/1471-2105-7-109. BMC Bioinformatics. 2006. PMID: 16519817 Free PMC article.
BACKGROUND: Recent advances with high-throughput methods in life-science research have increased the need for automatized data analysis and visual exploration techniques. ...Statistical methods allow analysis and comparison of multiple data sets such a …
BACKGROUND: Recent advances with high-throughput methods in life-science research have increased the need for automatized data ana
Mapping connections in signaling networks with ambiguous modularity.
Lill D, Rukhlenko OS, Mc Elwee AJ, Kashdan E, Timmer J, Kholodenko BN. Lill D, et al. NPJ Syst Biol Appl. 2019 May 23;5:19. doi: 10.1038/s41540-019-0096-1. eCollection 2019. NPJ Syst Biol Appl. 2019. PMID: 31149348 Free PMC article.
Modular Response Analysis (MRA) is a suite of methods that under certain assumptions permits the precise reconstruction of both the directions and strengths of connections between network modules from network responses to perturbations. ...Although not …
Modular Response Analysis (MRA) is a suite of methods that under certain assumptions permits the precise reconstruction of bot …
GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.
Vlasblom J, Wu S, Pu S, Superina M, Liu G, Orsi C, Wodak SJ. Vlasblom J, et al. Bioinformatics. 2006 Sep 1;22(17):2178-9. doi: 10.1093/bioinformatics/btl356. Bioinformatics. 2006. PMID: 16921162
MOTIVATION: Analyzing the networks of interactions between genes and proteins has become a central theme in systems biology. ...RESULTS: We present GenePro, a plugin to Cytoscape featuring a set of versatile tools that greatly facilitates the visualization and analysis
MOTIVATION: Analyzing the networks of interactions between genes and proteins has become a central theme in systems biology. ...RESUL …
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