Discrete dynamic modeling with asynchronous update, or how to model complex systems in the absence of quantitative information
SM Assmann, R Albert - Plant systems biology, 2009 - Springer
A major aim of systems biology is the study of the inter-relationships found within and
between large biological data sets. Here we describe one systems biology method, in which …
between large biological data sets. Here we describe one systems biology method, in which …
Discrete dynamic modeling of signal transduction networks
A Saadatpour, R Albert - Computational Modeling of Signaling Networks, 2012 - Springer
Newly available experimental data characterizing different processes involved in signaling
pathways have provided the opportunity for network analysis and modeling of these …
pathways have provided the opportunity for network analysis and modeling of these …
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 …
Network inference, analysis, and modeling in systems biology
R Albert - The Plant Cell, 2007 - academic.oup.com
Cells use signaling and regulatory pathways connecting numerous constituents, such as
DNA, RNA, proteins, and small molecules, to coordinate multiple functions, allowing them to …
DNA, RNA, proteins, and small molecules, to coordinate multiple functions, allowing them to …
Numeric simulation of plant signaling networks
T Genoud, MB Trevino Santa Cruz… - Plant …, 2001 - academic.oup.com
Plants have evolved an intricate signaling apparatus that integrates relevant information and
allows an optimal response to environmental conditions. For instance, the coordination of …
allows an optimal response to environmental conditions. For instance, the coordination of …
Automatic inference of regulatory and dynamical properties from incomplete gene interaction and expression data
F Corblin, E Fanchon, L Trilling, C Chaouiya… - … Processign in Cells and …, 2012 - Springer
Advanced mathematical methods and computational tools are required to properly
understand the behavior of large and complex regulatory networks that control cellular …
understand the behavior of large and complex regulatory networks that control cellular …
Predictive modelling of complex agronomic and biological systems
JJB Keurentjes, J Molenaar… - Plant, Cell & …, 2013 - Wiley Online Library
Biological systems are tremendously complex in their functioning and regulation. Studying
the multifaceted behaviour and describing the performance of such complexity has …
the multifaceted behaviour and describing the performance of such complexity has …
Elementary signaling modes predict the essentiality of signal transduction network components
Background Understanding how signals propagate through signaling pathways and
networks is a central goal in systems biology. Quantitative dynamic models help to achieve …
networks is a central goal in systems biology. Quantitative dynamic models help to achieve …
A semiquantitative framework for gene regulatory networks: increasing the time and quantitative resolution of Boolean networks
J Kerkhofs, L Geris - PLoS One, 2015 - journals.plos.org
Boolean models have been instrumental in predicting general features of gene networks
and more recently also as explorative tools in specific biological applications. In this study …
and more recently also as explorative tools in specific biological applications. In this study …
Systematic component selection for gene-network refinement
Motivation: A quantitative description of interactions between cell components is a major
challenge in Computational Biology. As a method of choice, differential equations are used …
challenge in Computational Biology. As a method of choice, differential equations are used …