共查询到20条相似文献,搜索用时 31 毫秒
1.
Sophie Lèbre Jennifer Becq Frédéric Devaux Michael PH Stumpf Gaëlle Lelandais 《BMC systems biology》2010,4(1):130
Background
Biological networks are highly dynamic in response to environmental and physiological cues. This variability is in contrast to conventional analyses of biological networks, which have overwhelmingly employed static graph models which stay constant over time to describe biological systems and their underlying molecular interactions. 相似文献2.
Arne B Gjuvsland Ben J Hayes Theo HE Meuwissen Erik Plahte Stig W Omholt 《BMC systems biology》2007,1(1):32-12
Background
Genetic variation explains a considerable part of observed phenotypic variation in gene expression networks. This variation has been shown to be located both locally (cis) and distally (trans) to the genes being measured. Here we explore to which degree the phenotypic manifestation of local and distant polymorphisms is a dynamic feature of regulatory design. 相似文献3.
Shuhei Kimura Katsuki Sonoda Soichiro Yamane Hideki Maeda Koki Matsumura Mariko Hatakeyama 《BMC bioinformatics》2008,9(1):23
Background
The inference of a genetic network is a problem in which mutual interactions among genes are deduced using time-series of gene expression patterns. While a number of models have been proposed to describe genetic regulatory networks, this study focuses on a set of differential equations since it has the ability to model dynamic behavior of gene expression. When we use a set of differential equations to describe genetic networks, the inference problem can be defined as a function approximation problem. On the basis of this problem definition, we propose in this study a new method to infer reduced NGnet models of genetic networks. 相似文献4.
Background
Biomolecular networks dynamically respond to stimuli and implement cellular function. Understanding these dynamic changes is the key challenge for cell biologists. As biomolecular networks grow in size and complexity, the model of a biomolecular network must become more rigorous to keep track of all the components and their interactions. In general this presents the need for computer simulation to manipulate and understand the biomolecular network model. 相似文献5.
I Emrah Nikerel Wouter A van Winden Walter M van Gulik Joseph J Heijnen 《BMC bioinformatics》2006,7(1):540-23
Background
Dynamic modeling of metabolic reaction networks under in vivo conditions is a crucial step in order to obtain a better understanding of the (dis)functioning of living cells. So far dynamic metabolic models generally have been based on mechanistic rate equations which often contain so many parameters that their identifiability from experimental data forms a serious problem. Recently, approximative rate equations, based on the linear logarithmic (linlog) format have been proposed as a suitable alternative with fewer parameters. 相似文献6.
7.
Background
Sex determination networks evolve rapidly and have been studied intensely across many species, particularly in insects, thus presenting good models to study the evolutionary plasticity of gene networks. 相似文献8.
Background
A central question for the understanding of biological reaction networks is how a particular dynamic behavior, such as bistability or oscillations, is realized at the molecular level. So far this question has been mainly addressed in well-mixed reaction systems which are conveniently described by ordinary differential equations. However, much less is known about how molecular details of a reaction mechanism can affect the dynamics in diffusively coupled systems because the resulting partial differential equations are much more difficult to analyze. 相似文献9.
Chen-Ching Lin Jen-Tsung Hsiang Chia-Yi Wu Yen-Jen Oyang Hsueh-Fen Juan Hsuan-Cheng Huang 《BMC systems biology》2010,4(1):138
Background
Molecular networks represent the backbone of molecular activity within cells and provide opportunities for understanding the mechanism of diseases. While protein-protein interaction data constitute static network maps, integration of condition-specific co-expression information provides clues to the dynamic features of these networks. Dilated cardiomyopathy is a leading cause of heart failure. Although previous studies have identified putative biomarkers or therapeutic targets for heart failure, the underlying molecular mechanism of dilated cardiomyopathy remains unclear. 相似文献10.
Background
The reconstruction of genetic regulatory networks from microarray gene expression data has been a challenging task in bioinformatics. Various approaches to this problem have been proposed, however, they do not take into account the topological characteristics of the targeted networks while reconstructing them. 相似文献11.
Steffen Klamt Julio Saez-Rodriguez Jonathan A Lindquist Luca Simeoni Ernst D Gilles 《BMC bioinformatics》2006,7(1):56-26
Background
Structural analysis of cellular interaction networks contributes to a deeper understanding of network-wide interdependencies, causal relationships, and basic functional capabilities. While the structural analysis of metabolic networks is a well-established field, similar methodologies have been scarcely developed and applied to signaling and regulatory networks. 相似文献12.
Background
Many complex random networks have been found to be scale-free. Existing literature on scale-free networks has rarely considered potential false positive and false negative links in the observed networks, especially in biological networks inferred from high-throughput experiments. Therefore, it is important to study the impact of these measurement errors on the topology of the observed networks. 相似文献13.
Background
Many biological networks such as protein-protein interaction networks, signaling networks, and metabolic networks have topological characteristics of a scale-free degree distribution. Preferential attachment has been considered as the most plausible evolutionary growth model to explain this topological property. Although various studies have been undertaken to investigate the structural characteristics of a network obtained using this growth model, its dynamical characteristics have received relatively less attention. 相似文献14.
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Background
The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological analysis of graph models has often been applied to study the structural characteristics of complex metabolic networks. 相似文献16.
Background
Understanding how signals propagate through signaling pathways and networks is a central goal in systems biology. Quantitative dynamic models help to achieve this understanding, but are difficult to construct and validate because of the scarcity of known mechanistic details and kinetic parameters. Structural and qualitative analysis is emerging as a feasible and useful alternative for interpreting signal transduction. 相似文献17.
Background
The abundant data available for protein interaction networks have not yet been fully understood. New types of analyses are needed to reveal organizational principles of these networks to investigate the details of functional and regulatory clusters of proteins. 相似文献18.
19.
Robert Sidney CoxIII Mary J Dunlop Michael B Elowitz 《Journal of biological engineering》2010,4(1):10
Background
Current methods for analyzing the dynamics of natural regulatory networks, and quantifying synthetic circuit function, are limited by the lack of well-characterized genetic measurement tools. Fluorescent reporters have been used to measure dynamic gene expression, but recent attempts to monitor multiple genes simultaneously in single cells have not focused on independent, isolated measurements. Multiple reporters can be used to observe interactions between natural genes, or to facilitate the 'debugging' of biologically engineered genetic networks. Using three distinguishable reporter genes in a single cell can reveal information not obtainable from only one or two reporters. One application of multiple reporters is the use of genetic noise to reveal regulatory connections between genes. Experiments in both natural and synthetic systems would benefit from a well-characterized platform for expressing multiple reporter genes and synthetic network components. 相似文献20.
Jing Zhao Guo-Hui Ding Lin Tao Hong Yu Zhong-Hao Yu Jian-Hua Luo Zhi-Wei Cao Yi-Xue Li 《BMC bioinformatics》2007,8(1):311