BMC Systems Biology
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From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data
BMC Systems Biology - Tập 1 - Trang 1-10 - 2007
The use of correlation networks is widespread in the analysis of gene expression and proteomics data, even though it is known that correlations not only confound direct and indirect associations but also provide no means to distinguish between cause and effect. For "causal" analysis typically the inference of a directed graphical model is required. However, this is rather difficult due to the curs......
Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network
BMC Systems Biology - Tập 7 - Trang 1-13 - 2013
Gene regulatory networks (GRNs) are models of molecule-gene interactions instrumental in the coordination of gene expression. Transcription factor (TF)-GRNs are an important subset of GRNs that characterize gene expression as the effect of TFs acting on their target genes. Although such networks can qualitatively summarize TF-gene interactions, it is highly desirable to quantitatively determine th......
Discovering conditional co-regulated protein complexes by integrating diverse data sources
BMC Systems Biology - Tập 4 - Trang 1-13 - 2010
Proteins interacting with each other as a complex play an important role in many molecular processes and functions. Directly detecting protein complexes is still costly, whereas many protein-protein interaction (PPI) maps for model organisms are available owing to the fast development of high-throughput PPI detecting techniques. These binary PPI data provides fundamental and abundant information f......
Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina
BMC Systems Biology - Tập 9 Số 1 - Trang 1-11 - 2015
Mortierella alpina is an oleaginous fungus used in the industrial scale production of arachidonic acid (ARA). In order to investigate the metabolic characteristics at a systems level and to explore potential strategies for enhanced lipid production, a genome-scale metabolic model of M. alpina was reconstructed. This model included 1106 genes, 1854 reactions and 1732 metabolites. On minimal growth ......
Highly sensitive inference of time-delayed gene regulation by network deconvolution
BMC Systems Biology - Tập 8 - Trang 1-10 - 2014
Gene regulatory network (GRN) is a fundamental topic in systems biology. The dynamics of GRN can shed light on the cellular processes, which facilitates the understanding of the mechanisms of diseases when the processes are dysregulated. Accurate reconstruction of GRN could also provide guidelines for experimental biologists. Therefore, inferring gene regulatory networks from high-throughput gene ......
A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network
BMC Systems Biology - Tập 6 - Trang 1-14 - 2012
Cell cycle process of budding yeast (Saccharomyces cerevisiae) consists of four phases: G1, S, G2 and M. Initiated by stimulation of the G1 phase, cell cycle returns to the G1 stationary phase through a sequence of the S, G2 and M phases. During the cell cycle, a cell verifies whether necessary conditions are satisfied at the end of each phase (i.e., checkpoint) since damages of any phase can caus......
Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans
BMC Systems Biology - Tập 2 - Trang 1-11 - 2008
Large-scale evaluation of gene expression variation among Caenorhabditis elegans lines that have diverged from a common ancestor allows for the analysis of a novel class of biological networks – evolutionary gene coexpression networks. Comparative analysis of these evolutionary networks has the potential to uncover the effects of natural selection in shaping coexpression network topologies since C......
Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory
BMC Systems Biology - Tập 2 - Trang 1-11 - 2008
Several approaches, including metabolic control analysis (MCA), flux balance analysis (FBA), correlation metric construction (CMC), and biochemical circuit theory (BCT), have been developed for the quantitative analysis of complex biochemical networks. Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS) biochemical reaction networks that unites these d......
TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networksAbstract
Background
Several methods have been developed for analyzing genome-scale models of metabolism and transcriptional regulation. Many of these methods, such as Flux Balance Analysis, use constrained optimization to predict relationships between metabolic flux and the genes that encode and ... ...
BMC Systems Biology - Tập 5 Số 1 - 2011
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