共查询到20条相似文献,搜索用时 15 毫秒
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Kazuharu Arakawa Yohei Yamada Kosaku Shinoda Yoichi Nakayama Masaru Tomita 《BMC bioinformatics》2006,7(1):168-11
Background
Successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. However, current modeling approaches to cell simulation are labor-intensive, manual affairs, and therefore constitute a major bottleneck in the evolution of computational cell biology. 相似文献2.
Background
With the accumulation of increasing omics data, a key goal of systems biology is to construct networks at different cellular levels to investigate cellular machinery of the cell. However, there is currently no satisfactory method to construct an integrated cellular network that combines the gene regulatory network and the signaling regulatory pathway. 相似文献3.
Rita Gupta Anna Stincone Philipp Antczak Sarah Durant Roy Bicknell Andreas Bikfalvi Francesco Falciani 《BMC systems biology》2011,5(1):52
Background
Reverse engineering in systems biology entails inference of gene regulatory networks from observational data. This data typically include gene expression measurements of wild type and mutant cells in response to a given stimulus. It has been shown that when more than one type of experiment is used in the network inference process the accuracy is higher. Therefore the development of generally applicable and effective methodologies that embed multiple sources of information in a single computational framework is a worthwhile objective. 相似文献4.
Robert W Byrnes Dawn Cotter Andreia Maer Joshua Li David Nadeau Shankar Subramaniam 《BMC systems biology》2009,3(1):99-10
Background
Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface. 相似文献5.
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Background
The characterization of the global functional structure of a cell is a major goal in bioinformatics and systems biology. Gene Ontology (GO) and the protein-protein interaction network offer alternative views of that structure. 相似文献7.
Monica Chagoyen Pedro Carmona-Saez Concha Gil Jose M Carazo Alberto Pascual-Montano 《BMC bioinformatics》2006,7(1):363-13
Background
Recent analyses in systems biology pursue the discovery of functional modules within the cell. Recognition of such modules requires the integrative analysis of genome-wide experimental data together with available functional schemes. In this line, methods to bridge the gap between the abstract definitions of cellular processes in current schemes and the interlinked nature of biological networks are required. 相似文献8.
Background
In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools. 相似文献9.
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Derek Gatherer 《BMC systems biology》2010,4(1):22
Background
An old debate has undergone a resurgence in systems biology: that of reductionism versus holism. At least 35 articles in the systems biology literature since 2003 have touched on this issue. The histories of holism and reductionism in the philosophy of biology are reviewed, and the current debate in systems biology is placed in context. 相似文献11.
Michael Baitaluk Xufei Qian Shubhada Godbole Alpan Raval Animesh Ray Amarnath Gupta 《BMC bioinformatics》2006,7(1):55-13
Background
The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. 相似文献12.
Tianwei Yu 《BMC bioinformatics》2010,11(1):440
Background
Modular structures are ubiquitous across various types of biological networks. The study of network modularity can help reveal regulatory mechanisms in systems biology, evolutionary biology and developmental biology. Identifying putative modular latent structures from high-throughput data using exploratory analysis can help better interpret the data and generate new hypotheses. Unsupervised learning methods designed for global dimension reduction or clustering fall short of identifying modules with factors acting in linear combinations. 相似文献13.
Jayson Gutiérrez Georges St LaurentIII Silvio Urcuqui-Inchima 《Theoretical biology & medical modelling》2010,7(1):7
Background
Signal transduction networks represent the information processing systems that dictate which dynamical regimes of biochemical activity can be accessible to a cell under certain circumstances. One of the major concerns in molecular systems biology is centered on the elucidation of the robustness properties and information processing capabilities of signal transduction networks. Achieving this goal requires the establishment of causal relations between the design principle of biochemical reaction systems and their emergent dynamical behaviors. 相似文献14.
Background
Inference of protein interaction networks from various sources of data has become an important topic of both systems and computational biology. Here we present a supervised approach to identification of gene expression regulatory networks. 相似文献15.
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Background
Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. 相似文献17.
Areejit Samal Shalini Singh Varun Giri Sandeep Krishna Nandula Raghuram Sanjay Jain 《BMC bioinformatics》2006,7(1):118
Background
Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational and systems biology is to go beyond identification towards an explanation of specific modules and essential genes and reactions in terms of specific structural or evolutionary constraints. 相似文献18.
Background
New techniques for determining relationships between biomolecules of all types – genes, proteins, noncoding DNA, metabolites and small molecules – are now making a substantial contribution to the widely discussed explosion of facts about the cell. The data generated by these techniques promote a picture of the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems. 相似文献19.
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