systems biology bmc
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- systems biology bmc
Background Interoperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one format to another. However, they have been developed independently, resulting in redundancy of efforts and lack of synergy. Results Here we present the …
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Background Network is a useful way for presenting many types of biological data including protein-protein interactions, gene regulations, cellular pathways, and signal transductions. We can measure nodes by their network features to infer their importance in the network, and it can help us identify central elements of biological networks. Results …
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Background The C4 photosynthetic cycle supercharges photosynthesis by concentrating CO2 around ribulose-1,5-bisphosphate carboxylase and significantly reduces the oxygenation reaction. …
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Background Despite decades of new discoveries in biomedical research, the overwhelming complexity of cells has been a significant barrier to a fundamental understanding of how cells work as a whole. As such, the holistic study of biochemical pathways requires computer modeling. Due to the complexity of cells, it is not feasible for …
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Background The koji mold, Aspergillus oryzae is widely used for the production of industrial enzymes due to its particularly high protein secretion capacity and ability to perform post-translational modifications. However, systemic analysis of its secretion system is lacking, generally due to the poorly annotated proteome. Results Here we …
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Numerous recent efforts in systems biology have tried to characterize the set of all possible pairwise physical interactions or the binary protein "interactome" of an organism [1–3].Most proteins perform their functions through interactions [].Thus, these large-scale maps are critical in elucidating the biological roles of functional products of …
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Moreover, the reviewers from the Program Committee of ISB2010 selected 16 papers for a special issue in BMC Systems Biology after significant extension of their original versions on the Proceedings. Each submission has been peer reviewed and evaluated by three independent reviewers on the quality, originality, soundness, and …
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From the point of view of systems biology ('from above'), functional modules bridge the gap between individual genes and emergent global properties [8–10]. Here we view modules as basic system components (i.e., nodes of a network) and describe their relationships using network language. We find that co-expression modules may …
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BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as …
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BMC Systems Biology is now closed. Please consider submitting to BMC Bioinformatics. BMC will continue to host an archive of all articles published in BMC Systems Biology …
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Background Predicting drug-protein interactions from heterogeneous biological data sources is a key step for in silico drug discovery. The difficulty of this prediction task lies in the rarity of known drug-protein interactions and myriad unknown interactions to be predicted. To meet this challenge, a manifold regularization semi …
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Background With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of research in systems biology. Models are often encoded in formats such as SBML, whose structure is very complex and difficult to evaluate due to …
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Citation: BMC Systems Biology 2016 10:100 Content type: Software Published on: 21 October 2016. View Full Text View PDF Generalized method of moments for estimating parameters of stochastic reaction networks. Discrete-state stochastic models have become a well-established approach to describe biochemical reaction networks …
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December 2017, issue 1. October 2017, issue 5. Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: systems biology. This is a supplement. September 2017, issue 4. Selected papers from the 10th International Conference on Systems Biology (ISB 2016) This is a supplement. March 2017, issue 3 ...
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Fig. 1. Structural systems biology emerges from the integration of networks and structural biology. Genome-scale models incorporate multi-omic data and large-scale curation from databases such as KEGG and UniProt. Molecular-level analyses enable atomic-level characterizations of secondary structure, substrate binding, and …
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The tremendous growth of interest in systems biology was driven by the simultaneous rise of genomics [1, 2], which is the field dedicated to the large-scale analysis of the properties of genomes.As the international human genome sequencing project ramped up, the scientific community in concert with funding agencies devoted increasing …
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Background Experimental datasets are becoming larger and increasingly complex, spanning different data domains, thereby expanding the requirements for respective tool support for their analysis. Networks provide a basis for the integration, analysis and visualization of multi-omics experimental datasets. Results Here we present …
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This issue of BMC Medical Genomics SBB-2019 ("Systems Biology and Bioinformatics") presents recent works discussed at the 11th Young Scientists School …
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Background Drug-drug interactions (DDIs) always cause unexpected and even adverse drug reactions. It is important to identify DDIs before drugs are used in the market. However, preclinical identification of DDIs requires much money and time. Computational approaches have exhibited their abilities to predict potential DDIs on a …
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BMC Systems Biology is an open access journal publishing original peer-reviewed research articles in experimental and theoretical aspects of the function of biological systems at the molecular, cellular or organismal level, in particular those addressing the engineering of biological systems, network modelling, quantitative analyses ...
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Systems biology intertwines with single cell and AI. Yong Wang, Xiang-Sun Zhang & Luonan Chen. BMC Bioinformatics 20, Article number: 204 ( 2019 ) Cite this …
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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 …
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The first crystal structure of the active μ opioid receptor (μOR) exhibited several unexplained features. The ligand BU72 exhibited many extreme deviations from ideal geometry, along with unexplained electron ... Thomas A. Munro. BMC Biology 2023 21 :213. Research article Published on: 10 October 2023.
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Background Identifying a proper model structure, using methods that address both structural and parameter uncertainty, is a crucial problem within the systems approach to biology. And yet, it has a marginal presence in the recent literature. While many existing approaches integrate methods for simulation and parameter estimation of a single model …
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BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems.The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a …
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BMC Systems Biology | Methods, software and technology. Methods, software and technology. Section edited by Nitin Baliga and Pedro Mendes. This section …
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Background Kinase inhibition in the mitogen activated protein kinase (MAPK) pathway is a standard therapy for cancer patients with activating BRAF mutations. However, the anti-tumorigenic effect and clinical benefit are only transient, and tumors are prone to treatment resistance and relapse. To elucidate mechanistic insights into drug resistance, …
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BMC Systems Biology. 2009, 3: 37- 10.1186/1752- Article PubMed Central PubMed Google Scholar Nookaew I, Jewett MC, Meechai A, Thammarongtham C, Laoteng K, Cheevadhanarak S, Nielsen J, Bhumiratana S: The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a …
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The Systems Biology Simulation Core Library is an efficient Java tool for the simulation of differential equation systems used in systems biology. It can be easily …
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BMC systems biology. 2008, 2: 47- 10.1186/1752-. Article PubMed PubMed Central Google Scholar Download references. Acknowledgements. We would like to thank all the authors who submitted their manuscripts to this Special Issue. We would also like to thank the reviewers for their invaluable contributions to the peer review …
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Background One of the eminent opportunities afforded by modern genomic technologies is the potential to provide a mechanistic understanding of the processes by which genetic change translates to phenotypic variation and the resultant appearance of distinct physiological traits. Indeed much progress has been made in this area, …
به خواندن ادامه دهیدThe model of Insulin Signaling Pathway obtained by integrating the PI3K-AKT pathway, the mTOR pathway and the RAS-MAPK pathway, depicted using the Systems Biology Graphical Notation. Coloured nodes resemble the clustering results obtained on simulated profiles (see Fig. 3 ). Coloured lines represent important feedback …
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