MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'BMC Systems Biology - Latest articles' source. Thu, 09 Feb 2012 16:56:39 +0100 http://www.medworm.com/index.php?rid=5673968&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F6%2F11 Conclusions: We find that the experimentally observed crosstalk between MITF and STAT3 via PIAS3 in melanocytes is faithfully reproduced in our model, offering mechanistic explanations for this behaviour, as well as providing a scaffold for further studies of MITF signalling in melanoma. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5673968 Wed, 08 Feb 2012 05:00:00 +0100 5673968 http://www.medworm.com/index.php?rid=5664289&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F6%2F10 Conclusions: We find the topological approach to be faster by several orders of magnitude than the steady state approach. Yet both methods are generally scalable in time with the number of pathways in the metabolic network. Therefore this work provides an efficient tool for pathway enumeration with direct application to biosynthetic pathway design. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5664289 Mon, 06 Feb 2012 05:00:00 +0100 5664289 http://www.medworm.com/index.php?rid=5643862&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F6%2F8 Conclusions: With FAME, we present the community with an open source, user-friendly, web-based "one stop shop" for stoichiometric modeling. We expect the application will be of substantial use to investigators and educators alike. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5643862 Mon, 30 Jan 2012 05:00:00 +0100 5643862 http://www.medworm.com/index.php?rid=5643861&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F6%2F9 Conclusions: While 13C analysis is a useful tool in systems biology, high redundancy in measurements limits the information that can be obtained from each experiment. It is however possible to compute potential limitations before an experiment is run and predict whether, and to what degree, the rate of each reaction can be resolved. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5643861 Mon, 30 Jan 2012 05:00:00 +0100 5643861 http://www.medworm.com/index.php?rid=5656508&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F6%2F6 Conclusions: This study presents an application of the typical Systems Biology circle and is based on cooperation between wet-lab experimentalists and in silico modellers. The results underline that using prior knowledge during network inference helps to predict biologically important interactions. Together with the experimental results, we indicate a novel iron homoeostasis regulating system sensing the amount of metabolically available iron and identify the binding site of iron-related SrbA target genes. It will be of high interest to study whether these regulatory interactions are also important for close relatives of A. fumigatus and other pathogenic fungi, such as Candida albicans. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5656508 Thu, 19 Jan 2012 05:00:00 +0100 5656508 http://www.medworm.com/index.php?rid=5617047&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F6%2F5 Conclusions: With gene expression and interactome data supported, our study points out possible pathways leading to the emergence of drug resistance under drug treatment. We develop a computational workflow for giving new insights to bacterial drug resistance which can be gained by a systematic and global analysis of the bacterial regulation network. Our study also discovers the potential co-targets with good properties in biological and graph theory aspects to overcome the problem of drug resistance. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5617047 Thu, 19 Jan 2012 05:00:00 +0100 5617047 http://www.medworm.com/index.php?rid=5617046&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F6%2F6 Conclusions: This study presents an application of the typical Systems Biology circle and is based on cooperation between wet-lab experimentalists and in silico modellers. The results underline that using prior knowledge during network inference helps to predict biologically important interactions. Together with the experimental results, we indicate a novel iron homoeostasis regulating system sensing the amount of metabolically available iron and identify the binding site of iron-related SrbA target genes. It will be of high interest to study whether these regulatory interactions are also important for close relatives of A. fumigatus and other pathogenic fungi, such as Candida albicans. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5617046 Thu, 19 Jan 2012 05:00:00 +0100 5617046 http://www.medworm.com/index.php?rid=5617045&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F6%2F7 Conclusions: The natural abundance pattern of the feed-forward loop can be reconstructed concerning its intrinsic plasticity. Intrinsic plasticity is associated to each motif in terms of its capacity of implementing a repertoire of possible functions and it is directly linked to the motif's evolvability. Since evolvability is defined as the potential phenotypic variation of the motif upon mutation, the link plausibly explains the abundance pattern. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5617045 Thu, 19 Jan 2012 05:00:00 +0100 5617045 http://www.medworm.com/index.php?rid=5593110&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F6%2F4 Conclusion: A subset of growth-regulated genes have HFC characteristics when grown in conditions where there are few, or no, external constraints on the rate of growth that cells may attain. This subset is enriched for genes that participate in the processes of gene expression, itself (i.e. transcription and translation). The fact that haploproficiency is exhibited by mutants grown at the previously determined maximum rate implies that the control of growth rate in this simple eukaryote represents a trade-off between the selective advantages of rapid growth and the need to maintain the integrity of the genome. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5593110 Fri, 13 Jan 2012 05:00:00 +0100 5593110 http://www.medworm.com/index.php?rid=5593111&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F6%2F3 Conclusion: The work presented here demonstrates, through the power of gene-expression networks, the criticality of the PDGF network in driving disease outcome. In uncovering the specific interactions within the network, that drive the phenotype, we catalyze targeted treatment, facilitate prognosis and offer a novel perspective into hidden disease heterogeneity. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5593111 Wed, 11 Jan 2012 05:00:00 +0100 5593111 http://www.medworm.com/index.php?rid=5568906&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F6%2F2 Conclusions: This study shows a successful example of a workflow deriving novel biological insight from transcriptome-wide gene expression. Importantly, we do not find any significant difference between TcdA and TcdB besides potency or kinetics. The role of each toxin in the inhibition of cell growth and proliferation, an important function of cells in the intestinal epithelium, is characterized. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5568906 Fri, 06 Jan 2012 05:00:00 +0100 5568906 http://www.medworm.com/index.php?rid=5568907&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F6%2F1 Conclusions: Our model can be used to identify the biological factors that must be changed to minimize parasite load in the host body, and contributes to the design of effective therapies. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5568907 Thu, 05 Jan 2012 05:00:00 +0100 5568907 http://www.medworm.com/index.php?rid=5549801&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F204 Conclusions: Cell ensemble modeling of a heterogeneous cell population including a global sensitivity analysis presented here allowed us to illuminate the role of the different elements and parameters on apoptotic signaling. The receptors serve to transmit the external stimulus; procaspases and their inhibitors control the switching from life to death, while NF-kappaB enhances the heterogeneity of the cell population. The global sensitivity analysis of the cell population model further revealed an unexpected impact of heterogeneity, i.e. the reduction of parametric sensitivity. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5549801 Wed, 28 Dec 2011 05:00:00 +0100 5549801 http://www.medworm.com/index.php?rid=5533464&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F202 Conclusions: Highly pathogenic viruses elicit expression of many of the same key genes as lower pathogenic viruses but to a higher degree. This increased degree of expression may result in the uncontrolled co-localization of inflammatory cell types and lead to irreversible host damage. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5533464 Thu, 22 Dec 2011 05:00:00 +0100 5533464 http://www.medworm.com/index.php?rid=5533463&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F203 Conclusions: We find that the interactions between the networks that we studied are highly complex and not intuitive: (i) points of maximum perturbation do not necessarily correspond to points of maximum proximity to influence; (ii) increased coupling strength does not necessarily increase perturbation; (iii) different perturbations do not necessarily sum and (iv) overall, susceptibility to perturbation is amplitude and frequency dependent and cannot easily be predicted by heuristic measures.Our methodology is particularly relevant for oscillatory systems, though not limited to these, and is most revealing when applied to the results of stochastic simulation. The technique is able to characterise precisely the distance in behaviour between different models, different systems and different ... BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5533463 Thu, 22 Dec 2011 05:00:00 +0100 5533463 http://www.medworm.com/index.php?rid=5533465&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F201 Conclusions: We find that a quantitative description of replication initiation by DnaA must rely on the dependency of the basic parameters on growth rate, in order to account for the timing of initiation of DNA replication at different cell doubling times. We isolate two main possible scenarios for this, depending on the roles of DnaA autoregulation and DnaA ATP-hydrolysis regulatory process. One possibility is that the basal rate of regulatory inactivation by ATP hydrolysis must vary with growth rate. Alternatively, some parameters defining promoter activity need to be a function of the growth rate. In either case, the basal rate of gene expression needs to increase with the growth rate, in accordance with the known characteristics of the dnaA promoter. Furthermore, both inactivation and ... BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5533465 Wed, 21 Dec 2011 05:00:00 +0100 5533465 http://www.medworm.com/index.php?rid=5533466&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F200 Conclusions: In this 'individualized case study' of personalized medicine, we carry out untargeted metabolomic profiling of a patient and healthy controls. Rather than filtering the data down to a single value, these data are analyzed in the context of a network model of metabolism, in order to simulate the biochemical phenotypic differences between healthy and disease states; the results then guide the therapy. This presents one approach to achieving the goals of individualized medicine through Systems Biology and causal models analysis. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5533466 Tue, 20 Dec 2011 05:00:00 +0100 5533466 http://www.medworm.com/index.php?rid=5512428&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F198 Conclusions: With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5512428 Thu, 15 Dec 2011 05:00:00 +0100 5512428 http://www.medworm.com/index.php?rid=5512429&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F197 Conclusions: We extended the PdhR regulon by 22 new genes contained in two operons and validated the regulation of the glcDEFGBA operon for glycolate utilisation and the dcw-cluster for cell division proteins experimentally. Our results provide, for the first time, a plausible regulatory link between the nutritional status of the cell and cell replication mediated by PdhR. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5512429 Wed, 14 Dec 2011 05:00:00 +0100 5512429 http://www.medworm.com/index.php?rid=5501131&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F196 Conclusions: Spatial noise impedes the extent, accuracy, and smoothness of cell polarization. A combined filtering strategy implemented by a filter-amplifier architecture with slow dynamics was effective. Modeling and experimental data suggest that yeast cells employ these elaborate mechanisms to filter gradient noise resulting in a slow but relatively accurate polarization response. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5501131 Tue, 13 Dec 2011 05:00:00 +0100 5501131 http://www.medworm.com/index.php?rid=5473666&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F195 Conclusions: Hierarchical and model-based clustering revealed multi-centrality hubs in a vitamin PPI network and redundancies among the centrality indices. Vitamin D-related proteins were strongly represented among network hubs, highlighting the pervasive effects of this nutrient. Our integrated approach to network construction identified promiscuous transcription factors, cytokines and enzymes - primarily related to immune system and cancer processes - representing potential gatekeepers linking vitamin intake to disease. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5473666 Fri, 02 Dec 2011 05:00:00 +0100 5473666 http://www.medworm.com/index.php?rid=5465216&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F194 Conclusion: This study provides a deeper systems level insight into how Cyanothece ATCC51142 modulates cellular functions to accommodate photosynthesis and N2-fixation within the single cell. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5465216 Thu, 01 Dec 2011 05:00:00 +0100 5465216 http://www.medworm.com/index.php?rid=5437292&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F192 Conclusion: Taken together, our findings indicate that 14-3-3 proteins play roles as crucial tuners of multiple primary metabolic processes including the TCA cycle and the shikimate pathway. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5437292 Mon, 21 Nov 2011 05:00:00 +0100 5437292 http://www.medworm.com/index.php?rid=5437291&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F193 Conclusions: This study explores the optimal drug characteristics required for an anti-VEGF agent to have a therapeutic effect and the tumor-specific properties that influence the response to therapy. Our model provides a framework for investigating the use of VEGF-neutralizing drugs for personalized medicine treatment strategies. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5437291 Mon, 21 Nov 2011 05:00:00 +0100 5437291 http://www.medworm.com/index.php?rid=5404769&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F191 Conclusion: Logic modeling of the TOL circuit accounted for the intricate regulatory topology of this otherwise simple metabolic device. The found MAM appears to ensure a simultaneous expression of the upper and lower segments of the m-xylene catabolic route that would be difficult to bring about with a standard substrate-responsive single promoter. Furthermore, it is plausible that the MAM helps to avoid biochemical conflicts between competing plasmid-encoded and chromosomally-encoded pathways in this bacterium. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5404769 Fri, 11 Nov 2011 05:00:00 +0100 5404769 http://www.medworm.com/index.php?rid=5396829&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F190 Conclusions: This is the first demonstration of a global regulatory network modeling conserved host response between in vitro and in vivo models. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5396829 Fri, 11 Nov 2011 05:00:00 +0100 5396829 http://www.medworm.com/index.php?rid=5396830&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F189 Conclusions: This work emphasizes that the metabolism of M. extorquens AM1 is adapted to its lifestyle not only in terms of enzymatic equipment, but also in terms of network-level structure and regulation. It suggests that the metabolism of the bacterium has evolved both structurally and functionally to an efficient but transitory utilization of methanol. Besides, this work provides a basis for metabolic engineering to convert methanol into value-added products. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5396830 Thu, 10 Nov 2011 05:00:00 +0100 5396830 http://www.medworm.com/index.php?rid=5396831&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F188 Conclusions: PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (realtime) access to the data in the database. PathCase-SB itself is already being used by researchers across the world. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5396831 Wed, 09 Nov 2011 05:00:00 +0100 5396831 http://www.medworm.com/index.php?rid=5396832&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F187 Conclusions: The construction of a stochastic model for a biochemical network requires the utilization of information associated with an equation-based model. The conversion strategy proposed here guides a model design process that ensures a valid transition between deterministic and stochastic models. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5396832 Tue, 08 Nov 2011 05:00:00 +0100 5396832 http://www.medworm.com/index.php?rid=5375446&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F186 Conclusions: The results provide rich mechanistic information regarding molecular aberrations and gene expressions in cancer genomes. This kind of integrative analysis will become an important tool for the diagnosis and treatment of cancer in the era of personalized medicine. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5375446 Fri, 04 Nov 2011 04:00:00 +0100 5375446 http://www.medworm.com/index.php?rid=5375449&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F183 Conclusions: We combined several sources of interaction and association data to analyse and place miRNAs within regulatory pathways that influence human OC. These results represent the first comprehensive miRNA regulatory network analysis for human OC. This suggests that miRNAs and their regulation may play a major role in OC and that further directed research in this area is of utmost importance to enhance our understanding of the molecular mechanisms underlying human cancer development and OC in particular. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5375449 Thu, 03 Nov 2011 04:00:00 +0100 5375449 http://www.medworm.com/index.php?rid=5375448&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F184 Conclusions: The architecture of the TGF-beta pathway enables the observed signaling plasticity. The observed range of signaling outputs to TGF-beta ligand in different cell types and under different conditions can be explained with differences in cellular protein concentrations and with changes in effective rate constants due to cross-talk with other signaling pathways. It will be interesting to uncover the exact cellular differences as well as the details of the cross-talks in future work. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5375448 Thu, 03 Nov 2011 04:00:00 +0100 5375448 http://www.medworm.com/index.php?rid=5375447&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F185 Conclusions: In our study we show that the existing models that have been investigated are not suitable for reuse without substantial modifications. We furthermore show that the minor adjacent pathways of the carbon metabolism, neglected in all kinetic models of Calvin-Benson cycle, cannot be substituted without consequences in the mass production dynamics. We further show that photorespiration or at least its first step (O2 fixation) has to be implemented in the model if this model is aimed for analyses out of the steady state. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5375447 Thu, 03 Nov 2011 04:00:00 +0100 5375447 http://www.medworm.com/index.php?rid=5375451&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F181 Conclusions: Overall, our results demonstrate that PLP slightly outperforms PLS in terms of predictive power. But more importantly, PLP is able to discriminate the subset of EFM with highest correlation with the envirome, thus providing in-depth knowledge of how the environment controls core cellular functions. This offers a significant advantage over PLS since its abstract structure cannot be associated with the underlying biological structure. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5375451 Tue, 01 Nov 2011 04:00:00 +0100 5375451 http://www.medworm.com/index.php?rid=5375450&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F182 Conclusion: Our findings demonstrate that a pangenome-scale metabolic model can be used to rapidly construct additional E. coli strain-specific models, and that quantitative models of different strains of E. coli can accurately predict strain-specific phenotypes. Such pangenome and strain-specific models can be further used to engineer metabolic phenotypes of interest, such as designing new industrial E. coli strains. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5375450 Tue, 01 Nov 2011 04:00:00 +0100 5375450 http://www.medworm.com/index.php?rid=5375453&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F179 Conclusions: We suggest that studying central nodes in mediator networks may contribute to better understanding and quantifying pleiotropy. Network analysis provides potentially useful tools here, as well as helps in improving databases. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5375453 Mon, 31 Oct 2011 04:00:00 +0100 5375453 http://www.medworm.com/index.php?rid=5375452&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F180 Conclusion: The multi-tissue type modeling approach presented provides a platform to study integrated metabolic states. As more cell and tissue-specific models are released, it is critical to develop a framework in which to study their interdependencies. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5375452 Mon, 31 Oct 2011 04:00:00 +0100 5375452 http://www.medworm.com/index.php?rid=5375455&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F176 Conclusions: Our results demonstrate the utility of metabolomics for linking traits with quantitative molecular data. This opens up new opportunities for trait prediction and construction of tailored germplasms to support modern plant breeding. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5375455 Fri, 28 Oct 2011 04:00:00 +0100 5375455 http://www.medworm.com/index.php?rid=5375454&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F178 Conclusions: On the basis of experimental data, literature mining and database screening we established a dynamic in silico model of cyclic nucleotide signaling and probed its signaling sensitivity. Thoroughly validated, it successfully predicts drug combination effects on platelet function, including synergism, antagonism and regulatory loops. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5375454 Fri, 28 Oct 2011 04:00:00 +0100 5375454 http://www.medworm.com/index.php?rid=5355402&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F173 Conclusions: Our systems biology approach has highlighted the multiple associations between subunits and assembly factors of complexes III and IV during their biogenesis. In addition, this approach has allowed the identification of a new factor, Usb1p, involved in the biogenesis of respiratory complexes, which could not have been found using classical genetic screens looking for respiratory deficient mutants. Thus, this systems biology approach appears to be a fruitful new way to study the biogenesis of mitochondrial multi-subunit complexes. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5355402 Tue, 25 Oct 2011 04:00:00 +0100 5355402 http://www.medworm.com/index.php?rid=5355404&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F171 Conclusions: The presented PPDK mechanism is a new way to achieve robustness using product inhibition as a feedback loop on a bifunctional regulatory enzyme. This mechanism exhibits robustness to protein and metabolite levels as well as to catalytic rate changes. At the same time, the output of the system remains tuned to input levels. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5355404 Mon, 24 Oct 2011 04:00:00 +0100 5355404 http://www.medworm.com/index.php?rid=5355403&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F172 Conclusion: This algorithm has been applied to the protein functional association network of Clostridium acetobutylicum ATCC 824, a hydrogen producing, acid-tolerant organism. The algorithm was able to verify relationships known to exist in literature and also some previously unknown relationships including those with regulatory and signaling functions. Additionally, we were also able to hypothesize that some uncharacterized proteins are likely associated with the target phenotype. The DENSE code can be downloaded fromhttp://www.freescience.org/cs/DENSE/ (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5355403 Mon, 24 Oct 2011 04:00:00 +0100 5355403 http://www.medworm.com/index.php?rid=5343530&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F170 Conclusions: These findings suggest that proteolytic damage at sites of tissue injury and inflammation has the potential to modulate the VEGF system through a complex process and highlight the need for quantitative analysis to reveal mechanisms of growth factor control. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5343530 Fri, 21 Oct 2011 04:00:00 +0100 5343530 http://www.medworm.com/index.php?rid=5330682&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F168 Conclusions: The results presented here describe the construction of a cellular stress network model and its application towards the analysis of environmental stress using transcriptomic data. The proof-of-principle analysis described here, coupled with the future development of additional network models covering distinct areas of biology, will help to further clarify the integrated biological responses elicited by complex environmental stressors such as CS, in pulmonary and cardiovascular cells. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5330682 Wed, 19 Oct 2011 04:00:00 +0100 5330682 http://www.medworm.com/index.php?rid=5330681&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F169 Conclusions: We show here that the bias against membrane proteins can and should be corrected in order to have a better representation of the interactions and topological properties of protein interaction networks. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5330681 Wed, 19 Oct 2011 04:00:00 +0100 5330681 http://www.medworm.com/index.php?rid=5330683&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F167 Conclusions: This study provides a genome-scale description of the metabolic variability regarding by-production among E. coli strains under different conditions and shows how metabolic differences can be used to identify metabolically interacting strain communities. This work also extends the existing stoichiometric models in order to describe batch co-cultures and provides the extent of metabolic interactions in a strain community revealing their importance for growth. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5330683 Tue, 18 Oct 2011 04:00:00 +0100 5330683 http://www.medworm.com/index.php?rid=5330684&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F166 Conclusions: Rule-based languages are a suitable starting point for developing a concise and compact language for multi-level modeling of cell biological systems. The combination of nesting species, assigning attributes, and constraining reactions according to these attributes is crucial in achieving the desired expressiveness. Rule schemata allow a concise and compact description of complex models. As a result, the presented approach facilitates developing and maintaining multi-level models that, for instance, interrelate intracellular and intercellular dynamics. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5330684 Mon, 17 Oct 2011 04:00:00 +0100 5330684 http://www.medworm.com/index.php?rid=5321534&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F165 Conclusions: Our results show that each of the five networks compared provides us with a valuable piece of the puzzle of the complete reconstruction of the human metabolic network. To enable integration of the networks, next to a need for standardizing the metabolite names and identifiers, the conceptual differences between the databases should be resolved. Considerable manual intervention is required to reach the ultimate goal of a unified and biologically accurate model for studying the systems biology of human metabolism. Our comparison provides a stepping stone for such an endeavor. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5321534 Fri, 14 Oct 2011 04:00:00 +0100 5321534 http://www.medworm.com/index.php?rid=5321536&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F163 Conclusions: Y. pestis continues to be a dangerous threat to human health during modern times. The Y. pestis genome-scale metabolic reconstruction presented here, which has been benchmarked against experimental data and correctly reproduces known phenotypes, thus provides an in silico platform with which to investigate the metabolism of this important human pathogen. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5321536 Thu, 13 Oct 2011 04:00:00 +0100 5321536 http://www.medworm.com/index.php?rid=5321535&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F164 Conclusions: Our results suggest that targeted reduction of redox enzyme expression leads to widespread changes in off-target protein expression that are well-insulated between cellular compartments but are compensatory in both the production of and protection against intracellular reactive oxygen species. Our observations suggest that the use of lentivirus can in itself have off-target effects on dynamic responses to oxidative stress due to the changes in species concentrations. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5321535 Thu, 13 Oct 2011 04:00:00 +0100 5321535 http://www.medworm.com/index.php?rid=5310780&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F162 Conclusions: Although the ANLSH is energetically more favorable for the neuron, it is not the case for the astrocyte in the long term. Considering the fact that astrocytes are more resilient to hypoxia, we would propose that there is likely a switch between the two models, based on the energy demand of the neuron, so as to maintain the survival of the neuron under hypoxic or glucose-and-oxygen-deprived conditions. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5310780 Thu, 13 Oct 2011 04:00:00 +0100 5310780 http://www.medworm.com/index.php?rid=5310782&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F160 Conclusions: Analysis of the phases at which transcription factor activities peak supports previous findings suggesting that the various cellular functions occur during specific phases of the yeast metabolic cycle. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5310782 Wed, 12 Oct 2011 04:00:00 +0100 5310782 http://www.medworm.com/index.php?rid=5310781&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F161 Conclusions: We have developed a network-based approach for cancer biomarker identification, netSVM, resulting in an improved prediction performance with network biomarkers. We have applied the netSVM approach to breast cancer gene expression data to predict metastasis in patients. Network biomarkers identified by netSVM reveal potential signaling pathways associated with breast cancer metastasis, and help improve the prediction performance across independent data sets. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5310781 Wed, 12 Oct 2011 04:00:00 +0100 5310781 http://www.medworm.com/index.php?rid=5310784&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F158 Conclusions: Here we have shown that network theory combined with epigenetic characteristics provides a favorable platform from which to identify cancer-related genes. We prioritized 154 potential cancer-related genes with aberrant methylation that might contribute to the further understanding of cancers. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5310784 Tue, 11 Oct 2011 04:00:00 +0100 5310784 http://www.medworm.com/index.php?rid=5310783&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F159 Conclusions: Overall, the global meta-heuristic methods (DASA, PSO, and DE) clearly and significantly outperform the local derivative-based method (A717). Among the three meta-heuristics, differential evolution (DE) performs best in terms of the objective function, i.e., reconstructing the output, and in terms of convergence. These results hold for both real and artificial data, for all observability scenarios considered, and for all amounts of noise added to the artificial data. In sum, the meta-heuristic methods considered are suitable for estimating the parameters in the ODE model of the dynamics of endocytosis under a range of conditions: With the model and conditions being representative of parameter estimation tasks in ODE models of biochemical systems, our results clearly highlight ... BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5310783 Tue, 11 Oct 2011 04:00:00 +0100 5310783 http://www.medworm.com/index.php?rid=5292953&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F157 Conclusions: We present here a data-driven method to reveal modes of toxicity of different agents that impair cellular growth. The results from this study complement previous genomic phenotyping studies as we have expanded the data to include essential genes and to provide detailed mutant growth analysis for each individual strain. This eukaryotic testing system could potentially be used to screen compounds for toxicity, to identify mechanisms of toxicity, and to reduce the need for animal testing. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5292953 Thu, 06 Oct 2011 04:00:00 +0100 5292953 http://www.medworm.com/index.php?rid=5292954&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F156 Conclusions: A proper and detailed characterization of a pathway's structure is important for identifying the optimal protein to target as well as what concentration of the targeted therapy is required to modulate the pathway in a safe and effective manner. We believe our results support the position that such characterizations should consider retroactivity as a robust potential source of off-target effects induced by kinase inhibitors and other targeted therapies. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5292954 Tue, 04 Oct 2011 04:00:00 +0100 5292954 http://www.medworm.com/index.php?rid=5281493&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F155 Conclusions: The results demonstrate how metabolic models can be utilized to direct hypotheses of novel metabolic functions in human metabolism; a process that we find is heavily reliant upon manual curation and biochemical insight. The effectiveness of a systems approach for novel biochemical pathway discovery in mammals is demonstrated and steps required to tailor future gap filling algorithms to mammalian metabolic networks are proposed. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5281493 Sat, 01 Oct 2011 04:00:00 +0100 5281493 http://www.medworm.com/index.php?rid=5268666&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F154 Conclusions: We present here a system-wide computational model of neuronal migration that integrates theory and data within a precise, testable framework. Our model accounts for a range of observable behaviors and affords a computational framework to study aspects of neuronal migration as a complex process that is driven by a relatively simple molecular program. Analysis of the model generated new hypotheses and yet unobserved phenomena that may guide future experimental studies. This paper thus reports a first step toward a comprehensive in-silico model of neuronal migration. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5268666 Fri, 30 Sep 2011 04:00:00 +0100 5268666 http://www.medworm.com/index.php?rid=5268668&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F152 Conclusions: Our findings suggest that the expression of tmem59 is an important factor contributing to AD. The parallelized SWNI algorithm increased the efficiency of network reconstruction significantly. This study enables us to highlight novel genes that may be involved in NSC differentiation and provides a shortcut to identifying genes for AD. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5268668 Thu, 29 Sep 2011 04:00:00 +0100 5268668 http://www.medworm.com/index.php?rid=5268667&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F153 Conclusions: The lux genes in V.fischeri do not appear to distinguish between the two HSL inputs, and even with two signal inputs the regulation of lux is extremely noisy. Hence the role of crosstalk from the C8HSL input may not be to improve sensing precision, but rather to suppress the sensitivity of the switch for as long as possible during colony growth. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5268667 Thu, 29 Sep 2011 04:00:00 +0100 5268667 http://www.medworm.com/index.php?rid=5268669&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F151 Conclusions: Our analysis allows us to address how cell-to-cell variation affects motor behaviour and the question of optimal pathway design. A similar comprehensive analysis can be applied to other two-component signalling pathways. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5268669 Tue, 27 Sep 2011 04:00:00 +0100 5268669 http://www.medworm.com/index.php?rid=5257299&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F148 Conclusions: The study provided important information on the temporal organization of transcriptomic organization and underlying regulatory events as a response to both carbon and nitrogen impulse. It has also revealed the importance of a long-term dynamic analysis of the response to the relaxation of a nutritional limitation to understand the molecular basis of the cells' dynamic behaviour. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5257299 Sun, 25 Sep 2011 04:00:00 +0100 5257299 http://www.medworm.com/index.php?rid=5257298&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F149 Conclusions: The two rate-limiting steps in initiation are found to be important regulators of the dynamics of RNA production under the control of the lar promoter in the regimes of weak and medium induction. Variability in the intervals between consecutive RNA productions is much lower than if there was only one rate-limiting step with a duration following an exponential distribution. The methodology proposed here to analyze the in vivo dynamics of transcription may be applicable at a genome-wide scale and provide valuable insight into the dynamics of prokaryotic genetic networks. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5257298 Sun, 25 Sep 2011 04:00:00 +0100 5257298 http://www.medworm.com/index.php?rid=5257297&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F150 Conclusions: Taken together, the metabolic model (i) explains various redox-related phenomena of the versatile metabolism of PNSB, (ii) delivers new hypotheses on the operation and relevance of several metabolic pathways, and (iii) holds significant potential as a tool for rational metabolic engineering of PNSB in biotechnological applications. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5257297 Sun, 25 Sep 2011 04:00:00 +0100 5257297 http://www.medworm.com/index.php?rid=5257300&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F147 Conclusion: The TIGER packages provides a consistent platform for algorithm development and extending genome-scale metabolic models with regulatory networks and high-throughput data. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5257300 Fri, 23 Sep 2011 04:00:00 +0100 5257300 http://www.medworm.com/index.php?rid=5246355&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F146 Immunotherapies, including vaccines, represent a potent tool to prevent or contain disease with high morbidity or mortality such as infections and cancer. However, despite their widespread use, we still have a limited understanding of the mechanisms underlying the induction of protective immune responses.Immunity is made of a multifaceted set of integrated responses involving a dynamic interaction of thousands of molecules; among those is a growing appreciation for the role the innate immunity (i.e. pathogen recognition receptors - PRRs) plays in determining the nature and duration (immune memory) of adaptive T and B cell immunity. The complex network of interactions between immune manipulation of the host (immunotherapy) on one side and innate and adaptive responses on the other might be ... BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5246355 Tue, 20 Sep 2011 04:00:00 +0100 5246355 http://www.medworm.com/index.php?rid=5233508&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F144 Conclusions: We introduced a new methodology to identify potential diagnostic biomarkers for OC. This report is the first bioinformatics study that explores multiple transcriptional regulators of OC-associated genes as potential diagnostic biomarkers in connection with estrogen responsiveness. We show that 64% of TF biomarkers identified in our study are validated based on real-time data from microarray expression studies. As an illustration, our method could identify CP2 that in combination with CA125 has been reported to be sensitive in diagnosing ovarian tumors. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5233508 Mon, 19 Sep 2011 04:00:00 +0100 5233508 http://www.medworm.com/index.php?rid=5233507&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F145 Conclusions: Considering the resilience phenomena in metabolic networks can improve the predictions of gene intervention and maximum synthesis rates in metabolic engineering. The proposed generalized fuzzy multi-objective optimization approach has the potential to be a good and practical framework in the design of metabolic networks. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5233507 Mon, 19 Sep 2011 04:00:00 +0100 5233507 http://www.medworm.com/index.php?rid=5233510&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F142 Conclusions: Our algorithm permits an efficient analysis of high-dimensional, nonconvex, and poorly connected viable spaces characteristic of complex biological circuitry. It allows a systematic use of robustness as a tool for model discrimination. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5233510 Thu, 15 Sep 2011 04:00:00 +0100 5233510 http://www.medworm.com/index.php?rid=5233509&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F143 A computational model of Calcium ion and membrane potential-dependent regulation of cilliary beating shows how environmental or genetic changes to the beating modes can lead to diseases associated with ciliary dysfunction. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5233509 Thu, 15 Sep 2011 04:00:00 +0100 5233509 http://www.medworm.com/index.php?rid=5204211&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F141 Conclusions: MiR-206 has a profound effect on the dynamic mechanism of the mammalian circadian clock, both by control of the amplitude and control or alteration of the frequency to affect the level of the gene expression and to interfere with the temporal sequence of the gene production or delivery. This undoubtedly uncovers a new mechanism for regulation of the circadian clock at a post-transcriptional level and provides important insights into the normal development as well as the pathological conditions of skeletal muscles, such as the aging, chronic disease and cancer. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5204211 Fri, 09 Sep 2011 04:00:00 +0100 5204211 http://www.medworm.com/index.php?rid=5191222&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F139 Conclusions: The results presented here were not only comparable with other in vitro studies but also with in vivo studies. Moreover, new insights on the molecular responses caused by TCDD exposure were gained by the cross-omics analysis. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5191222 Tue, 30 Aug 2011 23:00:00 +0100 5191222 http://www.medworm.com/index.php?rid=5179237&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F138 Conclusions: Our results show that meta-analysis identified more differentially expressed genes than the individual studies, and that these genes act together in networks. These results provide new insight into E2 regulated mechanisms, especially in the context of breast cancer. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5179237 Mon, 29 Aug 2011 23:00:00 +0100 5179237 http://www.medworm.com/index.php?rid=5233511&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F136 Conclusions: Our findings indicate a coordinate posttranscriptional regulation of protein complexes by miRNAs. These provide a sound basis for designing experiments to study miRNA function at a systems level. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5233511 Thu, 25 Aug 2011 04:00:00 +0100 5233511 http://www.medworm.com/index.php?rid=5168897&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F136 Conclusions: Our findings indicate a coordinate posttranscriptional regulation of protein complexes by miRNAs. These provide a sound basis for designing experiments to study miRNA function at a systems level. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5168897 Wed, 24 Aug 2011 23:00:00 +0100 5168897 http://www.medworm.com/index.php?rid=5168896&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F137 Conclusions: Our results show that recasting non-linear kinetic models into GMA models is indeed an appropriate strategy that helps overcoming some of the numerical difficulties that arise during the global optimization task. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5168896 Wed, 24 Aug 2011 23:00:00 +0100 5168896 http://www.medworm.com/index.php?rid=5155682&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F135 Conclusions: Our work shows that modularity in metabolic networks can be a by-product of functional constraints, e.g., the need to sustain life in multiple environments. This organizational principle is insensitive to the environments we consider and to the number of reactions in a metabolic network. Because we observe this principle not just in one or few biological networks, but in large random samples of networks, we propose that it may be a generic principle of metabolic network organization. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5155682 Tue, 23 Aug 2011 23:00:00 +0100 5155682 http://www.medworm.com/index.php?rid=5155683&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F134 Conclusions: We show that conservation is maintained between species, but mainly at the module level. Our results indicate that interactions within modules are much more likely to be conserved than interactions between proteins in different modules. This provides a network based explanation to the observed conservation rates that can also help explain why so many biological processes are well conserved despite the lower levels of conservation for the interactions of proteins participating in these processes. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5155683 Mon, 22 Aug 2011 23:00:00 +0100 5155683 http://www.medworm.com/index.php?rid=5155684&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F133 Conclusion: We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5155684 Sun, 21 Aug 2011 23:00:00 +0100 5155684 http://www.medworm.com/index.php?rid=5155685&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F132 Conclusions: Our findings indicate that the observed degeneration is attributed to a significant decrease of the levels of the first two enzymes of the penicillin biosynthesis pathway, ACVS and IPNS. This decrease is not caused by genetic instability of the penicillin amplicon, neither by down regulation of the penicillin biosynthesis pathway. Furthermore no indications were obtained for degradation of these enzymes as a result of autophagy. Possible causes for the decreased enzyme levels could be a decrease of the translation efficiency of ACVS and IPNS during degeneration, or the presence of a culture variant impaired in the biosynthesis of functional proteins of these enzymes, which outcompeted the high producing part of the population. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5155685 Thu, 18 Aug 2011 23:00:00 +0100 5155685 http://www.medworm.com/index.php?rid=5155686&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F131 Conclusions: Our integrated probabilistic Models 1 and 2 explained GCN4 translation and helped to elucidate the role of a yet unidentified factor. The ensuing stochastic simulations evaluated different factors that may impact on the translation of GCN4 mRNA, and integrated translation status with ribosomal density. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5155686 Wed, 17 Aug 2011 23:00:00 +0100 5155686 http://www.medworm.com/index.php?rid=5137858&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F128 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5137858 Mon, 15 Aug 2011 23:00:00 +0100 5137858 http://www.medworm.com/index.php?rid=5137857&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F129 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5137857 Mon, 15 Aug 2011 23:00:00 +0100 5137857 http://www.medworm.com/index.php?rid=5137856&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F130 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5137856 Mon, 15 Aug 2011 23:00:00 +0100 5137856 http://www.medworm.com/index.php?rid=5129944&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F126 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5129944 Sun, 14 Aug 2011 23:00:00 +0100 5129944 http://www.medworm.com/index.php?rid=5129943&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F127 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5129943 Sun, 14 Aug 2011 23:00:00 +0100 5129943 http://www.medworm.com/index.php?rid=5124420&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F125 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5124420 Thu, 11 Aug 2011 23:00:00 +0100 5124420 http://www.medworm.com/index.php?rid=5117131&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F124 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5117131 Wed, 10 Aug 2011 23:00:00 +0100 5117131 http://www.medworm.com/index.php?rid=5102770&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F122 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5102770 Thu, 04 Aug 2011 23:00:00 +0100 5102770 http://www.medworm.com/index.php?rid=5085274&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F121 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5085274 Sun, 31 Jul 2011 23:00:00 +0100 5085274 http://www.medworm.com/index.php?rid=5076398&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F119 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5076398 Thu, 28 Jul 2011 23:00:00 +0100 5076398 http://www.medworm.com/index.php?rid=5076397&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F120 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5076397 Thu, 28 Jul 2011 23:00:00 +0100 5076397 http://www.medworm.com/index.php?rid=5076399&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F118 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5076399 Wed, 27 Jul 2011 23:00:00 +0100 5076399 http://www.medworm.com/index.php?rid=5068600&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F117 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5068600 Mon, 25 Jul 2011 23:00:00 +0100 5068600 http://www.medworm.com/index.php?rid=5048328&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F116 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5048328 Wed, 20 Jul 2011 23:00:00 +0100 5048328 http://www.medworm.com/index.php?rid=5048329&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F115 ${item.shortDescription} (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5048329 Mon, 18 Jul 2011 23:00:00 +0100 5048329 http://www.medworm.com/index.php?rid=5035420&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F112 Conclusion: Our model was validated against a number of experimental findings and the observed synergistic effects of low concentrations of thrombin and histamine in mediating the activation of MLC. It can be used to predict the effects of altered pathway components, collective actions of multiple mediators and the potential impact to various diseases. Similar to the published models of other pathways, our model can potentially be used to identify important disease genes through sensitivity analysis of signalling components. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5035420 Thu, 14 Jul 2011 23:00:00 +0100 5035420 http://www.medworm.com/index.php?rid=5035419&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F113 Conclusions: The new exact algorithm reconstructs extended Petri nets from time series data sets by finding all alternative minimal networks that are consistent with the data. It suggested alternative molecular mechanisms for certain reactions in the network. The algorithm is useful to combine data from wild-type and mutant cells and may potentially integrate physiological, biochemical, pharmacological, and genetic data in the form of a single model. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5035419 Thu, 14 Jul 2011 23:00:00 +0100 5035419 http://www.medworm.com/index.php?rid=5035418&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F114 Conclusion: The relapsing dynamic in MS derives from the emergent properties of the immune system operating in a pathological state, a fact that has implications for predicting disease course and developing new therapies for MS. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5035418 Thu, 14 Jul 2011 23:00:00 +0100 5035418 http://www.medworm.com/index.php?rid=5017851&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F110 Conclusion: The advancement of proteomic technologies and increased generation of high-throughput proteomic data have created the need for a means to analyze these data in a coherent manner. Network reconstructions provide a systematic means to integrate and analyze proteomic data in a biologically meaning manner. Analysis of the red cell proteome has revealed an unexpected level of complexity in the functional capabilities of human erythrocyte metabolism. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5017851 Mon, 11 Jul 2011 23:00:00 +0100 5017851 http://www.medworm.com/index.php?rid=5017850&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F111 Conclusions: Here we demonstrate that the negative auto-regulation motif in the native arabinose system of Escherichia coli increases the range of arabinose signals over which the system can respond. In this way, negative auto-regulation may help to increase the input dynamic-range while maintaining the specificity of cooperative regulatory systems. This function may contribute to explaining the common occurrence of negative auto-regulation in biological systems. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5017850 Mon, 11 Jul 2011 23:00:00 +0100 5017850 http://www.medworm.com/index.php?rid=5017852&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F109 Conclusion: A systematic analysis of the results following differential stimulation of this model by growth factors and cytokines suggests that: (a) using Boolean network ensembles with asynchronous updating provides biologically plausible noisy individual cellular responses with reproducible mean behavior for large cell populations, and (b) with sufficient data our model can estimate the response to different concentrations of extracellular ligands. Our results suggest that this approach is both quantitative, allowing statistical verification and calibration, and extensible, allowing modification and revision as guided by experimental evidence. The simulation methodology is part of the US EPA Virtual Liver, which is investigating the effects of everyday contaminants on living tissues. Fut... BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5017852 Sun, 10 Jul 2011 23:00:00 +0100 5017852 http://www.medworm.com/index.php?rid=5006359&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F108 Conclusions: We strongly recommend the use of these two modules either when pluripotent cell types of different origins are involved or when the comparisons made are constrained to the in vivo embryos during early human organogenesis (and an equivalent in vitro differentiation models). Network-based comparative transcriptome analysis will contribute to an increase in knowledge about human embryogenesis, particularly when only transcriptome data are currently available. These advances will add an extra dimension to network applications. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5006359 Tue, 05 Jul 2011 23:00:00 +0100 5006359 http://www.medworm.com/index.php?rid=5006361&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F106 Conclusions: It can be concluded that acetate metabolism is one of the major regulating factors of central carbon metabolism. More importantly, our model calculations with actual biomass composition and detailed carbon balance analysis in steady state conditions with -omics data comparison demonstrate the importance of a comprehensive systems biology approach for more advanced understanding of metabolism and carbon re-routing mechanisms potentially leading to more successful metabolic engineering. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5006361 Mon, 04 Jul 2011 23:00:00 +0100 5006361 http://www.medworm.com/index.php?rid=5006360&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F107 Conclusions: We developed a method for constructing extended pathways that start at the receptor level and via a complex intracellular signalling pathway identify those mechanisms that drive cellular behaviour. Our results constitute a proof-of-principle for construction of "extended pathways" that are capable of linking pathway activity to diverse responses such as growth, death, differentiation, gene expression, or cytokine secretion. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5006360 Mon, 04 Jul 2011 23:00:00 +0100 5006360 http://www.medworm.com/index.php?rid=4991793&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F105 Conclusions: To the best of our knowledge, this lung-focused Cell Proliferation Network provides the most comprehensive connectivity map in existence of the molecular mechanisms regulating cell proliferation in the lung. The network is based on fully referenced causal relationships obtained from extensive evaluation of the literature. The computable structure of the network enables its application to the qualitative and quantitative evaluation of cell proliferation using systems biology data sets. The network is available for public use. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4991793 Fri, 01 Jul 2011 23:00:00 +0100 4991793 http://www.medworm.com/index.php?rid=4983307&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F102 Conclusion: The results of simulations using the new model corresponded closely with phenotypic data under normal conditions and provided insight into the complicated and unintuitive phenotypes of the three disorders, including the effect of interventions that may be of therapeutic benefit, such as low glucose diets or amino acid supplements. The model offers the ability to investigate other mitochondrial disorders and can provide the framework for the integration of experimental data in future studies. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4983307 Tue, 28 Jun 2011 23:00:00 +0100 4983307 http://www.medworm.com/index.php?rid=4983306&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F103 Conclusions: We have developed and analyzed a common systems platform for examining the effects of coupling of processes through shared components. This can be the basis for subsequent expansion and understanding the many biologically observed variations on this common theme. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4983306 Tue, 28 Jun 2011 23:00:00 +0100 4983306 http://www.medworm.com/index.php?rid=4983305&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F104 Conclusions: Concluding, our models show that the control of transposon activity can be achieved by alternative pathways that lack RdRP and act through different feedback mechanisms. Thus, although RdRP activity is ubiquitous in eukaryotes, it need not be a general requirement for transposon control. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4983305 Tue, 28 Jun 2011 23:00:00 +0100 4983305 http://www.medworm.com/index.php?rid=4974678&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F100 Conclusions: Integrating multi-omic datasets from Salmonella mutants lacking virulence regulators not only identified novel virulence factors but also defined a new class of translocated effectors involved in pathogenesis. The success of this strategy at discovery of known and novel virulence factors suggests that the approach may have applicability for other bacterial pathogens. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4974678 Mon, 27 Jun 2011 23:00:00 +0100 4974678 http://www.medworm.com/index.php?rid=4974677&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F101 Conclusions: The genome-scale metabolic model, RehMBEL1391, successfully represented metabolic characteristics of R. eutropha H16 at systems level. The reconstructed genome-scale metabolic model can be employed as an useful tool for understanding its metabolic capabilities, predicting its physiological consequences in response to various environmental and genetic changes, and developing strategies for systems metabolic engineering to improve its metabolic performance. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4974677 Mon, 27 Jun 2011 23:00:00 +0100 4974677 http://www.medworm.com/index.php?rid=4967608&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F99 Conclusions: This study provides a novel method to identify active oncomirs and their potential functions in gastric cancer progression. The present data suggest that miR-148a could be a potential prognostic biomarker of gastric cancer and function as a tumor suppressor through repressing the activity of its regulated PIN. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4967608 Sat, 25 Jun 2011 23:00:00 +0100 4967608 http://www.medworm.com/index.php?rid=4967610&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F97 Conclusions: Modelling in systems biology often builds on the study of time-dependent phenomena. Fourier Transforms are a convenient tool for analysing the frequency domain of time series. However, there are well-known limitations of this method, such as the introduction of spurious frequencies when handling short and noisy time series, and the requirement for uniformly sampled data. Biological time series often deviate significantly from the requirements of optimality for Fourier transformation. In this paper we present an alternative approach based on Bayesian inference. We show the value of placing spectral analysis in the framework of Bayesian inference and demonstrate how model comparison can automate this procedure. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4967610 Thu, 23 Jun 2011 23:00:00 +0100 4967610 http://www.medworm.com/index.php?rid=4967609&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F98 Conclusions: This result implies the expansion of metabolic networks due to this chaperonin, and it supports the existing hypothesis of acceleration of evolution by chaperonins. The distribution of chaperonin substrate enzymes in the metabolic network is inexplicable because it does not seem to be associated with individual protein features such as protein abundance, which has been observed characteristically in chaperonin substrates in previous works. However, it becomes clear by considering this expansion process due to chaperonin. This finding provides new insights into metabolic evolution and the roles of chaperonins in living systems. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4967609 Thu, 23 Jun 2011 23:00:00 +0100 4967609 http://www.medworm.com/index.php?rid=4951359&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F95 Conclusion: This consistency between EFM analysis and experimental flux measurements, validated on two metabolic systems allows us to conclude that elementary flux mode analysis could be a useful tool to complement 13C metabolic flux analysis, by allowing the prediction of changes in internal fluxes before carbon labelling experiments. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4951359 Sun, 19 Jun 2011 23:00:00 +0100 4951359 http://www.medworm.com/index.php?rid=4944248&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F94 Conclusions: We find that in the reference steady state, starch cleavage is the most significant determinant of carbon flux, with turnover of oligosaccharides playing a secondary role. Independence of stationary point with respect to initial dynamic variable values confirms a unique stationary point in the phase space of dynamically varying concentrations of the model network. Stromal maltooligosaccharide metabolism was highly coupled to the available starch concentration. From the most highly converged trajectories, distances between unique fixed points of phase spaces show that cytosolic maltose levels depend on the total concentrations of arabinogalactan and glucose present in the cytosol. In addition, cellular compartmentalization serves to dampen much, but not all, of the effects of o... BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4944248 Fri, 17 Jun 2011 23:00:00 +0100 4944248 http://www.medworm.com/index.php?rid=4932313&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F93 Conclusions: Herpesvirus miRNAs preferentially target hubs and bottlenecks. There are significant differences between common and specific targets. Moreover, common targets are more intensely connected and occupy the central part of the network. These results will help unravel the complex mechanism of herpesvirus-host interactions and may provide insight into the development of novel anti-herpesvirus drugs. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4932313 Sun, 12 Jun 2011 23:00:00 +0100 4932313 http://www.medworm.com/index.php?rid=4901301&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F92 Conclusion: Our results support the feasibility of cellular function reconstruction guided by the analysis and manipulation of dynamic envirome data. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4901301 Sun, 05 Jun 2011 23:00:00 +0100 4901301 http://www.medworm.com/index.php?rid=4901302&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F91 Conclusions: Our method can achieve computational time improvements exceeding 2000-fold and requires only several seconds to generate elementary mode decompositions on genome-scale networks. These improvements arise from not having to generate all relevant elementary modes prior to initiating the decomposition. The decompositions from our method are useful for understanding complex flux distributions and debugging genome-scale models. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4901302 Thu, 02 Jun 2011 23:00:00 +0100 4901302 http://www.medworm.com/index.php?rid=4891612&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F90 Conclusions: HC-PLSR is a promising approach for metamodelling in systems biology, especially for highly nonlinear or non-monotone parameter to phenotype maps. The algorithm can be flexibly adjusted to suit the complexity of the dynamic model behaviour, inviting automation in the metamodelling of complex systems. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4891612 Tue, 31 May 2011 23:00:00 +0100 4891612 http://www.medworm.com/index.php?rid=4882737&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F89 Conclusions: Our results suggest that GGM can be used to formally evaluate differences in global interactome connectivity across disease states, and can serve as a powerful tool for exploring the molecular events that contribute to disease at a systems level. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4882737 Mon, 30 May 2011 23:00:00 +0100 4882737 http://www.medworm.com/index.php?rid=4882738&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F88 Conclusions: This approach can facilitate development of systems biology and optimal drug combination therapies for cancer and other diseases and for understanding key interactions within the cellular network upon treatment with multiple signals. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4882738 Sun, 29 May 2011 23:00:00 +0100 4882738 http://www.medworm.com/index.php?rid=4882739&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F87 Conclusions: Our results suggest that molecular-level responses to diverse chemical and genetic perturbations are heavily interconnected in a modular fashion. Also, shared molecular pathways can be identified by comparing newly defined gene expression signatures with databases of previously published gene expression signatures. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4882739 Sat, 28 May 2011 23:00:00 +0100 4882739 http://www.medworm.com/index.php?rid=4870717&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F84 Conclusions: We show that systems mapping implemented by design principles of biological systems is quite versatile for deciphering the genetic machineries for size-shape, structural-functional, sink-source and pleiotropic relationships underlying plant physiology and development. Systems mapping should enable geneticists to shed light on the genetic complexity of any biological system in plants and other organisms and predict its physiological and pathological states. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4870717 Thu, 26 May 2011 23:00:00 +0100 4870717 http://www.medworm.com/index.php?rid=4870716&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F85 Conclusions: This quantitative map of the epigenetic landscape underlying cell fate choice provides mechanistic insights into the "forces" that direct cellular differentiation in the context of physiological development, as well as during artificially induced cell lineage reprogramming. Our generalized approach to mapping the landscape is applicable to non-gradient gene regulatory systems for which an analytical potential function cannot be derived, and also to high-dimensional gene networks. Rigorous quantification of the gene regulatory circuits that govern cell lineage choice and subsequent mapping of the epigenetic landscape can potentially help identify optimal routes of cell fate reprogramming. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4870716 Thu, 26 May 2011 23:00:00 +0100 4870716 http://www.medworm.com/index.php?rid=4870715&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F86 Conclusion: POBN provides a systematic way to integrate known transcriptional networks with observed gene expression data to better identify which transcriptional pathways are likely responsible for the observed gene expression pattern. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4870715 Thu, 26 May 2011 23:00:00 +0100 4870715 http://www.medworm.com/index.php?rid=4861250&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F83 Conclusions: As the first genome-scale metabolic network of B. cenocepacia J2315, iKF1028 allows a systematic study of the metabolic properties of B. cenocepacia and its key metabolic virulence factors affecting the CF community. The model can be used as a discovery tool to design novel drugs against diseases caused by this notorious pathogen. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4861250 Tue, 24 May 2011 23:00:00 +0100 4861250 http://www.medworm.com/index.php?rid=4861253&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F80 Conclusion: Overall, our data support a modular model of yeast cell protein network organization and show how prediction methods can considerably extend the information that can be extracted from overlapping E-MAP screens. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4861253 Sun, 22 May 2011 23:00:00 +0100 4861253 http://www.medworm.com/index.php?rid=4861252&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F81 Conclusions: We were able to find symbolic solutions for the steady state flux distribution of large metabolic networks. The ability to choose a flux basis was found to be useful in the constraint process and provides a strong argument for using symbolic Gauss-Jordan elimination in place of singular value decomposition. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4861252 Sun, 22 May 2011 23:00:00 +0100 4861252 http://www.medworm.com/index.php?rid=4861251&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F82 Conclusion: In this work, we carried out a microarray-based temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization using GAGE method. This novel temporal analysis is more informative and powerful than the classical static pathway analysis in that: (1) it captures the interconnections between signaling pathways or functional modules and demonstrates the even higher level organization of molecular biological systems; (2) it describes the temporal perturbation patterns of each pathway or module and their dynamic roles in osteoblast differentiation. The same set of experimental and computational strategies employed in our work could be useful for studying other complex biological processes. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4861251 Sun, 22 May 2011 23:00:00 +0100 4861251 http://www.medworm.com/index.php?rid=4847249&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F79 Conclusions: The phenotype-gene heterogeneous network contains abundant information for not only disease genes discovery but also disease subtypes detection. The CIPHER-HIT method presented here is effective for network inference, particularly on credible prediction of disease genes and the subtype analysis of diseases, for example Breast cancer. This method provides a promising way to analyze heterogeneous biological networks, both globally and locally. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4847249 Thu, 19 May 2011 23:00:00 +0100 4847249 http://www.medworm.com/index.php?rid=4839736&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F75 Conclusion: A useful tool to describe, understand and predict metabolite production in batch yeast cultures was developed. The resulting model, if used wisely, could help to search for new metabolic engineering strategies to manage ethanol content in batch fermentations. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4839736 Wed, 18 May 2011 23:00:00 +0100 4839736 http://www.medworm.com/index.php?rid=4839735&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F76 Conclusions: We foresee a wide range of potential applications at different sub-cellular or supra-cellular levels of biological interactions given the natural bipartivity of many biological networks. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4839735 Wed, 18 May 2011 23:00:00 +0100 4839735 http://www.medworm.com/index.php?rid=4839734&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F77 Conclusions: This analysis provides compelling evidence to suggest that coordinated transcriptional regulation of isoprenoid-related biosynthesis pathway genes plays a major role in coordinating the synthesis of functionally related chloroplast localized isoprenoid-derived compounds. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4839734 Wed, 18 May 2011 23:00:00 +0100 4839734 http://www.medworm.com/index.php?rid=4839733&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F78 Conclusion: Our model reveals how animals will alter their energy budget when food availability is low, and offers better understanding of the tradeoffs between growth and somatic maintenance; therefore shedding new light on aging research from an energetic viewpoint. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4839733 Wed, 18 May 2011 23:00:00 +0100 4839733 http://www.medworm.com/index.php?rid=4839738&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F73 Conclusion: The identification of domain genetic interactions helps the understanding of originality of functional relationship in SLGIs at domain level. Our study significantly improved the understanding of yeast mulitdomain proteins, the synthetic lethal genetic interactions and the functional relationships between proteins and pathways. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4839738 Mon, 16 May 2011 23:00:00 +0100 4839738 http://www.medworm.com/index.php?rid=4839737&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F74 Conclusions: The impact of our results is twofold: on the one hand, we highlight that classical and simple control theory methods are extremely useful to characterize the behavior of biological networks analytically. On the other hand, we are able to demonstrate that some biological networks are robust thanks to their structure and some qualitative properties of the interactions, regardless of the specific values of their parameters. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4839737 Mon, 16 May 2011 23:00:00 +0100 4839737 http://www.medworm.com/index.php?rid=4827625&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F72 We present and justify a new technique for comparing pairs of networks - in our case these networks are based on the same set of nodes and there are two distinct types of weighted edges. The algorithm is based on the Generalized Singular Value Decomposition (GSVD), which may be regarded as an extension of Principle Components Analysis to the case of two data sets. We show how the GSVD can be interpreted as a technique for reordering the two networks in order to reveal clusters that are exclusive to only one. Here we apply this algorithm to a new set of metabolomic data from the prefrontal cortex (PFC) of a translational model relevant to schizophrenia, rats treated subchronically with the N-methyl-D-Aspartic acid (NMDA) receptor antagonist phencyclidine (PCP). This provides us with a means... BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4827625 Sun, 15 May 2011 23:00:00 +0100 4827625 http://www.medworm.com/index.php?rid=4827626&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F71 Conclusions: Molecule distributions, reaction rate constants and structural parameters can be adjusted separately in the simulation allowing a comprehensive study of individual effects in the context of a realistic cell environment. As such, the present simulation can help to bridge the gap between in vivo and in vitro kinetics. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4827626 Fri, 13 May 2011 23:00:00 +0100 4827626 http://www.medworm.com/index.php?rid=4819684&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F70 Conclusions: The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4819684 Thu, 12 May 2011 23:00:00 +0100 4819684 http://www.medworm.com/index.php?rid=4819686&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F68 Conclusions: This work demonstrates a powerful integrative approach to study drug resistance and mode of action. Our findings are informative to the development of novel therapeutic strategies against Staphylococcus aureus and particularly MRSA. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4819686 Wed, 11 May 2011 23:00:00 +0100 4819686 http://www.medworm.com/index.php?rid=4819685&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F69 Conclusions: We have developed the first mechanistic model of the Psp response in E. coli. This model allows us to predict the possible qualitative stochastic and deterministic dynamic behaviours of key molecular players in the stress response. Our inferential approach can be applied to stress response and signalling systems more generally: in the ABC framework we can condition mathematical models on qualitative data in order to delimit e.g. parameter ranges or the qualitative system dynamics in light of available end-point or qualitative information. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4819685 Wed, 11 May 2011 23:00:00 +0100 4819685 http://www.medworm.com/index.php?rid=4801620&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F67 Background: Estrogens regulate diverse physiological processes in various tissues through genomic and non-genomic mechanisms that result in activation or repression of gene expression. Transcription regulation upon estrogen stimulation is a critical biological process underlying the onset and progress of the majority of breast cancer. Dynamic gene expression changes have been shown to characterize the breast cancer cell response to estrogens, the every molecular mechanism of which is still not well understood. Results: We developed a modulated empirical Bayes model, and constructed a novel topological and temporal transcription factor (TF) regulatory network in MCF7 breast cancer cell line upon stimulation by 17beta-estradiol stimulation. In the network, significant TF genomic hubs were id... BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4801620 Sun, 08 May 2011 23:00:00 +0100 4801620 http://www.medworm.com/index.php?rid=4794215&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F64 Conclusions: TCMC is a simple and flexible method for obtaining physically plausible values for the kinetic parameters of open biochemical reaction systems. It can be effectively used to recalculate a thermodynamically consistent set of parameter values for existing thermodynamically infeasible biochemical reaction models of cellular function as well as to estimate thermodynamically feasible values for the parameters of new models. Furthermore, TCMC can provide dimensionality reduction, better estimation performance, and lower computational complexity, and can help to alleviate the problem of data overfitting. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4794215 Thu, 05 May 2011 23:00:00 +0100 4794215 http://www.medworm.com/index.php?rid=4788154&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F60 Conclusions: In conclusion, our results demonstrated that the balance between ECM synthesis and degradation, controlled by interactions of specific key factors, determines the LV remodeling outcomes. Our mathematical model, based on the balance between ECM construction and destruction, provides a useful tool for studying the regulatory mechanisms and for predicting LV remodeling outcomes. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4788154 Wed, 04 May 2011 23:00:00 +0100 4788154 http://www.medworm.com/index.php?rid=4788153&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F61 Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4788153 Wed, 04 May 2011 23:00:00 +0100 4788153 http://www.medworm.com/index.php?rid=4788152&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F62 Conclusions: We suggest that these observations can be best understood as resulting from the higher fitness cost of misexpression in epistatic genes and a commensurate greater regulatory control of them. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4788152 Wed, 04 May 2011 23:00:00 +0100 4788152 http://www.medworm.com/index.php?rid=4774780&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F59 Conclusions: Isoform-specific VEGF degradation provides a possible explanation for numerous examples of isoform specificity in VEGF patterning and examples of proteases relocation of VEGF upon release. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4774780 Sun, 01 May 2011 23:00:00 +0100 4774780 http://www.medworm.com/index.php?rid=4762223&cid=s_34051_67_f&fid=34051&url=http%3A%2F%2Fwww.biomedcentral.com%2F1752-0509%2F5%2F58 Conclusions: This study provides the first look at transcription factor networks in corals. We identified a transcription factor repertoire encoded by the coral genome and found consistencies of the domain architectures of transcription factors and conserved regulatory subnetworks across eumetazoan species, providing insight into how regulatory networks have evolved. (Source: BMC Systems Biology - Latest articles) BMC Systems Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4762223 Wed, 27 Apr 2011 23:00:00 +0100 4762223