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DASMiner: discovering and integrating data from DAS sourcesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The support of the DAS protocol allows that hundreds of molecular biology databases to be treated as a federated, online collection of resources. DASMiner enables full exploration of these resources, and can be used to deploy applications and create integrated views of biological systems using the information deposited in DAS repositories. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - November 17, 2009 Category: Molecular Biology Authors: Diogo VeigaHelena DeusCaner AkdemirAna Tereza VasconcelosJonas Almeida Source Type: journals

Network analysis of the transcriptional pattern of young and old cells of Escherichia coli during lag phaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Network analysis revealed very different transcriptional activities during the lag period in old and young cells. Rejuvenation seems to take place during exponential growth by replicative dilution of old cellular components. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - November 16, 2009 Category: Molecular Biology Authors: Carmen PinMatthew RolfeMarina Munoz-CuevasJay HintonMichael PeckNicholas WaltonJozsef Baranyi Source Type: journals

Long-term prediction of fish growth under varying ambient temperatures using a multiscale dynamic modelEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We demonstrate that, despite thedifficulties involved, multiscale models in biology can yieldreasonable and useful results. The model predictions are reliableover several timescales and in the presence of strong temperaturefluctuations, which are crucial factors for modeling marine organismgrowth. The model provides important improvements over existingmodels. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - November 10, 2009 Category: Molecular Biology Authors: Nadav BarNicole Radde Source Type: journals

Using the ratio of means as the effect size measure in combining results of microarray experimentsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results show that the proposed effect size measure (log ratio of means) has better power to identify differentially expressed genes, and that the detected genes have better performance in predicting cancer outcomes than the commonly used effect size measure, the standardized mean difference (SMD), under both quality-weighted and quality-unweighted data integration frameworks. The new effect size measure and the quality-weighted microarray data integration framework provide efficient ways to combine microarray results. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - November 5, 2009 Category: Molecular Biology Authors: Pingzhao HuCelia GreenwoodJoseph Beyene Source Type: journals

Inferring branching pathways in genome-scale metabolic networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: ReTrace is a useful method in metabolic path finding tasks, combining some of the best aspects in constraint-based and graph-theoretic methods. It finds use in a multitude of tasks ranging from metabolic engineering to metabolic reconstruction of recently sequenced organisms. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - October 29, 2009 Category: Molecular Biology Authors: Esa PitkanenPaula JouhtenJuho Rousu Source Type: journals

13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucoseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: High similarity between the biosynthetic pathways of amino acids in T. reesei and yeast S. cerevisiae was concluded. In vivo flux distributions confirmed that T. reesei uses primarily the respirative pathway also when growing on the repressive carbon source glucose in contrast to Saccharomyces cerevisiae, which substantially diminishes the respirative pathway flux under glucose repression. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - October 29, 2009 Category: Molecular Biology Authors: Paula JouhtenEsa PitkanenTiina PakulaMarkku SaloheimoMerja PenttilaHannu Maaheimo Source Type: journals

How to identify essential genes from molecular networks?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The method reported here describes a reliable procedure to predict essential genes from molecular networks. Our results show that essential genes may be predicted only by combining centrality measures, revealing the complex nature of the function of essential genes. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - October 12, 2009 Category: Molecular Biology Authors: Gabriel del RioDirk KoschutzkiGerardo Coello Source Type: journals

Investigating the robustness of the classical enzyme kinetic equations in small intracellular compartmentsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The derived mesoscopic rate equations describe subcellular enzyme reaction kinetics, taking into account, for the first time, the simultaneous influence of both intrinsic noise and the mode of transport. They clearly show the range of applicability of the conventional deterministic equation models, namely intracellular conditions compatible with diffusive transport and simple enzyme mechanisms in several hundred nanometre-sized compartments. An active transport mechanism coupled with large intrinsic noise in enzyme concentrations is shown to lead to huge deviations from the predictions of deterministic models....
Source: BMC Systems Biology - Latest articles - October 7, 2009 Category: Molecular Biology Authors: Ramon Grima Source Type: journals

Computational modelling of cancerous mutations in the EGFR/ERK signalling pathwayEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results suggest that different routes to ERK activation are being utilised in different cancerous situations which therefore has interesting implications for drug selection strategies. We also conducted a comparison of the critical differences between signalling from different growth factor receptors (namely EGFR, mutated EGFR, NGF, and Insulin) with our results suggesting the difference between the systems are large scale and can be attributed to the presence/absence of entire pathways rather than subtle difference in individual rate constants between the systems. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - October 4, 2009 Category: Molecular Biology Authors: Richard OrtonMichiel AdriaensAmelie GormandOliver SturmWalter KolchDavid Gilbert Source Type: journals

Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infectionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: A network model for apoptosis and crosstalk in hepatocytes shows four different system states and reproduces a number of different conditions around apoptosis including effects of different growth substrates and viral infections. It produces semi-quantitative predictions on the activity of individual nodes, agreeing with experimental data. The model (SBML format) and all data are available for further predictions and development (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - September 21, 2009 Category: Molecular Biology Authors: Nicole PhilippiDorothee WalterRebekka SchlatterKarine FerreiraMichael EdererOliver SawodnyJens TimmerChristoph BornerThomas Dandekar Source Type: journals

A method for determining the robustness of bio-molecular oscillator modelsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The method here proposed for quantifying the robustness of biochemical oscillator models is computationally less demanding than similar multiparamter variation techniques available in the literature. It also provides tighter bounds on two models previously analyzed in the literature. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - September 20, 2009 Category: Molecular Biology Authors: Reza GhaemiJing SunPablo IglesiasDomitilla Del Vecchio Source Type: journals

Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Parameter sensitivity analysis allows one to discriminate between circuits having significant parameter and qualitative differences but exhibiting the same quantitative pattern. Furthermore, we show that using a stochastic model derived from a deterministic solution, one can introduce fluctuations within the model to analyze the circuits' robustness. Ultimately, we show that there is a close relation between circuit sensitivity and robustness to fluctuation, and that circuit robustness is rather modular than global. The current study shows that reverse engineering of GRNs should not only focus on estimating pa...
Source: BMC Systems Biology - Latest articles - September 20, 2009 Category: Molecular Biology Authors: Yves Fomekong-NanfackMarten PostmaJaap Kaandorp Source Type: journals

A Method for determining the dobustness of bio-molecular oscillator modelsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The method here proposed for quantifying the robustness of biochemical oscillator models is computationally less demanding than similar multiparamter variation techniques available in the literature. It also provides tighter bounds on two models previously analyzed in the literature. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - September 20, 2009 Category: Molecular Biology Authors: Reza GhaemiJing SunPablo IglesiasDomitilla Del Vecchio Source Type: journals

A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The predicted results quantitatively reproduced the experimentally measured dose-response curves, ranging over three orders of magnitude in inhibitor concentration. Thus, by allowing for detailed specifications of the underlying enzymatic kinetics, metabolic reactions/constraints, and growth media, our model captured the essential chemical and biological factors that determine the effects of drug inhibition on in vitro growth of M. tuberculosis cells. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - September 14, 2009 Category: Molecular Biology Authors: Xin FangAnders WallqvistJaques Reifman Source Type: journals

Metabolism as means for hypoxia adaptation: metabolic profiling and flux balance analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We suggest a network-level hypothesis of metabolic regulation in hypoxia-adapted flies, in which lower baseline rates of biosynthesis in adapted flies draws less anaplerotic flux, resulting in lower rates of glycolysis, less acidosis, and more efficient use of substrate during acute hypoxic stress. In addition we suggest new specific hypothesis, which were found to be consistent with existing data. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - September 8, 2009 Category: Molecular Biology Authors: Jacob FealaLaurence CoquinDan ZhouGabriel HaddadGiovanni PaternostroAndrew McCulloch Source Type: journals

The smallest chemical reaction system with bistabilityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The presented minimal bistable system finally clarifies the often discussed question for the necessary conditions for bistability. The three necessary conditions are: positive feedback, a mechanism to filter out small stimuli and a mechanism to prevent explosions. This is important for modelling bistability with simple systems and for synthetically designing new bistable systems. Our simple model system is also well suited for corresponding teaching purposes. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - September 7, 2009 Category: Molecular Biology Authors: Thomas Wilhelm Source Type: journals

Hybrid stochastic simplifications for multiscale gene networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Hybrid simplifications can be used for onion-like (multilayered) approaches to multi-scale biochemical systems, in which various descriptions are used at various scales. Sets of discrete and continuous variables are treated with different methods and are coupled together in a physically justified approach. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - September 6, 2009 Category: Molecular Biology Authors: Alina CruduArnaud DebusscheOvidiu Radulescu Source Type: journals

The genotype-phenotype relationship in multicellular pattern-generating models - the neglected role of pattern descriptorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The results suggest that our approach may qualify as a general procedure for how to relate relevant features and characteristics of emergent patterns to the functional relationships, parameter values and initial values of an underlying pattern-generating mathematical model. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - September 3, 2009 Category: Molecular Biology Authors: Harald MartensSiren VeflingstadErik PlahteMagni MartensDominique BertrandStig Omholt Source Type: journals

The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The simple model implemented in this paper provides a valuable first step in modeling signaling networks. However, to obtain a fully predictive model, a more detailed knowledge regarding parameters of individual interactions might be necessary. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - September 3, 2009 Category: Molecular Biology Authors: Rafal ZielinskiPawel PrzytyckiJie ZhengDavid ZhangTeresa PrzytyckaJacek Capala Source Type: journals

Monte-Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm NetworkEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The method described in this paper enables an evaluation of network topologies of GRNs withoutrequiring any parameter values. The benefit of this method is exemplified in the first mathematical analysis ofthe complete Endomesoderm Network Model. The predictions we provide deliver candidate nodes in the networkthat are likely to be erroneous or miss unknown connections, which may need additional experiments to improvethe network topology. This mathematical model can serve as a scaffold for detailed and more realistic models.We propose that our method can be used to assess a completeness grade of any GRN. This c...
Source: BMC Systems Biology - Latest articles - August 22, 2009 Category: Molecular Biology Authors: Clemens KuhnChristoph WierlingAlexander KuhnEdda KlippGeorgia PanopoulouHans LehrachAlbert Poustka Source Type: journals

Visualizing Post Genomics Data-sets on customized Pathway Maps by ProMeTra - aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We demonstrate the functionality of ProMeTra with quantitative metabolomics and trasncriptomics data obtained from a fermentation experiment of the L-lysine producing strain Corynebacterium glutamicum DM1730. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - August 22, 2009 Category: Molecular Biology Authors: Heiko NeuwegerMarcus PersickeStefan AlbaumThomas BekelMichael DondrupAndrea HuserJorn WinnebaldJessica SchneiderJorn KalinowskiAlexander Goesmann Source Type: journals

Optimal drug combinations and minimal hitting setsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The drug-response graph and the associated minimal hitting set method can be use to uncover effective drug combinations in anticancer drug screens and drug development programs targeting heterogeneous populations of infectious agents such as HIV. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - August 5, 2009 Category: Molecular Biology Authors: Alexei Vazquez Source Type: journals

Knowledge based identification of essential signaling from genome-scale siRNA experimentsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: PIPA provides an analytical framework to interpret siRNA screen data by merging biologically annotated gene sets with the human interactome. As a result we identify pathways and signaling hypotheses that are statistically enriched to effect cell growth in human cell lines. This method provides a complementary approach to standard gene set enrichment that utilizes the additional knowledge of specific interactions within biological gene sets. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - August 4, 2009 Category: Molecular Biology Authors: Armand BankheadIliana SachChester NiNolwenn LeMeurMark KrugerMarc FerrerRobert GentlemanCarol Rohl Source Type: journals

A possibilistic framework for constraint-based metabolic flux analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We introduce a possibilistic framework for the estimation of metabolic fluxes, which is shown to be flexible, reliable, usable in scenarios lacking data and computationally efficient. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - July 30, 2009 Category: Molecular Biology Authors: Francisco LlanerasAntonio SalaJesus Pico Source Type: journals

A dynamic network of transcription in LPS-treated human subjectsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Using NCA, we were able to build a network that accounted for between 8-11% genes in the known transcriptional response to LPS in humans. The dynamic network illustrated changes of transcription factor activities and gene expressions as well as interactions of signaling proteins, transcription factors and target genes. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - July 27, 2009 Category: Molecular Biology Authors: Junhee SeokWenzhong XiaoLyle MoldawerRonald DavisMarkus Covert Source Type: journals

Adapted Boolean network models for extracellular matrix formationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The newly developed method successfully and iteratively integrated expert knowledge at different steps, resulting in a promising solution for the in-depth understanding of regulatory pathways in disease dynamics. The knowledge base containing all the temporal rules may be queried to predict the functional consequences of observed or hypothetical gene expression disturbances. Furthermore, new hypotheses about gene relations were derived which await further experimental validation. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - July 20, 2009 Category: Molecular Biology Authors: Johannes WollboldRene HuberDirk PohlersDirk KoczanReinhard GuthkeRaimund KinneUlrike Gausmann Source Type: journals

Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Aside from the results obtained for the cell cycle of yeast our approach could be exemplary for the analysis of general pathways by exploiting the rich causal structure of inferred and/or curated gene networks including protein or signaling networks. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - July 19, 2009 Category: Molecular Biology Authors: Frank Emmert-StreibMatthias Dehmer Source Type: journals

An Integrative ChIP-chip and Gene Expression Profiling to Model SMAD Regulatory ModulesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Together, the computational results further the understanding of the interactions between SMAD and other transcription factors at specific target promoters, and provide the basis for more targeted experimental verification of the co-regulatory modules. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - July 16, 2009 Category: Molecular Biology Authors: Huaxia QinMichael ChanSandya LiyanarachchiCurtis BalchDustin PotterIrene SourirajAlfred ChengFrancisco Agosto-PerezElena NikonovaPearlly YanHuey-Jen LinKenneth NephewJoel SaltzLouise ShoweTim HuangRamana Davuluri Source Type: journals

Cascading signaling pathways improve the fidelity of a stochastically and deterministically simulated molecular RS latchEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Thus, the common biological theme of cascading signaling pathways is advantageous for maintaining the fidelity of a memory latch in the presence of crosstalk. The experimental implementation of such a latch system will lead to novel approaches to cell control using synthetic proteins and contribute to our understanding of why cells behave differently even when given the same stimulus. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - July 16, 2009 Category: Molecular Biology Authors: Evan MillsKevin Truong Source Type: journals

Mechanism of PP2A-mediated IKKbeta dephosphorylation: a systems biological approachEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The model developed here can be used as a reliable building block of larger NFkappaB models and offers comprehensive simplification potential for future modeling of NFkappaB signaling. It gives more insight into the newly discovered mechanisms for IKK deactivation and allows for substantiated predictions and investigation of different hypotheses.The evidence of constitutive activity of PP2Ac at the IKK complex provides new insights into the feedback regulation of NFkappaB, which is crucial for the development of new anti-cancer strategies. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - July 15, 2009 Category: Molecular Biology Authors: Johannes WittSandra BarisicEva SchumannFrank AllgowerOliver SawodnyThomas SauterDagmar Kulms Source Type: journals

Deterministic mathematical models of the cAMP Pathway in Saccharomyces cerevisiaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We suggest that the lower number of reactions and parameters makes these models suitable for integrating them with models of metabolism or of the cell cycle in S. cerevisiae. Similar models could be also useful for studies in the human pathogen Candida albicans as well as other less well-characterized fungal species. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - July 15, 2009 Category: Molecular Biology Authors: Thomas WilliamsonJean-Marc SchwartzDouglas KellLubomira Stateva Source Type: journals

Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cellEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The structures of the yeast cell deduced from GO and interactome are substantially congruent. However, some significant differences were also detected, which may contribute to a better understanding of cell function and also to a refinement of the current ontologies. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - July 14, 2009 Category: Molecular Biology Authors: Antonio MarcoIgnacio Marin Source Type: journals

Computing phenomenologic Adair-Klotz constants from microscopic MWC parametersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The validation of computational models requires methods to relate model parameters to experimentally observable quantities. We provide such a method for comparing generalised MWC allosteric models to experimentally determined Adair-Klotz constants. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - July 13, 2009 Category: Molecular Biology Authors: Melanie StefanStuart EdelsteinNicolas Le Novere Source Type: journals

A systematic design method for robust synthetic biology to satisfy design specificationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Based on four design specifications, a systematic design procedure is developed for designers to engineer a robust synthetic biology network that can achieve its desired steady state behavior under parameter fluctuations, external disturbances and functional variations in the host cell. Therefore, the proposed systematic design method has good potential for the robust synthetic gene network design. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - June 29, 2009 Category: Molecular Biology Authors: Bor-Sen ChenChih-Hung Wu Source Type: journals

BowTieBuilder: modeling signal transduction pathwaysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We show that BowTieBuilder, given multiple source and/or target proteins, infers pathways with satisfactory recall and precision rates and detects the core proteins of each pathway. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - June 29, 2009 Category: Molecular Biology Authors: Jochen SupperLucia SpangenbergHannes PlanatscherAndreas DraegerAdrian SchroederAndreas Zell Source Type: journals

Clustered microRNAs' coordination in regulating protein-protein interaction networkEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: In summary, this work supports the hypothesis of intra-cluster coordination and investigates the extent of this coordination. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - June 25, 2009 Category: Molecular Biology Authors: Xiongying YuanChangning LiuPengcheng YangShunmin HeQi LiaoShuli KangYi Zhao Source Type: journals

Stochastic simulation and analysis of biomolecular reaction networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The two main factors affecting the analysis of stochastic simulations are: (1) the selection of time intervals to compute or average state variables and (2) the number of simulations generated to evaluate the system behavior. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - June 16, 2009 Category: Molecular Biology Authors: John FrazierYaroslav ChushakBrent Foy Source Type: journals

Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strainsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results indicate that serial evolutionary networks of HIV sequences enable systematic statistical analysis of the implicit relations embedded in the topology of the structure and can greatly facilitate identification of patterns of evolution that can lead to specific hypotheses and new insights. The conclusions of applying our method to empirical HIV data support the conventional wisdom of the new generation HIV treatments, that in order to keep the virus in check, viral loads need to be suppressed to almost undetectable levels (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - June 15, 2009 Category: Molecular Biology Authors: Patricia BuendiaGiri Narasimhan Source Type: journals

The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium melilotiEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our 'systems-based model' represents a novel framework for studying host-microbe interactions, provides a theoretical basis for further experimental validations, and can also be applied to the study of other complex processes such as diseases. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - June 15, 2009 Category: Molecular Biology Authors: Ignacio Rodriguez-LlorenteMiguel CaviedesMohammed DaryAntonio PalomaresFrancisco CanovasJose Peregrin-Alvarez Source Type: journals

Intervention in gene regulatory networks via greedy control policies based on long-run behaviorEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The newly proposed control policies have better performance in general than the MFPT policy and, as indicated by the results on the mammalian cell cycle network, they can potentially serve as future gene therapeutic intervention strategies. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - June 14, 2009 Category: Molecular Biology Authors: Xiaoning QianIvan IvanovNoushin GhaffariEdward Dougherty Source Type: journals

The mathematics of tanningEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Despite the paucity of experimental validation data the model is constrained enough to serve as a foundation for the establishment of a theoretical-experimental research programme aimed at elucidating the more fine-grained regulatory anatomy underlying the tanning response. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - June 9, 2009 Category: Molecular Biology Authors: Josef ThingnesLeiv OyehaugEivind HovigStig Omholt Source Type: journals

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientistsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: ChemChains combines the advantages of logical and continuous modeling and provides a way for laboratory biologists to perform in silico experiments on mathematical models easily, a necessary component of laboratory research in the systems biology era. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - June 6, 2009 Category: Molecular Biology Authors: Tomas HelikarJim Rogers Source Type: journals

A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule"Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: This systems analysis enabled us to derive a hypothesis in which hormone signals are proposed to enhance the nitrate response, providing a potential mechanistic explanation for the link between nitrate signaling and the control of plant development. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - June 6, 2009 Category: Molecular Biology Authors: Damion NeroGabriel KroukDaniel TranchinaGloria Coruzzi Source Type: journals

LeishCyc: a biochemical pathways database for Leishmania majorEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The LeishCyc database describes Leishmania major genes, gene products, metabolites, their relationships and biochemical organization into metabolic pathways. LeishCyc provides a systematic approach to organizing the evolving information about Leishmania biochemical networks and is a tool for analysis, interpretation, and visualization of Leishmania 'omics (transcriptomics, proteomics, metabolomics) data in the context of metabolic pathways. LeishCyc is the first such database for the Trypanosomatidae family, which includes a number of other important human parasites. Flexible query/visualization capabilities a...
Source: BMC Systems Biology - Latest articles - June 5, 2009 Category: Molecular Biology Authors: Maria DoyleJames MacRaeDavid De SouzaEleanor SaundersMalcolm McConvilleVladimir Likic Source Type: journals

Computational disease modeling - fact or fiction?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: During the workshop it became obvious that diverse scientific modeling cultures (from computational neuroscience, theory, data-driven machine-learning approaches, agent-based modeling, network modeling and stochastic-molecular simulations) would benefit from intense cross-talk on shared theoretical issues in order to make progress on clinically relevant problems. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - June 4, 2009 Category: Molecular Biology Authors: Jesper TegnerAlbert CompteCharles AuffrayGary AnGunnar CedersundGilles ClermontBoris GutkinZoltan OltvaiKlaas Enno StephanRandy ThomasPablo Villoslada Source Type: journals

A graphical model approach for inferring large-scale networks integrating gene expression and genetic polymorphismEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results suggest that graphical models based on integrative genomic data are computationally efficient, work well with small samples, and can describe complex interactions among genes and polymorphisms that could not be identified by pair-wise association testing. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - May 27, 2009 Category: Molecular Biology Authors: Jen-hwa ChuScott WeissVincent CareyBenjamin Raby Source Type: journals

Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruziEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This work demonstrates the utility of constraint-based models for integrating various sources of data (e.g., genomics, primary biochemical literature, proteomics) to generate testable hypotheses. This model represents an approach for the systematic study of T. cruzi metabolism under a wide range of conditions and perturbations, and should eventually aid in the identification of urgently needed novel chemotherapeutic targets. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - May 16, 2009 Category: Molecular Biology Authors: Seth B Roberts, Jennifer L Robichaux, Arvind K Chavali, Patricio A Manque, Vladimir Lee, Ana M Lara, Jason A Papin and Gregory A Buck Source Type: journals

On the functional diversity of dynamical behaviour in genetic and metabolic feedback systemsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The analytical methods and insights presented in this study demonstrate that reallocation of the feedback loop may or may not make the system more stable; the specific effect is determined by the degradation rates of the newly inhibited molecular species. As the loop moves closer to the end of the pathway, the minimum Hill coefficient for oscillation is reduced. Furthermore, under general (unequal) values of the degradation rates, system extension becomes more stable only when the added species degrades slower than it is being produced; otherwise the system is more prone to oscillation. The coupling of loops si...
Source: BMC Systems Biology - Latest articles - May 11, 2009 Category: Molecular Biology Authors: Lan K Nguyen and Don Kulasiri Source Type: journals

miRNA-regulated dynamics in circadian oscillator modelsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: miRNAs can have a profound effect on the dynamics of regulatory modules, both by control of amplitude, namely by affecting the level of gene expression, as well as by control or alteration of frequency, namely by interference with the temporal sequence of gene production or delivery. We believe that our results are valid for a variety of regulatory systems, beyond the exemplars discussed here. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - May 5, 2009 Category: Molecular Biology Authors: Amitabha Nandi, Candida Vaz, Alok Bhattacharya and Ramakrishna Ramaswamy Source Type: journals

Genetic and environmental pathways to complex diseasesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Identification of key regulatory pathways that integrate genetic and environmental modulators define disease associated targets that will allow for efficient screening of large numbers of environmental factors, screening that could set priorities for further research and guide public health decisions. (Source: BMC Systems Biology - Latest articles)
Source: BMC Systems Biology - Latest articles - May 5, 2009 Category: Molecular Biology Authors: Julia M Gohlke, Reuben Thomas, Yonqing Zhang, Michael C Rosenstein, Allan P Davis, Cynthia Murphy, Kevin G Becker, Carolyn J Mattingly and Christopher J Portier Source Type: journals