MedWorm: Bioinformatics

Adaptation of Salmonella enterica Hadar under static magnetic field: effects on outer membrane protein pattern

Proteome Science — Fri, 03 Feb 2012 05:00:00 +0100

Conclusions: SMF (200 mT) seems to maintain the cell envelope integrity and to submit the exposed cells to an oxidative stress. Some alterations suggest an increase of the ability of exposed cells to form biofilms. (Source: Proteome Science)

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Markov Chain Ontology Analysis (MCOA)

BMC Bioinformatics - Latest articles — Fri, 03 Feb 2012 05:00:00 +0100

Conclusion: A methodology based on Markov chain models and network analytic metrics can help detect the relevant signal within large, highly interdependent and noisy data sets and, for applications such as enrichment analysis, has been shown to generate superior performance on both real and simulated data relative to existing state-of-the-art approaches. (Source: BMC Bioinformatics - Latest articles)

Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets

BMC Bioinformatics - Latest articles — Fri, 03 Feb 2012 05:00:00 +0100

Conclusions: On simulation studies and real data sets, we showed that IPCA offers a better visualization of thedata than ICA and with a smaller number of components than PCA. Furthermore, a preliminary investigation of the list of genes selected with sIPCA demonstrate that the approach is well able to highlight relevant genes inthe data with respect to the biological experiment.IPCA and sIPCA are both implemented in the R package mixOmics dedicated to the analysis and exploration ofhigh dimensional biological data sets, and on mixOmics' web-interface. (Source: BMC Bioinformatics - Latest articles)

Age or Stage Structure? : A Comparison of Dynamic Outcomes from Discrete Age- and Stage-Structured Population Models.

Bulletin of Mathematical Biology — Thu, 02 Feb 2012 05:00:00 +0100

Authors: Wikan A Abstract Discrete stage-structured density-dependent and discrete age-structured density-dependent population models are considered. Regarding the former, we prove that the model at hand is permanent (i.e., that the population will neither go extinct nor exhibit explosive oscillations) and given density dependent fecundity terms we also show that species with delayed semelparous life histories tend to be more stable than species which possess precocious semelparous life histories. Moreover, our findings together with results obtained from other stage-structured models seem to illustrate a fairly general ecological principle, namely that iteroparous species are more stable than semelparous species. Our analysis of various age-structured models does not necessarily s...

Analysis of Biochemical Equilibria Relevant to the Immune Response: Finding the Dissociation Constants.

Bulletin of Mathematical Biology — Thu, 02 Feb 2012 05:00:00 +0100

Authors: Cummings LJ, Perez-Castillejos R, Mack ET Abstract This paper analyzes the biochemical equilibria between bivalent receptors, homo-bifunctional ligands, monovalent inhibitors, and their complexes. Such reaction schemes arise in the immune response, where immunoglobulins (bivalent receptors) bind to pathogens or allergens. The equilibria may be described by an infinite system of algebraic equations, which accounts for complexes of arbitrary size n (n being the number of receptors present in the complex). The system can be reduced to just 3 algebraic equations for the concentrations of free (unbound) receptor, free ligand and free inhibitor. Concentrations of all other complexes can be written explicitly in terms of these variables. We analyze how concentrations of key (exp...

Caipirini: using gene sets to rank literature

BioData Mining — Wed, 01 Feb 2012 05:00:00 +0100

'Caipirini', a new software program, allows ranking of biomedical literature based on biological relevance to gene sets, thereby enabling data from these high-throughput experiments to be more easily accessed. (Source: BioData Mining)

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Analysis of Energy-based Algorithms for RNA Secondary Structure Prediction

BMC Bioinformatics - Latest articles — Wed, 01 Feb 2012 05:00:00 +0100

Conclusions: Large datasets should be used to obtain reliable measures of the accuracy of RNA structure prediction algorithms, and average accuracies on specific classes (such as Group I introns and Transfer RNAs) should be interpreted with caution, considering the relatively small size of currently available datasets for such classes. The accuracy of the MEA-based methods is significantly higher when using the BL* parameter set of Andronescu et al. than when using the parameters of Mathews and Turner, and there is no significant difference between the accuracy of MEA-based methods and MFE when using the BL* parameters. The pseudo-MEA-based method of Hamada et al. with the BL* parameter set significantly outperforms all other MFE and MEA-based algorithms on our large data sets. (Source: BM...

TranscriptomeBrowser 3.0 : introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

BMC Bioinformatics - Latest articles — Tue, 31 Jan 2012 05:00:00 +0100

Conclusions: The InteractomeBrowser plugin is a powerful tool to get quick access to a knowledge database that includes both predicted and validated molecular interactions. InteractomeBrowser is available through the TranscriptomeBrowser framework and can be found at : http://tagc.univ-mrs.fr/tbrowser/. Our database is updated on a regular basis. (Source: BMC Bioinformatics - Latest articles)

graphite - a Bioconductor package to convert pathway topology to gene network

BMC Bioinformatics - Latest articles — Tue, 31 Jan 2012 05:00:00 +0100

Conclusions: graphite is an innovative package able to gather and make easily available the contents of the four major pathway databases. In the field of topological analysis graphite acts as a provider of biological information by reducing the pathway complexity considering the biological meaning of the pathway elements. (Source: BMC Bioinformatics - Latest articles)

Fast automatic quantitative cell replication with fluorescent live cell imaging

BMC Bioinformatics - Latest articles — Tue, 31 Jan 2012 05:00:00 +0100

Background: live cell imaging is a useful tool to monitor cellular activities in living systems. It is often necessary in cancer research or experimental research to quantify the dividing capabilities of cells or the cell proliferation level when investigating manipulations of the cells or their environment. Manual quantification of fluorescence microscopic image is difficult because human is neither sensitive to fine differences in color intensity nor effective to count and average fluorescence level among cells. However, auto-quantification is not a straightforward problem to solve. As the sampling location of the microscopy changes, the amount of cells in individual microscopic images varies, which makes simple measurement methods such as the sum of stain intensity values or the total n...

Training text chunkers on a silver standard corpus: can silver replace gold?

BMC Bioinformatics - Latest articles — Mon, 30 Jan 2012 05:00:00 +0100

Conclusions: We conclude that an SSC can be a viable alternative for or a supplement to a GSC when training chunkers in a biomedical domain. A combined system only shows improvement if the SSC is used to supplement a GSC. Whether the approach is applicable to other systems in a natural-language processing pipeline has to be further investigated. (Source: BMC Bioinformatics - Latest articles)

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Propagating semantic information in biochemical network models

BMC Bioinformatics - Latest articles — Mon, 30 Jan 2012 05:00:00 +0100

Conclusions: Semantic propagation and model alignment are included in the open-source library semanticSBML, available on sourceforge. Online services for model alignment and for annotation prediction can be used at http://www.semanticsbml.org. (Source: BMC Bioinformatics - Latest articles)

seeQTL: a searchable database for human eQTLs