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Adaptation of Salmonella enterica Hadar under static magnetic field: effects on outer membrane protein patternEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Proteome Science - February 3, 2012 Category: Bioinformatics Authors: Sarra SnoussiAlya El MayLaurent CoquetPhilippe ChanThierry JouenneAhmed LandoulsiEmmanuelle De Source Type: research

Markov Chain Ontology Analysis (MCOA)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Bioinformatics - Latest articles - February 3, 2012 Category: Bioinformatics Authors: H FrostAlexa McCray Source Type: research

Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data setsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Bioinformatics - Latest articles - February 3, 2012 Category: Bioinformatics Authors: Fangzhou YaoJeff CoqueryKim-Anh Le Cao Source Type: research

Age or Stage Structure? : A Comparison of Dynamic Outcomes from Discrete Age- and Stage-Structured Population Models.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Bulletin of Mathematical Biology - February 2, 2012 Category: Bioinformatics Authors: Wikan A Tags: Bull Math Biol Source Type: research

Analysis of Biochemical Equilibria Relevant to the Immune Response: Finding the Dissociation Constants.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Bulletin of Mathematical Biology - February 2, 2012 Category: Bioinformatics Authors: Cummings LJ, Perez-Castillejos R, Mack ET Tags: Bull Math Biol Source Type: research

Caipirini: using gene sets to rank literatureEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
'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)
Source: BioData Mining - February 1, 2012 Category: Bioinformatics Authors: Theodoros SoldatosSean O'DonoghueVenkata SatagopamAdriano Barbosa-SilvaGeorgios PavlopoulosAna Carolina Wanderley-NogueiraNina Mota Soares-CavalcantiReinhard Schneider Source Type: research

Analysis of Energy-based Algorithms for RNA Secondary Structure PredictionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. Th...
Source: BMC Bioinformatics - Latest articles - February 1, 2012 Category: Bioinformatics Authors: Monir HajiaghayiAnne CondonHolger Hoos Source Type: research

TranscriptomeBrowser 3.0 : introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Bioinformatics - Latest articles - January 31, 2012 Category: Bioinformatics Authors: Cyrille LepoivreAurelie BergonFabrice LopezNarayanan PerumalCatherine NguyenJean ImbertDenis Puthier Source Type: research

graphite - a Bioconductor package to convert pathway topology to gene networkEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Bioinformatics - Latest articles - January 31, 2012 Category: Bioinformatics Authors: Gabriele SalesEnrica CaluraDuccio CavalieriChiara Romualdi Source Type: research

Fast automatic quantitative cell replication with fluorescent live cell imagingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 micros...
Source: BMC Bioinformatics - Latest articles - January 31, 2012 Category: Bioinformatics Authors: Ching-Wei Wang Source Type: research

Training text chunkers on a silver standard corpus: can silver replace gold?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Bioinformatics - Latest articles - January 30, 2012 Category: Bioinformatics Authors: Ning KangErik van MulligenJan Kors Source Type: research

Propagating semantic information in biochemical network modelsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: BMC Bioinformatics - Latest articles - January 30, 2012 Category: Bioinformatics Authors: Marvin SchulzEdda KlippWolfram Liebermeister Source Type: research

seeQTL: a searchable database for human eQTLsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: seeQTL is a comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information. The database presents eQTL association results in a convenient browser, using both segmented local-association plots and genome-wide Manhattan plots. Availability and implementation: seeQTL is freely available for non-commercial use at http://www.bios.unc.edu/research/genomic_software/seeQTL/. Contact: fred_wright@unc.edu; kxia@bios.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online. (Source: Bioinformatics)
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Xia, K., Shabalin, A. A., Huang, S., Madar, V., Zhou, Y.-H., Wang, W., Zou, F., Sun, W., Sullivan, P. F., Wright, F. A. Tags: DATABASES AND ONTOLOGIES Source Type: research

An infrastructure for ontology-based information systems in biomedicine: RICORDO case studyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: The article presents an infrastructure for supporting the semantic interoperability of biomedical resources based on the management (storing and inference-based querying) of their ontology-based annotations. This infrastructure consists of: (i) a repository to store and query ontology-based annotations; (ii) a knowledge base server with an inference engine to support the storage of and reasoning over ontologies used in the annotation of resources; (iii) a set of applications and services allowing interaction with the integrated repository and knowledge base. The infrastructure is being prototyped and developed and...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Wimalaratne, S. M., Grenon, P., Hoehndorf, R., Gkoutos, G. V., de Bono, B. Tags: DATABASES AND ONTOLOGIES Source Type: research

PathVar: analysis of gene and protein expression variance in cellular pathways using microarray dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: Finding significant differences between the expression levels of genes or proteins across diverse biological conditions is one of the primary goals in the analysis of functional genomics data. However, existing methods for identifying differentially expressed genes or sets of genes by comparing measures of the average expression across predefined sample groups do not detect differential variance in the expression levels across genes in cellular pathways. Since corresponding pathway deregulations occur frequently in microarray gene or protein expression data, we present a new dedicated web application, PathVar, to ...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Glaab, E., Schneider, R. Tags: SYSTEMS BIOLOGY Source Type: research

GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: The GWAtoolbox is an R package that standardizes and accelerates the handling of data from genome-wide association studies (GWAS), particularly in the context of large-scale GWAS meta-analyses. A key feature of GWAtoolbox is its ability to perform quality control (QC) of any number of files in a matter of minutes. The implemented workflow has been structured to check three particular data quality aspects: (i) data formatting, (ii) quality of the GWAS results and (iii) data consistency across studies. Output consists of an extensive list of quality statistics and plots which allow inspection of individual files and...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Fuchsberger, C., Taliun, D., Pramstaller, P. P., Pattaro, C., on behalf of the CKDGen consortium Tags: GENETICS AND POPULATION ANALYSIS Source Type: research

MTBindingSim: simulate protein binding to microtubulesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: Many protein–protein interactions are more complex than can be accounted for by 1:1 binding models. However, biochemists have few tools available to help them recognize and predict the behaviors of these more complicated systems, making it difficult to design experiments that distinguish between possible binding models. MTBindingSim provides researchers with an environment in which they can rapidly compare different models of binding for a given scenario. It is written specifically with microtubule polymers in mind, but many of its models apply equally well to any polymer or any protein–protein interac...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Philip, J. T., Pence, C. H., Goodson, H. V. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experimentsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: Differential scanning fluorimetry (DSF) is a rapid technique that can be used in structural biology to study protein–ligand interactions. We have developed DMAN, a novel tool to analyse multi-well plate data obtained in DSF experiments. DMAN is easy to install and provides a user-friendly interface. Multi-well plate layouts can be designed by the user and experimental data can be annotated and analysed by DMAN according to the specified plate layout. Statistical tests for significance are performed automatically, and graphical tools are also provided to assist in data analysis. The modular concept of this so...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Wang, C. K., Weeratunga, S. K., Pacheco, C. M., Hofmann, A. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

SitePainter: a tool for exploring biogeographical patternsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
As microbial ecologists take advantage of high-throughput analytical techniques to describe microbial communities across ever-increasing numbers of samples, the need for new analysis tools that reveal the intrinsic spatial patterns and structures of these populations is crucial. Here we present SitePainter, an interactive graphical tool that allows investigators to create or upload pictures of their study site, load diversity analyses data and display both diversity and taxonomy results in a spatial context. Features of SitePainter include: visualizing α -diversity, using taxonomic summaries; visualizing β -dive...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Gonzalez, A., Stombaugh, J., Lauber, C. L., Fierer, N., Knight, R. Tags: SEQUENCE ANALYSIS Source Type: research

Identification and removal of ribosomal RNA sequences from metatranscriptomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications. Availability and implementation: This open-source application was implemented in Perl and can be used as stand-alone version or accessed online through a...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Schmieder, R., Lim, Y. W., Edwards, R. Tags: SEQUENCE ANALYSIS Source Type: research

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: Reduced representation bisulfite sequencing (RRBS) is a powerful yet cost-efficient method for studying DNA methylation on a genomic scale. RRBS involves restriction-enzyme digestion, bisulfite conversion and size selection, resulting in DNA sequencing data that require special bioinformatic handling. Here, we describe RRBSMAP, a short-read alignment tool that is designed for handling RRBS data in a user-friendly and scalable way. RRBSMAP uses wildcard alignment, and avoids the need for any preprocessing or post-processing steps. We benchmarked RRBSMAP against a well-validated MAQ-based pipeline for RRBS read alig...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Xi, Y., Bock, C., Muller, F., Sun, D., Meissner, A., Li, W. Tags: SEQUENCE ANALYSIS Source Type: research

B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: Bisulfite sequencing, a combination of bisulfite treatment and high-throughput sequencing, has proved to be a valuable method for measuring DNA methylation at single base resolution. Here, we present B-SOLANA, an approach for the analysis of two-base encoding (colorspace) bisulfite sequencing data on the SOLiD platform of Life Technologies. It includes the alignment of bisulfite sequences and the determination of methylation levels in CpG as well as non-CpG sequence contexts. B-SOLANA enables a fast and accurate analysis of large raw sequence datasets. Availability and implementation: The source code, released und...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Kreck, B., Marnellos, G., Richter, J., Krueger, F., Siebert, R., Franke, A. Tags: SEQUENCE ANALYSIS Source Type: research

NRPSsp: non-ribosomal peptide synthase substrate predictorEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: Non-ribosomal peptide synthetases (NRPSs) are multi-modular enzymes, which biosynthesize many important peptide compounds produced by bacteria and fungi. Some studies have revealed that an individual domain within the NRPSs shows significant substrate selectivity. The discovery and characterization of non-ribosomal peptides are of great interest for the biotechnological industries. We have applied computational mining methods in order to build a database of NRPSs modules that bind to specific substrates. We have used this database to build a hidden Markov model predictor of substrates that bind to a given NRPS. Av...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Prieto, C., Garcia-Estrada, C., Lorenzana, D., Martin, J. F. Tags: SEQUENCE ANALYSIS Source Type: research

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: More and more cancer studies use next-generation sequencing (NGS) data to detect various types of genomic variation. However, even when researchers have such data at hand, single-nucleotide polymorphism arrays have been considered necessary to assess copy number alterations and especially loss of heterozygosity (LOH). Here, we present the tool Control-FREEC that enables automatic calculation of copy number and allelic content profiles from NGS data, and consequently predicts regions of genomic alteration such as gains, losses and LOH. Taking as input aligned reads, Control-FREEC constructs copy number and B-allele...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Boeva, V., Popova, T., Bleakley, K., Chiche, P., Cappo, J., Schleiermacher, G., Janoueix-Lerosey, I., Delattre, O., Barillot, E. Tags: GENOME ANALYSIS Source Type: research

Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant toolsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Storing, annotating and analyzing variants from next-generation sequencing projects can be difficult due to the availability of a wide array of data formats, tools and annotation sources, as well as the sheer size of the data files. Useful tools, including the GATK, ANNOVAR and BEDTools can be integrated into custom pipelines for annotating and analyzing sequence variants. However, building flexible pipelines that support the tracking of variants alongside their samples, while enabling updated annotation and reanalyses, is not a simple task. Results: We have developed variant tools, a flexible annotation and an...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: San Lucas, F. A., Wang, G., Scheet, P., Peng, B. Tags: GENOME ANALYSIS Source Type: research

GenomeRunner: automating genome explorationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: One of the challenges in interpreting high-throughput genomic studies such as a genome-wide associations, microarray or ChIP-seq is their open-ended nature—once a set of experimentally identified regions is identified as statistically significant, at least two questions arise: (i) besides P-value, do any of these significant regions stand out in terms of biological implications? (ii) Does the set of significant regions, as a whole, have anything in common genome wide? These issues are difficult to address because of the growing number of annotated genomic features (e.g. single nucleotide polymorphisms, tr...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Dozmorov, M. G., Cara, L. R., Giles, C. B., Wren, J. D. Tags: GENOME ANALYSIS Source Type: research

PGAP: pan-genomes analysis pipelineEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed. We have developed a new pan-genome analysis pipeline (PGAP), which can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters. PGA...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Zhao, Y., Wu, J., Yang, J., Sun, S., Xiao, J., Yu, J. Tags: GENOME ANALYSIS Source Type: research

The Virtual Fly Brain browser and query interfaceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present an online resource that provides a convenient way to study and query fly brain anatomy, expression and genetic data. We extended the newly developed BrainName nomenclature for the adult fly brain into a logically structured ontology that relates a comprehensive set of published neuron classes to the brain regions they innervate. The Virtual Fly Brain interface allows users to explore the structure of the Drosophila brain by browsing 3D images of a brain with subregions displayed as coloured overlays. An integrated query mechanism allows complex searches of underlying anatomy, cells, expression and other data fro...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Milyaev, N., Osumi-Sutherland, D., Reeve, S., Burton, N., Baldock, R. A., Armstrong, J. D. Tags: DATABASES AND ONTOLOGIES Source Type: research

SNPxGE2: a database for human SNP-coexpression associationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Recently, gene–coexpression relationships have been found to be often conditional and dynamic. Many studies have suggested that single nucleotide polymorphisms (SNPs) have impacts on gene expression variations in human populations. Results: The SNPxGE2 database contains the computationally predicted human SNP–coexpression associations, i.e. the differential coexpression between two genes is associated with the genotypes of an SNP. These data were generated from a large-scale association study that was based on the HapMap phase I data, which covered 269 individuals from 4 human populations, 556 873 S...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Wang, Y., Joseph, S. J., Liu, X., Kelley, M., Rekaya, R. Tags: DATABASES AND ONTOLOGIES Source Type: research

Integrating human and murine anatomical gene expression data for improved comparisonsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Information concerning the gene expression pattern in four dimensions (species, genes, anatomy and developmental stage) is crucial for unraveling the roles of genes through time. There are a variety of anatomical gene expression databases, but extracting information from them can be hampered by their diversity and heterogeneity. Results: aGEM 3.1 (anatomic Gene Expression Mapping) addresses the issues of diversity and heterogeneity of anatomical gene expression databases by integrating six mouse gene expression resources (EMAGE, GXD, GENSAT, Allen Brain Atlas data base, EUREXPRESS and BioGPS) and three human ge...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Jimenez-Lozano, N., Segura, J., Macias, J. R., Vega, J., Carazo, J. M. Tags: DATABASES AND ONTOLOGIES Source Type: research

Construction and completion of flux balance models from pathway databasesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP). The method suggests corrections to the sets of reactions, biomass metabolites, nutrients and secretions. The method generates FBA models directly from Pathway/Genome Databases. Thus, FBA models developed in this framework are easily queried and visualized using the Pathway Tools software. Predicted fluxes are more easily comprehended by visualizing them on diagrams of individual metabolic pathways or of metabolic maps. MetaFlux can also remove redundant hi...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Latendresse, M., Krummenacker, M., Trupp, M., Karp, P. D. Tags: SYSTEMS BIOLOGY Source Type: research

Minimal cut sets in a metabolic network are elementary modes in a dual networkEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Elementary modes (EMs) and minimal cut sets (MCSs) provide important techniques for metabolic network modeling. Whereas EMs describe minimal subnetworks that can function in steady state, MCSs are sets of reactions whose removal will disable certain network functions. Effective algorithms were developed for EM computation while calculation of MCSs is typically addressed by indirect methods requiring the computation of EMs as initial step. Results: In this contribution, we provide a method that determines MCSs directly without calculating the EMs. We introduce a duality framework for metabolic networks where the...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Ballerstein, K., von Kamp, A., Klamt, S., Haus, U.-U. Tags: SYSTEMS BIOLOGY Source Type: research

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe a new, substantially redesigned version of our tool Metscape that allows users to enter experimental data for metabolites, genes and pathways and display them in the context of relevant metabolic networks. Metscape 2 uses an internal relational database that integrates data from KEGG and EHMN databases. The new version of the tool allows users to identify enriched pathways from expression profiling data, build and analyze the networks of genes and metabolites, and visualize changes in the gene/metabolite data. We demonstrate the applications of Metscape to annotate molecular pathways for human and mouse metabol...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Karnovsky, A., Weymouth, T., Hull, T., Tarcea, V. G., Scardoni, G., Laudanna, C., Sartor, M. A., Stringer, K. A., Jagadish, H. V., Burant, C., Athey, B., Omenn, G. S. Tags: SYSTEMS BIOLOGY Source Type: research

Gaussian process modelling for bicoid mRNA regulation in spatio-temporal Bicoid profileEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Bicoid protein molecules, translated from maternally provided bicoid mRNA, establish a concentration gradient in Drosophila early embryonic development. There is experimental evidence that the synthesis and subsequent destruction of this protein is regulated at source by precise control of the stability of the maternal mRNA. Can we infer the driving function at the source from noisy observations of the spatio-temporal protein profile? We use non-parametric Gaussian process regression for modelling the propagation of Bicoid in the embryo and infer aspects of source regulation as a posterior function. Results: Wi...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Liu, W., Niranjan, M. Tags: SYSTEMS BIOLOGY Source Type: research

M3: an improved SNP calling algorithm for Illumina BeadArray dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: Genotype calling from high-throughput platforms such as Illumina and Affymetrix is a critical step in data processing, so that accurate information on genetic variants can be obtained for phenotype–genotype association studies. A number of algorithms have been developed to infer genotypes from data generated through the Illumina BeadStation platform, including GenCall, GenoSNP, Illuminus and CRLMM. Most of these algorithms are built on population-based statistical models to genotype every SNP in turn, such as GenCall with the GenTrain clustering algorithm, and require a large reference population to perform ...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Li, G., Gelernter, J., Kranzler, H. R., Zhao, H. Tags: GENETICS AND POPULATION ANALYSIS Source Type: research

Inhibition of HIV-1 protease: the rigidity perspectiveEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: HIV-1 protease is a key drug target due to its role in the life cycle of the HIV-1 virus. Rigidity analysis using the software First is a computationally inexpensive method for inferring functional information from protein crystal structures. We evaluate the rigidity of 206 high-resolution (2 Å or better) X-ray crystal structures of HIV-1 protease and compare the effects of different inhibitors binding to the enzyme. Results: Inhibitor binding has little effect on the overall rigidity of the protein homodimer, including the rigidity of the active site. The principal effect of inhibitor binding on rigidity...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Heal, J. W., Jimenez-Roldan, J. E., Wells, S. A., Freedman, R. B., Romer, R. A. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroidsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Protein–protein interfaces contain important information about molecular recognition. The discovery of conserved patterns is essential for understanding how substrates and inhibitors are bound and for predicting molecular binding. When an inhibitor binds to different enzymes (e.g. dissimilar sequences, structures or mechanisms what we call cross-inhibition), identification of invariants is a difficult task for which traditional methods may fail. Results: To clarify how cross-inhibition happens, we model the problem, propose and evaluate a methodology called HydroPaCe to detect conserved patterns. Interfac...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Goncalves-Almeida, V. M., Pires, D. E. V., de Melo-Minardi, R. C., da Silveira, C. H., Meira, W., Santoro, M. M. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Nucleotides are multifunctional molecules that are essential for numerous biological processes. They serve as sources for chemical energy, participate in the cellular signaling and they are involved in the enzymatic reactions. The knowledge of the nucleotide–protein interactions helps with annotation of protein functions and finds applications in drug design. Results: We propose a novel ensemble of accurate high-throughput predictors of binding residues from the protein sequence for ATP, ADP, AMP, GTP and GDP. Empirical tests show that our NsitePred method significantly outperforms existing predictors and...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Chen, K., Mizianty, M. J., Kurgan, L. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

SCPC: a method to structurally compare protein complexesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Protein–protein interactions play vital functional roles in various biological phenomena. Physical contacts between proteins have been revealed using experimental approaches that have solved the structures of protein complexes at atomic resolution. To examine the huge number of protein complexes available in the Protein Data Bank, an efficient automated method that compares protein complexes is required. Results: We have developed Structural Comparison of Protein Complexes (SCPC), a novel method to structurally compare protein complexes. SCPC compares the spatial arrangements of subunits in a complex with...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Koike, R., Ota, M. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

Detection of microRNAs in color spaceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Deep sequencing provides inexpensive opportunities to characterize the transcriptional diversity of known genomes. The AB SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw data is a sequence of colors, where each color represents 2 nt and each nucleotide is represented by two consecutive colors. This strategy is purported to have several advantages, including increased ability to distinguish sequencing errors from polymorphisms. Several programs have been developed to map short reads to genomes in color space. However, a number of previously unexplored technical issu...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Marco, A., Griffiths-Jones, S. Tags: SEQUENCE ANALYSIS Source Type: research

SomaticSniper: identification of somatic point mutations in whole genome sequencing dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: The sequencing of tumors and their matched normals is frequently used to study the genetic composition of cancer. Despite this fact, there remains a dearth of available software tools designed to compare sequences in pairs of samples and identify sites that are likely to be unique to one sample. Results: In this article, we describe the mathematical basis of our SomaticSniper software for comparing tumor and normal pairs. We estimate its sensitivity and precision, and present several common sources of error resulting in miscalls. Availability and implementation: Binaries are freely available for download at htt...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Larson, D. E., Harris, C. C., Chen, K., Koboldt, D. C., Abbott, T. E., Dooling, D. J., Ley, T. J., Mardis, E. R., Wilson, R. K., Ding, L. Tags: SEQUENCE ANALYSIS Source Type: research

InFiRe -- a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: InFiRe, Insertion Finder via Restriction digest, is a novel software tool that allows for the computational identification of transposon insertion sites in known bacterial genome sequences after transposon mutagenesis experiments. The approach is based on the fact that restriction endonuclease digestions of bacterial DNA yield a unique pattern of DNA fragments with defined sizes. Transposon insertion changes the size of the hosting DNA fragment by a known number of base pairs. The exact size of this fragment can be determined by Southern blot hybridization. Subsequently, the position of insertion can be identif...
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Shevchuk, O., Roselius, L., Gunther, G., Klein, J., Jahn, D., Steinert, M., Munch, R. Tags: GENOME ANALYSIS Source Type: research

A simple statistical test to infer the causality of target/phenotype correlation from small molecule phenotypic screensEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study indicates that, empowered by appropriate statistical adjustment, small molecule inhibitor perturbation remains a powerful tool to pin down the relevant biomarker for drug safety and efficacy research. Contact: xin.wei@roche.com Supplementary information: Supplementary data are available at Bioinformatics online. (Source: Bioinformatics)
Source: Bioinformatics - January 30, 2012 Category: Bioinformatics Authors: Wei, X., Hoffman, A. F., Hamilton, S. M., Xiang, Q., He, Y., So, W. V., So, S.-S., Mark, D. Tags: SYSTEMS BIOLOGY Source Type: research

Identification of aberrant pathways and network activities from high-throughput data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract Many complex diseases such as cancer are associated with changes in biological pathways and molecular networks rather than being caused by single gene alterations. A major challenge in the diagnosis and treatment of such diseases is to identify characteristic aberrancies in the biological pathways and molecular network activities and elucidate their relationship to the disease. This review presents recent progress in using high-throughput biological assays to decipher aberrant pathways and network activities. In particular, this review provides specific examples in which high-throughput data have been appl...
Source: Briefings in Bioinformatics - January 27, 2012 Category: Bioinformatics Authors: Wang J, Zhang Y, Marian C, Ressom HW Tags: Brief Bioinform Source Type: research

The EnzymeTracker: an open-source laboratory information management system for sample trackingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at http://cubique.concordia.ca/enzymedb/index.html under the GNU GPLv3 licence. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - January 26, 2012 Category: Bioinformatics Authors: Thomas TripletGregory Butler Source Type: research

Protein and phosphoprotein levels in glioma and adenocarcinoma cell lines grown in normoxia and hypoxia in monolayer and three-dimensional culturesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We identified subsets of proteins with clearly concordant/discordant behavior between gliomas and adenocarcinomas. In general, monolayer to 3D culture differences are clearer than normoxia to hypoxia differences, with anti-apoptotic, cytoskeletal rearrangement and cell survival pathways emphasized in the former and mTOR pathway, transcription, cell-cycle arrest modulation, and increased cell motility in the latter. (Source: Proteome Science)
Source: Proteome Science - January 25, 2012 Category: Bioinformatics Authors: Victor LevinSonali PanchabhaiLi ShenKeith Baggerly Source Type: research

Feature extraction for ECG heartbeats using higher order statistics of WPD coefficientsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: This paper describes feature extraction methods using higher order statistics (HOS) of wavelet packet decomposition (WPD) coefficients for the purpose of automatic heartbeat recognition. The method consists of three stages. First, the wavelet package coefficients (WPC) are calculated for each different type of ECG beat. Then, higher order statistics of WPC are derived. Finally, the obtained feature set is used as input to a classifier, which is based on k-NN algorithm. The MIT-BIH arrhythmia database is used to obtain the ECG records used in this study. All heartbeats in the arrhythmia database are grouped into f...
Source: Computer Methods and Programs in Biomedicine - January 24, 2012 Category: Bioinformatics Authors: Yakup Kutlu, Damla Kuntalp Tags: Section III: Experiences with Systems and Programs Source Type: research

Cone Beam CT using motion-compensated algebraic reconstruction methods with limited dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Cone Beam Computed Tomography (CBCT) is widely used in radiation therapy for verifying treatment areas, since it provides three-dimensional image reconstruction of those tumour regions under inspection. However, organ motion is problematic during the scanning process, it causes motion artefacts on the CBCT image and can lead to mispositioning for the subsequent treatment. Moreover, patient dose is also considerable and there is a need for methods which yield acceptable image quality with as few X-ray images as possible. Although methods have been developed to handle limited projection data, such as the Algebraic ...
Source: Computer Methods and Programs in Biomedicine - January 24, 2012 Category: Bioinformatics Authors: T. Pengpan, W. Qiu, N.D. Smith, M. Soleimani Tags: Section II: Systems and Programs Source Type: research

Fuzzy cognitive map software tool for treatment management of uncomplicated urinary tract infectionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Uncomplicated urinary tract infection (uUTI) is a bacterial infection that affects individuals with normal urinary tracts from both structural and functional perspective. The appropriate antibiotics and treatment suggestions to individuals suffer of uUTI is an important and complex task that demands a special attention. How to decrease the unsafely use of antibiotics and their consumption is an important issue in medical treatment. Aiming to model medical decision making for uUTI treatment, an innovative and flexible approach called fuzzy cognitive maps (FCMs) is proposed to handle with uncertainty and missing in...
Source: Computer Methods and Programs in Biomedicine - January 24, 2012 Category: Bioinformatics Authors: Elpiniki I. Papageorgiou Tags: Section II: Systems and Programs Source Type: research

Simulation of the human TMJ behavior based on interdependent joints topologyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: The temporomandibular joint (TMJ) is one of the most important and complex joints of the body and its pathologies affect a great percentage of the human population. The simulation of the TMJ behavior during opening, closing and chewing movements can be very useful to the understanding of this articulation by physicians, helping them to prevent or fix problems due to accidents or diseases. This work proposes a model to simulate the human TMJ behavior based on the concept of two interdependent joints. The model was conceived using multimodal information acquired from CT and MRI images of a live person, as well as m...
Source: Computer Methods and Programs in Biomedicine - January 24, 2012 Category: Bioinformatics Authors: Marta B. Villamil, Luciana P. Nedel, Carla M.D.S. Freitas, Benoit Macq Tags: Section I: Methodology Source Type: research