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This page shows you the most recent publications within this specialty of the MedWorm directory. This is page number 27.

New moment closures based on a priori distributions with applications to epidemic dynamics.
Abstract Recently, research that focuses on the rigorous understanding of the relation between simulation and/or exact models on graphs and approximate counterparts has gained lots of momentum. This includes revisiting the performance of classic pairwise models with closures at the level of pairs and/or triples as well as effective-degree-type models and those based on the probability generating function formalism. In this paper, for a fully connected graph and the simple SIS (susceptible-infected-susceptible) epidemic model, a novel closure is introduced. This is done via using the equations for the moments of the...
Source: Bulletin of Mathematical Biology - July 1, 2012 Category: Bioinformatics Authors: Kiss IZ, Simon PL Tags: Bull Math Biol Source Type: research

Analytical optimal controls for the state constrained addition and removal of cryoprotective agents.
Abstract Cryobiology is a field with enormous scientific, financial, and even cultural impact. Successful cryopreservation of cells and tissues depends on the equilibration of these materials with high concentrations of permeating chemicals (CPAs) such as glycerol or 1,2 propylene glycol. Because cells and tissues are exposed to highly anisosmotic conditions, the resulting gradients cause large volume fluctuations that have been shown to damage cells and tissues. On the other hand, there is evidence that toxicity to these high levels of chemicals is time dependent, and therefore it is ideal to minimize exposure tim...
Source: Bulletin of Mathematical Biology - July 1, 2012 Category: Bioinformatics Authors: Benson JD, Chicone CC, Critser JK Tags: Bull Math Biol Source Type: research

Influence of the nuclear membrane, active transport, and cell shape on the Hes1 and p53-Mdm2 pathways: insights from spatio-temporal modelling.
Abstract There are many intracellular signalling pathways where the spatial distribution of the molecular species cannot be neglected. These pathways often contain negative feedback loops and can exhibit oscillatory dynamics in space and time. Two such pathways are those involving Hes1 and p53-Mdm2, both of which are implicated in cancer. In this paper we further develop the partial differential equation (PDE) models of Sturrock et al. (J. Theor. Biol., 273:15-31, 2011) which were used to study these dynamics. We extend these PDE models by including a nuclear membrane and active transport, assuming that proteins ar...
Source: Bulletin of Mathematical Biology - July 1, 2012 Category: Bioinformatics Authors: Sturrock M, Terry AJ, Xirodimas DP, Thompson AM, Chaplain MA Tags: Bull Math Biol Source Type: research

Persistence probabilities for stream populations.
Abstract Individuals in streams and rivers are constantly at risk of being washed downstream and thereby lost to their population. The possibility of diffusion-mediated persistence of populations in advective environments has been the focus of a multitude of recent modeling efforts. Most of these recent models are deterministic, and they predict the existence of a critical advection velocity, above which a population cannot persist. In this work, we present a stochastic approach to the persistence problem in streams and rivers. We use the dominant eigenvalue of the advection-diffusion operator to transition from a ...
Source: Bulletin of Mathematical Biology - July 1, 2012 Category: Bioinformatics Authors: Samia Y, Lutscher F Tags: Bull Math Biol Source Type: research

Interspecific competition models derived from competition among individuals.
Abstract This paper demonstrates how discrete-time models describing population dynamics of two competing species can be derived in a bottom-up manner by considering competition for resources among individuals and the spatial distribution of individuals. The competition type of each species is assumed to be either scramble, contest, or an intermediate between them. Individuals of two species are distributed over resource sites or patches following one of three distribution functions. According to the combination of competition types of the two species and the distribution of individuals, various interspecific compe...
Source: Bulletin of Mathematical Biology - July 1, 2012 Category: Bioinformatics Authors: Anazawa M Tags: Bull Math Biol Source Type: research

Combining perturbations and parameter variation to influence mean first passage times.
Abstract Perturbations are relatively large shocks to state variables that can drive transitions between stable states, while drift in parameter values gradually alters equilibrium magnitudes. This latter effect can lead to equilibrium bifurcation, the generation, or annihilation of equilibria. Equilibrium annihilations reduce the number of equilibria and so are associated with catastrophic population collapse. We study the combination of perturbations and parameter drift, using a two-species intraguild predation (IGP) model. For example, we use bifurcation analysis to understand how parameter drift affects equilib...
Source: Bulletin of Mathematical Biology - July 1, 2012 Category: Bioinformatics Authors: Drury KL, Lodge DM Tags: Bull Math Biol Source Type: research

Latently infected cell activation: a way to reduce the size of the HIV reservoir?
Abstract While antiretroviral drugs can drive HIV to undetectably low levels in the blood, eradication is hindered by the persistence of long-lived, latently infected memory CD4 T cells. Immune activation therapy aims to eliminate this latent reservoir by reactivating these memory cells, exposing them to removal by the immune system and the cytotoxic effects of active infection. In this paper, we develop a mathematical model that investigates the use of immune activation strategies while limiting virus and latent class rebound. Our model considers infection of two memory classes, central and transitional CD4 T cell...
Source: Bulletin of Mathematical Biology - July 1, 2012 Category: Bioinformatics Authors: Forde J, Volpe JM, Ciupe SM Tags: Bull Math Biol Source Type: research

Sensory irritation response in rats II: recovery and dose-dependence.
Abstract Inhaled irritants can cause respiratory depression by simulating trigeminal nerves in the nasal cavity. This decrease in inhalation rate results in a decrease in the rate of the irritant gases flowing to the stimulated nerves, creating a complex feedback response. Previously, a model was created to describe how the presence of formaldehyde affects respiration in the rat. This ordinary differential equation model incorporated a model of the physiology of the upper respiratory tract of the rat and a model of the neurological control of the respiration rate due to signaling from the stimulated nerves in the n...
Source: Bulletin of Mathematical Biology - July 1, 2012 Category: Bioinformatics Authors: Yokley KA Tags: Bull Math Biol Source Type: research

Subject Index
Source: Artificial Intelligence in Medicine - July 1, 2012 Category: Bioinformatics Source Type: research

Author Index
Source: Artificial Intelligence in Medicine - July 1, 2012 Category: Bioinformatics Source Type: research

Editorial Board
Source: Artificial Intelligence in Medicine - July 1, 2012 Category: Bioinformatics Source Type: research

CONFORMATIONAL DYNAMICS OF HIV-1 PROTEASE: A COMPARATIVE MOLECULAR DYNAMICS SIMULATION STUDY WITH MULTIPLE AMBER FORCE FIELDS.
Abstract Flap dynamics of HIV-1 protease (HIV-pr) controls the entry of inhibitors and substrates to the active site. Dynamical models from previous simulations are not all consistent with each other and not all are supported by the NMR results. In the present work, the effect of force field on the dynamics of HIV-pr is investigated by MD simulations using three AMBER force fields ff99, ff99SB, and ff03. The generalized order parameters for amide backbone are calculated from the three force fields and compared with the NMR S2 values. We found that the ff99SB and ff03 force field calculated order parameters agree re...
Source: Journal of Bioinformatics and Computational Biology - June 29, 2012 Category: Bioinformatics Authors: Meher BR, Satish Kumar MV, Sharma S, Bandyopadhyay P Tags: J Bioinform Comput Biol Source Type: research

DAVID-WS: a stateful web service to facilitate gene/protein list analysis
Summary: The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ~1200 gene lists from ~400 unique researchers, and has been cited by more than 6000 scientific publications. However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL)-bas...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Jiao, X., Sherman, B. T., Huang, D. W., Stephens, R., Baseler, M. W., Lane, H. C., Lempicki, R. A. Tags: DATABASES AND ONTOLOGIES Source Type: research

Ka-me: a Voronoi image analyzer
Summary: Ka-me is a Voronoi image analyzer that allows users to analyze any image with a convex polygonal tessellation or any spatial point distribution by fitting Voronoi polygons and their dual, Delaunay triangulations, to the pattern. The analytical tools include a variety of graph theoretic and geometric tools that summarize the distribution of the numbers of edges per face, areas, perimeters, angles of Delaunay triangle edges (anglograms), Gabriel graphs, nearest neighbor graphs, minimal spanning trees, Ulam trees, Pitteway tests, circumcircles and convexhulls, as well as spatial statistics (Clark–Evans Nearest ...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Khiripet, N., Khantuwan, W., Jungck, J. R. Tags: DATA AND TEXT MINING Source Type: research

easyFRAP: an interactive, easy-to-use tool for qualitative and quantitative analysis of FRAP data
We present easyFRAP, a versatile tool that assists quantitative and qualitative analysis of fluorescence recovery after photobleaching (FRAP) data. The user can handle simultaneously large data sets of raw data, visualize fluorescence recovery curves, exclude low quality data, perform data normalization, extract quantitative parameters, perform batch analysis and save the resulting data and figures for further use. Our tool is implemented as a single-screen Graphical User Interface (GUI) and is highly interactive, as it permits parameterization and visual data quality assessment at various points during the analysis. Avail...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Rapsomaniki, M. A., Kotsantis, P., Symeonidou, I.-E., Giakoumakis, N.-N., Taraviras, S., Lygerou, Z. Tags: SYSTEMS BIOLOGY Source Type: research

INRICH: interval-based enrichment analysis for genome-wide association studies
Summary: Here we present INRICH (INterval enRICHment analysis), a pathway-based genome-wide association analysis tool that tests for enriched association signals of predefined gene-sets across independent genomic intervals. INRICH has wide applicability, fast running time and, most importantly, robustness to potential genomic biases and confounding factors. Such factors, including varying gene size and single-nucleotide polymorphism density, linkage disequilibrium within and between genes and overlapping genes with similar annotations, are often not accounted for by existing gene-set enrichment methods. By using a genomic ...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Lee, P. H., O'Dushlaine, C., Thomas, B., Purcell, S. M. Tags: GENETICS AND POPULATION ANALYSIS Source Type: research

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads
Summary: We introduce BRAT-BW, a fast, accurate and memory-efficient tool that maps bisulfite-treated short reads (BS-seq) to a reference genome using the FM-index (Burrows–Wheeler transform). BRAT-BW is significantly more memory efficient and faster on longer reads than current state-of-the-art tools for BS-seq data, without compromising on accuracy. BRAT-BW is a part of a software suite for genome-wide single base-resolution methylation data analysis that supports single and paired-end reads and includes a tool for estimation of methylation level at each cytosine. Availability: The software is available in the publ...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Harris, E. Y., Ponts, N., Le Roch, K. G., Lonardi, S. Tags: SEQUENCE ANALYSIS Source Type: research

CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation
Summary: CalMaTe calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. The resulting ASCNs are on average more accurate, which increases the power of segmentation methods for detecting changes between copy number states in tumor studies including copy neutral loss of heterozygosity. CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. Affymetrix and Illumina. Availability: The method is available on CRAN (http://cran.r-project.org/) in the open-source R package calmat...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Ortiz-Estevez, M., Aramburu, A., Bengtsson, H., Neuvial, P., Rubio, A. Tags: GENOME ANALYSIS Source Type: research

CNVRuler: a copy number variation-based case-control association analysis tool
Summary: The method for genome-wide association study (GWAS) based on copy number variation (CNV) is not as well established as that for single nucleotide polymorphism (SNP)–GWAS. Although there are several tools for CNV association studies, most of them do not provide appropriate definitions of CNV regions (CNVRs), which are essential for CNV-association studies. Here we present a user-friendly program called CNVRuler for CNV-association studies. Outputs from the 10 most common CNV defining algorithms can be directly used as input files for determining the three different definitions of CNVRs. Once CNVRs are defined...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Kim, J.-H., Hu, H.-J., Yim, S.-H., Bae, J. S., Kim, S.-Y., Chung, Y.-J. Tags: GENOME ANALYSIS Source Type: research

Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
In this study, we present the outline of a theory and its implementation for an ontology of physiology-related phenotypes. We provide a formal description of process attributes and relate them to the attributes of their temporal parts and participants. We apply our theory to create the Cellular Phenotype Ontology (CPO). The CPO is an ontology of morphological and physiological phenotypic characteristics of cells, cell components and cellular processes. Its prime application is to provide terms and uniform definition patterns for the annotation of cellular phenotypes. The CPO can be used for the annotation of observed abnor...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Hoehndorf, R., Harris, M. A., Herre, H., Rustici, G., Gkoutos, G. V. Tags: DATABASES AND ONTOLOGIES Source Type: research

Two effective methods for correcting experimental high-throughput screening data
We describe two new methods for eliminating systematic error from HTS data based on a prior knowledge of the error location. This information can be obtained using a specific version of the t-test or of the 2 goodness-of-fit test as discussed in Dragiev et al. (2011). We will show that both new methods constitute an important improvement over the standard practice of not correcting for systematic error at all as well as over the B-score correction procedure (Brideau et al., 2003) which is widely used in the modern HTS. We will also suggest a more general data preprocessing framework where the new methods can be applied in ...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Dragiev, P., Nadon, R., Makarenkov, V. Tags: DATA AND TEXT MINING Source Type: research

Statistical interpretation of machine learning-based feature importance scores for biomarker discovery
Motivation: Univariate statistical tests are widely used for biomarker discovery in bioinformatics. These procedures are simple, fast and their output is easily interpretable by biologists but they can only identify variables that provide a significant amount of information in isolation from the other variables. As biological processes are expected to involve complex interactions between variables, univariate methods thus potentially miss some informative biomarkers. Variable relevance scores provided by machine learning techniques, however, are potentially able to highlight multivariate interacting effects, but unlike the...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Huynh-Thu, V. A., Saeys, Y., Wehenkel, L., Geurts, P. Tags: DATA AND TEXT MINING Source Type: research

Boosting automatic event extraction from the literature using domain adaptation and coreference resolution
Motivation: In recent years, several biomedical event extraction (EE) systems have been developed. However, the nature of the annotated training corpora, as well as the training process itself, can limit the performance levels of the trained EE systems. In particular, most event-annotated corpora do not deal adequately with coreference. This impacts on the trained systems' ability to recognize biomedical entities, thus affecting their performance in extracting events accurately. Additionally, the fact that most EE systems are trained on a single annotated corpus further restricts their coverage. Results: We have enhanced o...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Miwa, M., Thompson, P., Ananiadou, S. Tags: DATA AND TEXT MINING Source Type: research

GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization
Motivation: Genome-scale metabolic network models have become an indispensable part of the increasingly important field of systems biology. Metabolic systems biology studies usually include three major components—network model construction, objective- and experiment-guided model editing and visualization, and simulation studies based mainly on flux balance analyses. Bioinformatics tools are required to facilitate these complicated analyses. Although some of the required functions have been served separately by existing tools, a free software resource that simultaneously serves the needs of the three major components ...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Liao, Y.-C., Tsai, M.-H., Chen, F.-C., Hsiung, C. A. Tags: SYSTEMS BIOLOGY Source Type: research

SEQCHIP: a powerful method to integrate sequence and genotype data for the detection of rare variant associations
Motivation: Next-generation sequencing greatly increases the capacity to detect rare-variant complex-trait associations. However, it is still expensive to sequence a large number of samples and therefore often small datasets are used. Given cost constraints, a potentially more powerful two-step strategy is to sequence a subset of the sample to discover variants, and genotype the identified variants in the remaining sample. If only cases are sequenced, directly combining sequence and genotype data will lead to inflated type-I errors in rare-variant association analysis. Although several methods have been developed to correc...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Liu, D. J., Leal, S. M. Tags: GENETICS AND POPULATION ANALYSIS Source Type: research

A novel variational Bayes multiple locus Z-statistic for genome-wide association studies with Bayesian model averaging
Motivation: For many complex traits, including height, the majority of variants identified by genome-wide association studies (GWAS) have small effects, leaving a significant proportion of the heritable variation unexplained. Although many penalized multiple regression methodologies have been proposed to increase the power to detect associations for complex genetic architectures, they generally lack mechanisms for false-positive control and diagnostics for model over-fitting. Our methodology is the first penalized multiple regression approach that explicitly controls Type I error rates and provide model over-fitting diagno...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Logsdon, B. A., Carty, C. L., Reiner, A. P., Dai, J. Y., Kooperberg, C. Tags: GENETICS AND POPULATION ANALYSIS Source Type: research

Analysis of case-control association studies with known risk variants
Motivation: The question of how to best use information from known associated variants when conducting disease association studies has yet to be answered. Some studies compute a marginal P-value for each Several Nucleotide Polymorphisms independently, ignoring previously discovered variants. Other studies include known variants as covariates in logistic regression, but a weakness of this standard conditioning strategy is that it does not account for disease prevalence and non-random ascertainment, which can induce a correlation structure between candidate variants and known associated variants even if the variants lie on d...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Zaitlen, N., Pasaniuc, B., Patterson, N., Pollack, S., Voight, B., Groop, L., Altshuler, D., Henderson, B. E., Kolonel, L. N., Marchand, L. L., Waters, K., Haiman, C. A., Stranger, B. E., Dermitzakis, E. T., Kraft, P., Price, A. L. Tags: GENETICS AND POPULATION ANALYSIS Source Type: research

Identifying differentially expressed transcripts from RNA-seq data with biological variation
We present Bayesian inference of transcripts from sequencing data (BitSeq), a Bayesian approach for estimation of transcript expression level from RNA-seq experiments. Inferred relative expression is represented by Markov chain Monte Carlo samples from the posterior probability distribution of a generative model of the read data. We propose a novel method for DE analysis across replicates which propagates uncertainty from the sample-level model while modelling biological variance using an expression-level-dependent prior. We demonstrate the advantages of our method using simulated data as well as an RNA-seq dataset with te...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Glaus, P., Honkela, A., Rattray, M. Tags: GENE EXPRESSION Source Type: research

Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data
In this study, we propose Bayesian inference of regulation of transcriptional activity (BIRTA) as a novel approach to infer both, TF and miRNA activities, from combined miRNA and mRNA expression data in a condition specific way. That means our model explains mRNA and miRNA expression for a specific experimental condition by the activities of certain miRNAs and TFs, hence allowing for differentiating between switches from active to inactive (negative switch) and inactive to active (positive switch) forms. Extensive simulations of our model reveal its good prediction performance in comparison to other approaches. Furthermore...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Zacher, B., Abnaof, K., Gade, S., Younesi, E., Tresch, A., Frohlich, H. Tags: GENE EXPRESSION Source Type: research

In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids
Motivation: Liquid chromatography–mass spectrometry-based metabolomics has gained importance in the life sciences, yet it is not supported by software tools for high throughput identification of metabolites based on their fragmentation spectra. An algorithm (ISIS: in silico identification software) and its implementation are presented and show great promise in generating in silico spectra of lipids for the purpose of structural identification. Instead of using chemical reaction rate equations or rules-based fragmentation libraries, the algorithm uses machine learning to find accurate bond cleavage rates in a mass spe...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Kangas, L. J., Metz, T. O., Isaac, G., Schrom, B. T., Ginovska-Pangovska, B., Wang, L., Tan, L., Lewis, R. R., Miller, J. H. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

Fast and sensitive mapping of bisulfite-treated sequencing data
In this study, we present a seed-based approach based on enhanced suffix arrays in conjunction with Myers bit-vector algorithm to efficiently extend seeds to optimal semi-global alignments while allowing for bisulfite-related substitutions. It outperforms most current approaches in terms of sensitivity and performs time-competitive in mapping hundreds of millions of sequencing reads to vertebrate genomes. Availability: The software segemehl is freely available at http://www.bioinf.uni-leipzig.de/Software/segemehl. Contact: E-mail: steve@bioinf.uni-leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Otto, C., Stadler, P. F., Hoffmann, S. Tags: SEQUENCE ANALYSIS Source Type: research

Speeding up tandem mass spectral identification using indexes
Motivation: Tandem mass spectrometry (MS/MS) has been routinely used in proteomics studies. Post-translational modification (PTM) identification is a challenging problem in tandem mass spectral analysis. Results: In this article, we define two scoring functions for identifying peptides/proteins with PTMs from MS/MS spectra: match scores and diagonal scores, as well as two spectral identification problems based on the two scores. We propose several index-based algorithms for the two problems. Both theoretical and experimental analyses show that the index-based algorithms significantly improve on speed when compared with exi...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Liu, X., Mammana, A., Bafna, V. Tags: SEQUENCE ANALYSIS Source Type: research

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
Motivation: Accurate alignment of large numbers of sequences is demanding and the computational burden is further increased by downstream analyses depending on these alignments. With the abundance of sequence data, an integrative approach of adding new sequences to existing alignments without their full re-computation and maintaining the relative matching of existing sequences is an attractive option. Another current challenge is the extension of reference alignments with fragmented sequences, as those coming from next-generation metagenomics, that contain relatively little information. Widely used methods for alignment ex...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Loytynoja, A., Vilella, A. J., Goldman, N. Tags: SEQUENCE ANALYSIS Source Type: research

OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing
Motivation: Next-generation DNA sequencing platforms are becoming increasingly cost-effective and capable of providing enormous number of reads in a relatively short time. However, their accuracy and read lengths are still lagging behind those of conventional Sanger sequencing method. Performance of next-generation sequencing platforms is fundamentally limited by various imperfections in the sequencing-by-synthesis and signal acquisition processes. This drives the search for accurate, scalable and computationally tractable base calling algorithms capable of accounting for such imperfections. Results: Relying on a statistic...
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Das, S., Vikalo, H. Tags: GENOME ANALYSIS Source Type: research

Statistical analysis of glycosylation profiles to compare tissue type and inflammatory disease state
We present a study on the testing and validation of statistical analysis tools to aid the structural elucidation of these analyses as well as using the results to answer biologically relevant questions. Results: We show the usefulness of data reduction and statistical analysis in the interpretation of complex glycosylation data. The reduction does not result in the loss of importance of the glycosylation information as shown by comparison of control and disease samples in two tissue types. Contact: catherine.hayes@medkem.gu.se Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - June 23, 2012 Category: Bioinformatics Authors: Hayes, C. A., Nemes, S., Karlsson, N. G. Tags: GENOME ANALYSIS Source Type: research

QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence
Conclusions: QuartetS-DB is one of the largest orthology resources available to date. Because its orthologypredictions are underpinned by evolutionary evidence obtained from sequenced genomes, weexpect its accuracy to continue to increase in future releases as the genomes of additionalspecies are sequenced.
Source: BMC Bioinformatics - Latest articles - June 22, 2012 Category: Bioinformatics Authors: Chenggang YuValmik DesaiLi ChengJaques Reifman Source Type: research

Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures
Conclusions: This approach automates the rapid creation of protein domain hierarchies and thus will eliminate one of the most time consuming aspects of conserved domain database curation. At the same time, it also facilitates protein domain annotation by identifying those pattern residues that most distinguish each protein domain subgroup from other related subgroups.
Source: BMC Bioinformatics - Latest articles - June 22, 2012 Category: Bioinformatics Authors: Andrew NeuwaldChristopher LanczyckiAron Marchler-Bauer Source Type: research

Error-correcting properties of the SOLiD Exact Call Chemistry
Conclusions: The Exact Call Chemistry increases the accuracy of the SOLiD platform, enabling manypotential miscalls to be prevented. However, single miscalls in the color sequence canproduce complex but localised patterns of error in the decoded nucleotide sequence.Analysis of similar codes shows that some exist that, if implemented in alternativechemistries, should have superior performance.
Source: BMC Bioinformatics - Latest articles - June 22, 2012 Category: Bioinformatics Authors: Tim MassinghamNick Goldman Source Type: research

Infantile Amoebiasis: A Case Report
Amoebiasis continues to be a major cause of morbidity and mortality in children in developing countries. Entamoeba histolytica infections are commonly observed in tropical and subtropical regions of the world including Iran. In developed countries Entamoeba histolytica infections are commonly seen in travelers, recent immigrants, homosexual men, and inmates of institutions. The disease is more severe in the two extremes of life. This paper paper describes a four-month-old male infant with Entamoeba histolytica presenting initially with refusal of feeds, hyperactive bowel sound, vomiting, and diarrhea. A fecal sample was po...
Source: EURASIP Journal on Bioinformatics and Systems Biology - June 21, 2012 Category: Bioinformatics Source Type: research

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools
Conclusions: The data and tools we present allow the creation of multiple result sets using a singlecomputation, permitting computational results to be shared between groups for largesequence data sets.
Source: BMC Bioinformatics - Latest articles - June 21, 2012 Category: Bioinformatics Authors: Andreas WilkeTravis HarrisonJared WilkeningDawn FieldElizabeth GlassNikos KyrpidesKonstantinos MavrommatisFolker Meyer Source Type: research

Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein's structural organization
Conclusions: The simple framework of protein contact networks and their subnetworks based on London van der Waalsforce is able to capture several known properties of protein structure as well as can unravel several newfeatures. The thermophiles do not only have the higher number of long-range interactions; they also havelarger cluster of connected residues at higher interaction strengths among amino acids, than their mesophiliccounterparts. It can reestablish the significant role of long-range hydrophobic clusters in protein folding andstabilization; at the same time, it shed light on the higher communication ability of hy...
Source: BMC Bioinformatics - Latest articles - June 21, 2012 Category: Bioinformatics Authors: Dhriti SenguptaSudip Kundu Source Type: research

Comparative study of classification algorithms for immunosignaturing data
Conclusions: 'Naive Bayes' algorithm appears to accommodate the complex patterns hidden within multilayered immunosignaturing microarray data due to its fundamental mathematical properties.
Source: BMC Bioinformatics - Latest articles - June 21, 2012 Category: Bioinformatics Authors: Muskan KukrejaStephen JohnstonPhillip Stafford Source Type: research

miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments
Conclusion: This work presents an integrated pipline, miREvo, for exploring the expressional and evolutionary dynamics of miRNAs across multiple species. MiREvo is standalone, modular, and freely available at http://evolution.sysu.edu.cn/software/mirevo.htm under the GNU/GPL license.
Source: BMC Bioinformatics - Latest articles - June 21, 2012 Category: Bioinformatics Authors: Ming WenYang ShenShu-Hua ShiTian Tang Source Type: research

System approach to modeling of liver glucose metabolism with physiologically interpreted model parameters outgoing from [18F]FDG concentrations measured by PET
Abstract: New mathematical models from physiologically interpreted parameters capable of evaluating glucose metabolism within the liver and/or the whole body were developed.The group of pigs in a fasting state and the group of pigs with euglycemic supraphysiological hyperinsulinemia were scanned by positron emission tomography after a single dose of [18F]FDG tracer. Simultaneously frequent sampling of the dynamic data of [18F]FDG plasma concentration in artery, portal vein and hepatic vein was obtained. A system approach to the liver and/or the whole-body system by the tools of linear dynamic sysztem theory was used.Three ...
Source: Computer Methods and Programs in Biomedicine - June 20, 2012 Category: Bioinformatics Authors: Zuzana Rausova, Jana Chrenova, Pirjo Nuutila, Patricia Iozzo, Ladislav Dedik Tags: Section III: Experiences with Methods, Systems and Programs Source Type: research

A warning concerning the estimation of multinomial logistic models with correlated responses in SAS
Abstract: Kuss and McLerran in a paper in this journal provide SAS code for the estimation of multinomial logistic models for correlated data. Their motivation derived from two papers that recommended to estimate such models using a Poisson likelihood, which is according to Kuss and McLerran “statistically correct but computationally inefficient”. Kuss and McLerran propose several estimating methods. Some of these are based on the fact that the multinomial model is a multivariate binary model. Subsequently a procedure proposed by Wright is exploited to fit the models. In this paper we will show that the new computation...
Source: Computer Methods and Programs in Biomedicine - June 20, 2012 Category: Bioinformatics Authors: Mark de Rooij, Hailemichael M. Worku Tags: Section III: Experiences with Methods, Systems and Programs Source Type: research

Wiener sliding-mode control for artificial pancreas: A new nonlinear approach to glucose regulation
Abstract: Type 1 diabetic patients need insulin therapy to keep their blood glucose close to normal. In this paper an attempt is made to show how nonlinear control-oriented model may be used to improve the performance of closed-loop control of blood glucose in diabetic patients. The nonlinear Wiener model is used as a novel modeling approach to be applied to the glucose control problem. The identified Wiener model is used in the design of a robust nonlinear sliding mode control strategy. Two configurations of the nonlinear controller are tested and compared to a controller designed with a linear model. The controllers are ...
Source: Computer Methods and Programs in Biomedicine - June 20, 2012 Category: Bioinformatics Authors: Amjad Abu-Rmileh, Winston Garcia-Gabin Tags: Section III: Experiences with Methods, Systems and Programs Source Type: research

Determination of nonlinear fibre-reinforced biphasic poroviscoelastic constitutive parameters of articular cartilage using stress relaxation indentation testing and an optimizing finite element analysis
Abstract: An inverse method was developed to determine the material constitutive parameters of human articular cartilage from stress relaxation indentation tests. The cartilage was modeled as a fibre-reinforced nonlinear biphasic poroviscoelastic material, and a finite element (FE) model was used with a simulated annealing (SA) optimization algorithm to determine the material parameters that minimized the error between the experimental and predicted time dependant indentation loads. The values of the 15 optimized material parameters were found to be insensitive to the initial guesses, and, when friction between the indente...
Source: Computer Methods and Programs in Biomedicine - June 20, 2012 Category: Bioinformatics Authors: A. Seifzadeh, D.C.D. Oguamanam, N. Trutiak, M. Hurtig, M. Papini Tags: Section II: Systems and Programs Source Type: research

RandoWeb, an online randomization tool for clinical trials
This article describes RandoWeb, a generic tool allowing online randomizations for clinical trials. It allows some users to specify the randomization methods to use, patient data to collect or compute, and other users authorized to access the tool and their rights. Randomization can be defined through a randomization list or by using a dynamic method such as minimization. The randomization lists can be stratified and use block decomposition to maintain the best possible balance between the arms of the trial, even for the case when a trial is stopped prematurely. The block definition used by RandoWeb is slightly different f...
Source: Computer Methods and Programs in Biomedicine - June 20, 2012 Category: Bioinformatics Authors: Vincent Morice Tags: Section II: Systems and Programs Source Type: research

A monitoring tool of workers’ activity at Video Display Terminals for investigating VDT-related risk of musculoskeletal disorders
Abstract: Today the risk factors related to the use of Video Display Terminals (VDT) are assessed by investigating the actual activities at the VDT through subjective questionnaires and/or quantitative measurements. Questionnaire outcomes are quite imprecise and seldom objective. Quantitative measurements (EMG recordings, electrogoniometers, motion analysis systems) mostly prevent subjects from moving freely while working at the VDT. The paper presents an automatic tool for the monitoring of activity at VDTs, using a quantitative, objective approach. The suitability of the proposed tool was fully tested in the laboratory, ...
Source: Computer Methods and Programs in Biomedicine - June 20, 2012 Category: Bioinformatics Authors: Sandra Morelli, Mauro Grigioni, Maurizio Ferrarin, Alberto Boschetto, Monica Brocco, Giovanni Maccioni, Daniele Giansanti Tags: Section II: Systems and Programs Source Type: research

Simple methods for segmentation and measurement of diabetic retinopathy lesions in retinal fundus images
Highlights: ► A complete segmentation system is developed for segmenting all types of DR. ► DR is segmented by using inverse segmentation and background image approach. ► Background image divides image into high and low intensity areas in segmentation. ► The method dynamically adapts itself to changing image conditions and segments DR.Abstract: Diabetic retinopathy (DR) is one of the most important complications of diabetes mellitus, which causes serious damages in the retina, consequently visual loss and sometimes blindness if necessary medical treatment is not applied on time. One of the difficulties in this illn...
Source: Computer Methods and Programs in Biomedicine - June 20, 2012 Category: Bioinformatics Authors: Cemal Köse, Uğur Şevik, Cevat İkibaş, Hidayet Erdöl Tags: Section II: Systems and Programs Source Type: research