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Prediction of protein binding sites in protein structures using hidden Markov support vector machineEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The improved prediction performance and computational efficiency of the method based on hidden Markov support vector machine can be attributed to the following three factors. Firstly, the relation between labels of neighbouring residues is useful for protein binding site prediction. Secondly, the kernel trick is very advantageous to this field. Thirdly, the complexity of the training step for hidden Markov support vector machine is linear with the number of training samples by using the cutting-plane algorithm. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 20, 2009 Category: Bioinformatics Authors: Bin LiuXiaolong WangLei LinBuzhou TangQiwen DongXuan Wang Source Type: journals

Automatic Clustering of Flow Cytometry Data with Density-Based MergingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe methodology and software to automatically identify cell populations in flow cytometry data. Our approach advances the paradigm of manually gating sequential two-dimensional projections of the data to a procedure that automatically produces gates based on statistical theory. Our approach is nonparametric and can reproduce nonconvex subpopulations that are known to occur in flow cytometry samples, but which cannot be produced with current parametric model-based approaches. We illustrate the methodology with a sample of mouse spleen and peritoneal cavity cells. (Source: Advances in Bioinformatics)
Source: Advances in Bioinformatics - November 19, 2009 Category: Bioinformatics Source Type: journals

SitesIdentify: a protein functional site prediction toolEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at www.manchester.ac.uk/bioinformatics/sitesidentify/ (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 18, 2009 Category: Bioinformatics Authors: Tracey BrayPedro ChanSalim BougouffaRichard GreavesAndrew DoigJim Warwicker Source Type: journals

The ontology of biological sequencesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 18, 2009 Category: Bioinformatics Authors: Robert HoehndorfJanet KelsoHeinrich Herre Source Type: journals

Nonlinear preprocessing method for detecting peaks from gas chromatogramsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results demonstrate that the proposed method can achieve near perfect peak detection performance while maintaining very small false alarm probabilities in case of gas chromatograms. Given the fact that biological signals appear in the form of peaks in various experimental data and that the propose method can easily be extended to such data, our approach will be a useful and robust tool that can help researchers highlight valid signals in their noisy measurements. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 18, 2009 Category: Bioinformatics Authors: Byonghyo ShimHyeyoung MinSungroh Yoon Source Type: journals

Fluorescence Intensity Normalisation: Correcting for Time Effects in Large-Scale Flow Cytometric AnalysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A next step to interpret the findings generated by genome-wide association studies is to associate molecular quantitative traits with disease-associated alleles. To this end, researchers are linking disease risk alleles with gene expression quantitative trait loci (eQTL). However, gene expression at the mRNA level is only an intermediate trait and flow cytometry analysis can provide more downstream and biologically valuable protein level information in multiple cell subsets simultaneously using freshly obtained samples. Because the throughput of flow cytometry is currently limited, experiments may need to span over several...
Source: Advances in Bioinformatics - November 17, 2009 Category: Bioinformatics Source Type: journals

In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: In their article entitled ‘Can sugars be produced from fatty acids? A test case for pathway analysis tools’ de Figueiredo and co-authors assess the performance of three pathway prediction tools (METATOOL, PathFinding and Pathway Hunter Tool) using the synthesis of glucose-6-phosphate (G6P) from acetyl-CoA in humans as a test case. We think that this article is biased for three reasons: (i) the metabolic networks used as input for the respective tools were of very different sizes; (ii) the ‘assessment’ is restricted to two study cases; (iii) developers are inherently more skilled to use t...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Faust, K., Croes, D., van Helden, J. Tags: SYSTEMS BIOLOGY Source Type: journals

ncRNAppi--a tool for identifying disease-related miRNA and siRNA targeting pathwaysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: Currently, there are a number of databases which store microRNA (miRNA) information, and tools available which provide miRNA target prediction. In this article, we describe a novel web-based tool that integrate the miRNA-targeted mRNA data, protein–protein interactions (PPI) records, tissues, biochemical pathways, human disease and gene function information to establish a disease-related miRNA target pathway database. This database is unique in the sense that it links miRNA target genes with their PPI partners according to being tissue- and diseases-specific or both. The same approach is also applied to siRN...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Ng, K.-L., Liu, H.-C., Lee, S.-C. Tags: DATABASES AND ONTOLOGIES Source Type: journals

SimCT: a generic tool to visualize ontology-based relationships for biological objectsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a web-based service, SimCT, which allows to graphically display the relationships between biological objects (e.g. genes or proteins) based on their annotations to a biomedical ontology. The result is presented as a tree of these objects, which can be viewed and explored through a specific java applet designed to highlight relevant features. Unlike the numerous tools that search for overrepresented terms, SimCT draws a simplified representation of biological terms present in the set of objects, and can be applied to any ontology for which annotation data is available. Being web-based, it does not require prior i...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Herrmann, C., Berard, S., Tichit, L. Tags: DATABASES AND ONTOLOGIES Source Type: journals

Client-side integration of life science literature resourcesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: The online resources in the life sciences are characterized by a great fragmentation and one of the pressing issues of bioinformatics is making the integration of these resources a smoother and more flexible process than it is currently. Here we present i-cite, a browser extension, which implements a client-side model of integration which improves the navigation within the rapidly increasing life science literature and links terms from it to corresponding non-textual data. Availability: http://i-cite.org. Contact: nan23@cam.ac.uk (Source: Bioinformatics)
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Easty, R., Nikolov, N. Tags: DATABASES AND ONTOLOGIES Source Type: journals

W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: W-ChIPMotifs is a web application tool that provides a user friendly interface for de novo motif discovery. The web tool is based on our previous ChIPMotifs program which is a de novo motif finding tool developed for ChIP-based high-throughput data and incorporated various ab initio motif discovery tools such as MEME, MaMF, Weeder and optimized the significance of the detected motifs by using a bootstrap resampling statistic method and a Fisher test. Use of a randomized statistical model like bootstrap resampling can significantly increase the accuracy of the detected motifs. In our web tool, we have modified the ...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Jin, V. X., Apostolos, J., Nagisetty, N. S. V. R., Farnham, P. J. Tags: SYSTEMS BIOLOGY Source Type: journals

Processing and population genetic analysis of multigenic datasets with ProSeq3 softwareEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: The current tendency in molecular population genetics is to use increasing numbers of genes in the analysis. Here I describe a program for handling and population genetic analysis of DNA polymorphism data collected from multiple genes. The program includes a sequence/alignment editor and an internal relational database that simplify the preparation and manipulation of multigenic DNA polymorphism datasets. The most commonly used DNA polymorphism analyses are implemented in ProSeq3, facilitating population genetic analysis of large multigenic datasets. Extensive input/output options make ProSeq3 a convenient hub ...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Filatov, D. A. Tags: GENETICS AND POPULATION ANALYSIS Source Type: journals

VDNA: The virtual DNA plug-in for VMDEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: The DNA inter base pair step parameters (Tilt, Roll, Twist, Shift, Slide, Rise) are a standard internal coordinate representation of DNA. In the absence of bend and shear, it is relatively easy to mentally visualize how Twist and Rise generate the familiar double helix. More complex structures do not readily yield to such intuition. For this reason, we developed a plug-in for VMD that accepts a set of mathematical expressions as input and generates a coarse-grained model of DNA as output. This feature of VDNA appears to provide a unique approach to DNA modeling. Predefined expressions include: linear, sheared, ben...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Bishop, T. C. Tags: STRUCTURAL BIOINFORMATICS Source Type: journals

EASYMIFS and SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structuresEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: SiteHound uses Molecular Interaction Fields (MIFs) produced by EasyMIFs to identify protein structure regions that show a high propensity for interaction with ligands. The type of binding site identified depends on the probe atom used in the MIF calculation. The input to EasyMIFs is a PDB file of a protein structure; the output MIF serves as input to SiteHound, which in turn produces a list of putative binding sites. Extensive testing of SiteHound for the detection of binding sites for drug-like molecules and phosphorylated ligands has been carried out. Availability: EasyMIFs and SiteHound executables for Linux, M...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Ghersi, D., Sanchez, R. Tags: STRUCTURAL BIOINFORMATICS Source Type: journals

PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: The increasing number of available atomic 3D structures of transmembrane channel proteins represents a valuable resource for better understanding their structure–function relationships and to eventually predict their selectivity. Herein, we present PoreLogo, an automatic tool for analysing, visualizing and comparing the amino acid composition of transmembrane channels and its conservation across the corresponding protein family. Availability: PoreLogo is accessible as a public web server at http://www.ebi.ac.uk/thornton-srv/software/PoreLogo/. Contacts: marial@ebi.ac.uk; romina.oliva@uniparthenope.it. (Source: Bioinformatics)
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Oliva, R., Thornton, J. M., Pellegrini-Calace, M. Tags: STRUCTURAL BIOINFORMATICS Source Type: journals

MOODS: fast search for position weight matrix matches in DNA sequencesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online matching algorithms, achieving considerably faster scanning speed than with a simple brute-force search. MOODS is written in C++, with bindings for the popular BioPerl and Biopython toolkits. It can easily be adapted for different purposes and integrated into existing workflows. It can also be used as a C++ library. Availability: The package with documentation and examples of usage is available at http://www.cs.helsinki.fi/group/pssmfind. The source co...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Korhonen, J., Martinmaki, P., Pizzi, C., Rastas, P., Ukkonen, E. Tags: SEQUENCE ANALYSIS Source Type: journals

Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and DiscussionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Discussion (IMRAD). Classifying sentences into these categories can benefit many other text-mining tasks. Although many studies have applied different approaches for automatically classifying sentences in MEDLINE abstracts into the IMRAD categories, few have explored the classification of sentences that appear in full-text biomedical articles. We first evaluated whether sentences in full-text biomedical articles could be reliably annotated into the IMRAD format and then explored different approaches for automatically classifying these sentences into the IMRAD categories. Our results show an overall annotation agreement of ...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Agarwal, S., Yu, H. Tags: DATA AND TEXT MINING Source Type: journals

Functionally guided alignment of protein interaction networks for module detectionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Functional module detection within protein interaction networks is a challenging problem due to the sparsity of data and presence of errors. Computational techniques for this task range from purely graph theoretical approaches involving single networks to alignment of multiple networks from several species. Current network alignment methods all rely on protein sequence similarity to map proteins across species. Results: Here we carry out network alignment using a protein functional similarity measure. We show that using functional similarity to map proteins across species improves network alignment in terms of ...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Ali, W., Deane, C. M. Tags: SYSTEMS BIOLOGY Source Type: journals

Computing the shortest elementary flux modes in genome-scale metabolic networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Elementary flux modes (EFMs) represent a key concept to analyze metabolic networks from a pathway-oriented perspective. In spite of considerable work in this field, the computation of the full set of elementary flux modes in large-scale metabolic networks still constitutes a challenging issue due to its underlying combinatorial complexity. Results: In this article, we illustrate that the full set of EFMs can be enumerated in increasing order of number of reactions via integer linear programming. In this light, we present a novel procedure to efficiently determine the K-shortest EFMs in large-scale metabolic net...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: de Figueiredo, L. F., Podhorski, A., Rubio, A., Kaleta, C., Beasley, J. E., Schuster, S., Planes, F. J. Tags: SYSTEMS BIOLOGY Source Type: journals

Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identificationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, a systematic method is proposed for identifying metabolic biomarkers in urine samples by selecting candidate biomarkers from altered genome-wide gene expression signatures of cancer cells. Biomarkers identified by the present study have increased coherence and robustness because the significances of biomarkers are validated in both gene expression profiles and metabolic profiles. Results: The proposed method was applied to the gene expression profiles and urine samples of 50 breast cancer patients and 50 normal persons. Nine altered metabolic pathways were identified from the breast cancer gene expression si...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Nam, H., Chung, B. C., Kim, Y., Lee, K., Lee, D. Tags: SYSTEMS BIOLOGY Source Type: journals

How and when should interactome-derived clusters be used to predict functional modules and protein function?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Clustering of protein–protein interaction networks is one of the most common approaches for predicting functional modules, protein complexes and protein functions. But, how well does clustering perform at these tasks? Results: We develop a general framework to assess how well computationally derived clusters in physical interactomes overlap functional modules derived via the Gene Ontology (GO). Using this framework, we evaluate six diverse network clustering algorithms using Saccharomyces cerevisiae and show that (i) the performances of these algorithms can differ substantially when run on the same networ...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Song, J., Singh, M. Tags: SYSTEMS BIOLOGY Source Type: journals

Automatic assignment of reaction operators to enzymatic reactionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The analysis and comparison of enzymatic reactions according to their electron shift patterns is defining enzyme groups characterised by unique reaction cores. Our results demonstrate the applicability of the Dugundji–Ugi model as a reasonable pre-classification system allowing an objective and rational view on biochemical reactions. Availability: The program to generate reaction matrix descriptors is available upon request. Contact: d.schomburg@tu-bs.de (Source: Bioinformatics)
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Leber, M., Egelhofer, V., Schomburg, I., Schomburg, D. Tags: SYSTEMS BIOLOGY Source Type: journals

Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experimentsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: The goal of present -omics sciences is to understand biological systems as a whole in terms of interactions of the individual cellular components. One of the main building blocks in this field of study is proteomics where tandem mass spectrometry (LC-MS/MS) in combination with isotopic labelling techniques provides a common way to obtain a direct insight into regulation at the protein level. Methods to identify and quantify the peptides contained in a sample are well established, and their output usually results in lists of identified proteins and calculated relative abundance values. The next step is to move a...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Albaum, S. P., Neuweger, H., Franzel, B., Lange, S., Mertens, D., Trotschel, C., Wolters, D., Kalinowski, J., Nattkemper, T. W., Goesmann, A. Tags: GENE EXPRESSION Source Type: journals

Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistanceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Type 2 diabetes is a chronic metabolic disease that involves both environmental and genetic factors. To understand the genetics of type 2 diabetes and insulin resistance, the DIabetes Genome Anatomy Project (DGAP) was launched to profile gene expression in a variety of related animal models and human subjects. We asked whether these heterogeneous models can be integrated to provide consistent and robust biological insights into the biology of insulin resistance. Results: We perform integrative analysis of the 16 DGAP data sets that span multiple tissues, conditions, array types, laboratories, species, genetic b...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Park, P. J., Kong, S. W., Tebaldi, T., Lai, W. R., Kasif, S., Kohane, I. S. Tags: GENE EXPRESSION Source Type: journals

Bayesian detection of non-sinusoidal periodic patterns in circadian expression dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present an analysis of variance (ANOVA) periodicity detector and its Bayesian extension that can be used to discover periodic transcripts of arbitrary shapes from replicated gene expression profiles. The models are applicable when the profiles are collected at comparable time points for at least two cycles. We provide an empirical Bayes procedure for estimating parameters of the prior distributions and derive closed-form expressions for the posterior probability of periodicity, enabling efficient computation. The model is applied to two datasets profiling circadian regulation in murine liver and skeletal muscle, reveali...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Chudova, D., Ihler, A., Lin, K. K., Andersen, B., Smyth, P. Tags: GENE EXPRESSION Source Type: journals

The interwinding nature of protein-protein interfaces and its implication for protein complex formationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Structural features at protein–protein interfaces can be studied to understand protein–protein interactions. It was noticed that in a dataset of 45 multimeric proteins the interface could either be described as flat against flat or protruding/interwound. In the latter, residues within one chain were surrounded by those in other chains, whereas in the former they were not. Results: A simple method was developed that could distinguish between these two types with results that matched those made by a human annotator. Applying this automatic method to a large dataset of 888 structures, chains at interfa...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Yura, K., Hayward, S. Tags: STRUCTURAL BIOINFORMATICS Source Type: journals

LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue predictionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Identifying residues that interact with ligands is useful as a first step to understanding protein function and as an aid to designing small molecules that target the protein for interaction. Several studies have shown that sequence features are very informative for this type of prediction, while structure features have also been useful when structure is available. We develop a sequence-based method, called LIBRUS, that combines homology-based transfer and direct prediction using machine learning and compare it to previous sequence-based work and current structure-based methods. Results: Our analysis shows that...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Kauffman, C., Karypis, G. Tags: STRUCTURAL BIOINFORMATICS Source Type: journals

Reproducing the manual annotation of multiple sequence alignments using a SVM classifierEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present here an automated editing method based on the classification of ‘valid’ and ‘invalid’ sites. Results: A support vector machine (SVM) classifier is trained to reproduce the decisions made during manual editing with an accuracy of 95.0%. This implies that manual editing can be made reproducible and applied to large-scale analyses. We further demonstrate that it is possible to retrain/extend the training of the classifier by providing examples of multiple sequence alignment (MSA) annotation. Near optimal training can be achieved with only 1000 annotated sites, or roughly three samples of pro...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Blouin, C., Perry, S., Lavell, A., Susko, E., Roger, A. J. Tags: PHYLOGENETICS Source Type: journals

Adaptive multi-agent architecture for functional sequence motifs recognitionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Accurate genome annotation or protein function prediction requires precise recognition of functional sequence motifs. Many computational motif prediction models have been proposed. Due to the complexity of the biological data, it may be desirable to apply an integrated approach that uses multiple models for analysis. Results: In this article, we propose a novel multi-agent architecture for the general purpose of functional sequence motif recognition. The approach takes advantage of the synergy provided by multiple agents through the employment of different agents equipped with distinctive problem solving skills...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Zeng, J., Alhajj, R., Demetrick, D. Tags: SEQUENCE ANALYSIS Source Type: journals

Detection of new protein domains using co-occurrence: application to Plasmodium falciparumEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Hidden Markov models (HMMs) have proved to be a powerful tool for protein domain identification in newly sequenced organisms. However, numerous domains may be missed in highly divergent proteins. This is the case for Plasmodium falciparum proteins, the main causal agent of human malaria. Results: We propose a method to improve the sensitivity of HMM domain detection by exploiting the tendency of the domains to appear preferentially with a few other favorite domains in a protein. When sequence information alone is not sufficient to warrant the presence of a particular domain, our method enables its detection on ...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Terrapon, N., Gascuel, O., Marechal, E., Breehelin, L. Tags: SEQUENCE ANALYSIS Source Type: journals

HHsvm: fast and accurate classification of profile-profile matches identified by HHsearchEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Recently developed profile–profile methods rival structural comparisons in their ability to detect homology between distantly related proteins. Despite this tremendous progress, many genuine relationships between protein families cannot be recognized as comparisons of their profiles result in scores that are statistically insignificant. Results: Using known evolutionary relationships among protein superfamilies in SCOP database, support vector machines were trained on four sets of discriminatory features derived from the output of HHsearch. Upon validation, it was shown that the automatic classification o...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Dlakic, M. Tags: SEQUENCE ANALYSIS Source Type: journals

Genome analysis with inter-nucleotide distancesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective of this work was to find a mapping scheme directly related to DNA characteristics and that would be useful in discriminating between different species. Mathematical models to explore DNA correlation structures may contribute to a better knowledge of the DNA and to find a concise DNA description. Results: We developed a methodology to process DNA sequences based on inter-nucleotide distances. Our main contribution is a method to obtain genomic signatures for complete genomes, based on the inter-nucleotide distances, that are able to discriminate between different species. Using these signatures and hierarchica...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Afreixo, V., Bastos, C. A. C., Pinho, A. J., Garcia, S. P., Ferreira, P. J. S. G. Tags: SEQUENCE ANALYSIS Source Type: journals

Quantitative measurement of aging using image texture entropyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: A key element in understanding the aging of Caenorhabditis elegans is objective quantification of the morphological differences between younger and older animals. Here we propose to use the image texture entropy as an objective measurement that reflects the structural deterioration of the C.elegans muscle tissues during aging. Results: The texture entropy and directionality of the muscle microscopy images were measured using 50 animals on Days 0, 2, 4, 6, 8, 10 and 12 of adulthood. Results show that the entropy of the C.elegans pharynx tissues increases as the animal ages, but a sharper increase was measured be...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Shamir, L., Wolkow, C. A., Goldberg, I. G. Tags: DATA AND TEXT MINING Source Type: journals

Identifiability of isoform deconvolution from junction arrays and RNA-SeqEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Splice junction microarrays and RNA-seq are two popular ways of quantifying splice variants within a cell. Unfortunately, isoform expressions cannot always be determined from the expressions of individual exons and splice junctions. While this issue has been noted before, the extent of the problem on various platforms has not yet been explored, nor have potential remedies been presented. Results: We propose criteria that will guarantee identifiability of an isoform deconvolution model on exon and splice junction arrays and in RNA-Seq. We show that up to 97% of 2256 alternatively spliced human genes selected fro...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Hiller, D., Jiang, H., Xu, W., Wong, W. H. Tags: GENE EXPRESSION Source Type: journals

Lost in translation: an assessment and perspective for computational microRNA target identificationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
MicroRNAs (miRNAs) are a class of short endogenously expressed RNA molecules that regulate gene expression by binding directly to the messenger RNA of protein coding genes. They have been found to confer a novel layer of genetic regulation in a wide range of biological processes. Computational miRNA target prediction remains one of the key means used to decipher the role of miRNAs in development and disease. Here we introduce the basic idea behind the experimental identification of miRNA targets and present some of the most widely used computational miRNA target identification programs. The review includes an assessment of...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Alexiou, P., Maragkakis, M., Papadopoulos, G. L., Reczko, M., Hatzigeorgiou, A. G. Tags: GENE EXPRESSION Source Type: journals

Interactive surface-guided segmentation of brain MRI dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: MRI segmentation is a process of deriving semantic information from volume data. For brain MRI data, segmentation is initially performed at a voxel level and then continued at a brain surface level by generating its approximation. While successful most of the time, automated brain segmentation may leave errors which have to be removed interactively by editing individual 2D slices. We propose an approach for correcting these segmentation errors in 3D modeling space. We actively use the brain surface, which is estimated (potentially wrongly) in the automated FreeSurfer segmentation pipeline. It allows us to work wi...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Konstantin Levinski, Alexei Sourin, Vitali Zagorodnov Source Type: journals

Adaptive threshold method for the peak detection of photoplethysmographic waveformEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Photoplethysmography (PPG)-based temporal analyses have been widely used as a useful analytical method in physiological and cardiovascular diagnosis. Most of temporal approaches of PPG are based on detected peak points, peak and foot of PPG. The aim of presented study is the development of improved peak detection algorithm of PPG waveform. The present study demonstrates a promising approach to overcome respiration effect and to detect PPG peak. More extensive investigation is necessary to adapt for the cardiovascular diseases, whose PPG morphology has different form. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Hang Sik H.S. Shin, Chungkeun Lee, Myoungho Lee Source Type: journals

Pleural nodule identification in low-dose and thin-slice lung computed tomographyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: A completely automated system for the identification of pleural nodules in low-dose and thin-slice computed tomography (CT) of the lung has been developed. The directional-gradient concentration method has been applied to the pleura surface and combined with a morphological opening-based procedure to generate a list of nodule candidates. Each nodule candidate is characterized by 12 morphological and textural features, which are analyzed by a rule-based filter and a neural classifier. This detection system has been developed and validated on a dataset of 42 annotated CT scans. The k-fold cross validation has been ...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: A. Retico, M.E. M.E. Fantacci, I. Gori, P. Kasae, B. Golosio, A. Piccioli, P. Cerello, G. De Nunzio, S. Tangaro Source Type: journals

Computer method for perinatal screening of cardiac murmur using fetal phonocardiographyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: The main purpose of this paper is to demonstrate the capability of fetal phonocardiographic measurements to indicate some congenital heart defects. It deals with the results of investigations carried out during the last four years involving 820 pregnant women. During the investigations fetal cardiac murmurs presenting typical waveforms and incidences of acoustic signals were recorded. Causes of these murmurs are suggested based on comparison with the well-known waveforms of infants and children. A sophisticated signal processing method for murmur discovery is presented, that is also useful for automatic perinatal...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: F. Kovács, N. Kersner, K. Kádár, G. Hosszú Source Type: journals

A computationally advantageous system for fitting probabilistic decompression models to empirical dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: To investigate the nature and mechanisms of decompression sickness (DCS), we developed a system for evaluating the success of decompression models in predicting DCS probability from empirical data. Model parameters were estimated using maximum likelihood techniques. Exact integrals of risk functions and tissue kinetics transition times were derived. Agreement with previously published results was excellent including: (a) maximum likelihood values within one log-likelihood unit of previous results and improvements by re-optimization; (b) mean predicted DCS incidents within 1.4% of observed DCS; and (c) time of DCS...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Laurens E. L.E. Howle, Paul W. Weber, Richard D. Vann Source Type: journals

An interactive graphical user interface for comprehensive analysis of human and swine cardiac monophasic action potentialEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: This research describes a novel monophasic action potential (MAP) annotation algorithm coupled with an interactive graphical user interface (GUI). This algorithm incorporates a number of features to reduce error. Additionally, the GUI has several convenient features to view and manipulate the annotation visually. We analyzed data from swine and human hearts in normal sinus rhythm, during myocardial ischemia, and while eliciting high rates. Validation results indicate correlation >90% between human and computer measurements. This analysis system has several clinical applications in electrophysiological interventio...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Maneesh Shrivastav, Paul A. Iaizzo Source Type: journals

Automated classification of cells in sub-epithelial connective tissue of oral sub-mucous fibrosis—An SVM based approachEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study segmentation and classification of sub-epithelial connective tissue (SECT) cells except endothelial cells in oral mucosa of normal and OSF conditions has been reported. Segmentation has been carried out using multi-level thresholding and subsequently the cell population has been classified using support vector machine (SVM) based classifier. Moreover, the geometric features used here have been observed to be statistically significant, which enhance the statistical learning potential and classification accuracy of the classifier. Automated classification of SECT cells characterizes this precancerous condition ...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: M. Muthu Rama Krishnan, Mousumi Pal, Suneel K S.K. Bomminayuni, Chandan Chakraborty, Ranjan Rashmi R.R. Paul, Jyotirmoy Chatterjee, Ajoy K. A.K. Ray Source Type: journals

A combinatorial feature selection approach to describe the QSAR of dual site inhibitors of acetylcholinesteraseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Regarding the great potential of dual binding site inhibitors of acetylcholinesterase as the future potent drugs of Alzheimer's disease, this study was devoted to extraction of the most effective structural features of these inhibitors from among a large number of quantitative descriptors. To do this, we adopted a unique approach in quantitative structure–activity relationships. An efficient feature selection method was emphasized in such an approach, using the confirmative results of different routine and novel feature selection methods. The proposed methods generated quite consistent results ensuring the effe...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Ebrahim Barzegari E.B. Asadabadi, Parviz Abdolmaleki, Seyyed Mohsen Hosseini S.M.H. Barkooie, Samad Jahandideh, Mohammad Ali M.A. Rezaei Source Type: journals

An EMG-driven model to estimate muscle forces and joint moments in stroke patientsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Individuals following stroke exhibit altered muscle activation and movement patterns. Improving the efficiency of gait can be facilitated by knowing which muscles are affected and how they contribute to the pathological pattern. In this paper we present an electromyographically (EMG) driven musculoskeletal model to estimate muscle forces and joint moments. Subject specific EMG for the primary ankle plantar and dorsiflexor muscles, and joint kinematics during walking for four subjects following stroke were used as inputs to the model to predict ankle joint moments during stance. The model's ability to predict the ...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Qi Shao, Daniel N. D.N. Bassett, Kurt Manal, Thomas S. T.S. Buchanan Source Type: journals

On the discrimination of patho-physiological states in epilepsy by means of dynamical measuresEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: In the present paper a number of techniques were applied to determine the effects of epileptic seizure on spontaneous ongoing EEG. The idea is that seizure represents transitions of an epileptic brain from its normal (chaotic) state to an abnormal (more ordered) state. Some nonlinear measures including correlation dimension, maximum Lyapunov exponent and wavelet entropy and a graphical tool, named recurrence plot, as well as a novel technique that collects some statistics of the state space organization were used to characterize interictal, preictal and ictal states and derivate a phase transition. The novelty of...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Somayeh Raiesdana, Seyed Mohammad Reza Hashemi Golpayegani, Seyed Mohammad P Firoozabadi, Jafar Mehvari Habibabadi Source Type: journals

Classification of breast tissues using Moran's index and Geary's coefficient as texture signatures and SVMEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Female breast cancer is the major cause of cancer-related deaths in western countries. Efforts in computer vision have been made in order to help improving the diagnostic accuracy by radiologists. In this paper, we present a methodology that uses Moran's index and Geary's coefficient measures in breast tissues extracted from mammogram images. These measures are used as input features for a support vector machine classifier with the purpose of distinguishing tissues between normal and abnormal cases as well as classifying them into benign and malignant cancerous cases. The use of both proposed techniques showed to...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Geraldo Braz Junior, Anselmo Cardoso de Paiva, Aristófanes Corrêa Silva, Alexandre Cesar Muniz de Oliveira Source Type: journals

Editorial Board & Publication informationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Source Type: journals

Algorithms for effective querying of compound graph-based pathway databasesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The PATIKA Project Web site is http://www.patika.org.PATIKAweb version 2.1 is available at http://web.patika.org. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 16, 2009 Category: Bioinformatics Authors: Ugur DogrusozAhmet CetintasEmek DemirOzgun Babur Source Type: journals

Assessing the Quality of Whole Genome Alignments in BacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Comparing genomes is an essential preliminary step to solve many problems in biology. Matching long similar segments between two genomes is a precondition for their evolutionary, genetic, and genome rearrangement analyses. Though various comparison methods have been developed in recent years, a quantitative assessment of their performance is lacking. Here, we describe two families of assessment measures whose purpose is to evaluate bacteria-oriented comparison tools. The first measure is based on how well the genome segmentation fits the gene annotation of the studied organisms; the second uses the number of segments creat...
Source: Advances in Bioinformatics - November 15, 2009 Category: Bioinformatics Source Type: journals

Response of Tumor Spheroids to Radiation: Modeling and Parameter Estimation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We propose a spatially distributed continuous model for the spheroid response to radiation, in which the oxygen distribution is represented by means of a diffusion-consumption equation and the radiosensitivity parameters depend on the oxygen concentration. The induction of lethally damaged cells by a pulse of radiation, their death, and the degradation of dead cells are included. The compartments of lethally damaged cells and of dead cells are subdivided into different subcompartments to simulate the delays that occur in cell death and cell degradation, with a gain in model flexibility. It is shown that, for a single i...
Source: Bulletin of Mathematical Biology - November 14, 2009 Category: Bioinformatics Authors: Bertuzzi A, Bruni C, Fasano A, Gandolfi A, Papa F, Sinisgalli C Tags: Bull Math Biol Source Type: journals