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

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PrePrint: Peakbin Selection in Mass Spectrometry Data Using a Consensus Approach with Estimation of Distribution AlgorithmsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Progress is continuously being made in the quest for stable biomarkers linked to complex diseases. Mass spectrometers are one of the devices for tackling this problem. The data profiles they produce are noisy and unstable. In these profiles, biomarkers are detected as signal regions (peaks), where control and disease samples behave differently. Mass spectrometry (MS) data generally contains a limited number of samples described by a high number of features. In this work, we present a novel class of evolutionary algorithms, estimation of distribution algorithms (EDA), as an efficient peak selector in this MS domain. There i...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - March 18, 2010 Category: Bioinformatics Source Type: journals

Proteome difference associated with fat accumulation in bovine subcutaneous adipose tissuesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The increased expression of annexin 1 protein has been found to be associated with higher BF thickness in both crossbred steers. This result lays the foundation for future studies to develop the protein marker for assessing animals with different BF. (Source: Proteome Science)
Source: Proteome Science - March 18, 2010 Category: Bioinformatics Authors: Yong Mei ZhaoUrmila BasuMichael DodsonJohn BasarabLe Luo Guan Source Type: journals

Gene regulatory networks modelling using a dynamic evolutionary hybridEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The results demonstrate the effectiveness of the ENFRN in retrieving biologically valid regulatory relations and providing meaningful insights for better understanding the dynamics of gene regulatory networks.The algorithms and methods described in this paper have been implemented in a Matlab toolbox and are available from:http://bioserver-1.bioacademy.gr/DataRepository/Project_ENFRN_GRN/. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 18, 2010 Category: Bioinformatics Authors: Ioannis MaraziotisAndrei DragomirDimitris Thanos Source Type: journals

MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: MISHIMA provides improved performance compared to the commonly used multiple alignment methods. As an example, six complete genome sequences of bacteria species Helicobacter pylori (about 1.7Mb each) were successfully aligned in about 6 hours using a single PC. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 18, 2010 Category: Bioinformatics Authors: Kirill KryukovNaruya Saitou Source Type: journals

PrePrint: A Practical Algorithm for Reconstructing Level-1 Phylogenetic NetworksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for reconstructing level-1 phylogenetic networks - a type of network slightly more general than a phylogenetic tree - from triplets. Our algorithm has been made publicly available as the program LEV1ATHAN. It combines ideas from several known theoretical algorithms for phylogenetic tree and network reconstruction with two novel subroutines. Namely, an exponential-time exact and a greedy algorithm bo...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - March 17, 2010 Category: Bioinformatics Source Type: journals

Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Correction for the effects of 13C natural abundance on a set of raw isotopologue intensities is computationally feasible when the raw isotopologues are isotopically resolved and identified. Such correction makes qualitative interpretation of stable isotope tracing easier and is required before attempting a more rigorous quantitative interpretation of the isotopologue data. The presented implementation is very robust with increasing metabolite size. Error analysis of the algorithm will be straightforward due to low relative error from the implementation itself. Furthermore, the algorithm may serve as an indepen...
Source: BMC Bioinformatics - Latest articles - March 17, 2010 Category: Bioinformatics Authors: Hunter Moseley Source Type: journals

Analysis of DNA strand-specific differential expression with high density tiling microarraysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We show that the information derived from TMA hybridization can be processed simultaneously for high-resolution qualitative and quantitative analysis of the differential expression of well-characterized genes and of previously non-annotated and antisense transcripts. The consistency of the performance of TMA, their genome-wide coverage and adaptability to updated genome annotations, and the possibility of measuring strand-specific differential expression makes them a tool of choice for the analysis of gene expression in any organism for which TMA platforms are available. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 17, 2010 Category: Bioinformatics Authors: Luis QuintalesMar SanchezFrancisco Antequera Source Type: journals

Indirect two-sided relative ranking: a robust similarity measure for gene expression dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We demonstrate the benefit of our proposed indirect method on several datasets. We first evaluate the ability of the indirect method to retrieve compounds with similar therapeutic effects across known experimental barriers, namely vehicle and batch effects, on two independent datasets (one private and one public). We show that our indirect method is able to significantly improve upon the previous state-of-the-art method with a substantial improvement in recall at rank 10 of 97.03% and 49.44%, on each dataset, respectively. Next, we demonstrate that our indirect method results in improved accuracy for classific...
Source: BMC Bioinformatics - Latest articles - March 17, 2010 Category: Bioinformatics Authors: Louis LicameleLise Getoor Source Type: journals

An optimized TOPS+ comparison method for enhanced TOPS modelsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our advanced TOPS+ comparison shows better performance on the PDB40 dataset [4] compared to our basic TOPS+ method, giving 90 percent accuracy for SCOP alpha+beta; a 6 percent increase in accuracy compared to the TOPS and basic TOPS+ methods. It also outperforms the TOPS, basic TOPS+ and SSAP comparison methods on the Chew-Kedem dataset [5], achieving 98 percent accuracy.Software Availability: The TOPS+ comparison server is available athttp://balabio.dcs.gla.ac.uk/mallika/WebTOPS/. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 17, 2010 Category: Bioinformatics Authors: Mallika VeeramalaiDavid GilbertGabriel Valiente Source Type: journals

PrePrint: Towards Better Understanding of Protein Secondary Structure: Extracting Prediction RulesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Although numerous computational techniques have been applied to predict protein secondary structure (PSS), only limited studies have dealt with discovery of logic rules underlying the prediction itself. Such rules offer interesting links between the prediction model and the underlying biology. In addition, they enhance interpretability of PSS prediction by providing a degree of transparency to the predicting model usually regarded as a black-box. In this paper, we explore the generation and use of C4.5 decision trees to extract relevant rules from PSS predictions modeled with two-stage support vector machines (TS-SVM). The...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - March 16, 2010 Category: Bioinformatics Source Type: journals

Coexistence and Spread of Competitors in Heterogeneous Landscapes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Competition between species is ubiquitous in nature and therefore widely studied in ecology through experiment and theory. One of the central questions is under which conditions a (rare) invader can establish itself in a landscape dominated by a resident species at carrying capacity. Applying the same question with the roles of the invader and resident reversed leads to the principle that "mutual invasibility implies coexistence." A related but different question is how fast a locally introduced invader spreads into a landscape (with or without competing resident), provided it can invade. We explore some aspects of the...
Source: Bulletin of Mathematical Biology - March 16, 2010 Category: Bioinformatics Authors: Samia Y, Lutscher F Tags: Bull Math Biol Source Type: journals

Structured and Unstructured Continuous Models for Wolbachia Infections.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We introduce and investigate a series of models for an infection of a diplodiploid host species by the bacterial endosymbiont Wolbachia. The continuous models are characterized by partial vertical transmission, cytoplasmic incompatibility and fitness costs associated with the infection. A particular aspect of interest is competitions between mutually incompatible strains. We further introduce an age-structured model that takes into account different fertility and mortality rates at different stages of the life cycle of the individuals. With only a few parameters, the ordinary differential equation models exhibit alread...
Source: Bulletin of Mathematical Biology - March 16, 2010 Category: Bioinformatics Authors: Farkas JZ, Hinow P Tags: Bull Math Biol Source Type: journals

A Stochastic Version of the Eigen Model.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We exhibit a stochastic discrete time model that produces the Eigen model (Naturwissenschaften 58:465-523, 1971) in the deterministic and continuous time limits. The model is based on the competition among individuals differing in terms of fecundity but with the same viability. We explicitly write down the Markov matrix of the discrete time stochastic model in the two species case and compute the master sequence concentration numerically for various values of the total population. We also obtain the master equation of the model and perform a Van Kampen expansion. The results obtained in the two species case are compare...
Source: Bulletin of Mathematical Biology - March 16, 2010 Category: Bioinformatics Authors: Musso F Tags: Bull Math Biol Source Type: journals

A parallel and incremental algorithm for efficient unique signature discovery on DNA databasesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The proposed algorithms discover implicit signatures efficiently. The presented CMD algorithm has up to 97% less execution time than typical sequential discovery algorithms in the discovery of implicit signatures in experiments, when eight processing cores are used. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 16, 2010 Category: Bioinformatics Authors: Hsiao Ping LeeTzu-Fang SheuChuan Yi Tang Source Type: journals

MapMi: automated mapping of microRNA lociEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The pipeline and an associated web-server for mapping miRNAs are freely available on http://www.ebi.ac.uk/enright-srv/MapMi/ . In addition precomputed miRNA mappings of miRBase miRNAs across a large number of species are provided. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 16, 2010 Category: Bioinformatics Authors: Jose Afonso Guerra-AssuncaoAnton Enright Source Type: journals

ProbABEL package for genome-wide association analysis of imputed dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: ProbABEL package provides fast efficient wayto analyze imputed data in genome-wide context and willfacilitate future identification of complex trait loci. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 16, 2010 Category: Bioinformatics Authors: Yurii AulchenkoMaksim StruchalinCornelia van Duijn Source Type: journals

miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literatureEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our database miRSel offers the currently largest collection of literature derived miRNA-gene associations. Comprehensive collections of miRNA-gene associations are important for the development of miRNA target prediction tools and the analysis of regulatory networks. miRSel is updated daily and can be queried using a web-based interface via microRNA identifiers, gene and protein names, PubMed queries as well as gene ontology (GO) terms. miRSel is freely available online at http://services.bio.ifi.lmu.de/mirsel. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 16, 2010 Category: Bioinformatics Authors: Haroon NaeemRobert KuffnerGergely CsabaRalf Zimmer Source Type: journals

Correlation method versus enhanced modified moving average method for automatic detection of T-wave alternansEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Enhanced modified moving average method (EMMAM) and correlation method (CM) for microvolt TWA identification are compared by aid of simulated ECG tracings (cases of absence of TWA and presence of stationary or time-varying TWA) and ECG recordings from healthy subjects (H-group) and patients who survived an acute myocardial infarction (AMI-group). The two competing methods were found to be equivalent when analyzing clean ECGs affected by stationary TWA. Non-stationary TWA is correctly tracked by the CM, whereas it is identified as stationary by the EMMAM. Moreover, the EMMAM suffers for its tendency to identify as...
Source: Computer Methods and Programs in Biomedicine - March 15, 2010 Category: Bioinformatics Authors: Laura Burattini, Silvia Bini, Roberto Burattini Tags: Section. III: Experiences with Methods, Systems and Programs Source Type: journals

From floated to conventional confidence intervals for the relative risks based on published dose–response dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: A dose–response meta-analysis of epidemiological studies can encounter different types of confidence intervals (floated vs. conventional). This paper illustrates how to back calculate conventional confidence intervals from a set of relative risks reported with floated confidence intervals or floated standard errors. Furthermore, we provide an implementation of the formulas in a user-friendly program developed for Stata software. I exemplify the point using published data about alcohol intake and endometrial cancer incidence from the Million Women Study. (Source: Computer Methods and Programs in Biomedicine)
Source: Computer Methods and Programs in Biomedicine - March 15, 2010 Category: Bioinformatics Authors: Nicola Orsini Tags: Section II: Systems and Programs Source Type: journals

KARDIA: A Matlab software for the analysis of cardiac interbeat intervalsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article presents KARDIA, a Matlab (MathWorks Inc., MA) software developed for the analysis of cardiac interbeat interval (IBI) data. Available functions are called through a graphical user interface and permit the study of phasic cardiac responses (PCRs) and the estimation of time and frequency domain heart rate variability (HRV) parameters. Scaling exponents of heartbeat fluctuations are calculated with the detrended fluctuation analysis (DFA) algorithm. Grand average and individual subject results can be exported to spreadsheets for further statistical analysis. KARDIA is distributed free of charge under the terms o...
Source: Computer Methods and Programs in Biomedicine - March 15, 2010 Category: Bioinformatics Authors: Pandelis Perakakis, Mateus Joffily, Michael Taylor, Pedro Guerra, Jaime Vila Tags: Section II: Systems and Programs Source Type: journals

A spreadsheet template compatible with Microsoft Excel and iWork Numbers that returns the simultaneous confidence intervals for all pairwise differences between multiple sample meansEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective of the method described in this paper is to develop a spreadsheet template for the purpose of comparing multiple sample means. An initial analysis of variance (ANOVA) test on the data returns F—the test statistic. If F is larger than the critical F value drawn from the F distribution at the appropriate degrees of freedom, convention dictates rejection of the null hypothesis and allows subsequent multiple comparison testing to determine where the inequalities between the sample means lie. A variety of multiple comparison methods are described that return the 95% confidence intervals for differences between m...
Source: Computer Methods and Programs in Biomedicine - March 15, 2010 Category: Bioinformatics Authors: Angus M. Brown Tags: Section II: Systems and Programs Source Type: journals

A tool developed in Matlab for multiple correspondence analysis of fuzzy coded data sets: Application to morphometric skull dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Multiple Correspondence factorial Analysis is a multivariate method for the exploratory study of multidimensional contingency tables. Its use can be extended to the analysis of a table of fuzzy coded data resulting from a distribution into fuzzy windows defined by linguistic properties. There are few existing software tools that allow performing this type of analysis on a data table; furthermore these tools are not interactive and do not allow defining and representing fuzzy windowing. This paper presents a software tool, developed with Matlab, to compute and represent results from multiple correspondence factori...
Source: Computer Methods and Programs in Biomedicine - March 15, 2010 Category: Bioinformatics Authors: Antonio Pinti, Fabienne Rambaud, Jean-Louis Griffon, Abdelmalik Taleb Ahmed Tags: Section II: Systems and Programs Source Type: journals

Design evaluation and optimisation in multiple response nonlinear mixed effect models: PFIM 3.0Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Nonlinear mixed effect models (NLMEM) with multiple responses are increasingly used in pharmacometrics, one of the main examples being the joint analysis of the pharmacokinetics (PK) and pharmacodynamics (PD) of a drug. Efficient tools for design evaluation and optimisation in NLMEM are necessary. The R functions PFIM 1.2 and PFIMOPT 1.0 were proposed for these purposes, but accommodate only single response models. The methodology used is based on the Fisher information matrix, developed using a linearisation of the model. In this paper, we present an extended version, PFIM 3.0, dedicated to both design evaluatio...
Source: Computer Methods and Programs in Biomedicine - March 15, 2010 Category: Bioinformatics Authors: Caroline Bazzoli, Sylvie Retout, France Mentré Tags: Section II: Systems and Programs Source Type: journals

A ligand predication tool based on modeling and reasoning with imprecise probabilistic knowledgeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Ligand prediction has been driven by a fundamental desire to understand more about how biomolecules recognize their ligands and by the commercial imperative to develop new drugs. Most of the current available software systems are very complex and time-consuming to use. Therefore, developing simple and efficient tools to perform initial screening of interesting compounds is an appealing idea.In this paper, we introduce our tool for very rapid screening for likely ligands (either substrates or inhibitors) based on reasoning with imprecise probabilistic knowledge elicited from past experiments. Probabilistic knowled...
Source: Computer Methods and Programs in Biomedicine - March 15, 2010 Category: Bioinformatics Authors: Weiru Liu, Anbu Yue, David J. Timson Tags: Section I. Methodology Source Type: journals

Prediction of externally applied forces to human hands using frequency content of surface EMG signalsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: In this work, a new signal processing method was proposed in order to predict externally applied forces to human hands by deriving a relationship between the surface electromyographic (SEMG) signals and experimentally known forces. This relationship was investigated by analyzing the spectral features of the SEMG signals. SEMG signals were recorded from three subjects during isometric contraction and from another three subjects during anisometric contraction. In order to determine force–SEMG signal relationship, higher order frequency moments (HOFMs) of the signals were calculated and used as characterizing feat...
Source: Computer Methods and Programs in Biomedicine - March 15, 2010 Category: Bioinformatics Authors: Yunus Ziya Arslan, Mehmet Arif Adli, Aydin Akan, Mehmet Baris Baslo Tags: Section I. Methodology Source Type: journals

A home environment test battery for status assessment in patients with advanced Parkinson's diseaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: A test battery for assessing patient state in advanced Parkinson's disease, consisting of self-assessments and motor tests, was constructed and implemented on a hand computer with touch screen in a telemedicine setting. The aim of this work was to construct an assessment device, applicable during motor fluctuations in the patient's home environment. Selection of self-assessment questions was based on questions from an e-diary, previously used in a clinical trial. Both un-cued and cued tapping tests and spiral drawing tests were designed for capturing upper limb stiffnes, slowness and involuntary movements. The pa...
Source: Computer Methods and Programs in Biomedicine - March 15, 2010 Category: Bioinformatics Authors: Jerker Westin, Mark Dougherty, Dag Nyholm, Torgny Groth Tags: Section I. Methodology Source Type: journals

Automatic computer-aided sacroiliac joint index analysis for bone scintigraphyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Bone scintigraphy helps to detect sacroiliitis before the radiographic changes. Nuclear medicine physicians interpret lesion on sacroiliac joint by the aid of sacroiliac joint-to-sacrum uptake ratios (sacroiliac joint index, SII). Usually, the SII is measured by manually drawing regions of interest (ROI) over the sacroiliac joints and sacrum, which is a tedious, time consuming, and highly operator dependent procedure. In this approach, we developed an automatic SII measurement program based on fuzzy sets histogram thresholding, anatomy-based image segmentation method and pelvis reference points located by morphol...
Source: Computer Methods and Programs in Biomedicine - March 15, 2010 Category: Bioinformatics Authors: Jia-Yann Huang, Ming-Fong Tsai, Pan-Fu Kao, Yung-Sheng Chen Tags: Section I. Methodology Source Type: journals

Methodology for automatic detection of lung nodules in computerized tomography imagesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective of the lung reconstruction stage is to prevent incorrect elimination of portions belonging to the parenchyma. Structures extraction stage comprises the selection of dense structures from inside the lung parenchyma. The next stage, tubular structures elimination eliminates a great part of the pulmonary trees. Finally, the false positive stage selects only structures with great probability to be nodule. Each of the several stages has very specific objectives in detection of particular cases of lung nodules, ensuring good matching rates even in difficult detection situations.We use 33 exams with diversified diag...
Source: Computer Methods and Programs in Biomedicine - March 15, 2010 Category: Bioinformatics Authors: João Rodrigo Ferreira da Silva Sousa, Aristófanes Corrěa Silva, Anselmo Cardoso de Paiva, Rodolfo Acatauassú Nunes Tags: Section I. Methodology Source Type: journals

Editorial BoardEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: Computer Methods and Programs in Biomedicine)
Source: Computer Methods and Programs in Biomedicine - March 15, 2010 Category: Bioinformatics Source Type: journals

Missing genes in the annotation of prokaryotic genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Prokaryotic gene finders and prokaryotic genome annotations require improvement for accurate prediction of small genes. The number of missing gene families found is likely a lower bound on the actual number, due to the conservative criteria used to determine whether an ORF corresponds to a real gene. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 15, 2010 Category: Bioinformatics Authors: Andrew WarrenJeremy ArchuletaWu-chun FengJoao Carlos Setubal Source Type: journals

Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An approach for module identification, Modules of Networks (MoNet), introduced an intuitive module definition and clear detection method using edges ranked by the Girvan-Newman algorithm. Modules from a yeast network showed significant association with biological processes, indicating the method's utility; however, systematic bias leads to varied results across trials. MoNet modules also exclude some network regions. To address these shortcomings, we developed a deterministic version of the Girvan-Newman algorithm and a new agglomerative algorithm, Deterministic Modularization of Networks (dMoNet). dMoNet simultaneousl...
Source: International Journal of Bioinformatics Research and Applications - March 13, 2010 Category: Bioinformatics Authors: Chang RL, Luo F, Johnson S, Scheuermann RH Tags: Int J Bioinform Res Appl Source Type: journals

Assessing and improving the accuracy of detecting protein adaptation with the TreeSAAP analytical software.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
TreeSAAP has been used in a variety of protein studies for detecting adaptation in terms of the physicochemical properties involved in amino acid replacement. The accuracy of TreeSAAP was here tested using simulated protein-coding DNA data. A sampling of 1402 simulated amino acid replacements resulted in a default accuracy of 81.1%, with most properties exhibiting >90% accuracy. More than half of the false-positive results were traced to just 11 of the 180 possible single-step amino acid exchanges. Overall accuracy increased as the number of magnitude partitions used in the analysis decreased. Sliding window size di...
Source: International Journal of Bioinformatics Research and Applications - March 13, 2010 Category: Bioinformatics Authors: McClellan DA, Ellison DD Tags: Int J Bioinform Res Appl Source Type: journals

Flavitrack analysis of the structure and function of West Nile non-structural proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Flavitrack database groups Flaviviruses (FV), evolutionarily related organisms with high subtype variability, according to their phenotypes. Here, PCPMer tools were used to calculate consensus sequences based on conservation of Physicochemical Properties (PCP) for 919 sequences of NS2a, a non-structural protein involved in preventing host interferon response to infection. Conserved PCP-motifs were detected, primarily in the N-terminal half of NS2a. One model structure, based on a nuclear receptor, groups residues essential for West Nile (WN) infectivity (I59, V61, and M103) in a pocket on the protein surface. These...
Source: International Journal of Bioinformatics Research and Applications - March 13, 2010 Category: Bioinformatics Authors: Danecek P, Schein CH Tags: Int J Bioinform Res Appl Source Type: journals

An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Interspersed repeats, mostly resulting from the activity and accumulation of transposable elements, occupy a significant fraction of many eukaryotic genomes. More than half of human genomic sequence consists of known repeats, however a very large part has not yet been associated with neither repetitive structures nor functional units. We have postulated that most of the seemingly unique content of mammalian genomes is also a result of transposon activity, written software to look for weak signals which would help us reconstruct the ancient elements with substantially mutated copies, and integrated it into a system for...
Source: International Journal of Bioinformatics Research and Applications - March 13, 2010 Category: Bioinformatics Authors: Singh A, Keswani U, Levine D, Feschotte C, Tags: Int J Bioinform Res Appl Source Type: journals

Strategies for enhanced annotation of a microarray probe set.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We aim to determine the biological relevance of genes identified through microarray-mediated transcriptional profiling of Xenopus sensory organs and brain. Difficulties with genetic data analysis arise because of limitations in probe set annotation and the lack of a universal gene nomenclature. To overcome these impediments, we used sequence based and semantic linking methods in combination with computational approaches to augment probe set annotation on a commercially available microarray. Our curation efforts enabled linkage of probe sets and expression data to public databases, increased the biological significance ...
Source: International Journal of Bioinformatics Research and Applications - March 13, 2010 Category: Bioinformatics Authors: Powers TR, Virk SM, Serrano EE Tags: Int J Bioinform Res Appl Source Type: journals

Ranking through integration of protein-similarity for identification of cell-cyclic genes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a unique schema to enable integration by employing QR-factorisation from the pair-wise similarity matrix formulation. Angular coefficients are derived and consequently employed for integrated gene ranking. Experimental results on an independent benchmark dataset signify the efficacy of the method. PMID: 20223739 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - March 13, 2010 Category: Bioinformatics Authors: Dua S, Chowriappa P, Alex AE Tags: Int J Bioinform Res Appl Source Type: journals

Scalable biomedical Named Entity Recognition: investigation of a database-supported SVM approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This paper explores scalability issues associated with the Named Entity Recognition problem in the biomedical publications domain using Support Vector Machines. The performance results using existing binary and multi-class SVMs with increasing training data are compared to results obtained using our new implementations. Our approach eliminates prior language or domain-specific knowledge and achieves good out-of-the-box accuracy measures comparable to those obtained using more complex approaches. The training time of multi-class SVMs is reduced by several orders of magnitude, which would make support vector machines a m...
Source: International Journal of Bioinformatics Research and Applications - March 13, 2010 Category: Bioinformatics Authors: Habib MS, Kalita J Tags: Int J Bioinform Res Appl Source Type: journals

Mining Cytochrome b561 proteins from plant genomes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cytochrome b561 (Cyt-b561) proteins are important for plant growth, development, and prevention of damage to plants. Because of their high sequence divergence, thorough mining of Cyt-b561 proteins from plant genomes are not easy. Currently there is only one Cyt-b561 gene found in the maize and none in the soybean genome. However, 22 have been identified in the Arabidopsis thaliana genome. We tested alignment-free protein classifiers based on partial least squares (PLS) and support vector machines to identify Cyt-b561. These classifiers performed better than profile hidden Markov models and PSI-BLAST. Using these classi...
Source: International Journal of Bioinformatics Research and Applications - March 13, 2010 Category: Bioinformatics Authors: Opiyo SO, Moriyama EN Tags: Int J Bioinform Res Appl Source Type: journals

Interactions Between the Immune System and Cancer: A Brief Review of Non-spatial Mathematical Models.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We briefly review spatially homogeneous mechanistic mathematical models describing the interactions between a malignant tumor and the immune system. We begin with the simplest (single equation) models for tumor growth and proceed to consider greater immunological detail (and correspondingly more equations) in steps. This approach allows us to clarify the necessity for expanding the complexity of models in order to capture the biological mechanisms we wish to understand. We conclude by discussing some unsolved problems in the mathematical modeling of cancer-immune system interactions. PMID: 20225137 [PubMed - as sup...
Source: Bulletin of Mathematical Biology - March 12, 2010 Category: Bioinformatics Authors: Eftimie R, Bramson JL, Earn DJ Tags: Bull Math Biol Source Type: journals

Proteomic analysis of PBMCs: characterization of potential HIV-associated proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Together, this work provided useful information to facilitate further investigation of the underlying mechanism of HIV and host cell protein interactions, and discovered novel potential biomarkers such as fragment of vinculin, filamin-A and talin-1 for anti-HIV research. (Source: Proteome Science)
Source: Proteome Science - March 12, 2010 Category: Bioinformatics Authors: Lijun ZhangXiaofang JiaXiaojun ZhangJianjun SunXia PengTangkai QiFang MaLin YinYamin YaoChao QiuHongzhou Lu Source Type: journals

Mocapy++ - A toolkit for inference and learning in dynamic Bayesian networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Mocapy++ is especially suitable for constructing probabilistic models of biomolecular structure, due to its support for directional statistics. In particular, it supports the Kent distribution on the sphere and the bivariate von Mises distribution on the torus. These distributions have proven useful to formulate probabilistic models of protein and RNA structure in atomic detail. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 12, 2010 Category: Bioinformatics Authors: Martin PaluszewskiThomas Hamelryck Source Type: journals

New statistical potential for quality assessment of protein models and a survey of energy functionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Among the most influential terms we observed a critical role of a proper reference state definition and the benefits of including information about the microenvironment of interaction centers. Molecular mechanical potentials were also tested and found to be over-sensitive to small local imperfections in a structure, requiring unfeasible long energy relaxation before energy scores started to correlate with model quality. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 12, 2010 Category: Bioinformatics Authors: Dmitry RykunovAndras Fiser Source Type: journals

KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterialsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results suggests that ligand-receptor binding interactions for DHDPS employing QSAR modeling seems to be a promising approach for prediction of antibacterial agents. To serve the experimentalist to develop novel/potent inhibitors, a webserver "KiDoQ" has been developed (http://crdd.osdd.net/raghava/kidoq), which allows the prediction of Ki value of a new ligand molecule against DHDPS. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 11, 2010 Category: Bioinformatics Authors: Aarti GargRupinder TewariGajendra Raghava Source Type: journals

A fast and robust hepatocyte quantification algorithm including vein processingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The proposed automatic procedure gives results with high sensitivity and low false positive fractionand can be applied to process entire stained sections. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 10, 2010 Category: Bioinformatics Authors: Tetyana IvanovskaAndrea SchenkAndre HomeyerMeihong DengUta DahmenOlaf DirschHorst HahnLars Linsen Source Type: journals

Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: By avoiding the use of a template or reference spectrum, PCANS allows for the creation of a consensus spectrum that enhances the signals within the spectra while maintaining sample-specific features. This approach is of greatest benefit when complex samples are being analyzed and where it is expected that there will be spectral features unique and/or strongly different between subgroups within the samples. Furthermore, this approach can be potentially applied to the alignment of any data having spectra-like properties. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 9, 2010 Category: Bioinformatics Authors: Jennifer StaabThomas O'ConnellShawn Gomez Source Type: journals

SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scaleEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Besides the spectral method, SCPS also implements connected component analysis and hierarchical clustering, it integrates TribeMCL, it provides different cluster quality tools, it can extract human-readable protein descriptions using GI numbers from NCBI, it interfaces with external tools such as BLAST and Cytoscape, and it can produce publication-quality graphical representations of the clusters obtained, thus constituting a comprehensive and effective tool for practical research in computational biology. Source code and precompiled executables for Windows, Linux and Mac OS X are freely available at http://ww...
Source: BMC Bioinformatics - Latest articles - March 9, 2010 Category: Bioinformatics Authors: Tamas NepuszRajkumar SasidharanAlberto Paccanaro Source Type: journals

Testing the Coding Potential of Conserved Short Genomic SequencesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Proposed is a procedure to test whether a genomic sequence contains coding DNA, called a coding potential region. The procedure tests the coding potential of conserved short genomic sequence, in which the assumptions on the probability models of gene structures are relaxed. Thus, it is expected to provide additional candidate regions that contain coding DNAs to the current genomic database. The procedure was applied to the set of highly conserved human-mouse sequences in the genome database at the University of California at Santa Cruz. For sequences containing RefSeq coding exons, the procedure detected 91.3% regions ...
Source: Advances in Bioinformatics - March 8, 2010 Category: Bioinformatics Source Type: journals

Prodigal: prokaryotic gene recognition and translation initiation site identificationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: We built a fast, lightweight, open source gene prediction program called Prodigal (http://compbio.ornl.gov/prodigal/). Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - March 8, 2010 Category: Bioinformatics Authors: Doug HyattGwo-Liang ChenPhilip LoCascioMiriam LandFrank LarimerLoren Hauser Source Type: journals

Network Properties for Ranking Predicted miRNA Targets in Breast CancerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
MicroRNAs control the expression of their target genes by translational repression and transcriptional cleavage. They are involved in various biological processes including development and progression of cancer. To uncover the biological role of miRNAs it is important to identify their target genes. The small number of experimentally validated target genes makes computer prediction methods very important. However, state-of-the-art prediction tools result in a great number of putative targets with an unpredictable number of false positives. In this paper, we propose and evaluate two approaches for ranking the biological rel...
Source: Advances in Bioinformatics - March 7, 2010 Category: Bioinformatics Source Type: journals

GPU computing for systems biology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The development of detailed, coherent, models of complex biological systems is recognized as a key requirement for integrating the increasing amount of experimental data. In addition, in-silico simulation of bio-chemical models provides an easy way to test different experimental conditions, helping in the discovery of the dynamics that regulate biological systems. However, the computational power required by these simulations often exceeds that available on common desktop computers and thus expensive high performance computing solutions are required. An emerging alternative is represented by general-purpose scientific ...
Source: Briefings in Bioinformatics - March 7, 2010 Category: Bioinformatics Authors: Dematté L, Prandi D Tags: Brief Bioinform Source Type: journals