International Journal of Bioinformatics Research and Applications This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

A linearly convergent first-order algorithm for total variation minimisation in image processing.
Abstract We introduce a new formulation for total variation minimisation in image denoising. We also present a linearly convergent first-order method for solving this reformulated problem and show that it possesses a nearly dimension-independent iteration complexity bound. PMID: 24449690 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - January 28, 2014 Category: Bioinformatics Authors: Dang CD, Dai K, Lan G Tags: Int J Bioinform Res Appl Source Type: research

Uses and challenges of bioinformatic tools in mass spectrometric-based proteomic brain perturbation studies.
Abstract Mass spectrometry (MS) has become the method of choice to study the proteome of brain injury. The high throughput nature of MS-based proteomic experiments generates massive amount of mass spectral data presenting great challenges in downstream interpretation. Currently, different bioinformatics platforms are available for functional analysis and data mining of MS-generated proteomic data. These tools provide a way to convert data sets to biologically interpretable results and functional outcomes. In this review, a brief overview of the currently available bioinformatics strategies applied to neuro...
Source: International Journal of Bioinformatics Research and Applications - January 28, 2014 Category: Bioinformatics Authors: Guingab-Cagmat JD, Cagmat EB, Kobeissy FH, Anagli J Tags: Int J Bioinform Res Appl Source Type: research

Learning dependence from samples.
Abstract Mutual information, conditional mutual information and interaction information have been widely used in scientific literature as measures of dependence, conditional dependence and mutual dependence. However, these concepts suffer from several computational issues; they are difficult to estimate in continuous domain, the existing regularised estimators are almost always defined only for real or vector-valued random variables, and these measures address what dependence, conditional dependence and mutual dependence imply in terms of the random variables but not finite realisations. In this paper, we ...
Source: International Journal of Bioinformatics Research and Applications - January 28, 2014 Category: Bioinformatics Authors: Seth S, Príncipe JC Tags: Int J Bioinform Res Appl Source Type: research

Space pruning monotonic search for the non-unique probe selection problem.
Abstract Identification of targets, generally viruses or bacteria, in a biological sample is a relevant problem in medicine. Biologists can use hybridisation experiments to determine whether a specific DNA fragment, that represents the virus, is presented in a DNA solution. A probe is a segment of DNA or RNA, labelled with a radioactive isotope, dye or enzyme, used to find a specific target sequence on a DNA molecule by hybridisation. Selecting unique probes through hybridisation experiments is a difficult task, especially when targets have a high degree of similarity, for instance in a case of closely rel...
Source: International Journal of Bioinformatics Research and Applications - January 28, 2014 Category: Bioinformatics Authors: Pappalardo E, Ozkok BA, Pardalos PM Tags: Int J Bioinform Res Appl Source Type: research

Perpendicular fibre tracking for neural fibre bundle analysis using diffusion MRI.
Abstract Information on the directionality and structure of axonal fibres in neural tissue can be obtained by analysing diffusion-weighted MRI data sets. Several fibre tracking algorithms have been presented in the literature that trace the underlying field of principal orientations of water diffusion, which correspond to the local primary eigenvectors of the diffusion tensor field. However, the majority of the existing techniques ignore the secondary and tertiary orientations of diffusion, which contain significant information on the local patterns of diffusion. In this paper, we introduce the idea of per...
Source: International Journal of Bioinformatics Research and Applications - January 28, 2014 Category: Bioinformatics Authors: Ray S, O'Dell W, Barmpoutis A Tags: Int J Bioinform Res Appl Source Type: research

Integrating edge detection and fuzzy connectedness for automated segmentation of anatomical branching structures.
Abstract Image segmentation algorithms are critical components of medical image analysis systems. This paper presents a novel and fully automated methodology for segmenting anatomical branching structures in medical images. It is a hybrid approach which integrates the Canny edge detection to obtain a preliminary boundary of the structure and the fuzzy connectedness algorithm to handle efficiently the discontinuities of the returned edge map. To ensure efficient localisation of weak branches, the fuzzy connectedness framework is applied in a sliding window mode and using a voting scheme the optimal connecti...
Source: International Journal of Bioinformatics Research and Applications - January 28, 2014 Category: Bioinformatics Authors: Skoura A, Nuzhnaya T, Megalooikonomou V Tags: Int J Bioinform Res Appl Source Type: research

Vectorial total variation regularisation of orientation distribution functions in diffusion weighted MRI.
Abstract We propose a model for simultaneous Orientation Distribution Function (ODF) reconstruction and regularisation. The ODFs are represented by real spherical harmonic functions, and we propose to solve the spherical harmonic coefficients of the ODFs, with spatial regularisation by minimising the Vectorial Total Variation (VTV) of the coefficients. The proposed model also incorporates angular regularisation of the ODFs using Laplace-Beltrami operator on the unit sphere. A modified primal-dual hybrid gradient algorithm is applied to solve the model efficiently. The experimental results indicate better d...
Source: International Journal of Bioinformatics Research and Applications - January 28, 2014 Category: Bioinformatics Authors: Ouyang Y, Chen Y, Wu Y Tags: Int J Bioinform Res Appl Source Type: research

Estimating relative noise to signal in DNA microarray data.
Abstract A method was proposed for estimating noise relative to signal in microarray data. A signal to noise index, SNI, was defined and used to measure the level of signal compared to the noise contained in two microarray data sets. Simulations were conducted to generate the quantitative relationship between the SNI and its measurement of relative noise. The method was applied to two well known microarray data sets. Relative noise was estimated for both data sets, and the results were consistent with the observations in the original papers, demonstrating the proposed method is reliable for estimating rela...
Source: International Journal of Bioinformatics Research and Applications - September 5, 2013 Category: Bioinformatics Authors: Hong H, Hong Q, Liu J, Tong W, Shi L Tags: Int J Bioinform Res Appl Source Type: research

Analysis of oxygen affinity in aquatic amphibian; homology modelling of the major Haemoglobin component HbA1 from the African clawed frog (Xenopus laevis, Anura).
Abstract The homology model of major haemoglobin component HbA1 of the African Clawed Frog was predicted using the pigeon (Columba livia) haemoglobin as a template. The model was built with the help of MODELLER9v8. The models were evaluated with ProSA and PROCHECK. In X. laevis Gln38α is unable to form a hydrogen bond with β97His or β99Asp, which is responsible for the increase in oxygen affinity of the Xenopus HbA1. The hydrogen bond between α34Thr and β124Pro, which stabilises the deoxy state of the haemoglobin, was absent in X. laevis. Hence it is predicted that the HbA1 component of X. laevis has ...
Source: International Journal of Bioinformatics Research and Applications - September 5, 2013 Category: Bioinformatics Authors: Ali R, Lutfullah G, Khan AA, Rashid MI Tags: Int J Bioinform Res Appl Source Type: research

An interval-based algorithm to represent conformational states of experimentally determined polypeptide templates and fast prediction of approximated 3D protein structures.
Abstract Predicting the three-dimensional (3-D) structure of a protein that has no templates in the Protein Data Bank (PDB) is a very hard, still an impossible task. Computational prediction methods have been developed during the last years, but the problem still remains challenging. In this paper we present a new strategy based on Interval Arithmetic to store structural information obtained from experimental protein templates and predict native-like approximate three-dimensional structures of proteins. Our objective is to perform the prediction in a very fast manner and predict native-like structures that...
Source: International Journal of Bioinformatics Research and Applications - September 5, 2013 Category: Bioinformatics Authors: Dorn M, Souza ON Tags: Int J Bioinform Res Appl Source Type: research

Receptor-based pharmacophore tool for design and development of next-generation drugs.
Abstract Drug discovery is an intricate process in which new drugs are designed or discovered. A pharmacophore is an essential ensemble of steric and electronic features for drug discovery, which is necessary to ensure optimal interactions with a specific target structure and to trigger its biological response. Here we present our innovative approach: the Receptor-Based Pharmacophoric Tool (RBPT), a transparent user friendly GUI sphere that generates pharmacophores using the structure of the target protein at the specified binding site. The pharmacophore generated for the specified binding site of a target...
Source: International Journal of Bioinformatics Research and Applications - September 5, 2013 Category: Bioinformatics Authors: Udayakumar M, Kumar PS, Hemavathi K, Shanmugapriya P, Seenivasagam R Tags: Int J Bioinform Res Appl Source Type: research

A novel strategy for plant breeding based on simulations of gene network models.
Abstract This paper describes a new computational method to make predictions on the outcome of pair-wise crosses of plant lines limiting expensive laboratory breeding experiments to carry out crosses of the most promising pairs of lines. Compared to the well-known marker assisted breeding, the proposed approach approximates plant gene regulatory networks to estimate outcomes of all possible crossovers, thereby taking into account epistatic relationships between alleles. The proposed method is tested and compare with various breeding approaches on artificial NK landscape models and an extensive synthetic mo...
Source: International Journal of Bioinformatics Research and Applications - September 5, 2013 Category: Bioinformatics Authors: Cai X, Das S, Welch SM Tags: Int J Bioinform Res Appl Source Type: research

Performance modelling of parallel BLAST using Intel and PGI compilers on an infiniband-based HPC cluster.
Abstract The Basic Local Alignment Search (BLAST) is one of the most widely used bioinformatics programs for searching all available sequence databases for similarities between a protein or DNA query and predefined sequences, using sequence alignment technique. Recently, many attempts have been made to make the algorithm practical to run against the publicly available genome databases. This paper presents our experience in mapping and evaluating both the serial and parallel BLAST algorithms onto a large Infiniband-based High Performance Cluster. The evaluation is performed using two commonly used parallel ...
Source: International Journal of Bioinformatics Research and Applications - September 5, 2013 Category: Bioinformatics Authors: Al-Mulhem M, Al-Shaikh R Tags: Int J Bioinform Res Appl Source Type: research

Historic demography and phylogenetic relationship of Euthynnus species based on COI sequence analyses.
Abstract Euthynnus species are epipelagic migratory tuna species, with global distribution. They occur in the open waters but usually remain close to the shoreline. In present study, historic demography and phylogenetic relationship of Euthynnus species were examined using sequence data from portions of the mitochondrial COI gene. A total of 35 sequences were retrieved from NCBI. Mismatch distribution analyses suggested a late Pleistocene population expansion of E. affinis and E. alletteratus. Neutrality test for E. alletteratus fails to reject the null hypothesis of neutral evolution while COI sequences o...
Source: International Journal of Bioinformatics Research and Applications - September 5, 2013 Category: Bioinformatics Authors: Kumar G, Kunal SP Tags: Int J Bioinform Res Appl Source Type: research

In silico analysis of mt 16S rRNA sequences of ocypodid crabs.
Abstract The family Ocypodidae comprises of four sub-families Dotillinae, Heloeciinae, Macrophthalminae and Ocypodinae. Ocypodidae mt 16S rRNA sequences were analysed for studying the conserved regions and phylogeny. Conserved regions will be helpful in molecular identification at the sub-family level and in interpretation of the species relationships in a better way. In the current phylogeny, the Ocypodidae family exhibits different lineages, indicating the family is polyphyletic along with its sub-families Dotillinae and Ocypodinae. The genera Ilyoplax of Dotillinae, with three different lineages, and th...
Source: International Journal of Bioinformatics Research and Applications - June 29, 2013 Category: Bioinformatics Authors: Prasad NK, Vindal V Tags: Int J Bioinform Res Appl Source Type: research