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.

Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.
Abstract Many non-coding RNAs (ncRNAs) can fold into alternate native structures and perform different biological functions. The computational prediction of an ncRNA's alternate native structures can be conducted by analysing the ncRNA's energy landscape. Previously, we have developed a computational approach, RNASLOpt, to predict alternate native structures for a single RNA. In this paper, in order to improve the accuracy of the prediction, we incorporate structural conservation information among a family of related ncRNA sequences to the prediction. We propose a comparative approach, RNAConSLOpt, to prod...
Source: International Journal of Bioinformatics Research and Applications - July 11, 2014 Category: Bioinformatics Authors: Li Y, Zhong C, Zhang S Tags: Int J Bioinform Res Appl Source Type: research

Parameter discovery in stochastic biological models using simulated annealing and statistical model checking.
We present a new parameter discovery algorithm that uses simulated annealing, sequential hypothesis testing, and statistical model checking to learn the parameters in a stochastic model. We apply our technique to a model of glucose and insulin metabolism used for in-silico validation of artificial pancreata and demonstrate its effectiveness by developing parallel CUDA-based implementation for parameter synthesis in this model. PMID: 24989866 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - July 11, 2014 Category: Bioinformatics Authors: Hussain F, Jha SK, Jha S, Langmead CJ Tags: Int J Bioinform Res Appl Source Type: research

Discovering rare behaviours in stochastic differential equations using decision procedures: applications to a minimal cell cycle model.
Abstract Stochastic Differential Equation (SDE) models are used to describe the dynamics of complex systems with inherent randomness. The primary purpose of these models is to study rare but interesting or important behaviours, such as the formation of a tumour. Stochastic simulations are the most common means for estimating (or bounding) the probability of rare behaviours, but the cost of simulations increases with the rarity of events. To address this problem, we introduce a new algorithm specifically designed to quantify the likelihood of rare behaviours in SDE models. Our approach relies on temporal lo...
Source: International Journal of Bioinformatics Research and Applications - July 11, 2014 Category: Bioinformatics Authors: Ghosh AK, Hussain F, Jha S, Langmead CJ, Jha SK Tags: Int J Bioinform Res Appl Source Type: research

Structure, evolution and virtual screening of NDM-1 strain from Kolkata.
Abstract β-lactam antibiotics are utilised to treat bacterial infection. β-lactamase enzymes (EC 3.5.2.6) are produced by several bacteria and are responsible for their resistance to β-lactam antibiotics like penicillin, cephamycins and carbapenems. New Delhi Metallo-β-lactamase (NDM-1) is a gene that makes bacteria resistant to β-lactam antibiotics. Preparing a compound against NDM-1 will require additional investment and development by drug manufacturers as the current antibiotics will not treat patients with NDM-1 resistance. NDM-1 of Kolkata showed convergent-type evolution with other NDM-1 produc...
Source: International Journal of Bioinformatics Research and Applications - May 11, 2014 Category: Bioinformatics Authors: Sahoo GC, Rani M, Ansari MY, Jha C, Rana S, Dikhit MR, Moharana KC, Kumar R, Das P Tags: Int J Bioinform Res Appl Source Type: research

Tools, resources and databases for SNPs and indels in sequences: a review.
Abstract Single Nucleotide Polymorphism (SNP) is a mutation where, a single base in the DNA differs from the usual base at that position. SNPs are the marker of choice in genetic analysis and also useful in locating genes associated with diseases. SNPs are important and frequently occurring point mutations in genomes and have many practical implications. In silico methods are easy to study the SNPs that are occurring in known genomes or sequences of a species of interest during the post genomic era. There are many on-line and stand alone tools to analyse the SNPs. We intend to guide the reader with the sof...
Source: International Journal of Bioinformatics Research and Applications - May 11, 2014 Category: Bioinformatics Authors: Seal A, Gupta A, Mahalaxmi M, Aykkal R, Singh TR, Arunachalam V Tags: Int J Bioinform Res Appl Source Type: research

In silico analysis of plant and animal transposable elements.
This study elucidated the molecular characteristics of TEs in land plants and animals using bioinformatics and in silico mutational approach. We discovered that the GC-rich class I TEs is the predominant class of TEs in animal, but the AT-rich class II TEs is prevalent in plants. The GC-rich class I TEs appears to be evolved within the animals. On contrary, the preserved in AT-rich in class II TEs is believed to be contributed in host defence systems. PMID: 24794071 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - May 11, 2014 Category: Bioinformatics Authors: Huang ML, Wattanachaisaereekul S, Han YJ, Vongsangnak W Tags: Int J Bioinform Res Appl Source Type: research

A classifier system for predicting RNA secondary structure.
We present a through experimental evaluation of 24 features, classified into five groups, to determine the most relevant feature groups. The system is evaluated using Rfam sequences and achieves an overall sensitivity, selectivity, and accuracy of 96.1%, 98%, and 96.1%, respectively. PMID: 24794072 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - May 11, 2014 Category: Bioinformatics Authors: Aldwairi M, Al-Hajasad B, Khamayseh Y Tags: Int J Bioinform Res Appl Source Type: research

Fast decision tree-based method to index large DNA-protein sequence databases using hybrid distributed-shared memory programming model.
Abstract In recent times, the size of biological databases has increased significantly, with the continuous growth in the number of users and rate of queries; such that some databases have reached the terabyte size. There is therefore, the increasing need to access databases at the fastest rates possible. In this paper, the decision tree indexing model (PDTIM) was parallelised, using a hybrid of distributed and shared memory on resident database; with horizontal and vertical growth through Message Passing Interface (MPI) and POSIX Thread (PThread), to accelerate the index building time. The PDTIM was imple...
Source: International Journal of Bioinformatics Research and Applications - May 11, 2014 Category: Bioinformatics Authors: Jaber KM, Abdullah R, Rashid NA Tags: Int J Bioinform Res Appl Source Type: research

Texture-based medical image retrieval in compressed domain using compressive sensing.
Abstract Content-based image retrieval has gained considerable attention in today's scenario as a useful tool in many applications; texture is one of them. In this paper, we focus on texture-based image retrieval in compressed domain using compressive sensing with the help of DC coefficients. Medical imaging is one of the fields which have been affected most, as there had been huge size of image database and getting out the concerned image had been a daunting task. Considering this, in this paper we propose a new model of image retrieval process using compressive sampling, since it allows accurate recovery...
Source: International Journal of Bioinformatics Research and Applications - March 7, 2014 Category: Bioinformatics Authors: Yadav K, Srivastava A, Mittal A, Ansari MA Tags: Int J Bioinform Res Appl Source Type: research

DNA-algorithm for timetable problem.
Abstract Using of DNA molecules for solving of NP-complete problems is discussed. Properties of DNA allow one to reduce the number of operations from exponential to polynomial. DNA-algorithm for solving of the timetable problem is suggested. The starting point is a set of classes, teachers and hours with some limitations. It is necessary to determine whether there is a timetable satisfying all limitations. The sets of classes, teachers and hours are coded by chains of nucleotides. After preparing of the input multi-set containing all possible timetables the filtering procedure should be made. It allows to ...
Source: International Journal of Bioinformatics Research and Applications - March 7, 2014 Category: Bioinformatics Authors: Popov IY, Vorobyova AV, Blinova IV Tags: Int J Bioinform Res Appl Source Type: research

Identification of unique repeated patterns, location of mutation in DNA finger printing using artificial intelligence technique.
Abstract In genetic engineering, conventional techniques and algorithms employed by forensic scientists to assist in identification of individuals on the basis of their respective DNA profiles involves more complex computational steps and mathematical formulae, also the identification of location of mutation in a genomic sequence in laboratories is still an exigent task. This novel approach provides ability to solve the problems that do not have an algorithmic solution and the available solutions are also too complex to be found. The perfect blend made of bioinformatics and neural networks technique result...
Source: International Journal of Bioinformatics Research and Applications - March 7, 2014 Category: Bioinformatics Authors: Mukunthan B, Nagaveni N Tags: Int J Bioinform Res Appl Source Type: research

A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments.
Abstract We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature. PMID: 24589836 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - March 7, 2014 Category: Bioinformatics Authors: Quinn T, Sinkala Z Tags: Int J Bioinform Res Appl Source Type: research

Real-time estimation and detection of non-linearity in bio-signals using wireless brain-computer interface.
Abstract In this paper, the work is mainly concentrated on removing non-linear parameters to make the physiological signals more linear and reducing the complexity of the signals. This paper discusses three different types of techniques that can be successfully utilised to remove non-linear parameters in EEG and ECG. (i) Transformation technique using Discrete Walsh-Hadamard Transform (DWHT); (ii) application of fuzzy logic control and (iii) building the Adaptive Neuro-Fuzzy Inference System (ANFIS) model for fuzzy. This work has been inspired by the need to arrive at an efficient, simple, accurate and qui...
Source: International Journal of Bioinformatics Research and Applications - March 7, 2014 Category: Bioinformatics Authors: Ganesan S, Victoire TA, Vijayalakshmy G Tags: Int J Bioinform Res Appl Source Type: research

Functional and structural analysis of mice TRPC6 with human analogue through homology modelling.
Abstract Homology models are increasingly used to determine structural and functional relationships of genes and proteins in biomedical research. In the current study, for the first time, we compared the TRPC6 gene in mouse and human. The protein encoded by this gene forms a receptor activated calcium channel in cell membrane. Defects in this gene have been implicated in a wide range of diseases including glioblastomas. To determine the structural similarities in mouse and human TRPC6, we used standard bioinformatics tools such as fold prediction to identify the protein 3D structure, sequence-structure com...
Source: International Journal of Bioinformatics Research and Applications - March 7, 2014 Category: Bioinformatics Authors: Chigurupati S, Bhasin A, Inampudi KK, Asuthkar S, Madarampalli B, Kammili RK, Velpula KK Tags: Int J Bioinform Res Appl Source Type: research

Understanding the importance of natural neuromotor strategy in upper extremity neuroprosthetic control.
Abstract A key challenge in upper extremity neuroprosthetics is variable levels of skill and inconsistent functional recovery. We examine the feasibility and benefits of using natural neuromotor strategies through the design and development of a proof-of-concept model for a feed-forward upper extremity neuroprosthetic controller. Developed using Artificial Neural Networks, the model is able to extract and classify neural correlates of movement intention from multiple brain regions that correspond to functional movements. This is unique compared to contemporary controllers that record from limited physiolog...
Source: International Journal of Bioinformatics Research and Applications - March 7, 2014 Category: Bioinformatics Authors: Nathan DE, Prost RW, Guastello SJ, Jeutter DC Tags: Int J Bioinform Res Appl Source Type: research