International Journal of Bioinformatics Research and ApplicationsThis is an RSS file. You can use it to subscribe to this data in your favourite RSS reader, such as GoogleReader, or to display this data on your own website or blog. Subscribe to this data using MyMedWorm.Subscribe to this data using GoogleReader.Subscribe to this data using Bloglines.Subscribe to this data using MyYahoo.

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A Lossless Compression Algorithm for DNA sequences.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The increase of the amount of DNA sequences requires efficient computational algorithms for performing sequence comparison and analysis. Standard compression algorithms are not able to compress DNA sequences because they do not consider special characteristics of DNA sequences (i.e., DNA sequences contain several approximate repeats and complimentary palindromes). Recently, new algorithms have been proposed to compress DNA sequences, often using detection of long approximate repeats. The current work proposes a Lossless Compression Algorithm (LCA), providing a new encoding method. LCA achieves a better compression rati...
Source: International Journal of Bioinformatics Research and Applications - November 7, 2009 Category: Bioinformatics Authors: Soliman TH, Gharib TF, Abo-Alian A, El Sharkawy MA Tags: Int J Bioinform Res Appl Source Type: journals

Insilico analysis of homocamptothecin (hCPT) analogues for anti-tumour activity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cancer being a leading cause of death, the development of anti-cancer drugs like Camptothecin (CPT) has been promoted. CPT has lactone ring instability and lacks lipophilicity resulting in drug efflux. Owing to these limitations, homocamptothecin (hCPT), a CPT analogue was developed, which due to seven membered beta-hydroxylactone ring has better lipophilicity leading to reduced drug efflux. Analogues of hCPT were designed and docked into catalytic site of 1t8i (PDB id) protein (top-I). The docking energies and formation of hydrogen-bonds between the analogue and protein were compared with the original hCPT. Further, A...
Source: International Journal of Bioinformatics Research and Applications - November 7, 2009 Category: Bioinformatics Authors: Vadwai V, Devaraj S Tags: Int J Bioinform Res Appl Source Type: journals

Modifications of ampicillin structure and its implication: an in-silico approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Structural modifications of the existing ampicillin are much needed for saving patients from ampicillin-resistant microorganisms. A number of new molecules were generated by side chain modification of the existing ampicillin structure. Armed with molecular docking softwares like FlexiDOC, GLIDE, and AutoDOCK, a docking study was performed. Interaction between new molecules and target protein (1W2N) was also executed. Finally, we arranged new molecules according to docking scores, which directly reflects the binding affinity to the receptor protein. PMID: 19887336 [PubMed - in process] (Source: International Journa...
Source: International Journal of Bioinformatics Research and Applications - November 7, 2009 Category: Bioinformatics Authors: Poddar R, Mathur A, Kawalekar OU, Rai A, Tags: Int J Bioinform Res Appl Source Type: journals

Identifying cell cycle regulators and combinatorial interactions among transcription factors with microarray data and ChIP-chip data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this paper, we integrate transcriptional regulatory modelling with temporal correlation analysis between one Transcription Factor (TF) and its corresponding cell cycle-regulated targets to investigate Cell Cycle Regulators (CCRs) and combinatorial interactions among TFs across the cell cycle in Saccharomyces cerevisiae. Our method is developed based on the rationale that if one TF or one TF combinatorial interaction takes more possibilities of sharing common cell cycle-regulated targets with other TFs, this TF or TF combinatorial interaction is more likely to control the cell cycle. Our results reveal abundant CCRs ...
Source: International Journal of Bioinformatics Research and Applications - November 7, 2009 Category: Bioinformatics Authors: Chen T, Li F Tags: Int J Bioinform Res Appl Source Type: journals

Investigating an Artificial Immune System to strengthen protein structure prediction and protein coding region identification using the Cellular Automata classifier.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genes carry the instructions for making proteins that are found in a cell as a specific sequence of nucleotides that are found in DNA molecules. But, the regions of these genes that code for proteins may occupy only a small region of the sequence. Identification of the coding regions plays a vital role in understanding these genes. In this paper we have explored an Artificial Immune System (AIS) that can be used to strengthen and identify the protein coding regions in a genomic DNA system in changing environments and the CA technique for protein structure prediction of small alpha/beta proteins using Rosetta. From an i...
Source: International Journal of Bioinformatics Research and Applications - November 7, 2009 Category: Bioinformatics Authors: Sree PK, Babu IR, Devi NS Tags: Int J Bioinform Res Appl Source Type: journals

SnS-Align: a graphic tool for alignment of distantly related proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genomic sequences for many animal species are now available in the public domain. Protein similarity search in evolutionarily distant organisms by sequence comparison often turns out to be difficult. Here, we present the Structure and Sequence Alignment (SnS-Align) tool that graphically presents pairwise local alignment of sandwiched protein sequences, a hybrid of the primary protein sequence and its secondary structure. The utility of the tool is demonstrated by sample analysis of the gap junction protein superfamily of innexins/pannexins and the classic myoglobin family. SnS-Align can also be used for demarcation of ...
Source: International Journal of Bioinformatics Research and Applications - November 7, 2009 Category: Bioinformatics Authors: Manyam G, Baranova A, Skoblov M, Mishra RK Tags: Int J Bioinform Res Appl Source Type: journals

microRNA: human disease and development.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
microRNAs or miRNAs are an abundant class of highly conversed, small non-coding RNAs that present an entirely new theme of post-transcriptional gene regulation. miRNAs play a key role in diverse biological systems, such as virology, embryogenesis, differentiation, inflammation and cancer research. Research showed the importance of these non-coding small RNAs on immune system development and response. It plays important regulatory roles in various metabolic pathways in most eukaryotes. miRNAs are found to be involved in the regulation of immunity, including the development and differentiation of immune cells, antibody p...
Source: International Journal of Bioinformatics Research and Applications - September 27, 2009 Category: Bioinformatics Authors: Gomase VS, Parundekar AN Tags: Int J Bioinform Res Appl Source Type: journals

Scatter Search algorithm for Protein Structure Prediction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this paper, we present a Scatter Search (SS) algorithm for predicting 3D structures of proteins based on torsion angles representation. Given the protein's sequence of Amino Acids (AAs), our algorithm produces a 3D structure that aims to minimise the energy function associated with the structure. SS is an evolutionary approach that is based on a population of candidate solutions. These candidates undergo evolutionary operations that combine search intensification and diversification over a number of iterations. We evaluate our algorithm on three proteins taken from a Protein Data Bank (PDB). The results show that ou...
Source: International Journal of Bioinformatics Research and Applications - September 27, 2009 Category: Bioinformatics Authors: Mansour N, Kehyayan C, Khachfe H Tags: Int J Bioinform Res Appl Source Type: journals

Three dimensional structure of the closed conformation (active) of human merlin reveals masking of actin binding site in the FERM domain.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We modelled the structure of human merlin using the structure of moesin from Spodoptera frugiperda as the template. The present model suggests an interaction of its extreme C-terminal region with the subdomains B and C of FERM domain, masking the binding site of beta II spectrin. Modelling the complete structure of merlin revealed a novel central alpha helical domain with a helix-coil-helix. The actin binding site in the carboxy terminal is absent in merlin and in its closed conformation the indirect actin binding site in the FERM domain is also not available for the interaction of other proteins with it. PMID: 197...
Source: International Journal of Bioinformatics Research and Applications - September 27, 2009 Category: Bioinformatics Authors: Sivakumar KC, Thomas B, Karunagaran D Tags: Int J Bioinform Res Appl Source Type: journals

In silico analysis of motifs in promoters of Differentially Expressed Genes in rice (Oryza sativa L.) under anoxia.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The aim of this study was to characterise the molecular mechanisms of transcriptional regulation of Differentially Expressed Genes (DEGs) in rice coleoptiles under anoxia by identifying motifs that are common in the promoter region of co-regulated genes. Un-changed DEGs (<2 fold and >-2), up-regulated DEGs (>/=2 fold) and down-regulated DEGs (</=2 fold) were separated in three different data sets. Their gene promoters were extracted from eukaryotic promoter database. Statistically significant consensus promoter motifs were detected by in silico method. A significant variation in the number of promoter motif...
Source: International Journal of Bioinformatics Research and Applications - September 27, 2009 Category: Bioinformatics Authors: Kumar A, Smita S, Sahu N, Sharma V, Shankaracharya S, Vidyarthi A, Pandey D Tags: Int J Bioinform Res Appl Source Type: journals

Phylogenomics: evolution and genomics intersection.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Phylogenomics is the analysis of genomes of a group of closely related species. Almost all functional prediction methods rely on the identification, characterisation and quantification of sequence similarity between the gene of interest and genes for which functional information is available. This is the new evolved branch that is developed from the ongoing genome sequencing projects that have led to a phylogenetic approach based on genome-scale data. The use of large data sets in phylogenomic analysis results in a global increase in resolution owing to a decrease in sampling error. PMID: 19778869 [PubMed - in proc...
Source: International Journal of Bioinformatics Research and Applications - September 27, 2009 Category: Bioinformatics Authors: Gomase VS, Tagore S Tags: Int J Bioinform Res Appl Source Type: journals

Grafta: A 3D environment for biomolecular networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The importance of a comprehensive environment for the depiction of biomolecular networks in the domain of system biology has been emphasised after the completion of genomic, proteomic and metabolomic initatives. Grafta is a software application developed for the three dimensional illustration of biomolecular interactions such as protein interaction networks. Grafta allows its user to move in a 3D environment through a complex assembly of biomolecules represented by 3D objects such as spheres. Their interactions are displayed by an array of 3D tubes. One novelty in Grafta is its anthropomorphic navigation of the viewpoi...
Source: International Journal of Bioinformatics Research and Applications - September 27, 2009 Category: Bioinformatics Authors: Najmabadi P, Lee HH, Aung T, Thuya A, Ng J, Clair J, Burkart M Tags: Int J Bioinform Res Appl Source Type: journals

The Double Digest Problem: finding all solutions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The strongly NP-complete Double Digest Problem (DDP), for physical mapping of DNA, is now used for efficient genotyping. Existing methods: are inefficient in tackling large instances; produce only one solution while an instance may have multiple distinct solutions. In this paper, we employ the notion of equivalence among the distinct solutions to obtain almost all of them. Our method comprises two phases: finding a representative from each equivalence class using an elitist Genetic Algorithm (GA); for each representative generating the entire class efficiently. Experimental results tally for known instances. Significan...
Source: International Journal of Bioinformatics Research and Applications - September 27, 2009 Category: Bioinformatics Authors: Sur-Kolay S, Banerjee S, Mukhopadhyaya S, Murthy CA Tags: Int J Bioinform Res Appl Source Type: journals

Identification of LTR retrotransposons in eukaryotic genomes: supports from structure and evolution.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this report we describe LTR_INSERT, a computational method for identifying LTR elements in genomic sequences. Our method provides structural and evolutionary supports to discover LTR elements. By applying LTR_INSERT to two rice genomes, we have identified 72 novel LTR families in the species of which LTR elements have been extensively mined. PMID: 19640825 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - August 1, 2009 Category: Bioinformatics Authors: Wang H, Xu Z Tags: Int J Bioinform Res Appl Source Type: journals

Recognition of DNase I hypersensitive sites in multiple cell lines.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, a method of Increment of Diversity with Quadratic Discriminant analysis (IDQD) is presented for DHSs prediction in K562, CD4+ T, Hela and GM06990 cell lines. The average accuracies of 10-fold cross-validation test are 98.52%, 96.50%, 99.25% and 97.58%, respectively, and the mean areas under ROC curves (auROC) are all greater than 0.90. The prediction results indicate that the IDQD method is an effective tool for DHSs recognition. PMID: 19640826 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - August 1, 2009 Category: Bioinformatics Authors: Chen W, Luo L, Zhang L, Lin H Tags: Int J Bioinform Res Appl Source Type: journals

GRASPm: an efficient algorithm for exact pattern-matching in genomic sequences.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this paper, we propose Genomic-oriented Rapid Algorithm for String Pattern-match (GRASPm), an algorithm centred on overlapped 2-grams analysis, which introduces a novel filtering heuristic - the compatibility rule - achieving significant efficiency gain. GRASPm's foundations rely especially on a wide searching window having the central duplet as reference for fast filtering of multiple alignments. Subsequently, superfluous detailed verifications are summarily avoided by filtering the incompatible alignments using the idcd (involving duplet of central duplet) concept combined with pre-processed conditions, allowing f...
Source: International Journal of Bioinformatics Research and Applications - August 1, 2009 Category: Bioinformatics Authors: Deusdado S, Carvalho P Tags: Int J Bioinform Res Appl Source Type: journals

Prot-2S: a new python web tool for protein secondary structure studies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Prot-2S is a bioinformatics web application devised to analyse the protein chain secondary structures (2S) (http:/ /www.requimte.pt:8080/Prot-2S/). The tool is built on the RCSB Protein Data Bank PDB and DSSP application/files and includes calculation/graphical display of amino acid propensities in 2S motifs based on any user amino acid classification/code (for any particular protein chain list). The interface can calculate the 2S composition, display the 2S subsequences and search for DSSP non-standard residues and for pairs/triplets/quadruplets (amino acid patterns in 2S motifs). This work presents some Prot-2S appli...
Source: International Journal of Bioinformatics Research and Applications - August 1, 2009 Category: Bioinformatics Authors: Munteanu CR, Magalhaes AL Tags: Int J Bioinform Res Appl Source Type: journals

Comparison of feature selection and classification combinations for cancer classification using microarray data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
High throughput gene expression data can be used to identify biomarker profiles for classification. The accuracy of microarray based sample classification depends on the algorithm employed for selecting the features (genes) used for classification, and the classification algorithm. We have evaluated the performance of over 2000 combinations of feature selection and classification algorithms in classifying cancer datasets. One of these combinations (SVM for ranking genes + SMO) shows excellent classification accuracy using a small number of genes across three cancer datasets tested. Notably, classification using 15 sele...
Source: International Journal of Bioinformatics Research and Applications - August 1, 2009 Category: Bioinformatics Authors: Vinaya V, Bulsara N, Gadgil CJ, Gadgil M Tags: Int J Bioinform Res Appl Source Type: journals

Application of the Burrows-Wheeler Transform for searching for tandem repeats in DNA sequences.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genomic sequences contain a variety of repeated structures of various lengths and types, interspersed or in tandem. Repetitive structures play an important role in molecular biology; they are related to the genetic backgrounds of inherited diseases, and they can also serve as markers for DNA mapping and DNA fingerprinting. Since biological databases keep growing in size and number there is a need for creating new tools for finding repeats in genomic sequences. This paper presents a new method for searching for tandem repeats in DNA sequences. It is based on the Burrows-Wheeler Transform (BWT), a very fast and effective...
Source: International Journal of Bioinformatics Research and Applications - August 1, 2009 Category: Bioinformatics Authors: Pokrzywa R Tags: Int J Bioinform Res Appl Source Type: journals

Exploration of homodimer receptor: homodimer protein interactions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Homodimerisation is producing a protein?protein complex composed of two identical molecules. Dimerisation is a phenomenon often occurring in the regulation of biochemical systems like signal transduction pathways. We investigated whether the existence of a homodimer-activated receptor and the activation of homodimer transducers correspond to a more general pattern in cell signalling. We developed a workflow to merge data from the Gene Ontology and the BIND database to produce a list of interactions between homodimer receptors and homodimer proteins. Finally, we found a prevalence of homodimer?homodimer interactions in...
Source: International Journal of Bioinformatics Research and Applications - August 1, 2009 Category: Bioinformatics Authors: Vera J, Kwon T, Schmitz U, Kolch W, Tags: Int J Bioinform Res Appl Source Type: journals

Frameshift detection in prokaryotic genomic sequences.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We have developed a new method for frameshift detection, a combination of ab initio and alignment-based algorithms, that can serve as a useful tool for sequencing quality control in the next generation sequencing. We evaluated the method's accuracy on test sets of annotated genomic sequences with artificial frameshifts in protein coding regions. These tests have shown that the new method performs comparably to the earlier developed FrameD. On the sets of sequences produced by 454 pyrosequencing with sequence errors recovered by Sanger re-sequencing the accuracy of the method was shown to hold at the same level. PMI...
Source: International Journal of Bioinformatics Research and Applications - August 1, 2009 Category: Bioinformatics Authors: Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M Tags: Int J Bioinform Res Appl Source Type: journals

Learning robust cell signalling models from high throughput proteomic data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We propose a framework for learning robust Bayesian network models of cell signalling from high-throughput proteomic data. We show that model averaging using Bayesian bootstrap resampling generates more robust structures than procedures that learn structures using all of the data. We also develop an algorithm for ranking the importance of network features using bootstrap resample data. We apply our algorithms to derive the T-cell signalling network from the flow cytometry data of Sachs et al. (2005). Our learning algorithm has identified, with high confidence, several new crosstalk mechanisms in the T-cell signalling n...
Source: International Journal of Bioinformatics Research and Applications - June 28, 2009 Category: Bioinformatics Authors: Koch M, Broom BM, Subramanian D Tags: Int J Bioinform Res Appl Source Type: journals

Simultaneous structure discovery and parameter estimation in gene networks using a multi-objective GP-PSO hybrid approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This paper presents a hybrid algorithm based on Genetic Programming (GP) and Particle Swarm Optimisation (PSO) for the automated recovery of gene network structure. It uses gene expression time series data as well as phenotypic data pertaining to plant flowering time as its input data. The algorithm then attempts to discover simple structures to approximate the plant gene regulatory networks that produce model gene expressions and flowering times that closely resemble the input data. To show the efficacy of the proposed approach, simulation results applied to flowering time control in Arabidopsis thaliana are demonstra...
Source: International Journal of Bioinformatics Research and Applications - June 28, 2009 Category: Bioinformatics Authors: Cai X, Koduru P, Das S, Welch SM Tags: Int J Bioinform Res Appl Source Type: journals

Development and evaluation of a new statistical model for structure-based high-throughput virtual screening.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We have developed a High-Performance Computing (HPC)-based molecular docking scheme, termed HiPCDock, for drug discovery and development. To improve the statistical significance of our screening results, a bioinformatics approach, motivated by a sequence alignment package BLAST, was implemented. The statistical model was validated with ten known Thymidine Kinase (TK) binders and the real inhibitors showed significant statistics, in terms of low probabilities and expectation values. Our HiPCDock has been implemented to be used by both computational experts and experimental scientists. Thus it is an automated, easy-to-us...
Source: International Journal of Bioinformatics Research and Applications - June 28, 2009 Category: Bioinformatics Authors: Zhang S, Du-Cuny L Tags: Int J Bioinform Res Appl Source Type: journals

Divergent evolution of a Rossmann fold and identification of its oldest surviving ancestor.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
beta-ketoacyl (acyl carrier protein) reductase (beta-k-ACPR) enzymes are essential to fatty acid synthesis in bacteria. The analyses revealed the most primitive member of the beta-k-ACPRs family was a NADP reductase where NADP was recognised by a Thr residue in the beta2alpha3 turn. Aromatic residue stacking at the dimer interface and a previously undetected conserved sequence at the C-terminus, stabilise the oligomeric assembly of these proteins. Our analysis indicates that the primordial members of the beta-k-ACPR family probably arose in the alpha-proteobacteria and are characterised by the presence of multiple ope...
Source: International Journal of Bioinformatics Research and Applications - June 28, 2009 Category: Bioinformatics Authors: Duax WL, Huether R, Pletnev V, Umland TC, Tags: Int J Bioinform Res Appl Source Type: journals

Mining the Arabidopsis and rice genomes for cyclophilin protein families.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cyclophilins, which possess peptidyl-prolyl isomerase activity, are cellular targets of immunosuppressant drugs and involved in a wide variety of functions. While the Arabidopsis thaliana genome contains the largest number of cyclophilins, the number of plant cyclophilins available in databases is small compared to that of other organisms. It implies that many cyclophilins are yet to be identified in plants. In order to identify cyclophilin candidates from available plant sequence data, we examined alignment-free methods based on Partial Least Squares (PLS). PLS classifier performed better than profile hidden Markov mo...
Source: International Journal of Bioinformatics Research and Applications - June 28, 2009 Category: Bioinformatics Authors: Opiyo SO, Moriyama EN Tags: Int J Bioinform Res Appl Source Type: journals

A new approach for clustering gene expression time series data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Identifying groups of genes that manifest similar expression patterns is crucial in the analysis of gene expression time series data. Choosing a similarity measure to determine the similarity or distance between profiles is an important task. This paper proposes a suitable dissimilarity measure for gene expression time series data sets. It also presents a graph-based clustering method for finding clusters in gene expression time series data using the new dissimilarity measure. A comparison with other similarity measures used for gene expression data is presented; the new dissimilarity measure is found effective. The cl...
Source: International Journal of Bioinformatics Research and Applications - June 28, 2009 Category: Bioinformatics Authors: Das R, Kalita J, Bhattacharyya DK Tags: Int J Bioinform Res Appl Source Type: journals

Beyond clustering of array expressions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Microarray technology provides an opportunity to view transcriptions at genomic level under different experimental conditions. Generally, co-expressed genes, which are members of the same cluster, are expected to have similar function, but unfortunately it is not true due to various reasons including co-expression does not necessarily imply co-regulation. To improve the results of clustering, we investigate a method based on singular value decomposition (SVD) for integrating diverse data sources. We also introduce a new cluster evaluation method based on mutual information. Using time series data sets on yeast, we have...
Source: International Journal of Bioinformatics Research and Applications - June 28, 2009 Category: Bioinformatics Authors: Loganantharaj R Tags: Int J Bioinform Res Appl Source Type: journals

An open source phylogenetic search and alignment package.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PSODA is a comprehensive phylogenetics package, including alignment, phylogenetic search under both parsimony and maximum likelihood, and visualisation and analysis tools. PSODA offers performance comparable to PAUP* in an open source package that aims to provide a foundation for researchers examining new phylogenetic algorithms. A key new feature is PsodaScript, an extension to the nearly ubiquitous NEXUS format, that includes conditional and loop constructs; thereby allowing complex meta-search techniques like the parsimony ratchet to be easily and compactly implemented. PSODA promises to be a valuable tool in the fu...
Source: International Journal of Bioinformatics Research and Applications - June 28, 2009 Category: Bioinformatics Authors: Carroll H, Teichert AR, Krein J, Sundberg K, Snell Q, Clement M Tags: Int J Bioinform Res Appl Source Type: journals

Polyhelices through n points.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A polyhelix is continuous space curve with continuous Frenet frame that consists of a sequence of connected helical segments. The main result of this paper is that given n points in space, there exist infinitely many polyhelices passing through these points. These curves are by construction continuous with continuous derivatives and are completely specified by 3n numbers, i.e., the initial position, the signed curvature, torsion, and length of each helical segment. Polyhelices can be parametrised by the arc length and easily expressed in terms of product of matrices. PMID: 19324599 [PubMed - in process] (Source: In...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2009 Category: Bioinformatics Authors: Goriely A, Neukirch S, Hausrath A Tags: Int J Bioinform Res Appl Source Type: journals

Homology modelling of pyrophosphosrylase, enzyme involved in chitin pathway of Moniliophthora perniciosa.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Moniliophthora perniciosa (Sthael) (Singer) Phillips-Mora is the causal agent of witches' broom disease, which can infect Theobroma cacao decreasing the production of cocoa about 60%. M. perniciosa has a set of potential enzymes that can be useful targets for design of new inhibitors. After the release of the aminoacid sequence of pyrophosphorylase of M. perniciosa, a comparative modelling approach was carried out to obtain the 3D structure of this target. This model can be useful to develop new inhibitors against witches' broom disease. PMID: 19324600 [PubMed - in process] (Source: International Journal of Bioinfo...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2009 Category: Bioinformatics Authors: Dos Santos MC, Taranto AG, De Assis SA, Goes-Neto A Tags: Int J Bioinform Res Appl Source Type: journals

Structural studies of PNP from Toxoplasma gondii.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Toxoplasmosis is a chronic infection that affects approximately 30% of the human population and is caused by Toxoplasma gondii. Determination of the three dimensional structure of PNP from T. gondii could provide new insights into the purine binding site and sub-strate binding, and could be used for future rational design of new drugs against toxoplasmosis. This work describes the molecular model for three dimensional structure of PNP from T.gondii using, as a template, PNP from Plasmodium falciparum. Molecular dynamics showed that this model is stable during a trajectory of 3 ns. PMID: 19324601 [PubMed - in proce...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2009 Category: Bioinformatics Authors: Vivan AL, Caceres RA, Basso LA, Santos DS, Tags: Int J Bioinform Res Appl Source Type: journals

Parallelisation of a multi-neighbourhood local search heuristic for a phylogeny problem.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this work we study a phylogeny problem. That is, given a collection of organisms, we want to reconstruct the evolutionary history of the organisms. We are interested in inferring relationships between the organisms. For a number of reasonable biological hypotheses the problem becomes NP-hard. Besides that, the problem data is large enough to inhibit anyone using exact algorithms to solve, in practical computational time, real instances of the problem. In this work, we propose an innovative technique based on local search procedures that use multiple starts and diversified neighbourhoods. PMID: 19324602 [PubMed -...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2009 Category: Bioinformatics Authors: Viana GV, Gomes FA, Ferreira CE, Meneses CN Tags: Int J Bioinform Res Appl Source Type: journals

Scaling properties of transcription profiles in gene networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Here we show that the transcriptional noise is an emergent property with scale invariance from genome level to the level of small Transcriptional Regulatory Genetic Networks (TRGN). We show that a small set of 9-12 genes reproduces the geometric mean value of transcriptional noise of the largest percolating networks and the whole 93-gene wide TRGN sub-network. Our results predict that the collapse of the standard deviation of the transcriptional noise as a function of gene sub-networks connectivity should occur for 1000 genes, the approximate size of the maximal interconnected percolating network cluster, which corresp...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2009 Category: Bioinformatics Authors: Ferreira RC, Bosco F, Briones MR Tags: Int J Bioinform Res Appl Source Type: journals

Optimisation and data mining techniques for the screening of epileptic patients.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Identifying abnormalities or anomalies by visual inspection on neurophysiologic signals such as ElectroEncephaloGrams (EEGs), is extremely challenging. We propose a novel Multi-Dimensional Time Series (MDTS) classification technique, called Connectivity Support Vector Machines (C-SVMs) that integrates brain connectivity network with SVMs. To alter noise in EEG data, Independent Component Analysis based on the Unbiased Quasi Newton Method was applied. C-SVM achieved 94.8% accuracy classifying subjects compared to 69.4% accuracy with standard SVMs. It suggests that C-SVM can be a rapid, yet accurate, technique for online...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2009 Category: Bioinformatics Authors: Fan YJ, Chaovalitwongse WA, Liu CC, Sachdeo RC, Iasemidis L, Pardalos P Tags: Int J Bioinform Res Appl Source Type: journals

Modelling biomolecular structure with geodesic curves through ordered sets of atom sites.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A study of the fundamental requirements which are used in the mathematical modelling of biomolecular structure is presented in this work. The visualisation of smooth spatial curves through an ordered set of points corresponding to atom sites is then considered. It is emphasised that the restrictions introduced by the choice of Euclidean Geometry as a natural paradigm lead usually to helices as the natural solution. However, some arguments are also presented for the consideration of curves which satisfy only one of the requirements or none. PMID: 19324605 [PubMed - in process] (Source: International Journal of Bioin...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2009 Category: Bioinformatics Authors: Mondaini RP Tags: Int J Bioinform Res Appl Source Type: journals

Fuzzy cluster stability analysis with missing values using resampling.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Exploratory data analysis is often necessary to evaluate potential hypotheses for subsequent studies such as grouping the data in clusters. In real data sets the occurrence of incompleteness is very common. We propose a method that tolerates missing values for fuzzy clustering using resampling (bootstrapping) and cluster stability analysis. The quality of classification is based on the measures like F1 and Hubert. The central idea is to compare a reference cluster with many clusters from sub-samples of the original data set. The results demonstrate that our method is capable of identifying relevant partitions even with...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2009 Category: Bioinformatics Authors: Milagre ST, Maciel CD, Pereira JC, Pereira AA Tags: Int J Bioinform Res Appl Source Type: journals

Correcting short reads with high error rates for improved sequencing result.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In the sequencing process, reads of the sequence are generated, then assembled to form contigs. New technologies can produce reads faster with lower cost and higher coverage. However, these reads are shorter. With errors, short reads make the assembly step more difficult. Chaisson et al. (2004) proposed an algorithm to correct the reads prior to the assembly step. The result is not satisfactory when the error rate is high (e.g., >/=3%). We improve their approach to handle reads of higher error rates. Experimental results show that our approach is much more effective in correcting errors, producing contigs of higher ...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2009 Category: Bioinformatics Authors: Wong TK, Lam TW, Chan PY, Yiu SM Tags: Int J Bioinform Res Appl Source Type: journals

RECOMBFLOW: a scientific workflow environment for Intragenomic Gene Conversion analysis in bacterial genomes, including the pathogen Streptococcus pyogenes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Intragenomic Gene Conversion (IGC) is important in the evolution of bacteria but has only been analysed computationally in a few strains of Escherichia coli. This paper describes a scientific workflow system, called RECOMBFLOW, that automates this complex procedure for the analysis of more than 400 bacterial genomes, with a median analysis time per genome of less than 5 minutes. Results show that IGC varies greatly, both between different species and among multiple genomes of the same species. We analyse for the first time the large variation of IGC in the pathogen Streptococcus pyogenes, and also in non-pathogenic bac...
Source: International Journal of Bioinformatics Research and Applications - January 13, 2009 Category: Bioinformatics Authors: Alhiyafi J, Sabesan C, Lu S, Ram JL Tags: Int J Bioinform Res Appl Source Type: journals

Analysis of protein phosphorylation site predictors with an independent dataset.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Protein phosphorylation plays a fundamental role in most of the cellular regulatory pathways. Experimental detection of protein phosphorylation sites is labour intensive and often limited by the availability and optimisation of enzymatic reactions. The in silico prediction of phosphorylation sites using protein's primary sequences may provide guidelines for further experimental consideration and interpretation of phosphoproteomic data. An array of such tools exists over the internet and provides the prediction for protein kinase families. We developed an independent dataset to compare the performances of these methods ...
Source: International Journal of Bioinformatics Research and Applications - January 13, 2009 Category: Bioinformatics Authors: Sikder AR, Zomaya AY Tags: Int J Bioinform Res Appl Source Type: journals

A practical algorithm for multiplex PCR primer set selection.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Selecting the minimum primer set with multiple constraints is an effective method for a successful and economical Multiplex Polymerase Chain Reaction (MP-PCR) experiment. However, there is no suitable algorithm for solving the problem. In this paper, a mathematical model is presented for the minimum primer set selection problem with multiple constraints. By introducing a novel genetic operator, we developed a parthenogenetic algorithm MG-PGA to solve the model. Experimental results show that MG-PGA can not only find a small primer set, but can also satisfy multiple biological constraints. Therefore, MG-PGA is a practic...
Source: International Journal of Bioinformatics Research and Applications - January 13, 2009 Category: Bioinformatics Authors: Wu J, Wang J, Chen J Tags: Int J Bioinform Res Appl Source Type: journals

Finding Significantly Expressed genes from time-course expression profiles.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This paper proposes a statistical method for finding Significantly Expressed (SE) genes from time-course expression. SE genes are time-dependent while non-SE genes are time-independent. This method models time-dependent gene expression profiles by autoregressive equations plus Gaussian noises, and time-independent ones by Gaussian noises. The statistical F-testing is used to calculate the probability (p-value) that a profile is time-independent. Both a synthetic dataset and a biological dataset were employed to evaluate the performance of this method, measured by the False Discovery Rate (FDR) and the False Non-discove...
Source: International Journal of Bioinformatics Research and Applications - January 13, 2009 Category: Bioinformatics Authors: Wu FX, Xia Z, Mu L Tags: Int J Bioinform Res Appl Source Type: journals

Stabbing balls and simplifying proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We address the problem of stabbing a sequence of indexed balls B = {B1,B2, . . . , Bn} in R(3), where Bi (1 </= i </= n) has centre pi and radius epsiloni; a solution is an increasing integer sequence i1, . . . , im such that i1 = 1, im = n and for ij </= k </= ij+1 the line segment Pij Pij+1 stabs the ball Bk; the goal is to minimise m. The problem finds applications in simplification of molecule chains for visualisation, matching and efficient searching in molecule and protein databases. We implemented the algorithm and created a web server where one can input a pdb file and get the simplified protein cha...
Source: International Journal of Bioinformatics Research and Applications - January 13, 2009 Category: Bioinformatics Authors: Daescu O, Luo J Tags: Int J Bioinform Res Appl Source Type: journals

An autonomous DNA model for finite state automata.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this paper we introduce an autonomous DNA model for finite state automata. This model called sticker automaton model is based on the hybridisation of single stranded DNA molecules (stickers) encoding transition rules and input data. The computation is carried out in an autonomous manner by one enzyme which allows us to determine whether a resulting double-stranded DNA molecule belongs to the automaton's language or not. PMID: 19136366 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - January 13, 2009 Category: Bioinformatics Authors: Martinez-Perez IM, Zimmermann KH, Ignatova Z Tags: Int J Bioinform Res Appl Source Type: journals

Alignment of biological sequences with quality scores.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this paper we consider the problem of sequence alignment with quality scores. DNA sequences produced by a base-calling program (as part of sequencing) have quality scores which represent the confidence level for individual bases. However, previous sequence alignment algorithms do not consider such quality scores. To solve sequence alignment with quality scores, we first consider a more general problem where the input is weighted sequences which are sequences with probabilities that characters occur in each position. We propose a meaningful measure of an alignment of two weighted sequences and show that an optimal al...
Source: International Journal of Bioinformatics Research and Applications - January 13, 2009 Category: Bioinformatics Authors: Na JC, Roh K, Apostolico A, Park K Tags: Int J Bioinform Res Appl Source Type: journals

Classification of proteomic data with multiclass Logistic Partial Least Squares algorithm.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Early detection of cancer is crucial for successful treatments. In this paper, we propose a multiclass Logistic Partial Least Squares (LPLS) algorithm for classification of normal vs. cancer using Mass Spectrometry (MS). LPLS combines the multiclass logistic regression with Partial Least Squares (PLS) algorithm. Wavelet decomposition is also proposed for pre-processing of original data. Wavelet decomposition and the proposed LPLS are applied to real life cancer data. Experimental comparisons show that LPLS with wavelet decomposition outperforms other methods in the analysis of MS data. PMID: 18283025 [PubMed - inde...
Source: International Journal of Bioinformatics Research and Applications - December 1, 2008 Category: Bioinformatics Authors: Liu Z, Chen D, Tian JP Tags: Int J Bioinform Res Appl Source Type: journals

A matrix-based multilevel approach to identify functional protein modules.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present an unweighted-graph version of a multilevel spectral algorithm which more accurately identifies protein complexes with less computational time. PMID: 18283026 [PubMed - indexed for MEDLINE] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - December 1, 2008 Category: Bioinformatics Authors: Oliveira S, Seok SC Tags: Int J Bioinform Res Appl Source Type: journals

CARIBIAM: constrained Association Rules using Interactive Biological IncrementAl Mining.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This paper analyses annotated genome data by applying a very central data-mining technique known as Association Rule Mining (ARM) with the aim of discovering rules and hypotheses capable of yielding deeper insights into this type of data. In the literature, ARM has been noted for producing an overwhelming number of rules. This work proposes a new technique capable of using domain knowledge in the form of queries in order to efficiently mine only the subset of the associations that are of interest to investigators in an incremental and interactive manner. PMID: 18283027 [PubMed - indexed for MEDLINE] (Source: Intern...
Source: International Journal of Bioinformatics Research and Applications - December 1, 2008 Category: Bioinformatics Authors: Rahal I, Rahhal R, Wang B, Perrizo W Tags: Int J Bioinform Res Appl Source Type: journals

High performance bio-image database retrieval using MPI.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Fast and accurate 3D object reconstruction and partial 3D component retrieval from 2D image slices represent a difficult and challenging problem. To group related objects on different layers in an image stack, image segmentation and sequential matching of adjacent 2D objects have to be preformed. Object matching involves heavy computing and is time consuming. In this paper, we propose a new approach for parallel implementation of object contour matching and partial 3D component retrieval based on image contour structure. The method has been implemented in MPI on a SGI Origin 2000 machine. The experimental results show ...
Source: International Journal of Bioinformatics Research and Applications - December 1, 2008 Category: Bioinformatics Authors: Li Y, Chen X, Belkasim S, Pan Y Tags: Int J Bioinform Res Appl Source Type: journals

Extracting Protein-Protein Interactions from MEDLINE using the Hidden Vector State model.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A major challenge in text mining for biomedicine is automatically extracting protein-protein interactions from the vast amount of biomedical literature. We have constructed an information extraction system based on the Hidden Vector State (HVS) model for protein-protein interactions. The HVS model can be trained using only lightly annotated data whilst simultaneously retaining sufficient ability to capture the hierarchical structure. When applied in extracting protein-protein interactions, we found that it performed better than other established statistical methods and achieved 61.5% in F-score with balanced recall and...
Source: International Journal of Bioinformatics Research and Applications - December 1, 2008 Category: Bioinformatics Authors: Zhou D, He Y, Kwoh CK Tags: Int J Bioinform Res Appl Source Type: journals