MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'International Journal of Bioinformatics Research and Applications' source. Sat, 28 Jan 2012 00:35:47 +0100 http://www.medworm.com/index.php?rid=5454261&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22112527%26dopt%3DAbstract Authors: Subramani P, Sahu R, Verma S, Prabakaran S Abstract Data mining is a boon to many fields like bioinformatics for processing a vast amount of data. In our previous paper, we proposed a novel feature selection method for microarray data classification using Wavelet Power Spectrum (WPS). In this paper, we present optimisation techniques to improve the quality of the features thus selected and to select 'tight genes' from various cancer microarrays. The results show that 'tight genes' thus selected were more qualitative and could be used for a wide variety of data sets. Also, 'tight genes' thus selected in this mining process could be used with any existing classification approach. PMID: 22112527 [PubMed - in process] (Source: International Journal of Bioinformatics Resear... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5454261 Tue, 29 Nov 2011 13:42:02 +0100 5454261 http://www.medworm.com/index.php?rid=5454260&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22112528%26dopt%3DAbstract Authors: Wang J, Griesmer S, Cervantes-Cervantes M, Griesmer SJ, Song Y, Wang JT Abstract We propose here a new approach for ncRNA prediction. Our approach selects features derived from RNA folding programs and ranks these features using a class separation method that measures the ability of the features to differentiate between positive and negative classes. The target feature set comprising top-ranked features is then used to construct several classifiers with different supervised learning algorithms. These classifiers are compared to the same supervised learning algorithms with the baseline feature set employed in a state-of-the-art method. Experimental results based on ncRNA families taken from the Rfam database demonstrate the good performance of the proposed approach. PMI... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5454260 Tue, 29 Nov 2011 13:42:02 +0100 5454260 http://www.medworm.com/index.php?rid=5454259&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22112529%26dopt%3DAbstract In this study, we predicted Single Exon Genes (SEGs) distributed in whole rice genome and their expressed proteins. Complete genome of rice was retrieved from TIGR. CDS annotation in the FEATURE (GenBank format) was used to predict SEGs sequences. Organelle gene sequences, pseudogenes, tRNA genes, rRNA genes and duplicated genes were eliminated through different bioinformatics tools. A sizeable number (8.1%) of SEGs in whole rice genome were detected. Predicted SEGs were further searched for their differential response under anoxia. Out of total detected SEGs, only 39.33% were anoxia responsive. Among the total detected anoxia-responsive SEG, only 23.48% encode the known proteins. PMID: 22112529 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applica... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5454259 Tue, 29 Nov 2011 13:42:02 +0100 5454259 http://www.medworm.com/index.php?rid=5454258&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22112530%26dopt%3DAbstract Authors: Messaoudi A, Belguith H, Ghram I, Hamida JB Abstract Lipase enzymes play an important role in lipid metabolism and are produced by a variety of species. Compared with animal, bacterial and fungal, little is known about plant lipases. Although lipases belong to many different protein families, they have the same architecture, the ?/?-hydrolase fold and a conserved active site signature, the Gly-Xaa-Ser-Xaa-Gly motif. Several studies on enzymatic activity and interfacial activation phenomenon of lipases confirm the presence of consensus sequence and a conserved domain. Lipases can be divided into two main groups: carboxylesterases (EC 3.1.1.1); 'true' lipases (EC 3.1.1.3), which differ in several biochemical features, which allow us to develop a database that regroups all 't... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5454258 Tue, 29 Nov 2011 13:42:02 +0100 5454258 http://www.medworm.com/index.php?rid=5454257&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22112531%26dopt%3DAbstract Authors: Vuskovic MI, Xu H, Bovin NV, Pass HI, Huflejt ME Abstract Procedures for data preprocessing, quality control, data analysis, evaluation and visualization of the new high-throughput biomarker platform based on printed glycan arrays (PGA) are presented in this paper. PGAs are similar in concept to DNA arrays but contain deposits of various carbohydrate structures (glycans) instead of spotted DNAs. PGA biomarker discovery for the early detection, diagnosis and prognosis of human malignancies and viral diseases is based on the response of the immune system as measured by the level of binding of anti-glycan antibodies from human serum to the glycans on the array. Procedures related to PGA data processing are herein demonstrated in a pilot study of cases representing 50 sera fro... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5454257 Tue, 29 Nov 2011 13:42:02 +0100 5454257 http://www.medworm.com/index.php?rid=5454256&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22112532%26dopt%3DAbstract Authors: Ahmad A, Lutfullah G, Ali R Abstract Streptolysin O, a 63 kDa exotoxin coded by slo gene, is a well-characterised thiol-activated cytolysin, which damages cholesterol-containing membranes resulting in disruption and lysis of the target cell. On the basis of homology model and secondary structure analysis, the toxin has four domains of which domain 4 is of particular importance and is directly linked to domain 2 by a glycine linker and remained consistent in initial membrane recognition. Domain 4 reduces the hydrophobic ratio when compared with its template, which would affect the activity of the toxin at low pH. PMID: 22112532 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5454256 Tue, 29 Nov 2011 13:42:02 +0100 5454256 http://www.medworm.com/index.php?rid=5244380&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919276%26dopt%3DAbstract Authors: Neelakanta P, Pavlovic M, Zhuang H PMID: 21919276 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5244380 Fri, 23 Sep 2011 01:24:06 +0100 5244380 http://www.medworm.com/index.php?rid=5140533&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21816712%26dopt%3DAbstract Authors: Pavlovic M, Cavallo M, Kats A, Kotlarchyk A, Zhuang H, Shoenfeld Y Abstract Specific entities of naturally-occurring DNA hydrolytic/cytotoxic antibodies (abzymes) are linked to autoimmune and lymphoproliferative disorders. Suggested sequence of underlying activities conform to such entities penetrating the living cells, trans-locating to nucleus and recognising specific binding sites within single- or double-stranded DNA. Their origin is unknown since corresponding immunogens are unidentified. These anti-DNA antibodies could be the organism's immune response to microbial attack. Their structure, function and pathogenicity were investigated in wet-lab and via bioinformatics in context of Rational Vaccine Designs. This paper offers a comprehensive critical review on the subj... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5140533 Fri, 19 Aug 2011 14:20:03 +0100 5140533 http://www.medworm.com/index.php?rid=5140532&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21816713%26dopt%3DAbstract Authors: Neelakanta PS, Chatterjee S, Thengum-Pallil GA Abstract The bioinformatic aspects of computing entropy and energetic profiles associated with a viral single-stranded DNA (ssDNA) are addressed. The analyses envisaged thereof determine the structural (stem and loop) features, identify the CpG motifs and delineate the boundaries of coding DNA segments along a test viral (B19) ssDNA. The analytical modelling and computational efforts conform to Shannon entropy and thermodynamic kinetics of the test genome. Results are presented toward validation against available data. Pertinent details are reviewed in the context of their possible uses in rational vaccine designs. PMID: 21816713 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applicatio... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5140532 Fri, 19 Aug 2011 14:20:03 +0100 5140532 http://www.medworm.com/index.php?rid=5140531&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21816714%26dopt%3DAbstract Authors: Arredondo TV Abstract In this paper, a novel discriminant algorithm based on Fisher linear discriminant that enables distinguishing the features of Codon DNA Segments (CDS) in a DNA sequence consistent with the underlying stochastic attributes is developed. It is specifically applied to a viral single-strand DNA (ssDNA). The Fisher discriminant adopted delineates judiciously, the codon and non-codon regions in the test ssDNA. With a complete description of the computational procedure, the efficacy of the algorithm is tested via simulated experiments on a real ssDNA of B19 virus. The results are validated against GenBank data available on the test viral sequence. Inferences with regard to CDS regions present in the test sequence are made indicating possible fuzzy transition... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5140531 Fri, 19 Aug 2011 14:20:03 +0100 5140531 http://www.medworm.com/index.php?rid=5140530&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21816715%26dopt%3DAbstract Authors: Kalpana R, Muttan S, Kumarasamy N Abstract Brain White Matter (BWM) is formed on nerve fibres (due to myelin coating) and it undergoes continuous changes with aging throughout the life of humans. This age-related morphology, however, also gets further modified when a subject is infected by a viral disease such as HIV. In the present study, textural variations in BWM specific to a set of control images vs. images of a HIV + subject are assayed via an algorithm based on the Grey Level Co-occurrence Matrix (GLCM); and the associated Haralick features that are extracted from the GLCM. The clinical images of the brain used in the study are gathered from the noninvasive technique of Diffusion Tensor Magnetic Resonance Imaging (DT MRI). Results observed in the images of normal (n... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5140530 Fri, 19 Aug 2011 14:20:03 +0100 5140530 http://www.medworm.com/index.php?rid=5140529&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21816716%26dopt%3DAbstract Authors: Amin MR, Siddiqui MS, Ahmed D, Ahmed F, Hossain A Abstract Human sapovirus is one of the major causes of viral gastroenteritis. Although the capsid protein (VP1) confers antigenic cross-reactivity, immunity against sapovirus is still unclear. Using immunoinformatics approach, we defined putative T- and B-cell epitopes of VP1 and mapped on to its predicted three-dimensional structure. Identified five putative T-cell epitopes also occupied the putative B-cell epitope region. These putative epitopes were conserved in all existing serotypes. Predicted epitopes can be generated through proteasome cleavage and may be useful in designing peptide-based subunit vaccine to confer both humoral and cell-mediated immunity. PMID: 21816716 [PubMed - in process] (Source: International... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5140529 Fri, 19 Aug 2011 14:20:03 +0100 5140529 http://www.medworm.com/index.php?rid=5140528&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21816717%26dopt%3DAbstract Authors: Sagar M, Yadav AK Abstract Hepatitis B Virus encodes HBX, which is considered to be responsible for virus infection in mammals. The HBx modulates the signal transduction pathways toward the aetiological aspects of establishing liver cancer. In this context, to predict epitopes from three HBX protein (for vaccine designs), use of certain computational tools are indicated. Relevant study shows that seven binding peptides for MHC class I and 16 for MHC class II molecule bear significant binding affinity. Epitope LSAMSTTDL for MHC I and LRFTSARRM, HLSLRGLPV for MHC II have highest log-values of 0.746 and (0.8628, 0.8048), respectively. Vaccine model is designed using predicted epitopes. Such patterns characterise possible biological activity of the vaccine of interest. PMI... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5140528 Fri, 19 Aug 2011 14:20:03 +0100 5140528 http://www.medworm.com/index.php?rid=5140527&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21816718%26dopt%3DAbstract Authors: Seoud RA Abstract Hepatitis C Virus (HCV) causes significant morbidity worldwide with restricted treatment options and lack of a universal cure which necessitate design of novel drugs. Researchers face an enormous growth of literature with very small portions of HCV knowledge accessible in structured way. This paper proposes the BioHCVKD that helps researchers to annotate relevant HCV information targeted to accelerate HCV drug discovery. BioHCVKD combines the dictionary based filtering and conditional random field (CRF) based gene mention tagger. BioHCVKD is supported by two modules, the Abstract Insertion module, and the Protein Insertion module. BioHCVKD achieves a recall of 73.25%, a precision of 70.5% and F-score of 71.85%, which improves the performance of the name e... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=5140527 Fri, 19 Aug 2011 14:20:03 +0100 5140527 http://www.medworm.com/index.php?rid=4853597&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21576071%26dopt%3DAbstract Authors: Gupta A, Agarwal S This paper introduces a novel algorithm for DNA sequence compression that makes use of a transformation and statistical properties within the transformed sequence. A word based tagged code is used for identification of end of code. The word based encoder uses frequency distribution for assigning the code of words. The designed compression algorithm is efficient and effective for DNA sequence compression. As a statistical compression method, it is able to search the pattern inside the compressed text which is useful in knowledge discovery. Experiments show that our algorithm is shown to outperform existing compressors on typical DNA sequence datasets. PMID: 21576071 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applic... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4853597 Tue, 24 May 2011 10:45:03 +0100 4853597 http://www.medworm.com/index.php?rid=4853596&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21576072%26dopt%3DAbstract Authors: Niranjan V, Ahmed R, Seenivasagam R, Sivakumar G A comprehensive analysis of the X-chromosome led to the discovery of an important region found to be Xq22.1. Xq22.1 was analysed in detail to locate a credible gene carrying segment on it, which may be implicated in various disorders related to the X-chromosome. Finding genes in a genomic sequence is a fiddly problem. Hence, we developed a new in-silico approach to identify the novel gene, based on homology methods (extrinsic methods) and gene prediction methods (intrinsic methods). PMID: 21576072 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4853596 Tue, 24 May 2011 10:45:03 +0100 4853596 http://www.medworm.com/index.php?rid=4853595&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21576073%26dopt%3DAbstract Authors: Wu D, Smith S, Mahan H, Jernigan RL, Flexibility and dynamics of protein structures are reflected in the B-factors and order parameters obtained experimentally with X-ray crystallography and Nuclear Magnetic Resonance (NMR). Methods such as Normal Mode Analysis (NMA) and Elastic Network Models (ENM) can be used to predict the fluctuations of protein structures for either atomic level or coarse-grained structures. Here, we introduce the Local-Distance Matrix Error (DME), an efficient and simple analytic method to study the fluctuations of protein structures, especially for the ensembles of NMR-determined protein structures. Comparisons with the fluctuations obtained by experiments and other by computations show strong correlations. PMID: 21576073 [PubMed - in process] (Sou... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4853595 Tue, 24 May 2011 10:45:03 +0100 4853595 http://www.medworm.com/index.php?rid=4853594&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21576074%26dopt%3DAbstract In this study, we carried out genome-wide analyses to explore expansin gene family in the genome of indica rice. Reference nucleotides were chosen as query sequences for searches in the indica rice genome database. Clones having genomic sequences similar to expansin were taken and converted to amino acid sequences. Putative sequences were subjected to PROSITE and Pfam databases, and 21 signature-sequences-related expansin gene family was obtained. The presence of transmembrane domains was also predicted for all 21 expansin proteins. A phylogenetic tree was generated from the alignments of the proteins sequences to examine the phylogenetic relationship of indica rice expansin proteins. PMID: 21576074 [PubMed - in process] (Source: International Journal of Bioinformatics Research and App... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4853594 Tue, 24 May 2011 10:45:03 +0100 4853594 http://www.medworm.com/index.php?rid=4853593&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21576075%26dopt%3DAbstract In this study, we propose a new multiple sequence strategy that extracts sequence information, sequence global and local similarities to provide different weights for each input sequence. A weighted pair-wise distance matrix is calculated from these sequences to build a dynamic alignment guiding tree. The tree can reorder its higher-level branches based on corresponding alignment results from lower tree levels to guarantee the highest alignment scores at each level of the tree. This technique improves the alignment accuracy up to 10% on many benchmarks tested against alignment tools such as CLUSTALW (Thompson et al., 1994), DIALIGN (Morgenstern, 1999), T-COFFEE (Notredame et al., 2000), MUSCLE (Edgar, 2004), and PROBCONS (Do et al., 2005) of the multiple sequence alignment. PMID: 21576... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4853593 Tue, 24 May 2011 10:45:03 +0100 4853593 http://www.medworm.com/index.php?rid=4853592&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21576076%26dopt%3DAbstract Authors: Elloumi Oueslati A, Lachiri Z, Ellouze N In this paper, synchronous analysis based on wavelet transform is applied to genomic sequences. To focus on the particular feature of periodicity 3 in the protein-coding region of genes, a coding method is applied on the sequence, which will be segmented to form a pitch synchronous representation. This modelling concept captures period of period fluctuation of signals. The wavelet transform enhances the periodicity, and a given threshold is used to make decision about exon's positions. The algorithm simulation shows the accuracy of the method in simultaneously locating exons and revealing the reading frame associated. PMID: 21576076 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4853592 Tue, 24 May 2011 10:45:03 +0100 4853592 http://www.medworm.com/index.php?rid=4853591&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21576077%26dopt%3DAbstract Authors: Sharma R, Gupta N, Narang V, Mittal A Positional Weight Matrices (PWMs) are widely used in representation and detection of Transcription Factor Of Binding Sites (TFBSs) on DNA. We implement online PWM search algorithm over parallel architecture. A large PWM data can be processed on Graphic Processing Unit (GPU) systems in parallel which can help in matching sequences at a faster rate. Our method employs extensive usage of highly multithreaded architecture and shared memory of multi-cored GPU. An efficient use of shared memory is required to optimise parallel reduction in CUDA. Our optimised method has a speedup of 230-280x over linear implementation on GPU named GeForce GTX 280. PMID: 21576077 [PubMed - in process] (Source: International Journal of Bioinformatics Research ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4853591 Tue, 24 May 2011 10:45:03 +0100 4853591 http://www.medworm.com/index.php?rid=4748097&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21441093%26dopt%3DAbstract This study sets out to check similar pattern, domain and residue-specific mutation, which may interact with expressions of P53 and BRCA1. PMID: 21441093 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4748097 Mon, 25 Apr 2011 19:45:03 +0100 4748097 http://www.medworm.com/index.php?rid=4748096&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21441094%26dopt%3DAbstract This study is useful in making more accurate prediction of results with better combination Highly Active Antiretroviral Therapy (HAART) and important mutations. PMID: 21441094 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4748096 Mon, 25 Apr 2011 19:45:03 +0100 4748096 http://www.medworm.com/index.php?rid=4748095&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21441095%26dopt%3DAbstract Authors: Chiu SK, Hsieh MH, Tzeng CM By taking advantage of the power of comparative genomics, we devised an algorithm, Unique Marker Finder (U-MarFin), to generate a collection of unique DNA sequences from a target organism. The whole target genome is partitioned into a scoring pool of less 4000 base-pair fragments, which are then subjected to elimination of homologous sequences in other bacterial genomes by BLAST alignment, and looked for all open reading frames as they may be applied as unique markers. Through regular, nested, multiplex and real time PCR and microarray technology, we empirically demonstrated that the sequences discovered were highly specific to the species that they are derived from, and they can serve as molecular biomarkers for diagnostic purpose. PMID: 214410... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4748095 Mon, 25 Apr 2011 19:45:03 +0100 4748095 http://www.medworm.com/index.php?rid=4748094&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21441096%26dopt%3DAbstract Authors: Jean G, Nikolski M Current methods for detecting synteny work well for genomes with high degrees of inter- and intra-species chromosomal homology, such as mammals. This paper presents a new algorithm for synteny computation that is well suited to genomes covering a large evolutionary span. It is based on a three-step process: identification of initial microsyntenic homologous regions, extension of homologous boundaries and reconstruction of syntenic blocks by identification of groups of homologous genomic segments that are conserved in every subject genome. Our method performs as well as GRIMM-Synteny on mammalian genomes, and outperforms it for clades with much greater evolutionary distances such as the Hemiascomycetous yeasts. PMID: 21441096 [PubMed - in process] (Source... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4748094 Mon, 25 Apr 2011 19:45:03 +0100 4748094 http://www.medworm.com/index.php?rid=4748093&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21441097%26dopt%3DAbstract We describe a novel approach to predict the structure of key TR features and to aid the identification of TRs in genomes, using a program we developed, TRFolder. We applied our method to confirm and improve previously studied core structures from Saccharomyces and Kluyveromyces TRs. We made novel structural predictions of core elements of the TRs from Schizosaccharomyces pombe, Candida albicans, and several other yeast species. PMID: 21441097 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4748093 Mon, 25 Apr 2011 19:45:03 +0100 4748093 http://www.medworm.com/index.php?rid=4696140&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21441098%26dopt%3DAbstract Authors: Khrustalev VV, Barkovsky EV The usage of cytosine in third codon positions of 22 complete Rubella virus genomes (52.4%) is significantly higher than the usage of guanine (28.9%), adenine (6.9%) and uracil (11.8%). The percentage of U ↔ C transitions (55%) between 22 Rubella virus genomes is two times higher than the percentage of A ↔ G transitions (23%). Predicted microRNA from ORF1 of Rubella virus may target human APOBEC1 mRNA, blocking APOBEC1-editing of viral RNA-minus and RNA-plus strands (preventing G → A and C → U transitions, respectively), while their ADAR-editing (causing U → C and A → G transitions, respectively) occurs frequently. PMID: 21441098 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4696140 Sun, 10 Apr 2011 09:45:06 +0100 4696140 http://www.medworm.com/index.php?rid=4696128&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21441099%26dopt%3DAbstract Authors: Chen Z, Cai Z, Li M, Liu B Prediction of protein function is one of the most challenging problems in the post-genomic era. In this paper, we propose a novel algorithm Improved ProteinRank (IPR) for protein function prediction, which is based on the search engine technology and the preferential attachment criteria. In addition, an improved algorithm IPRW is developed from IPR to be used in the weighted protein?protein interaction (PPI) network. The proposed algorithms IPR and IPRW are applied to the PPI network of S.cerevisiae. The experimental results show that both IPR and IPRW outweigh the previous methods for the prediction of protein functions. PMID: 21441099 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4696128 Sun, 10 Apr 2011 09:45:06 +0100 4696128 http://www.medworm.com/index.php?rid=4075591&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20940121%26dopt%3DAbstract Authors: Broom BM, Sulman EP, Do KA, Edgerton ME, The analysis of high-throughput data sets, such as microarray data, often requires that individual variables (genes, for example) be grouped into clusters of variables with highly correlated values across all samples. Gene shaving is an established method for generating such clusters, but is overly sensitive to the input data: changing just one sample can determine whether or not an entire cluster is found. This paper describes a clustering method based on the bootstrap aggregation of gene shaving clusters, which overcomes this and other problems, and applies the new method to a large gene expression microarray dataset from brain tumour samples. PMID: 20940121 [PubMed - in process] (Source: International Journal of Bioinformatics R... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4075591 Mon, 18 Oct 2010 08:55:03 +0100 4075591 http://www.medworm.com/index.php?rid=4075590&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20940122%26dopt%3DAbstract In this study, we develop a two-class classification system based on a committee of k-Nearest Neighbour (kNN) classifiers. The system includes a sequence of simple data preprocessing steps. Each committee consists of 5 kNN classifiers of different architectures. Each classifier on the committee takes in a different set of features. The classification system is then applied to a set of microarray gene expression profiles from leukaemia patients. We show that the system can be effectively used for classifying microarray gene expression data. The results demonstrate the committee approach consistently outperforms individual kNN classifiers in terms of both classification accuracy and stability. PMID: 20940122 [PubMed - in process] (Source: International Journal of Bioinformatics Research ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4075590 Mon, 18 Oct 2010 08:55:03 +0100 4075590 http://www.medworm.com/index.php?rid=4075589&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20940123%26dopt%3DAbstract Authors: Lai Y Deep sequencing techniques have shown a promising impact on biomedical studies. Based on a recently published two-sample Digital Gene Expression (DGE) data set, we compared three widely used t-type tests for the differential expression analysis. Both the 'soft' and 'hard' filtering strategies were considered. For the 'hard' filtering strategy, we also considered a genome-wide co-expression based adjustment for each t-type test. Our results suggest that excluding RNA-tags at an appropriate level of data variability can improve the control of false positives. Furthermore, the genome-wide co-expression based adjustments consistently provide comparably low levels of false positive control for different exclusion criteria. PMID: 20940123 [PubMed - in process] (Source: Int... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4075589 Mon, 18 Oct 2010 08:55:03 +0100 4075589 http://www.medworm.com/index.php?rid=4075588&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20940124%26dopt%3DAbstract Authors: Ma F, Deogun JS In this paper, we present a simple and efficient algorithm for multiple genome sequence alignment. Sequences of Maximal Unique Matches (MUMs) are first transformed into a multi-bipartite diagram. The diagram is then converted into a Directed Acyclic Graph (DAG). Therefore, finding the alignment is reduced to finding the longest path in the DAG, which is solvable in linear time. The experiments show that the algorithm can correctly find the alignment, and runs faster than MGA and EMAGEN. In addition, our algorithm can handle the alignments with overlapping MUMs and has both weighted and unweighted options. It provides the flexibility for the alignments depending on different needs. PMID: 20940124 [PubMed - in process] (Source: International Journal of Bioinf... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4075588 Mon, 18 Oct 2010 08:55:03 +0100 4075588 http://www.medworm.com/index.php?rid=4075587&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20940125%26dopt%3DAbstract We present an alignment algorithm that bounds processing by selecting optimal subtrees to align and show that this improves efficiency without significant reduction in precision. We apply the algorithm in conjunction with our approach that includes modelling ontology alignment in a Support Vector Machine. PMID: 20940125 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4075587 Mon, 18 Oct 2010 08:55:03 +0100 4075587 http://www.medworm.com/index.php?rid=4075586&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20940126%26dopt%3DAbstract Authors: Ko Y, Zhai C, Rodriguez-Zas SL Gene networks have been predicted using the expression profiles from microarray experiments that include multiple samples representing each of several classes or states (e.g., treatments, developmental stages, health status). A framework that integrates Bayesian networks, mixture of gene co-expression models and clustering is proposed to further mine information from the variation of samples within and across classes and enhance the understanding of gene networks. The approach was evaluated on two independent pathways using data from two microarray experiments. Our algorithm succeeded on reconstructing the topology of the gene pathways when benchmarked against empirical reports and randomised data sets. The majority or all the samples within a cl... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4075586 Mon, 18 Oct 2010 08:55:03 +0100 4075586 http://www.medworm.com/index.php?rid=4075585&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20940127%26dopt%3DAbstract Authors: Bhattacharya M, Das A Breast cancer throughout the world is a significant health problem for women. Small clusters of microcalcifications appearing as collection of white spots on mammograms indicate an early warning of breast cancer. In present work we have initiated computer?aided analysis of mammograms to automate the diagnostic procedures for breast cancer screening using multiresolution and FCM based clustering algorithms. Further region growing approach has been applied to segment considerably larger calcifications and the masses. The advantage of the proposed method is its ability to detect both tiny and comparatively larger calcifications in a single image and to reduce the false-positive appearance of microcalcifications in breast. PMID: 20940127 [PubMed - in proc... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=4075585 Mon, 18 Oct 2010 08:55:03 +0100 4075585 http://www.medworm.com/index.php?rid=3742548&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20615831%26dopt%3DAbstract Authors: Shardiwal RK, Sohrab SS Relative Synonymous Codon Usage (RSCU) and Relative Adaptiveness of a Codon (RAC) table bias importance in gene expression are well documented in the literature. However, to improve the gene expression we need to figure out which codons are optimal for the expression in order to synthesise an appropriate DNA sequence. An alternative to the manual approach, which is obviously a tedious task, is to set up software on your computer to perform this. Though such kinds of programs are available on the internet, none of them are open-source libraries. Here, one can use our Perl program to do his or her task more easily and efficiently. It is free for everyone. PMID: 20615831 [PubMed - in process] (Source: International Journal of Bioinformatics Research an... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3742548 Sun, 11 Jul 2010 11:27:03 +0100 3742548 http://www.medworm.com/index.php?rid=3742547&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20615832%26dopt%3DAbstract Authors: Sohpal VK, Dey A, Singh A Biocomputing has moved into central position in molecular biology research. Enormous improvements in genetic engineering have led to the accumulation of a vast amount of biological information. With the advent of this extensive repertoire of raw sequence information, the next major challenge for a modern researcher is to interpret this biological information. Molecular Evolutionary Genetic Analysis (MEGA) is bio-computational software to fill the vacuum between data development and analysis. In this paper, an attempt to review the evolution of MEGA software, working and application has been made. Moreover, data analysis, implementation and advantages over other bioinformatics software have been discussed systematically. PMID: 20615832 [PubMed - in... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3742547 Sun, 11 Jul 2010 11:27:03 +0100 3742547 http://www.medworm.com/index.php?rid=3742546&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20615833%26dopt%3DAbstract Authors: Prasad VR, Tripathi BN, Sethumadhavan R In this work, the role of cation-pi and CH...pi interactions in the activity of glutaredoxins is analysed. Among the proteins, an average of 1 cation-pi interaction per 109 residues and an average of 1 CH...pi interaction per 16 residues were found. These interactions were influenced by long-range contacts whereas short- and medium-range contacts were found insignificant. Significant differences in these interactions were noticed when the same glutaredoxin was analysed in its glutathionylated, reduced and oxidised states. Since activities of glutaredoxins depend on its state, the role of these interactions in regulation of these proteins might be significant. PMID: 20615833 [PubMed - in process] (Source: International Journal of Bioi... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3742546 Sun, 11 Jul 2010 11:27:03 +0100 3742546 http://www.medworm.com/index.php?rid=3742545&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20615834%26dopt%3DAbstract Authors: Arock M, Reddy S, Reddy AV In bioinformatics, motif finding is one of the most common problems. It is to locate recurring patterns in the sequence of nucleotides or amino acids. The main difficulty of the problem is that the patterns are not exact matches owing to biological mutations. It is NP-complete. Within the literature many solutions have been provided for this challenging problem. Nevertheless, they do not address certain subtleties. Among them, one is addressed by Hu (2003). In this paper, we propose a parallel combinatorial algorithm for subtle motif finding on a Shared Memory Multiprocessor model. We suggest a method of implementation for the same. PMID: 20615834 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3742545 Sun, 11 Jul 2010 11:27:03 +0100 3742545 http://www.medworm.com/index.php?rid=3742544&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20615835%26dopt%3DAbstract Authors: Al-Mubaid H, Singh RK We propose a new text mining technique to identify associations between biological entities, specifically genes-diseases associations, from the biomedical literature. The proposed method is very simple and straightforward; it uses two sets (a positive set and a negative set) of documents and utilises the concepts of expectation (ex), evidence (ev), and Z-scores in combining positive and negative evidences in determining the significant gene-disease associations from Medline documents. Moreover, the method offers an efficient way to handle gene names, aliases, symbols, and abbreviations. We evaluated the method in discovering gene-to-disease associations from literature and the experimental results are impressive. We verified our results and confirmed the ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3742544 Sun, 11 Jul 2010 11:27:03 +0100 3742544 http://www.medworm.com/index.php?rid=3742543&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20615836%26dopt%3DAbstract Authors: Kumar A, Bulusu S, Kasu V, Rao K The aim of the present analysis is to create a complete database of Simple Sequence Repeats (SSRs) occurring in the Expressed Sequence Tags (ESTs) of Human Genome. For the recognition of SSRs, various Bioinformatics Tools, Databases and Softwares are employed. The data are analysed statistically for Mean, Density and Frequency distribution of the identified Repeats. A consolidated Database is created and maintained in SAS Environment. This database can provide comprehensive information regarding: 1) the complete sequence of microsatellites/tandem repeats; 2) the number of times each one is repeated; 3) the starting and ending position of each repeat; 4) its length. In addition the database can also provide the location of the gene and also its ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3742543 Sun, 11 Jul 2010 11:27:03 +0100 3742543 http://www.medworm.com/index.php?rid=3742542&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20615837%26dopt%3DAbstract Authors: Song M, Rajasekaran S Microarrays serve scientists as a powerful and efficient tool to observe thousands of genes and analyse their activeness in normal or cancerous tissues. In general, microarrays are used to measure the expression levels of thounsands of genes in a cell mixture. Gene expression data obtained from microarrays can be used for various applications. One such application is that of gene selection. Gene selection is very similar to the feature selection problem addressed in the machine-learning area. In a nutshell, gene selection is the problem of identifying a minimum set of genes that are responsible for certain events (for example the presence of cancer). Informative gene selection is an important problem arising in the analysis of microarray data. In this pap... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3742542 Sun, 11 Jul 2010 11:27:03 +0100 3742542 http://www.medworm.com/index.php?rid=3742541&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20615838%26dopt%3DAbstract Authors: Li Z, Gao S, Du H, Shi Y, Pooling design is an important mathematical tool in DNA library screening. It has been showed that using pooling design, the number of tests in DNA library screening can be greatly reduced. In this paper, we present some new algebraic constructions for pooling design. PMID: 20615838 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3742541 Sun, 11 Jul 2010 11:27:03 +0100 3742541 http://www.medworm.com/index.php?rid=3362672&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20223734%26dopt%3DAbstract Authors: Chang RL, Luo F, Johnson S, Scheuermann RH 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 simultaneously processes structurally equivalent edges while preserving intuitive foundations of the MoNet algorithm and generates ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3362672 Sat, 13 Mar 2010 19:32:02 +0100 3362672 http://www.medworm.com/index.php?rid=3362671&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20223735%26dopt%3DAbstract Authors: McClellan DA, Ellison DD 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 did not significantly affect accuracy. PMID: 20223735 [PubMed - in process] (Source: International Journal of Bioinformatics Research ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3362671 Sat, 13 Mar 2010 19:32:02 +0100 3362671 http://www.medworm.com/index.php?rid=3362670&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20223736%26dopt%3DAbstract Authors: Danecek P, Schein CH 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 methods will aid in the design of vaccines and specific therapies against FV. PMID: 20223736 [PubMed - in process] (Source: Internation... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3362670 Sat, 13 Mar 2010 19:32:02 +0100 3362670 http://www.medworm.com/index.php?rid=3362669&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20223737%26dopt%3DAbstract Authors: Singh A, Keswani U, Levine D, Feschotte C, 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 de novo identification and classification of interspersed repeats. In this manuscript we describe our approach, and r... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3362669 Sat, 13 Mar 2010 19:32:02 +0100 3362669 http://www.medworm.com/index.php?rid=3362668&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20223738%26dopt%3DAbstract Authors: Powers TR, Virk SM, Serrano EE 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 of our microarray data, and assisted with the tentative identification of unidentified probe sets. PMID: 20223738 [PubMed - in... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3362668 Sat, 13 Mar 2010 19:32:02 +0100 3362668 http://www.medworm.com/index.php?rid=3362667&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20223739%26dopt%3DAbstract 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) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3362667 Sat, 13 Mar 2010 19:32:02 +0100 3362667 http://www.medworm.com/index.php?rid=3362666&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20223740%26dopt%3DAbstract Authors: Habib MS, Kalita J 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 more viable and practical solution for real-world problems with large datasets. PMID: 20223740 [PubMed - in process] (Source: International... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3362666 Sat, 13 Mar 2010 19:32:02 +0100 3362666 http://www.medworm.com/index.php?rid=3362665&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20223741%26dopt%3DAbstract Authors: Opiyo SO, Moriyama EN 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 classifiers we identified new Cyt-b561-related proteins from four plant genomes. PMID: 20223741 [PubMed - in process] (Source: International ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3362665 Sat, 13 Mar 2010 19:32:02 +0100 3362665 http://www.medworm.com/index.php?rid=3224721&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20110205%26dopt%3DAbstract Authors: Jang Y, Wan XF Here we proposed a Chemical Bond based Elastic Network Model (CB-ENM) method, which was demonstrated with a better performance in representing functional movements, especially the local motions, than the conventional normal mode analysis. CB-ENM was applied in characterising functional motions in surface glycoprotein Haemagglutinin (HA) of H5N1 highly pathogenic avian influenza virus. Eleven local peaks were identified amongst HA fluctuation spectrum, and eight of these peaks were correlated with the reported five antigenic binding sites and Receptor Binding Sites (RBS) in influenza viruses. Our study showed that CB-ENM has a potential in identifying functional residues in protein structure. PMID: 20110205 [PubMed - in process] (Source: International Journal... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3224721 Sun, 31 Jan 2010 16:08:03 +0100 3224721 http://www.medworm.com/index.php?rid=3224720&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20110206%26dopt%3DAbstract Authors: Liu G, Ding M, Wang H, Huang J, Jing Q, Shen B MicroRNAs (miRNAs) are non-coding RNAs, which regulate gene expression by promoting degradation or repressing translation of targeted transcripts. Current researches indicate that microRNAs play essential roles in heart development, but their regulating mechanisms are still elusive. Using computational methods, we analysed microRNAs associated pathways in mouse heart development and found that 24 pathways were enriched with target genes of microRNAs. Some of these pathways are reported important in heart development, while others are associated with cancer. The computational results could be used to guide experimental design for the further understanding of the microRNAs function in heart development. PMID: 20110206 [PubMed - ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3224720 Sun, 31 Jan 2010 16:08:03 +0100 3224720 http://www.medworm.com/index.php?rid=3224719&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20110207%26dopt%3DAbstract Authors: Phan V, Thomas A, Malasri K, Sutter CH We propose a novel method to estimate editing efficiency by adenosine deaminases that act on RNA (ADARs). The method employs the notion of stability of secondary structure in the vicinity of edited sites during transcription. Such an analysis of 'dynamic' structural motifs of RNA is important because as a pre-spliced RNA is being transcribed and elongated, its entire structure, and thus its local structures, may change drastically. Our simulation showed that the stability of structures in the vicinity of edited sites correlates moderately highly with editing efficiency of edited sites recently established in laboratory experiments. PMID: 20110207 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Appli... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3224719 Sun, 31 Jan 2010 16:08:03 +0100 3224719 http://www.medworm.com/index.php?rid=3224718&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20110208%26dopt%3DAbstract Authors: Taheri J, Zomaya AY This paper presents a novel approach to solve the Multiple Sequence Alignment (MSA) problem. The Rubber Band Technique: Location Base (RBT-L) introduced in this paper, is inspired by the elastic behaviour of a Rubber Band (RB) on a plate with poles. RBT-L is an iterative optimisation algorithm designed and implemented to find the optimal alignment for a set of input protein sequences. RBT-L is tested with one of the well-known benchmarks (BALiBASE 2.0) in this field. The obtained results show the superiority of the proposed technique even in the case of formidable sequences. PMID: 20110208 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3224718 Sun, 31 Jan 2010 16:08:03 +0100 3224718 http://www.medworm.com/index.php?rid=3224717&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20110209%26dopt%3DAbstract Authors: Liu J, Wang L, Zhu S Peptides binding to MHC molecules is of great importance in the process of triggering and initiating immune responses. There are two main kinds of MHC molecules, MHC class I and class II, and the prediction of MHC-II binding peptides is much more difficult due to their variable lengths, which makes it difficult to construct a preferable prediction model by using most of the existing methods. This paper presents a method, called as SVR-PAIRWISE, to combine Support Vector Regression (SVR) and pairwise alignment, to quantitatively predict the MHC-II binding peptides. The comparison results with some popular methods show its satisfying performances. PMID: 20110209 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applicati... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3224717 Sun, 31 Jan 2010 16:08:03 +0100 3224717 http://www.medworm.com/index.php?rid=3224716&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20110210%26dopt%3DAbstract Authors: Zou Q, Guo M, Liu Y, Xuan P It is an important work to search unknown microRNA gene from genome or EST sequences. There are several ab initio methods to classify microRNA precursors from random hairpins. However, the exact position of the mature part in the precursor remains unknown only from these ab initio classification methods. In this paper, we propose four significant position distribution features, and then give a computational method to predict the miRNA?miRNA* duplex from the animal precursors. It is helpful for classifying miRNA precursor and detecting unknown miRNA genes. PMID: 20110210 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3224716 Sun, 31 Jan 2010 16:08:03 +0100 3224716 http://www.medworm.com/index.php?rid=3224715&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20110211%26dopt%3DAbstract Authors: Torgasin S, Zimmermann KH A careful design of DNA strands is crucial for several biological applications such as microarray techniques, Polymerase Chain Reaction (PCR), and DNA computing. For this, the important criterion under laboratory conditions is the hybridisation energy of two DNA strands. During the last decade, a thermodynamic model was developed that allows for the calculation of the DNA/DNA hybridisation energy and recently also the cross-hybridisation energy of structural motifs. Employing this model a new algorithm for the secondary structure prediction of DNA/DNA cross-hybridisation complexes called HYBGRAPH is introduced. The method is based on Gibbs free energy minimisation and the paradigm of dynamic programming. PMID: 20110211 [PubMed - in process] (Sourc... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=3224715 Sun, 31 Jan 2010 16:08:03 +0100 3224715 http://www.medworm.com/index.php?rid=2968142&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19887334%26dopt%3DAbstract Authors: Soliman TH, Gharib TF, Abo-Alian A, El Sharkawy MA 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 ratio than that of existing DNA-oriented compression algorithms, when compared to GenCompress, DNACompress, and DN... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2968142 Sat, 07 Nov 2009 07:10:03 +0100 2968142 http://www.medworm.com/index.php?rid=2968141&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19887335%26dopt%3DAbstract Authors: Vadwai V, Devaraj S 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, ADME properties, LogP and IC50 values were determined computationally. PMID: 19887335 [PubMed - in process] (Source: International Journal... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2968141 Sat, 07 Nov 2009 07:10:03 +0100 2968141 http://www.medworm.com/index.php?rid=2968140&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19887336%26dopt%3DAbstract Authors: Poddar R, Mathur A, Kawalekar OU, Rai A, 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 Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2968140 Sat, 07 Nov 2009 07:10:03 +0100 2968140 http://www.medworm.com/index.php?rid=2968139&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19887337%26dopt%3DAbstract Authors: Chen T, Li F 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 and TF co-operativities supported by biological experiments or other computational methods. PMID: 19887337 [PubMed - in process] (Source: Intern... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2968139 Sat, 07 Nov 2009 07:10:03 +0100 2968139 http://www.medworm.com/index.php?rid=2968138&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19887338%26dopt%3DAbstract Authors: Sree PK, Babu IR, Devi NS 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 initial round of Rosetta sampling, we learn properties of the energy landscape that guide a subsequent round of sampling toward lower-en... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2968138 Sat, 07 Nov 2009 07:10:03 +0100 2968138 http://www.medworm.com/index.php?rid=2968137&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19887339%26dopt%3DAbstract Authors: Manyam G, Baranova A, Skoblov M, Mishra RK 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 the structurally conserved domains within superfamilies of paralogous genes. PMID: 19887339 [PubMed - in process] ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2968137 Sat, 07 Nov 2009 07:10:03 +0100 2968137 http://www.medworm.com/index.php?rid=2834985&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19778865%26dopt%3DAbstract Authors: Gomase VS, Parundekar AN 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 production and the inflammatory mediator release. PMID: 19778865 [PubMed - in process] (Source: International Journal of Bioinformati... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2834985 Sun, 27 Sep 2009 11:56:02 +0100 2834985 http://www.medworm.com/index.php?rid=2834984&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19778866%26dopt%3DAbstract Authors: Mansour N, Kehyayan C, Khachfe H 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 our algorithm is able to produce 3D structures with good sub-optimal energy values. Also, the Root Mean Square Deviations (RMSD) o... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2834984 Sun, 27 Sep 2009 11:56:02 +0100 2834984 http://www.medworm.com/index.php?rid=2834983&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19778867%26dopt%3DAbstract Authors: Sivakumar KC, Thomas B, Karunagaran D 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: 19778867 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2834983 Sun, 27 Sep 2009 11:56:02 +0100 2834983 http://www.medworm.com/index.php?rid=2834982&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19778868%26dopt%3DAbstract Authors: Kumar A, Smita S, Sahu N, Sharma V, Shankaracharya S, Vidyarthi A, Pandey D 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 motifs, consensus promoter motif and their sequences between UR-DEGs and DR-DEGs were dete... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2834982 Sun, 27 Sep 2009 11:56:02 +0100 2834982 http://www.medworm.com/index.php?rid=2834981&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19778869%26dopt%3DAbstract Authors: Gomase VS, Tagore S 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 process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2834981 Sun, 27 Sep 2009 11:56:02 +0100 2834981 http://www.medworm.com/index.php?rid=2834980&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19778870%26dopt%3DAbstract Authors: Najmabadi P, Lee HH, Aung T, Thuya A, Ng J, Clair J, Burkart M 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 viewpoint with respect to the displayed biomolecular network. PMID: 19778870 [PubMed - in process] (S... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2834980 Sun, 27 Sep 2009 11:56:02 +0100 2834980 http://www.medworm.com/index.php?rid=2834979&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19778871%26dopt%3DAbstract Authors: Sur-Kolay S, Banerjee S, Mukhopadhyaya S, Murthy CA 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. Significant reduction in search space provides notable efficiency. PMID: 19778871 [PubMed - in process] (Source: In... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2834979 Sun, 27 Sep 2009 11:56:02 +0100 2834979 http://www.medworm.com/index.php?rid=2659345&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19640825%26dopt%3DAbstract 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) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2659345 Sat, 01 Aug 2009 11:12:03 +0100 2659345 http://www.medworm.com/index.php?rid=2659344&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19640826%26dopt%3DAbstract 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) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2659344 Sat, 01 Aug 2009 11:12:03 +0100 2659344 http://www.medworm.com/index.php?rid=2659343&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19640827%26dopt%3DAbstract Authors: Deusdado S, Carvalho P 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 fast parallel testing for multiple alignments. Comparative performance analysis, using diverse genomic data, shows that GRASPm is faster th... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2659343 Sat, 01 Aug 2009 11:12:03 +0100 2659343 http://www.medworm.com/index.php?rid=2659342&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19640828%26dopt%3DAbstract Authors: Munteanu CR, Magalhaes AL 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 applications showing its usefulness in protein research and as an e-learning tool as well. PMID: 19640828 [PubMed - in process] (Source:... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2659342 Sat, 01 Aug 2009 11:12:03 +0100 2659342 http://www.medworm.com/index.php?rid=2659341&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19640829%26dopt%3DAbstract Authors: Vinaya V, Bulsara N, Gadgil CJ, Gadgil M 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 selected genes yields 96% accuracy for a dataset obtained on an independent microarray platform. PMID: 19640829 [PubMed ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2659341 Sat, 01 Aug 2009 11:12:03 +0100 2659341 http://www.medworm.com/index.php?rid=2659338&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19640830%26dopt%3DAbstract Authors: Pokrzywa R 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 data compression algorithm. PMID: 19640830 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2659338 Sat, 01 Aug 2009 11:12:03 +0100 2659338 http://www.medworm.com/index.php?rid=2659334&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19640831%26dopt%3DAbstract Authors: Vera J, Kwon T, Schmitz U, Kolch W, 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 signalling systems in human cells. PMID: 19640831 [PubMed - in process] (Source: International Journal of Bioinformatics... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2659334 Sat, 01 Aug 2009 11:12:03 +0100 2659334 http://www.medworm.com/index.php?rid=2659333&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19640832%26dopt%3DAbstract Authors: Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M 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. PMID: 19640832 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2659333 Sat, 01 Aug 2009 11:12:03 +0100 2659333 http://www.medworm.com/index.php?rid=2548724&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19525198%26dopt%3DAbstract Authors: Koch M, Broom BM, Subramanian D 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 network. Many of them have already been confirmed experimentally in the recent literature and six new crosstalk mechanisms await e... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2548724 Sun, 28 Jun 2009 05:55:03 +0100 2548724 http://www.medworm.com/index.php?rid=2548723&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19525199%26dopt%3DAbstract Authors: Cai X, Koduru P, Das S, Welch SM 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 demonstrated and discussed. PMID: 19525199 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applic... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2548723 Sun, 28 Jun 2009 05:55:03 +0100 2548723 http://www.medworm.com/index.php?rid=2548722&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19525200%26dopt%3DAbstract Authors: Zhang S, Du-Cuny L 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-use, and efficient package for molecular docking-based high-throughput virtual screening in drug discovery. PMID: 19525200 [PubMed - in proc... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2548722 Sun, 28 Jun 2009 05:55:03 +0100 2548722 http://www.medworm.com/index.php?rid=2548721&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19525201%26dopt%3DAbstract Authors: Duax WL, Huether R, Pletnev V, Umland TC, 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 open reading frames and an extreme codon and amino acid bias. PMID: 19525201 [PubMed - in process] (Source: Internatio... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2548721 Sun, 28 Jun 2009 05:55:03 +0100 2548721 http://www.medworm.com/index.php?rid=2548720&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19525202%26dopt%3DAbstract Authors: Opiyo SO, Moriyama EN 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 models and PSI-BLAST in identifying cyclophilins from the Arabidopsis and rice genomes. PMID: 19525202 [PubMed - in process] (Source: Int... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2548720 Sun, 28 Jun 2009 05:55:03 +0100 2548720 http://www.medworm.com/index.php?rid=2548719&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19525203%26dopt%3DAbstract Authors: Das R, Kalita J, Bhattacharyya DK 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 clustering method is used in experiments that use real-life datasets and has been found to perform satisfactorily. PMID: 1952... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2548719 Sun, 28 Jun 2009 05:55:03 +0100 2548719 http://www.medworm.com/index.php?rid=2548718&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19525204%26dopt%3DAbstract Authors: Loganantharaj R 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 empirically demonstrated the effectiveness of SVD as a data integrator. PMID: 19525204 [PubMed - in process] (Source: International Journal ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2548718 Sun, 28 Jun 2009 05:55:03 +0100 2548718 http://www.medworm.com/index.php?rid=2548717&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19525205%26dopt%3DAbstract Authors: Carroll H, Teichert AR, Krein J, Sundberg K, Snell Q, Clement M 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 future development of novel phylogenetic techniques. This paper seeks to familiarise researchers wi... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2548717 Sun, 28 Jun 2009 05:55:03 +0100 2548717 http://www.medworm.com/index.php?rid=2297391&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19324599%26dopt%3DAbstract Authors: Goriely A, Neukirch S, Hausrath A 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: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2297391 Sun, 29 Mar 2009 11:39:07 +0100 2297391 http://www.medworm.com/index.php?rid=2297388&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19324600%26dopt%3DAbstract Authors: Dos Santos MC, Taranto AG, De Assis SA, Goes-Neto A 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 Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2297388 Sun, 29 Mar 2009 11:39:06 +0100 2297388 http://www.medworm.com/index.php?rid=2297385&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19324601%26dopt%3DAbstract Authors: Vivan AL, Caceres RA, Basso LA, Santos DS, 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 process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2297385 Sun, 29 Mar 2009 11:39:06 +0100 2297385 http://www.medworm.com/index.php?rid=2297381&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19324602%26dopt%3DAbstract Authors: Viana GV, Gomes FA, Ferreira CE, Meneses CN 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 - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2297381 Sun, 29 Mar 2009 11:39:06 +0100 2297381 http://www.medworm.com/index.php?rid=2297379&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19324603%26dopt%3DAbstract Authors: Ferreira RC, Bosco F, Briones MR 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 corresponds to the minimal genome size. PMID: 19324603 [PubMed - in process] (Source: International Journal of Bioinformatics Resea... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2297379 Sun, 29 Mar 2009 11:39:06 +0100 2297379 http://www.medworm.com/index.php?rid=2297377&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19324604%26dopt%3DAbstract Authors: Fan YJ, Chaovalitwongse WA, Liu CC, Sachdeo RC, Iasemidis L, Pardalos P 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 differentiation between epileptic and normal subjects. It may solve other classification... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2297377 Sun, 29 Mar 2009 11:39:06 +0100 2297377 http://www.medworm.com/index.php?rid=2297375&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19324605%26dopt%3DAbstract Authors: Mondaini RP 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 Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2297375 Sun, 29 Mar 2009 11:39:06 +0100 2297375 http://www.medworm.com/index.php?rid=2297374&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19324606%26dopt%3DAbstract Authors: Milagre ST, Maciel CD, Pereira JC, Pereira AA 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 high presence of missing values. PMID: 19324606 [PubMed - in process] (Source: International Journal of Bioinf... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2297374 Sun, 29 Mar 2009 11:39:06 +0100 2297374 http://www.medworm.com/index.php?rid=2297372&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19324607%26dopt%3DAbstract Authors: Wong TK, Lam TW, Chan PY, Yiu SM 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 quality. PMID: 19324607 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2297372 Sun, 29 Mar 2009 11:39:06 +0100 2297372 http://www.medworm.com/index.php?rid=2098656&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19136361%26dopt%3DAbstract Authors: Alhiyafi J, Sabesan C, Lu S, Ram JL 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 bacteria. PMID: 19136361 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2098656 Tue, 13 Jan 2009 15:00:19 +0100 2098656 http://www.medworm.com/index.php?rid=2098655&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19136362%26dopt%3DAbstract Authors: Sikder AR, Zomaya AY 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 to provide scientists with a better understanding of which method to use for their research. PMID: 19136362 [PubMed - in process] (Sourc... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2098655 Tue, 13 Jan 2009 15:00:19 +0100 2098655 http://www.medworm.com/index.php?rid=2098654&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19136363%26dopt%3DAbstract Authors: Wu J, Wang J, Chen J 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 practical solution for MP-PCR primer design. PMID: 19136363 [PubMed - in process] (Source: International Journal of Bioinformatics Research and... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2098654 Tue, 13 Jan 2009 15:00:19 +0100 2098654 http://www.medworm.com/index.php?rid=2098653&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19136364%26dopt%3DAbstract Authors: Wu FX, Xia Z, Mu L 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-discovery Rate (FNR). Results show that the proposed method outperforms traditional methods. PMID: 19136364 [PubMed - in process] (Source: Intern... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2098653 Tue, 13 Jan 2009 15:00:19 +0100 2098653 http://www.medworm.com/index.php?rid=2098652&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19136365%26dopt%3DAbstract Authors: Daescu O, Luo J 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 chains. We did experiments on thousands of proteins from the PDB Bank to estimate the simplification ratio achieved. PMID: 19136365 [PubMed - in... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2098652 Tue, 13 Jan 2009 15:00:19 +0100 2098652 http://www.medworm.com/index.php?rid=2098651&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19136366%26dopt%3DAbstract Authors: Martinez-Perez IM, Zimmermann KH, Ignatova Z 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) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2098651 Tue, 13 Jan 2009 15:00:19 +0100 2098651 http://www.medworm.com/index.php?rid=2098650&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19136367%26dopt%3DAbstract Authors: Na JC, Roh K, Apostolico A, Park K 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 alignment in this measure can be found by dynamic programming. Sequence alignment with quality scores can be solved as a special... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2098650 Tue, 13 Jan 2009 15:00:19 +0100 2098650 http://www.medworm.com/index.php?rid=2000067&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18283025%26dopt%3DAbstract Authors: Liu Z, Chen D, Tian JP 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 - indexed for MEDLINE] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000067 Mon, 01 Dec 2008 16:22:41 +0100 2000067 http://www.medworm.com/index.php?rid=2000066&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18283026%26dopt%3DAbstract 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) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000066 Mon, 01 Dec 2008 16:22:41 +0100 2000066 http://www.medworm.com/index.php?rid=2000065&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18283027%26dopt%3DAbstract Authors: Rahal I, Rahhal R, Wang B, Perrizo W 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: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000065 Mon, 01 Dec 2008 16:22:41 +0100 2000065 http://www.medworm.com/index.php?rid=2000064&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18283028%26dopt%3DAbstract Authors: Li Y, Chen X, Belkasim S, Pan Y 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 a good speedup for sequential object matching and partial 3D component retrieval. PMID: 18283028 [PubMed - indexed for MEDLIN... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000064 Mon, 01 Dec 2008 16:22:41 +0100 2000064 http://www.medworm.com/index.php?rid=2000063&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18283029%26dopt%3DAbstract Authors: Zhou D, He Y, Kwoh CK 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 precision values. Moreover, the statistical nature of the pure data-driven HVS model makes it intrinsically robust and it can be easily ad... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000063 Mon, 01 Dec 2008 16:22:41 +0100 2000063 http://www.medworm.com/index.php?rid=2000062&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18283030%26dopt%3DAbstract Authors: Schulz MH, Bauer S, Robinson PN Efficient searching for specific subsequences in a set of longer sequences is an important component of many bioinformatics algorithms. Generalised suffix trees and suffix arrays allow searches for a pattern of length n in time proportional to n independent of the length of the sequences, and are thus attractive for a variety of applications. Here, we present an algorithm termed the generalised k-Truncated Suffix Tree (kTST), that represents an adaption of Ukkonen's linear-time suffix tree construction algorithm. The kTST algorithm creates a k-deep tree in linear time that allows rapid searches for short patterns of length of up to k characters. The kTST can offer advantages in computational time and memory usage for searches for short sequences... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000062 Mon, 01 Dec 2008 16:22:41 +0100 2000062 http://www.medworm.com/index.php?rid=2000061&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18283031%26dopt%3DAbstract Authors: Wang J, Yang D Motif discovery is a significant problem in Bioinformatics. According to the complexity of most signals in biologic sequences, there are no extremely good models or dependable algorithms to solve this problem. This paper introduces the Uniform Projection and Neighbourhood Thresholding (UPNT) algorithm, which is based on two efficient strategies: Uniform Projection and Neighbourhood-based Thresholding. In the UPNT algorithm, the policy of uniform projection leads to fewer projections, while the strategy of refining the buckets after aggregation results in great abatement of the number of buckets to be refined. This paper further demonstrates its superiority over other projection algorithms by the experiments. PMID: 18283031 [PubMed - indexed for MEDLINE] (Sou... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000061 Mon, 01 Dec 2008 16:22:41 +0100 2000061 http://www.medworm.com/index.php?rid=2000060&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18283032%26dopt%3DAbstract Authors: Buendia P, Collins TM, Narasimhan G Algorithms that infer phylogenetic relationships between serially-sampled sequences have been developed in recent years to assist in the analysis of rapidly-evolving human pathogens. Our study consisted of evaluating seven relevant methods using empirical as well as simulated data sets. In particular, we investigated how the molecular clock hypothesis affected their relative performance, as three of the algorithms that accept serially-sampled data as input assume a molecular clock. Our results show that the standard phylogenetic methods and MinPD had a better overall performance. Surprisingly, when all internal node sequences were included in the data, the topological performance measure of all the methods, with the exception of MinPD, dropp... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000060 Mon, 01 Dec 2008 16:22:41 +0100 2000060 http://www.medworm.com/index.php?rid=2000059&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18490258%26dopt%3DAbstract Authors: Chen P, Huang DS, Zhao XM, Li X Contact map, which is important to understand and reconstruct protein's three-dimensional (3D) structure, may be helpful to solve the protein's 3D structure. This paper presents a novel approach to predict the contact map using Radial Basis Function Neural Network (RBFNN) optimised by Conformational Energy Function (CEF) based on chemico-physical knowledge of amino acids. Finally, the results are trimmed by Short-Range Contact Function (SRCF). Consequently, it can be found that our proposed method is better than the existing methods such as PROFcon and the PE-based method. Particularly, this method can accurately predict 35% of contacts at a distance cutoff of 8 A. PMID: 18490258 [PubMed - indexed for MEDLINE] (Source: International Journal ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000059 Mon, 01 Dec 2008 16:22:41 +0100 2000059 http://www.medworm.com/index.php?rid=2000058&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18490259%26dopt%3DAbstract Authors: Chen Y, Li G Identification of the short DNA sequence motif, which serves as binding targets for transcription factors, is a fundamental problem in both computer science and molecular biology. Especially, finding the subtle motifs with variable gaps is more challenging. In this paper, a new algorithm is presented, which explores some new strategies. Based on a neighbourhood set concept, a new probability matrix is defined, which can capture the target motifs effectively. An iterative restart strategy is used, by which we can use several similar motifs' information to detect the real motif to demonstrate the effectiveness of our algorithm. We test it on several kinds of data and compare it with some other current representation algorithms. Simulation shows that the algorithm ca... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000058 Mon, 01 Dec 2008 16:22:41 +0100 2000058 http://www.medworm.com/index.php?rid=2000057&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18490260%26dopt%3DAbstract Authors: Li J Large-scale Genome-Wide Association Studies (GWAS) for complex diseases are increasingly common, due to recent advances in genotyping technology. Gene-gene interactions play an important role in the etiology of complex diseases and have to be addressed in GWAS. In this paper, an efficient strategy based on two-stage analysis is proposed. It combines a single-locus approach with a Goodness-Of-Fit (GOF) test in stage one, and selects a promising subset of SNPs to be modelled using a full interaction model in stage two. Extensive simulations using different disease models with different levels of epistasis demonstrate that it achieves higher power than existing approaches. PMID: 18490260 [PubMed - indexed for MEDLINE] (Source: International Journal of Bioinformatics Rese... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000057 Mon, 01 Dec 2008 16:22:41 +0100 2000057 http://www.medworm.com/index.php?rid=2000056&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18490261%26dopt%3DAbstract Authors: Cui J, Chen C, Lu H, Shen P In this paper, we performed an experimental observation-based computer simulation of the regulatory network of mitochondrial apoptosis. By modelling we obtained dynamical understandings of various apoptosis-related proteins, including cytochrome c (cyt c) release and caspase activation. Through parameter analysis, we examined the role of Bcl-2 family proteins and the natural inhibitors of apoptosis in the regulatory network of apoptosis. Furthermore, the effects of several amplified loops in the network were found to enhance caspase activation and make the decision of apoptosis switch like. Consistent with most available experimental evidences, our results yield insights into the complex regulatory mechanism of mitochondrial apoptosis. PMID: 184... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000056 Mon, 01 Dec 2008 16:22:41 +0100 2000056 http://www.medworm.com/index.php?rid=2000055&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18490262%26dopt%3DAbstract Authors: Han A, Zhu D, Pan J Sequence alignment reveals the relations between the characters in different sequences, and there are the reverse complement relations between the characters in DNA double strand. We introduce sequence alignment to the field of DNA computing, propose the definitions of complement alignment and reverse complement alignment, give a method of computing the scores of complement alignment and reverse complement alignment, and devise a DNA encoding method and the corresponding DNA algorithm for the Minimum Spanning Tree (MST) problem by means of reverse complement alignments. Our work enriches the theory of DNA computing and extends the range of DNA computing to solve optimisation problems. PMID: 18490262 [PubMed - indexed for MEDLINE] (Source: International ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000055 Mon, 01 Dec 2008 16:22:41 +0100 2000055 http://www.medworm.com/index.php?rid=2000054&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18490263%26dopt%3DAbstract Authors: Tian J, Guo X, Chu X, Wu N, Guo J, Yao B Six motifs of Methyl Parathion Hydrolase (MPH) were discovered using a method based on the Hidden Markov Model (HMM). Most MPH from TrEMBL (Release 48.6) could be recognised by these six motifs. When these six motifs were projected onto the 3D enzyme structure, we discovered that all of them closely surrounded the active centre and might play an important role in structure and function of the enzyme. By comparing the motifs of MPH with PH and analysing the phylogenetic tree, we found that these two enzymes, with substrates differing from only two methyl groups, belonged to two different protein families. The MPH belonged to the Lactamase family, and the PH belonged to the Phosphotriesterase (PTE) family. PMID: 18490263 [PubMed - ind... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000054 Mon, 01 Dec 2008 16:22:41 +0100 2000054 http://www.medworm.com/index.php?rid=2000053&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18490264%26dopt%3DAbstract Authors: Liu ZH, Sun X With more and more complete genome sequences having been released, phylogenetic analysis is entering a new era--that of phylogenomics. In this paper, a novel phylogenomic method, named as Base-Base Correlation (BBC), has been proposed to infer phylogenetic relationships from complete genomes, with particular emphasis on coronavirus phylogeny. Following the high-profile publicity of SARS outbreaks, a renewed interest in coronavirus has been promoted and two novel human coronaviruses (NL63 and HKU1) have been identified. Coronavirus phylogenomics based on BBC is well consistent with that of previous studies. BBC, to study genome information structure based on information theory, provides a novel alignment-free phylogenomic methodology in postgenome informatics. ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000053 Mon, 01 Dec 2008 16:22:41 +0100 2000053 http://www.medworm.com/index.php?rid=2000052&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18640901%26dopt%3DAbstract Authors: Merelli I, Orro A, D'Agostino D, Clematis A, In this paper we propose a parallel system for protein surface reconstruction based on techniques of computational geometry. The advantage of our modelling system is the production of both superficial and volumetric description of proteins. This is very important in protein analysis from the functional point of view, because many binding sites are buried inside the macromolecule. However the amount of data to process, both in the volume modelling and in extraction phase, may be huge, in proportion to the selected resolution of the output. For this reason the parallel implementation of the system represents a fundamental aspect in reducing the processing time. PMID: 18640901 [PubMed - indexed for MEDLINE] (Source: International ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000052 Mon, 01 Dec 2008 16:22:41 +0100 2000052 http://www.medworm.com/index.php?rid=2000051&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18640902%26dopt%3DAbstract Authors: Ahmad J, Roux O, Bernot G, Comet JP, In this paper, we propose a refinement of the modelling of biological regulatory networks based on the discrete approach of Rene Thomas. We refine and automatise the use of delays of activation/inhibition in order to specify which variable is more quickly affected by a change of its regulators. The formalism of linear hybrid automata is well suited to allow such refinement. We then use HyTech for two purposes: to find automatically all paths from a specified initial state to another one; to synthesise constraints on the delay parameters in order to follow any specific path. PMID: 18640902 [PubMed - indexed for MEDLINE] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000051 Mon, 01 Dec 2008 16:22:41 +0100 2000051 http://www.medworm.com/index.php?rid=2000050&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18640903%26dopt%3DAbstract Authors: Deng X, Geng H, Ali HH Existing data mining tools can only achieve about 40% precision in function prediction of unannotated genes. We developed a gene function prediction tool based on profile Hidden Markov Models (HMMs). Each function class was modelled using a distinct HMM whose parameters were trained using yeast time-series gene expression profiles. Two structural variants of HMMs were designed and tested, each of them on 40 function classes. The highest overall prediction precision achieved was 67% using double-split HMM with leave-one-out cross-validation. We also attempted to generalise HMMs to dynamic Bayesian networks for gene function prediction using heterogeneous data sets. PMID: 18640903 [PubMed - indexed for MEDLINE] (Source: International Journal of Bioinfo... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000050 Mon, 01 Dec 2008 16:22:41 +0100 2000050 http://www.medworm.com/index.php?rid=2000049&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18640904%26dopt%3DAbstract We present a new method for semantic comparison of biological pathways, aiming to discover evolutionary conservation of pathways between species. Our method uses all three sub-ontologies of Gene Ontology (GO) and a measure of semantic similarity to calculate match scores between gene products. These scores are used for finding local pairwise pathway alignments. This approach has the advantage of being applicable to all types of pathways where nodes are gene products, e.g., regulatory pathways, signalling pathways and metabolic enzyme-to-enzyme pathways. We demonstrate the usefulness of the method using regulatory and metabolic pathways from E. coli and S. cerevisiae as examples. PMID: 18640904 [PubMed - indexed for MEDLINE] (Source: International Journal of Bioinformatics Research and ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000049 Mon, 01 Dec 2008 16:22:41 +0100 2000049 http://www.medworm.com/index.php?rid=2000048&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18640905%26dopt%3DAbstract Authors: Zhang K, Xu Y, Chen G In the post-genome era, huge numbers of protein structures accumulate, but little is known about their function. It is time consuming and labour intensive to investigate them, e.g., enzyme catalytic properties, through in vivo or in vitro work. So in silico predictions could be a promising strategy to greatly shrink the list of potential targets. This work incorporated both structural and physico-chemical information into a Naive Bayes classification system, and gained much better performance. The ten-fold cross validation results of this method could reach 88.6% of sensitivity and 93.7% of specificity. The improvement of prediction accuracy is detailed in this paper. The PECB is also applied to predict other important sites. PMID: 18640905 [PubMed - ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000048 Mon, 01 Dec 2008 16:22:41 +0100 2000048 http://www.medworm.com/index.php?rid=2000047&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18640906%26dopt%3DAbstract Authors: Knijnenburg TA, Wessels LF, Reinders MJ The use of predefined gene sets has become crucial in the interpretation of genomewide expression data. A limitation of the existing techniques that relate gene expression levels to gene sets is that they cannot readily be applied to time-course microarray data. The ability to attach statistical significance to the behaviour of biological processes over time would greatly contribute to understanding the complex regulatory mechanisms in the cell. We propose a statistical testing procedure based on the central limit theorem to assess the enrichment of a gene set. The technique is applied on time-course microarray data to generate gene-set specific 'activity profiles'. PMID: 18640906 [PubMed - indexed for MEDLINE] (Source: International... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000047 Mon, 01 Dec 2008 16:22:41 +0100 2000047 http://www.medworm.com/index.php?rid=2000046&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18640907%26dopt%3DAbstract Authors: Larsen LS, Wassman CD, Hatfield GW, Lathrop RH Gene synthesis is hampered by two obstacles: improper assembly of oligonucleotides; oligonucleotide defects incurred during chemical synthesis. To overcome the first problem, we describe the employment of a Computationally Optimised DNA Assembly (CODA) algorithm that uses the degeneracy of the genetic code to design overlapping oligonucleotides with thermodynamic properties for self-assembly into a single, linear, DNA product. To address the second problem, we describe a hierarchical assembly strategy that reduces the incorporation of defective oligonucleotides into full-length gene constructs. The CODA algorithm and these biological methods enable fast, simple and reliable assemblies of sequence-correct full-length genes. PMI... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000046 Mon, 01 Dec 2008 16:22:41 +0100 2000046 http://www.medworm.com/index.php?rid=2000045&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18640908%26dopt%3DAbstract Authors: Du L, Wu S, Liew AW, Smith DK, We propose a new strategy to analyse the periodicity of gene expression profiles using Singular Spectrum Analysis (SSA) and Autoregressive (AR) model based spectral estimation. By combining the advantages of SSA and AR modelling, more periodic genes are extracted in the Plasmodium falciparum data set, compared with the classical Fourier analysis technique. We are able to identify more gene targets for new drug discovery, and by checking against the seven well-known malaria vaccine candidates, we have found five additional genes that warrant further biological verification. PMID: 18640908 [PubMed - indexed for MEDLINE] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000045 Mon, 01 Dec 2008 16:22:41 +0100 2000045 http://www.medworm.com/index.php?rid=2000044&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18649439%26dopt%3DAbstract Authors: Qi X, Wu J, Li S, Li G For the first time, we study the sorting of permutations by length-weighted transpositions under a wide class of cost functions, namely f(l)=l(alpha), where l is the length of the transposition. For different alpha, we give corresponding upper and lower bounds of the cost of sorting any binary sequences or any permutations. Furthermore, an O(log n)-approximation algorithm and an exact algorithm are given to determine the optimal transposition series of sorting a permutation of length n when 1< alpha < 2 and alpha > or =2 respectively. Our work poses some interesting questions to both biologists and computer scientists and suggests some new bioinformatic insights that are currently being studied. PMID: 18649439 [PubMed - indexed for MEDLINE] ... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000044 Mon, 01 Dec 2008 16:22:41 +0100 2000044 http://www.medworm.com/index.php?rid=2000043&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19008180%26dopt%3DAbstract Authors: Wu Z, Zhang Y The double digestion problem for DNA restriction mapping has been proved to be NP-complete and intractable if the numbers of the DNA fragments become large. Several approaches to the problem have been tested and proved to be effective only for small problems. In this paper, we formulate the problem as a mixed-integer linear program (MIP) by following (Waterman, 1995) in a sightly different form. With this formulation and using state-of-the-art integer programming techniques, we can solve randomly generated problems whose search space sizes are many-magnitude larger than previously reported testing sizes. PMID: 19008180 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000043 Mon, 01 Dec 2008 16:22:41 +0100 2000043 http://www.medworm.com/index.php?rid=2000040&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19008183%26dopt%3DAbstract Authors: Brown M, He F, Yeung LF As a general lack of quantitative measurement data for pathway modelling and parameter identification process, time-series experimental design is particularly important in current systems biology research. This paper mainly investigates state measurement/observer selection problem when parametric uncertainties are considered. Based on the extension of optimal design criteria, two robust experimental design strategies are investigated, one is the regularisation-based design method, and the other is Taguchi-based design approach. By implementing to a simplified IkappaBalpha - NF - kappaB signalling pathway system, two design approaches are comparatively studied. When large parametric uncertainty is present, by assuming that different parametric uncertaint... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000040 Mon, 01 Dec 2008 16:22:41 +0100 2000040 http://www.medworm.com/index.php?rid=2000039&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19008184%26dopt%3DAbstract Authors: Liao H, Ng M, Fung E, Sham PC The main aim of this paper is to propose and develop a unidimensional nonnegative scaling model to construct Linkage Disequilibrium (LD) maps. The proposed constrained scaling model can be efficiently solved by transforming it to an unconstrained model. The method is implemented in PC Clusters at Hong Kong Baptist University. The LD maps are constructed for four populations from Hapmap data sets with chromosomes of several ten thousand Single Nucleotide Polymorphisms (SNPs). The similarities and dissimilarities of the LD maps are studied and analysed. Computational results are also reported to show the effectiveness of the method using parallel computation. PMID: 19008184 [PubMed - in process] (Source: International Journal of Bioinformatics R... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000039 Mon, 01 Dec 2008 16:22:41 +0100 2000039 http://www.medworm.com/index.php?rid=2000037&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19008186%26dopt%3DAbstract Authors: Liu ZP, Wu LY, Wang Y, Zhang XS, Functions of a protein are mainly determined by its structure. Surface cavities, also called pockets or clefts, are ordinarily regarded as potentially active sites where the protein carries out the functions. Clustering these pockets is a challenging task in structural genomics. In this paper, we introduce pocket similarity network which possesses the feature of community structure to systematically describe structural similarity among pockets, then a straightforward classification scheme is developed based on this special feature. The surface pockets are clustered into structurally similar pocket groups via a hierarchical process. We identify these small pocket groups as structural templates which represent similar functions in diverse protei... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000037 Mon, 01 Dec 2008 16:22:41 +0100 2000037 http://www.medworm.com/index.php?rid=2000042&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19008181%26dopt%3DAbstract In this study, we compare Bayesian Method, which is used in previous work, with several regression models. We apply the models to known reactions in E. coli and three other bacteria. It is shown that the proposed regression models obtain favourable performance when compared with the Bayesian method. PMID: 19008181 [PubMed - as supplied by publisher] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000042 Tue, 01 Jan 2008 05:00:00 +0100 2000042 http://www.medworm.com/index.php?rid=2000041&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19008182%26dopt%3DAbstract Authors: Zhao XM, Chen L, Aihara K Annotating proteins with biological functions is one of the main goals in post genomic era. Various high-throughout technologies, e.g., yeast two-hybrid systems and microarray, have provided an alternative way to protein function prediction. Despite the success obtained by high-throughout data, the errors in the data have not been handled well. In this work, a new technique for protein function prediction is presented, where a weighted functional linkage graph is generated by exploiting the existing protein-protein interaction data, complex data and gene expression data. By finding the shortest path in the functional linkage graph, the functional links among proteins can be captured. With the functional links available, the functions of unknown protei... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000041 Tue, 01 Jan 2008 05:00:00 +0100 2000041 http://www.medworm.com/index.php?rid=2000038&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19008185%26dopt%3DAbstract Authors: Tozaki H, Kobe T, Aihara K, Iwasaki H The use of synthetic biology to design artificial gene circuits is an important approach for understanding the principles underlying the complicated dynamic behaviours of biomolecular networks, such as genetic switching and biological rhythms. The synthetic approach is also useful in systems biology in that it can be used to create artificial bypasses for processes related to cellular phenomena of interest for their easier analysis. To validate the role of transcription feedback in the cyanobacterial circadian system, we propose an experimental design for a 'semi-synthetic' approach that involves transplantation of the kaiABC genes into Escherichia coli and the construction of chimeric transcriptional outputs. The design principle and prel... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000038 Tue, 01 Jan 2008 05:00:00 +0100 2000038 http://www.medworm.com/index.php?rid=2000107&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048170%26dopt%3DAbstract Authors: Parvini F, Shahabi C We propose a novel approach for recognising static and dynamic hand gestures by analysing the raw data streams generated by the sensors attached to the human hands. We utilise the concept of 'range of motion' in the movement of fingers and exploit this characteristic to analyse the acquired data for recognising hand signs. Our approach for hand gesture recognition addresses two major problems: user-dependency and device-dependency. Furthermore, we show that our approach neither requires calibration nor involves training. We apply our approach for recognising American Sign Language (ASL) signs and show that more than 75% accuracy in sign recognition can be achieved. PMID: 18048170 [PubMed - indexed for MEDLINE] (Source: International Journal of Bioinfor... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000107 Mon, 01 Jan 2007 05:00:00 +0100 2000107 http://www.medworm.com/index.php?rid=2000106&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048171%26dopt%3DAbstract Authors: Morse M, Patel JM, Grosky WI We propose a novel indexing structure, called the target tree, which is designed to answer a new type of spatial query, called the radial query. A radial query finds all objects in the spatial data set that intersect with line segments emanating from a single target point. Many biomedical applications use radial queries, including neurosurgical planning. A target tree uses a regular hierarchical decomposition of space using wedge shapes that emanate from the target point. We compare the target tree with the R*-tree and quadtree, and show that the target tree is significantly faster than these methods. PMID: 18048171 [PubMed - indexed for MEDLINE] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000106 Mon, 01 Jan 2007 05:00:00 +0100 2000106 http://www.medworm.com/index.php?rid=2000105&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048172%26dopt%3DAbstract Authors: Cheung L, Cheung DW, Kao B, Yip KY, We study the problem of pattern-based subspace clustering which is clustering by pattern similarity finds objects that exhibit a coherent pattern of rises and falls in subspaces. Applications of pattern-based subspace clustering include DNA micro-array data analysis. Our goal is to devise pattern-based clustering methods that are capable of: discovering useful patterns of various shapes, and discovering all significant patterns. Our approach is to extend the idea of Order-Preserving Submatrix (OPSM). We devise a novel algorithm for mining OPSM, show that OPSM can be generalised to cover most existing pattern-based clustering models and propose a number of extensions to the original OPSM model. PMID: 18048172 [PubMed - indexed for MEDLIN... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000105 Mon, 01 Jan 2007 05:00:00 +0100 2000105 http://www.medworm.com/index.php?rid=2000104&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048173%26dopt%3DAbstract Authors: Andreopoulos B, An A, Huang X, Wang X Clustering protein-protein interaction networks (PINs) helps to identify complexes that guide the cell machinery. Clustering algorithms often create a flat clustering, without considering the layered structure of PINs. We propose the MULIC clustering algorithm that produces layered clusters. We applied MULIC to five PINs. Clusters correlate with known MIPS protein complexes. For example, a cluster of 79 proteins overlaps with a known complex of 88 proteins. Proteins in top cluster layers tend to be more representative of complexes than proteins in bottom layers. Lab work on finding unknown complexes or determining drug effects can be guided by top layer proteins. PMID: 18048173 [PubMed - indexed for MEDLINE] (Source: International Jour... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000104 Mon, 01 Jan 2007 05:00:00 +0100 2000104 http://www.medworm.com/index.php?rid=2000103&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048174%26dopt%3DAbstract Authors: Zhou J, Sander J, Lin G Automatically identifying frequent composite patterns in DNA sequences is an important task in bioinformatics, especially when all the basic elements (or monad patterns) of a composite pattern are weak. In this paper, we compare one straightforward approach to assemble the monad patterns into composite patterns to two other rather complex approaches. Both our theoretical analysis and empirical results show that this overlooked straightforward method can be several orders of magnitude faster. Furthermore, different from the previous understandings, the empirical results show that the runtime superiority among the three approaches is closely related to the insignificance of the monad patterns. PMID: 18048174 [PubMed - indexed for MEDLINE] (Source: Int... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000103 Mon, 01 Jan 2007 05:00:00 +0100 2000103 http://www.medworm.com/index.php?rid=2000102&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048175%26dopt%3DAbstract Authors: Zhu X, Wei D Computer simulation of intracardiac potentials was performed based on a whole-heart model, emphasising applications to Electrophysiology Study (EPS) and catheter ablation. A numerical method was proposed based on a volume conductor model with multiple interfaces and piecewise homogeneity. A model of a normal heart and a model of Wolff-Parkinson-White (WPW) Syndrome with a right free-wall Accessory Pathway (AP) were employed to simulate intracardiac electrograms. The study was validated by comparing the simulated electrograms with those in catheter-based EPS and ablations. Applying whole-heart modelling to the EPS and ablation is regarded as a new direction of electrocardiologic forward problem. PMID: 18048175 [PubMed - indexed for MEDLINE] (Source: Internation... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000102 Mon, 01 Jan 2007 05:00:00 +0100 2000102 http://www.medworm.com/index.php?rid=2000093&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048184%26dopt%3DAbstract Authors: Wang Y, Wu LY, Chen L, Zhang XS One of the central problems in functional genomics is to establish the classification schemes of protein structures. In this paper the relationship of protein structures is uncovered within the framework of supervised learning. Specifically, the novel patterns based on convex hull representation are firstly extracted from a protein structure, then the classification system is constructed and machine learning methods such as neural networks, Hidden Markov Models (HMM) and Support Vector Machines (SVMs) are applied. The CATH scheme is highlighted in the classification experiments. The results indicate that the proposed supervised classification scheme is effective and efficient. PMID: 18048184 [PubMed - indexed for MEDLINE] (Source: Internatio... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000093 Mon, 01 Jan 2007 05:00:00 +0100 2000093 http://www.medworm.com/index.php?rid=2000092&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048185%26dopt%3DAbstract We present a novel decoding algorithm identifying all positive clones in the presence of inhibitors and experimental errors. PMID: 18048185 [PubMed - indexed for MEDLINE] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000092 Mon, 01 Jan 2007 05:00:00 +0100 2000092 http://www.medworm.com/index.php?rid=2000091&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048186%26dopt%3DAbstract Authors: Chen XW, Gerlach B, Chen D, Liu Z For microarray based cancer classification, feature selection is a common method for improving classifier generalisation. Most wrapper methods use cross validation methods to evaluate feature sets. For small sample problems like microarray, however, cross validation methods may overfit the data. In this paper, we propose a Structural Risk Minimisation (SRM) based method for gene selection in cancer classification. SRM principle allows for reducing the probable bound on generalisation error and thus avoids overfitting problems. The experimental results show that the proposed method produces significantly better performance than general wrapper methods that use cross validations. PMID: 18048186 [PubMed - indexed for MEDLINE] (Source: Interna... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000091 Mon, 01 Jan 2007 05:00:00 +0100 2000091 http://www.medworm.com/index.php?rid=2000090&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048187%26dopt%3DAbstract We report a heuristic search algorithm called Two-Level Simulated Annealing (TLSA) that is more likely to find the global optimal network structure compared to conventional simulated annealing and other searching schemes. We have applied this method to search for a global optimised network structure from a synthetic data set and an expression data set of S. cerevisiae mutants. We have achieved better precision and recall compared to other searching algorithms and are able to map relationships more accurately among functionally-linked genes. PMID: 18048187 [PubMed - indexed for MEDLINE] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000090 Mon, 01 Jan 2007 05:00:00 +0100 2000090 http://www.medworm.com/index.php?rid=2000089&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048188%26dopt%3DAbstract Authors: Nair PS, John EB Aligning specific sequences against a very large number of other sequences is a central aspect of bioinformatics. With the widespread availability of personal computers in biology laboratories, sequence alignment is now often performed locally. This makes it necessary to analyse the performance of personal computers for sequence aligning bioinformatics benchmarks. In this paper, we analyse the performance of a personal computer for the popular BLAST and FASTA sequence alignment suites. Results indicate that these benchmarks have a large number of recurring operations and use memory operations extensively. It seems that the performance can be improved with a bigger L1-cache. PMID: 18048188 [PubMed - indexed for MEDLINE] (Source: International Journal of Bio... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000089 Mon, 01 Jan 2007 05:00:00 +0100 2000089 http://www.medworm.com/index.php?rid=2000088&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048189%26dopt%3DAbstract Authors: Wang Y, Wang S High-throughput microarrays have recently been developed to detect DNA Copy Number (DCN) aberrations. The resulting DCN data is often very noisy. Previous denoising methods proposed for DCN data assumed uniform spacing between adjacent probes, which is not true and can potentially result in erroneous output. To address this issue, we developed a novel stationary wavelet denoising scheme for DCN data. Empirical results on synthetic data showed that our method outperformed the best previous method by 4.612.7% in terms of the root mean squared error. Experiments on a real data set also confirmed the applicability of our method. PMID: 18048189 [PubMed - indexed for MEDLINE] (Source: International Journal of Bioinformatics Research and Applications) International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000088 Mon, 01 Jan 2007 05:00:00 +0100 2000088 http://www.medworm.com/index.php?rid=2000087&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048190%26dopt%3DAbstract Authors: Du A, Hu X, Pan Y Disulphide bonds link distant portions of protein chains and provide strong structural constraints in the form of long-range interactions. Prediction and knowledge of disulphide bond connectivity is important in reducing the search space of protein conformation. In this research, we present an effective way to predict disulphide bridges by Support Vector Machine (SVM). The SVM encoding was based on experimental results on the binding motifs of protein disulphide isomerases. The physical-chemical characteristics of the flanking sequences and the linear distance between the concerned cysteine pairs were also included in the encoding. An overall pair wise accuracy of 92% was obtained for the SP39 dataset. PMID: 18048190 [PubMed - indexed for MEDLINE] (Source... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000087 Mon, 01 Jan 2007 05:00:00 +0100 2000087 http://www.medworm.com/index.php?rid=2000086&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048191%26dopt%3DAbstract Authors: Brylinski M, Konieczny L, Roterman I The model for protein folding (in silico) simulation is presented. Three steps have been implemented: early stage folding based on the backbone conformation; hydrophobic collapse based on the fuzzy-oil-drop model; aim-oriented structure modification by the function-related ligand. The model has been verified taking alpha and beta haemoglobin chains as examples to fold them in two different conditions: with and without haem being present in the folding environment. The presence of haem and its participation in the folding simulation led to the structure more similar to the crystal one. It suggests that the haem presence directs the folding process towards the function-related structure. PMID: 18048191 [PubMed - indexed for MEDLINE] (Sour... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000086 Mon, 01 Jan 2007 05:00:00 +0100 2000086 http://www.medworm.com/index.php?rid=2000085&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048192%26dopt%3DAbstract Authors: Digiampietri LA, Perez-Alcazar Jde J, Medeiros CB The proliferation of bioinformatics activities brings new challenges - how to understand and organise these resources, how to exchange and reuse successful experimental procedures, and to provide interoperability among data and tools. This paper describes an effort toward these directions. It is based on combining research on ontology management, AI and scientific workflows to design, reuse and annotate bioinformatics experiments. The resulting framework supports automatic or interactive composition of tasks based on AI planning techniques and takes advantage of ontologies to support the specification and annotation of bioinformatics workflows. We validate our proposal with a prototype running on real data. PMID: 18048192 [... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000085 Mon, 01 Jan 2007 05:00:00 +0100 2000085 http://www.medworm.com/index.php?rid=2000084&cid=s_38179_79_f&fid=38179&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18048193%26dopt%3DAbstract We describe a new ontology-driven semantic data integration approach for post-genome biology studies. Here, a view-based global schema can be automatically generated by merging RDF schemas from local databases. The semantic inconsistency of the merged schema is resolved by the creation of 'RDF ontology maps'. Data querying capability is accomplished with a virtual data repository, in which a D2RQ-based 'relational-to-RDF' map is developed to link schema to the relational database backend. With sample RDQL queries, we demonstrate that our approach significantly simplifies the retrieval of human protein interaction data from different databases containing hundreds of thousands of records. PMID: 18048193 [PubMed - indexed for MEDLINE] (Source: International Journal of Bioinformatics Resea... International Journal of Bioinformatics Research and Applications journals http://www.medworm.com/rss/comments.php?id=2000084 Mon, 01 Jan 2007 05:00:00 +0100 2000084