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 'Advances in Bioinformatics' source. Tue, 10 Jan 2012 05:19:21 +0100 http://www.medworm.com/index.php?rid=5404990&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fdrp%2F2011%2F436952%2F The objective of the present study was to identify the causative bacterial of nosocomial infection and to determine the incidence of nosocomial infection and their changing during hospitalization in burned patients admitted to in the Motahari Hospital, Tehran, Iran. During the second part of 2010, 164 patients were included in this study. Samples were taken the first 48 hours and the fourth week after admission to Motahari Burn hospital. Isolation and identification of microorganisms was performed using the standard procedure. Of the 164 patients, 717 samples were taken and 812 bacteria were identified, 610 patients were culture positive on day 7 while 24 (17.2%) on 14 days after admission. The bacteria causing infections were 325 Pseudomonas, 140 Acinetobacter, 132 Staphylococcus aure... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=5404990 Mon, 14 Nov 2011 14:34:28 +0100 5404990 http://www.medworm.com/index.php?rid=4454948&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F268925.html Biochemical systems biology augments more traditional disciplines, such as genomics, biochemistry and molecular biology, by championing (i) mathematical and computational modeling; (ii) the application of traditional engineering practices in the analysis of biochemical systems; and in the past decade increasingly (iii) the use of near-comprehensive data sets derived from ‘omics platform technologies, in particular “downstream” technologies relative to genome sequencing, including transcriptomics, proteomics and metabolomics. The future progress in understanding biological principles will increasingly depend on the development of temporal and spatial analytical techniques that will provide high-resolution data for systems analyses. To date, particularly successful we... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4454948 Thu, 10 Feb 2011 00:53:26 +0100 4454948 http://www.medworm.com/index.php?rid=4275027&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F454671.html Understanding mechanisms of protein flexibility is of great importance to structural biology. The ability to detect similarities between proteins and their patterns is vital in discovering new information about unknown protein functions. A Distance Constraint Model (DCM) provides a means to generate a variety of flexibility measures based on a given protein structure. Although information about mechanical properties of flexibility is critical for understanding protein function for a given protein, the question of whether certain characteristics are shared across homologous proteins is difficult to assess. For a proper assessment, a quantified measure of similarity is necessary. This paper begins to explore image processing techniques to quantify similarities in signals and images that char... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4275027 Tue, 21 Dec 2010 11:47:03 +0100 4275027 http://www.medworm.com/index.php?rid=4012184&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F289301.html Carbohydrate-binding proteins are proteins that can interact with sugar chains but do not modify them. They are involved in many physiological functions, and we have developed a method for predicting them from their amino acid sequences. Our method is based on support vector machines (SVMs). We first clarified the definition of carbohydrate-binding proteins and then constructed positive and negative datasets with which the SVMs were trained. By applying the leave-one-out test to these datasets, our method delivered 0.92 of the area under the receiver operating characteristic (ROC) curve. We also examined two amino acid grouping methods that enable effective learning of sequence patterns and evaluated the performance of these methods. When we applied our method in combination with the homol... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=4012184 Wed, 29 Sep 2010 21:22:50 +0100 4012184 http://www.medworm.com/index.php?rid=3976244&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F708501.html The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications.We propose a rigorous and flexible algorithmic solution to mapping SOLiD color-space reads to a reference genome. The solution relies on an advanced method of seed design that uses a faithful probabilistic model of read matches and, on the other hand, a novel seeding principle especially adapted to read mapping. Our method can handle both lossy and lossless frameworks and is able to distinguish, at the level of seed design, between SNPs and reading errors. We illustrate our approach by several seed designs and demonstrate their efficiency. (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3976244 Fri, 17 Sep 2010 09:10:27 +0100 3976244 http://www.medworm.com/index.php?rid=3884996&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F976792.html Previous work has established a genomic signature based on relative counts of the 16 possible dinucleotides. Until now, it has been generally accepted that the dinucleotide signature is characteristic of a genome and is relatively homogeneous across a genome. However, we found some local regions of the soybean genome with a signature differing widely from that of the rest of the genome. Those regions were mostly centromeric and pericentromeric, and enriched for repetitive sequences. We found that DNA binding energy also presented large-scale patterns across soybean chromosomes. These two patterns were helpful during assembly and quality control of soybean whole genome shotgun scaffold sequences into chromosome pseudomolecules. (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3884996 Fri, 20 Aug 2010 09:31:46 +0100 3884996 http://www.medworm.com/index.php?rid=3771852&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F749848.html An important objective in systems biology is to infer gene regulatory networks from postgenomic data, and dynamic Bayesian networks have been widely applied as a popular tool to this end. The standard approach for nondiscretised data is restricted to a linear model and a homogeneous Markov chain. Recently, various generalisations based on changepoint processes and free allocation mixture models have been proposed. The former aim to relax the homogeneity assumption, whereas the latter are more flexible and, in principle, more adequate for modelling nonlinear processes. In our paper, we compare both paradigms and discuss theoretical shortcomings of the latter approach. We show that a model based on the changepoint process yields systematically better results than the free allocation model wh... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3771852 Wed, 21 Jul 2010 07:47:37 +0100 3771852 http://www.medworm.com/index.php?rid=3726444&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F428325.html We present a comprehensive study of cytogenetic alterations that occur during the progression of clear cell renal cell carcinoma (ccRCC). We used high-density high-throughput Affymetrix 100 K SNP arrays to obtain the whole genome SNP copy number information from 71 pretreatment tissue samples with RCC tumors; of those, 42 samples were of human ccRCC subtype. We analyzed patterns of cytogenetic loss and gain from different RCC subtypes and in particular, different stages and grades of ccRCC tumors, using a novel algorithm that we have designed. Based on patterns of cytogenetic alterations in chromosomal regions with frequent losses and gains, we inferred the involvement of candidate genes from these regions in ccRCC tumorigenesis and development. We then proposed a new model of ccRC... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3726444 Tue, 06 Jul 2010 07:42:59 +0100 3726444 http://www.medworm.com/index.php?rid=3723260&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F318573.html Detection of discriminating patterns in gene expression data can be accomplished by using various methods of statistical learning. It has been proposed that sample pooling in this context would have negative effects; however, pooling cannot always be avoided. We propose a simulation framework to explicitly investigate the parameters of patterns, experimental design, noise, and choice of method in order to find out which effects on classification performance are to be expected. We use a two-group classification task and simulated gene expression data with independent differentially expressed genes as well as bivariate linear patterns and the combination of both. Our results show a clear increase of prediction error with pool size. For pooled training sets powered partial least squares discr... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3723260 Sun, 04 Jul 2010 07:38:57 +0100 3723260 http://www.medworm.com/index.php?rid=3710222&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F436036.html Understanding of the three-dimensional structures of proteins that interact with carbohydrates covalently (glycoproteins) as well as noncovalently (protein-carbohydrate complexes) is essential to many biological processes and plays a significant role in normal and disease-associated functions. It is important to have a central repository of knowledge available about these protein-carbohydrate complexes as well as preprocessed data of predicted structures. This can be significantly enhanced by tools de novo which can predict carbohydrate-binding sites for proteins in the absence of structure of experimentally known binding site. PROCARB is an open-access database comprising three independently working components, namely, (i) Core PROCARB module, consisting of three-dimensional structures of... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3710222 Wed, 30 Jun 2010 07:41:27 +0100 3710222 http://www.medworm.com/index.php?rid=3599135&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F257512.html We describe these nodes taking into account their position in the primary structure to study their apparition frequency in the folded proteins. Finally, we observe that their interaction level is a consequence of the general rules which govern the folding process. (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3599135 Wed, 26 May 2010 15:26:46 +0100 3599135 http://www.medworm.com/index.php?rid=3537843&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F167408.html Evolutionary binary characters are features of species or genes, indicating the absence (value zero) or presence (value one) of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus), gene content, and morphological characters. In many studies, the acquisition of such binary characters is assumed to represent a rare evolutionary event, and consequently, their evolution is analyzed using various flavors of parsimony. However, when gain and loss of the character are not rare enough, a probabilistic analysis becomes essential. Here, we present a comprehensive probabilistic model to describe the evolution of binary characters on a bifurcating phylogenetic tree. A fast software tool, EREM, is provided, using maximum likelihood t... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3537843 Thu, 06 May 2010 15:34:51 +0100 3537843 http://www.medworm.com/index.php?rid=3526347&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F856825.html We recently reported that the human genome is ‘‘splitting’’ into two gene subgroups characterised by polarised GC content (Tang et al, 2007), and that such evolutionary change may be accelerated by programmed genetic instability (Zhao et al, 2008). Here we extend this work by mapping the presence of two separate high-evolutionary-rate (Ka/Ks) hotspots in the human genome—one characterized by low GC content, high intron length, and low gene expression, and the other by high GC content, high exon number, and high gene expression. This finding suggests that at least two different mechanisms mediate adaptive genetic evolution in higher organisms: (1) intron lengthening and reduced repair in hypermethylated lowly-transcribed genes, and (2) duplication and/or inser... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3526347 Mon, 03 May 2010 15:40:25 +0100 3526347 http://www.medworm.com/index.php?rid=3415666&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F423589.html High-throughput “omics” technologies bring new opportunities for biological and biomedical researchers to ask complex questions and gain new scientific insights. However, the voluminous, complex, and context-dependent data being maintained in heterogeneous and distributed environments plus the lack of well-defined data standard and standardized nomenclature imposes a major challenge which requires advanced computational methods and bioinformatics infrastructures for integration, mining, visualization, and comparative analysis to facilitate data-driven hypothesis generation and biological knowledge discovery. In this paper, we present the challenges in high-throughput “omics” data integration and analysis, introduce a protein-centric approach for systems integration ... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3415666 Mon, 29 Mar 2010 15:51:54 +0100 3415666 http://www.medworm.com/index.php?rid=3342212&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F287070.html Proposed is a procedure to test whether a genomic sequence contains coding DNA, called a coding potential region. The procedure tests the coding potential of conserved short genomic sequence, in which the assumptions on the probability models of gene structures are relaxed. Thus, it is expected to provide additional candidate regions that contain coding DNAs to the current genomic database. The procedure was applied to the set of highly conserved human-mouse sequences in the genome database at the University of California at Santa Cruz. For sequences containing RefSeq coding exons, the procedure detected 91.3% regions having coding potential in this set, which covers 83% of the human RefSeq coding exons, at a 2.6% false positive rate. The procedure detected 12,688 novel short r... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3342212 Mon, 08 Mar 2010 17:55:04 +0100 3342212 http://www.medworm.com/index.php?rid=3339597&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F182689.html MicroRNAs control the expression of their target genes by translational repression and transcriptional cleavage. They are involved in various biological processes including development and progression of cancer. To uncover the biological role of miRNAs it is important to identify their target genes. The small number of experimentally validated target genes makes computer prediction methods very important. However, state-of-the-art prediction tools result in a great number of putative targets with an unpredictable number of false positives. In this paper, we propose and evaluate two approaches for ranking the biological relevance of putative targets of miRNAs which are associated with breast cancer. (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3339597 Sun, 07 Mar 2010 16:19:19 +0100 3339597 http://www.medworm.com/index.php?rid=3326590&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F532989.html Classification of cancers based on gene expressions produces better accuracy when compared to that of the clinical markers. Feature selection improves the accuracy of these classification algorithms by reducing the chance of overfitting that happens due to large number of features. We develop a new feature selection method called Biological Pathway-based Feature Selection (BPFS) for microarray data. Unlike most of the existing methods, our method integrates signaling and gene regulatory pathways with gene expression data to minimize the chance of overfitting of the method and to improve the test accuracy. Thus, BPFS selects a biologically meaningful feature set that is minimally redundant. Our experiments on published breast cancer datasets demonstrate that all of the top 20 genes found by... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3326590 Wed, 03 Mar 2010 16:46:41 +0100 3326590 http://www.medworm.com/index.php?rid=3301960&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F323654.html Human hepatitis delta virus (HDV) is the smallest RNA virus in genome. HDV genome is divided into a viroid-like sequence and a protein-coding sequence which could have originated from different resources and the HDV genome was eventually constituted through RNA recombination. The genome subsequently diversified through accumulation of mutations selected by interactions between the mutated RNA and proteins with host factors to successfully form the infectious virions. Therefore, we propose that the conservation of HDV nucleotide sequence is highly related with its functionality. Genome analysis of known HDV isolates shows that the C-terminal coding sequences of large delta antigen (LDAg) are the highest diversity than other regions of protein-coding sequences but they still retain biologica... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3301960 Wed, 24 Feb 2010 17:07:46 +0100 3301960 http://www.medworm.com/index.php?rid=3297979&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F787128.html A protein network shows physical interactions as well as functional associations. An important usage of such networks is to discover unknown members of partially known complexes and pathways. A number of methods exist for such analyses, and they can be divided into two main categories based on their treatment of highly connected proteins. In this paper, we show that methods that are not affected by the degree (number of linkages) of a protein give more accurate predictions for certain complexes and pathways. We propose a network flow-based technique to compute the association probability of a pair of proteins. We extend the proposed technique using hierarchical clustering in order to scale well with the size of proteome. We also show that top-k queries are not suitable for a large number o... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3297979 Tue, 23 Feb 2010 16:56:46 +0100 3297979 http://www.medworm.com/index.php?rid=3254111&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F461763.html (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3254111 Tue, 09 Feb 2010 16:40:01 +0100 3254111 http://www.medworm.com/index.php?rid=3227348&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F316936.html Synonymous codon usage of protein coding genes of thirty two completely sequenced mycobacteriophage genomes was studied using multivariate statistical analysis. One of the major factors influencing codon usage is identified to be compositional bias. Codons ending with either C or G are preferred in highly expressed genes among which C ending codons are highly preferred over G ending codons. A strong negative correlation between effective number of codons (Nc) and GC3s content was also observed, showing that the codon usage was effected by gene nucleotide composition. Translational selection is also identified to play a role in shaping the codon usage operative at the level of translational accuracy. High level of heterogeneity is seen among and between the genomes. Length of genes is also ... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3227348 Mon, 01 Feb 2010 17:37:52 +0100 3227348 http://www.medworm.com/index.php?rid=3227347&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2010%2F178069.html Posttrial assessment of a vaccine's selective pressure on infecting strains may be realized through a bioinformatic tool such as parsimony phylogenetic analysis. Following a failed gonococcal pilus vaccine trial of Neisseria gonorrhoeae, we conducted a phylogenetic analysis of pilin DNA and predicted peptide sequences from clinical isolates to assess the extent of the vaccine's effect on the type of field strains that the volunteers contracted. Amplified pilin DNA sequences from infected vaccinees, placebo recipients, and vaccine specimens were phylogenetically analyzed. Cladograms show that the vaccine peptides have diverged substantially from their paternal isolate by clustering distantly from each other. Pilin genes of the field clinical isolates were heterogeneous, and their pe... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3227347 Mon, 01 Feb 2010 17:37:52 +0100 3227347 http://www.medworm.com/index.php?rid=3193358&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F235320.html We demonstrate the application and comparative interpretations of three tree-based algorithms for the analysis of data arising from flow cytometry: classification and regression trees (CARTs), random forests (RFs), and logic regression (LR). Specifically, we consider the question of what best predicts CD4 T-cell recovery in HIV-1 infected persons starting antiretroviral therapy with CD4 count between 200 and 350 cell/μL. A comparison to a more standard contingency table analysis is provided. While contingency table analysis and RFs provide information on the importance of each potential predictor variable, CART and LR offer additional insight into the combinations of variables that together are predictive of the outcome. In all cases considered, baseline CD3-DR-CD56+CD16+ eme... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3193358 Thu, 21 Jan 2010 16:29:47 +0100 3193358 http://www.medworm.com/index.php?rid=3061365&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F584603.html Flow cytometry (FCM) is widely used in health research and in treatment for a variety of tasks, such as in the diagnosis and monitoring of leukemia and lymphoma patients, providing the counts of helper-T lymphocytes needed to monitor the course and treatment of HIV infection, the evaluation of peripheral blood hematopoietic stem cell grafts, and many other diseases. In practice, FCM data analysis is performed manually, a process that requires an inordinate amount of time and is error-prone, nonreproducible, nonstandardized, and not open for re-evaluation, making it the most limiting aspect of this technology. This paper reviews state-of-the-art FCM data analysis approaches using a framework introduced to report each of the components in a data analysis pipeline. Current challenges and poss... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3061365 Sun, 06 Dec 2009 15:58:41 +0100 3061365 http://www.medworm.com/index.php?rid=3007701&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F686759.html We describe methodology and software to automatically identify cell populations in flow cytometry data. Our approach advances the paradigm of manually gating sequential two-dimensional projections of the data to a procedure that automatically produces gates based on statistical theory. Our approach is nonparametric and can reproduce nonconvex subpopulations that are known to occur in flow cytometry samples, but which cannot be produced with current parametric model-based approaches. We illustrate the methodology with a sample of mouse spleen and peritoneal cavity cells. (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=3007701 Thu, 19 Nov 2009 16:18:58 +0100 3007701 http://www.medworm.com/index.php?rid=2999229&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F476106.html A next step to interpret the findings generated by genome-wide association studies is to associate molecular quantitative traits with disease-associated alleles. To this end, researchers are linking disease risk alleles with gene expression quantitative trait loci (eQTL). However, gene expression at the mRNA level is only an intermediate trait and flow cytometry analysis can provide more downstream and biologically valuable protein level information in multiple cell subsets simultaneously using freshly obtained samples. Because the throughput of flow cytometry is currently limited, experiments may need to span over several weeks or months to obtain a sufficient sample size to demonstrate genetic association. Therefore, normalisation methods are needed to control for technical variability a... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2999229 Tue, 17 Nov 2009 16:26:51 +0100 2999229 http://www.medworm.com/index.php?rid=2993685&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F749027.html Comparing genomes is an essential preliminary step to solve many problems in biology. Matching long similar segments between two genomes is a precondition for their evolutionary, genetic, and genome rearrangement analyses. Though various comparison methods have been developed in recent years, a quantitative assessment of their performance is lacking. Here, we describe two families of assessment measures whose purpose is to evaluate bacteria-oriented comparison tools. The first measure is based on how well the genome segmentation fits the gene annotation of the studied organisms; the second uses the number of segments created by the segmentation and the percentage of the two genomes that are conserved. The effectiveness of the two measures is demonstrated by applying them to the results of ... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2993685 Sun, 15 Nov 2009 15:56:35 +0100 2993685 http://www.medworm.com/index.php?rid=2984544&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F247646.html We present a framework for the identification of cell subpopulations in flow cytometry data based on merging mixture components using the flowClust methodology. We show that the cluster merging algorithm under our framework improves model fit and provides a better estimate of the number of distinct cell subpopulations than either Gaussian mixture models or flowClust, especially for complicated flow cytometry data distributions. Our framework allows the automated selection of the number of distinct cell subpopulations and we are able to identify cases where the algorithm fails, thus making it suitable for application in a high throughput FCM analysis pipeline. Furthermore, we demonstrate a method for summarizing complex merged cell subpopulations in a simple manner that integrat... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2984544 Thu, 12 Nov 2009 16:20:24 +0100 2984544 http://www.medworm.com/index.php?rid=2984543&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F103839.html Flow cytometry (FCM) has become an important analysis technology in health care and medical research, but the large volume of data produced by modern high-throughput experiments has presented significant new challenges for computational analysis tools. The development of an FCM software suite in Bioconductor represents one approach to overcome these challenges. In the spirit of the R programming language (Tree Star Inc., “FlowJo”), these tools are predominantly console-driven, allowing for programmatic access and rapid development of novel algorithms. Using this software requires a solid understanding of programming concepts and of the R language. However, some of these tools|in particular the statistical graphics and novel analytical methods|are also useful for nonprogrammers.... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2984543 Thu, 12 Nov 2009 16:20:24 +0100 2984543 http://www.medworm.com/index.php?rid=2881117&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F356141.html Flow cytometry (FCM) software packages from R/Bioconductor, such as flowCore and flowViz, serve as an open platform for development of new analysis tools and methods. We created plateCore, a new package that extends the functionality in these core packages to enable automated negative control-based gating and make the processing and analysis of plate-based data sets from high-throughput FCM screening experiments easier. plateCore was used to analyze data from a BD FACS CAP screening experiment where five Peripheral Blood Mononucleocyte Cell (PBMC) samples were assayed for 189 different human cell surface markers. This same data set was also manually analyzed by a cytometry expert using the FlowJo data analysis software package (TreeStar, USA). We show that the expression values for markers... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2881117 Sun, 11 Oct 2009 18:39:13 +0100 2881117 http://www.medworm.com/index.php?rid=2868700&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F809469.html We present this package and illustrate some of the ways in which it can be used. (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2868700 Wed, 07 Oct 2009 16:31:53 +0100 2868700 http://www.medworm.com/index.php?rid=2868699&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F284251.html We present a statistical method to rank observed genes in gene expression time series experiments according to their degree of regulation in a biological process. The ranking may be used to focus on specific genes or to select meaningful subsets of genes from which gene regulatory networks can be built. Our approach is based on a state space model that incorporates hidden regulators of gene expression. Kalman (K) smoothing and maximum (M) likelihood estimation techniques are used to derive optimal estimates of the model parameters upon which a proposed regulation criterion is based. The statistical power of the proposed algorithm is investigated, and a real data set is analyzed for the purpose of identifying regulated genes in time dependent gene expression data. This statistical approach ... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2868699 Wed, 07 Oct 2009 16:31:53 +0100 2868699 http://www.medworm.com/index.php?rid=2827955&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F193947.html A new software package called flowFP for the analysis of flow cytometry data is introduced. The package, which is tightly integrated with other Bioconductor software for analysis of flow cytometry, provides tools to transform raw flow cytometry data into a form suitable for direct input into conventional statistical analysis and empirical modeling software tools. The approach of flowFP is to generate a description of the multivariate probability distribution function of flow cytometry data in the form of a “fingerprint.” As such, it is independent of a presumptive functional form for the distribution, in contrast with model-based methods such as Gaussian Mixture Modeling. FlowFP is computationally efficient and able to handle extremely large flow cytometry data sets of arbitrar... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2827955 Thu, 24 Sep 2009 18:03:21 +0100 2827955 http://www.medworm.com/index.php?rid=2653427&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F480486.html Different from significant gene expression analysis which looks for genes that are differentially regulated, feature selection in the microarray-based prognostic gene expression analysis aims at finding a subset of marker genes that are not only differentially expressed but also informative for prediction. Unfortunately feature selection in literature of microarray study is predominated by the simple heuristic univariate gene filter paradigm that selects differentially expressed genes according to their statistical significances. We introduce a combinatory feature selection strategy that integrates differential gene expression analysis with the Gram-Schmidt process to identify prognostic genes that are both statistically significant and highly informative for predicting tumour survival out... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2653427 Thu, 30 Jul 2009 12:30:52 +0100 2653427 http://www.medworm.com/index.php?rid=2616581&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F926450.html Motivation. Independent Components Analysis (ICA) maximizes the statistical independence of the representational components of a training gene expression profiles (GEP) ensemble, but it cannot distinguish relations between the different factors, or different modes, and it is not available to high-order GEP Data Mining. In order to generalize ICA, we introduce Multilinear-ICA and apply it to tumor classification using high order GEP. Firstly, we introduce the basis conceptions and operations of tensor and recommend Support Vector Machine (SVM) classifier and Multilinear-ICA. Secondly, the higher score genes of original high order GEP are selected by using t-statistics and tabulate tensors. Thirdly, the tensors are performed by Multilinear-ICA. Finally, the SVM is used to classify the tumor ... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2616581 Mon, 20 Jul 2009 12:13:09 +0100 2616581 http://www.medworm.com/index.php?rid=2583893&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2009%2F598241.html Within clinical proteomics, mass spectrometry analysis of biological samples is emerging as an important high-throughput technology, capable of producing powerful diagnostic and prognostic models and identifying important disease biomarkers. As interest in this area grows, and the number of such proteomics datasets continues to increase, the need has developed for efficient, comprehensive, reproducible methods of mass spectrometry data analysis by both experts and nonexperts. We have designed and implemented a stand-alone software system, FAST-AIMS, which seeks to meet this need through automation of data preprocessing, feature selection, classification model generation, and performance estimation. FAST-AIMS is an efficient and user-friendly stand-alone software for predictive analysis of ... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2583893 Thu, 09 Jul 2009 12:14:58 +0100 2583893 http://www.medworm.com/index.php?rid=2468708&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2008%2F897019.html Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pf... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2468708 Wed, 10 Jun 2009 05:46:48 +0100 2468708 http://www.medworm.com/index.php?rid=2468707&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2008%2F257864.html Population genetics is the study of allele frequency changes driven by various evolutionary forces such as mutation, natural selection, and random genetic drift. Although natural selection is widely recognized as a bona-fide phenomenon, the extent to which it drives evolution continues to remain unclear and controversial. Various qualitative techniques, or so-called “tests of neutrality”, have been introduced to detect signatures of natural selection. A decade and a half ago, Stanley Sawyer and Daniel Hartl provided a mathematical framework, referred to as the Poisson random field (PRF), with which to determine quantitatively the intensity of selection on a particular gene or genomic region. The recent availability of large-scale genetic polymorphism data has sparked widespread... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2468707 Wed, 10 Jun 2009 05:46:48 +0100 2468707 http://www.medworm.com/index.php?rid=2468706&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2008%2F420747.html The Web-based software tool Genevestigator provides powerful tools for biologists to explore gene expression across a wide variety of biological contexts. Its first releases, however, were limited by the scaling ability of the system architecture, multiorganism data storage and analysis capability, and availability of computationally intensive analysis methods. Genevestigator V3 is a novel meta-analysis system resulting from new algorithmic and software development using a client/server architecture, large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis. In addition to improved querying features, Genevestigator V3 provides new tools to analyze the expression of genes in many different contexts, to id... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2468706 Wed, 10 Jun 2009 05:46:48 +0100 2468706 http://www.medworm.com/index.php?rid=2468705&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2008%2F719818.html We develop methods to compare the positions of quantitative trait loci (QTL) with a set of genes selected by other methods, such as microarray experiments, from a sequenced genome. We apply our methods to QTL for addictive behavior in mouse, and a set of genes upregulated in a region of the brain associated with addictive behavior, the nucleus accumbens (NA). The association between the QTL and NA genes is not significantly stronger than expected by chance. However, chromosomes 2 and 16 do show strong associations suggesting that genes on these chromosomes might be associated with addictive behavior. The statistical methodology developed for this study can be applied to similar studies to assess the mutual information in microarray and QTL analyses. (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2468705 Wed, 10 Jun 2009 05:46:48 +0100 2468705 http://www.medworm.com/index.php?rid=2468704&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2008%2F369830.html Conclusion. Our analyses show that integration of chromatin immunoprecipitation data with conserved TFBS analysis can be used to generate accurate predictions of functional TFBS. They also show that TFBS cooccurrence can be used to predict transcription factor binding to promoters in vivo. (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2468704 Wed, 10 Jun 2009 05:46:48 +0100 2468704 http://www.medworm.com/index.php?rid=2468703&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2008%2F205969.html A vast amount of microbial sequencing data is being generated through large-scale projects in ecology, agriculture, and human health. Efficient high-throughput methods are needed to analyze the mass amounts of metagenomic data, all DNA present in an environmental sample. A major obstacle in metagenomics is the inability to obtain accuracy using technology that yields short reads. We construct the unique N-mer frequency profiles of 635 microbial genomes publicly available as of February 2008. These profiles are used to train a naive Bayes classifier (NBC) that can be used to identify the genome of any fragment. We show that our method is comparable to BLAST for small 25 bp fragments but does not have the ambiguity of BLAST's tied top scores. We demonstrate that this approach is scalable... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2468703 Wed, 10 Jun 2009 05:46:48 +0100 2468703 http://www.medworm.com/index.php?rid=2468702&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2008%2F789026.html Conclusions. The PCOPGene tools are especially suitable for microarrays with large sample series. This application helps to identify cellular states and the genes involved in it in a flexible way. The application takes advantage of the ability of our system to relate gene expressions; even when these relationships are noncontinuous and cannot be found using linear or nonlinear analytical methods. (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2468702 Wed, 10 Jun 2009 05:46:48 +0100 2468702 http://www.medworm.com/index.php?rid=2468701&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fabi%2F2008%2F719468.html Pathway information provides insight into the biological processes underlying microarray data. Pathway information is widely available for humans and laboratory animals in databases through the internet, but less for other species, for example, livestock. Many software packages use species-specific gene IDs that cannot handle genomics data from other species. We developed a species-independent method to search pathways databases to analyse microarray data. Three PERL scripts were developed that use the names of the genes on the microarray. (1) Add synonyms of gene names by searching the Gene Ontology (GO) database. (2) Search the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database for pathway information using this GO-enriched gene list. (3) Combine the pathway data with the microarra... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2468701 Wed, 10 Jun 2009 05:46:48 +0100 2468701 http://www.medworm.com/index.php?rid=2028829&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F789026 Conclusions. The PCOPGene tools are especially suitable for microarrays with large sample series. This application helps to identify cellular states and the genes involved in it in a flexible way. The application takes advantage of the ability of our system to relate gene expressions; even when these relationships are noncontinuous and cannot be found using linear or nonlinear analytical methods. (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=2028829 Thu, 11 Dec 2008 15:03:07 +0100 2028829 http://www.medworm.com/index.php?rid=1964737&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F205969 A vast amount of microbial sequencing data is being generated through large-scale projects in ecology, agriculture, and human health. Efficient high-throughput methods are needed to analyze the mass amounts of metagenomic data, all DNA present in an environmental sample. A major obstacle in metagenomics is the inability to obtain accuracy using technology that yields short reads. We construct the unique N-mer frequency profiles of 635 microbial genomes publicly available as of February 2008. These profiles are used to train a naive Bayes classifier (NBC) that can be used to identify the genome of any fragment. We show that our method is comparable to BLAST for small 25 bp fragments but does not have the ambiguity of BLAST's tied top scores. We demonstrate that this approach is scalable... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=1964737 Mon, 17 Nov 2008 11:41:42 +0100 1964737 http://www.medworm.com/index.php?rid=1918524&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F369830 Conclusion. Our analyses show that integration of chromatin immunoprecipitation data with conserved TFBS analysis can be used to generate accurate predictions of functional TFBS. They also show that TFBS cooccurrence can be used to predict transcription factor binding to promoters in vivo. (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=1918524 Thu, 30 Oct 2008 15:14:29 +0100 1918524 http://www.medworm.com/index.php?rid=1795200&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F719818 We develop methods to compare the positions of quantitative trait loci (QTL) with a set of genes selected by other methods, such as microarray experiments, from a sequenced genome. We apply our methods to QTL for addictive behavior in mouse, and a set of genes upregulated in a region of the brain associated with addictive behavior, the nucleus accumbens (NA). The association between the QTL and NA genes is not significantly stronger than expected by chance. However, chromosomes 2 and 16 do show strong associations suggesting that genes on these chromosomes might be associated with addictive behavior. The statistical methodology developed for this study can be applied to similar studies to assess the mutual information in microarray and QTL analyses. (Source: Advances in Bioinformatics) Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=1795200 Tue, 16 Sep 2008 15:13:58 +0100 1795200 http://www.medworm.com/index.php?rid=1594283&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F420747 The Web-based software tool Genevestigator provides powerful tools for biologists to explore gene expression across a wide variety of biological contexts. Its first releases, however, were limited by the scaling ability of the system architecture, multiorganism data storage and analysis capability, and availability of computationally intensive analysis methods. Genevestigator V3 is a novel meta-analysis system resulting from new algorithmic and software development using a client/server architecture, large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis. In addition to improved querying features, Genevestigator V3 provides new tools to analyze the expression of genes in many different contexts, to id... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=1594283 Tue, 08 Jul 2008 12:09:59 +0100 1594283 http://www.medworm.com/index.php?rid=1561793&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F257864 Population genetics is the study of allele frequency changes driven by various evolutionary forces such as mutation, natural selection, and random genetic drift. Although natural selection is widely recognized as a bona-fide phenomenon, the extent to which it drives evolution continues to remain unclear and controversial. Various qualitative techniques, or so-called “tests of neutrality”, have been introduced to detect signatures of natural selection. A decade and a half ago, Stanley Sawyer and Daniel Hartl provided a mathematical framework, referred to as the Poisson random field (PRF), with which to determine quantitatively the intensity of selection on a particular gene or genomic region. The recent availability of large-scale genetic polymorphism data has sparked widespread... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=1561793 Wed, 02 Jul 2008 12:17:40 +0100 1561793 http://www.medworm.com/index.php?rid=1554960&cid=s_37043_79_f&fid=37043&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F897019 Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pf... Advances in Bioinformatics journals http://www.medworm.com/rss/comments.php?id=1554960 Mon, 30 Jun 2008 12:47:36 +0100 1554960