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 'BMC Bioinformatics - Latest articles' source. Thu, 09 Feb 2012 22:12:26 +0100 http://www.medworm.com/index.php?rid=5674724&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F28 Conclusions: We demonstrate the accuracy of our method to detect inversions and classify individuals on principled-simulated genotypes, produced by the evolution of an inversion event within a coalescent model [2]. We applied our method to real genotype data from HapMap Phase III to characterize the inversion status of two known inversions within the regions 17q21 and 8p23 across 1184 individuals. Finally, we scan the full genomes of the European Origin (CEU) and Yoruba (YRI) HapMap samples. We find population-based evidence for 9 out of 15 well-established autosomic inversions, and for 52 regions previously predicted by independent experimental methods in ten (9+1) individuals [3, 4]. We provide efficient implementations of both genotype and haplotype methods as a unified R package inveRs... BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5674724 Thu, 09 Feb 2012 05:00:00 +0100 5674724 http://www.medworm.com/index.php?rid=5674723&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F29 Conclusions: We demonstrated that texture based methods for mitochondria segmentation can be enhanced with multiple steps that form an image processing pipeline. While we used a random-forest based patch classifier to recognize texture, it would be possible to replace this with other texture identifiers, and we plan to explore this in future work. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5674723 Thu, 09 Feb 2012 05:00:00 +0100 5674723 http://www.medworm.com/index.php?rid=5674726&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F26 Conclusions: We have presented a novel framework termed consensus embedding which leverages ensemble classification theory within dimensionality reduction, allowing for application to a wide range of high-dimensional biomedical data classification and segmentation problems. Our generalizable framework allows for improved representation and classification in the context of both imaging and non-imaging data. The algorithm offers a promising solution to problems that currently plague DR methods, and may allow for extension to other areas of biomedical data analysis. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5674726 Wed, 08 Feb 2012 05:00:00 +0100 5674726 http://www.medworm.com/index.php?rid=5674725&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F27 Conclusions: We developed a model-based peak alignment method to process both homogeneous and heterogeneous experimental data. The unique feature of our method is the only model-based peak alignment method coupled with metabolite identification in an unified framework. Through the comparison with other existing method, we demonstrated that our method has better performance. Data are available at http://stage.louisville.edu/faculty/x0zhan17/software/software-development/mspa. The R source codes are available at http://www.biostat.iupui.edu/~ChangyuShen/CodesPeakAlignment.zip.Trial Registration: 2136949528613691 (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5674725 Wed, 08 Feb 2012 05:00:00 +0100 5674725 http://www.medworm.com/index.php?rid=5674727&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F25 Conclusion: These results suggest that CrmMiner predictions are accurate and likely to be tissue-specific CRMs. We expect that the predicted tissue-specific CRMs and the regulatory signatures broaden our knowledge of gene transcription regulation. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5674727 Tue, 07 Feb 2012 05:00:00 +0100 5674727 http://www.medworm.com/index.php?rid=5657267&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F23 Conclusion: A methodology based on Markov chain models and network analytic metrics can help detect the relevant signal within large, highly interdependent and noisy data sets and, for applications such as enrichment analysis, has been shown to generate superior performance on both real and simulated data relative to existing state-of-the-art approaches. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5657267 Fri, 03 Feb 2012 05:00:00 +0100 5657267 http://www.medworm.com/index.php?rid=5657266&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F24 Conclusions: On simulation studies and real data sets, we showed that IPCA offers a better visualization of thedata than ICA and with a smaller number of components than PCA. Furthermore, a preliminary investigation of the list of genes selected with sIPCA demonstrate that the approach is well able to highlight relevant genes inthe data with respect to the biological experiment.IPCA and sIPCA are both implemented in the R package mixOmics dedicated to the analysis and exploration ofhigh dimensional biological data sets, and on mixOmics' web-interface. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5657266 Fri, 03 Feb 2012 05:00:00 +0100 5657266 http://www.medworm.com/index.php?rid=5657268&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F22 Conclusions: Large datasets should be used to obtain reliable measures of the accuracy of RNA structure prediction algorithms, and average accuracies on specific classes (such as Group I introns and Transfer RNAs) should be interpreted with caution, considering the relatively small size of currently available datasets for such classes. The accuracy of the MEA-based methods is significantly higher when using the BL* parameter set of Andronescu et al. than when using the parameters of Mathews and Turner, and there is no significant difference between the accuracy of MEA-based methods and MFE when using the BL* parameters. The pseudo-MEA-based method of Hamada et al. with the BL* parameter set significantly outperforms all other MFE and MEA-based algorithms on our large data sets. (Source: BM... BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5657268 Wed, 01 Feb 2012 05:00:00 +0100 5657268 http://www.medworm.com/index.php?rid=5644438&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F19 Conclusions: The InteractomeBrowser plugin is a powerful tool to get quick access to a knowledge database that includes both predicted and validated molecular interactions. InteractomeBrowser is available through the TranscriptomeBrowser framework and can be found at : http://tagc.univ-mrs.fr/tbrowser/. Our database is updated on a regular basis. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5644438 Tue, 31 Jan 2012 05:00:00 +0100 5644438 http://www.medworm.com/index.php?rid=5644437&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F20 Conclusions: graphite is an innovative package able to gather and make easily available the contents of the four major pathway databases. In the field of topological analysis graphite acts as a provider of biological information by reducing the pathway complexity considering the biological meaning of the pathway elements. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5644437 Tue, 31 Jan 2012 05:00:00 +0100 5644437 http://www.medworm.com/index.php?rid=5644436&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F21 Background: live cell imaging is a useful tool to monitor cellular activities in living systems. It is often necessary in cancer research or experimental research to quantify the dividing capabilities of cells or the cell proliferation level when investigating manipulations of the cells or their environment. Manual quantification of fluorescence microscopic image is difficult because human is neither sensitive to fine differences in color intensity nor effective to count and average fluorescence level among cells. However, auto-quantification is not a straightforward problem to solve. As the sampling location of the microscopy changes, the amount of cells in individual microscopic images varies, which makes simple measurement methods such as the sum of stain intensity values or the total n... BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5644436 Tue, 31 Jan 2012 05:00:00 +0100 5644436 http://www.medworm.com/index.php?rid=5644440&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F17 Conclusions: We conclude that an SSC can be a viable alternative for or a supplement to a GSC when training chunkers in a biomedical domain. A combined system only shows improvement if the SSC is used to supplement a GSC. Whether the approach is applicable to other systems in a natural-language processing pipeline has to be further investigated. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5644440 Mon, 30 Jan 2012 05:00:00 +0100 5644440 http://www.medworm.com/index.php?rid=5644439&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F18 Conclusions: Semantic propagation and model alignment are included in the open-source library semanticSBML, available on sourceforge. Online services for model alignment and for annotation prediction can be used at http://www.semanticsbml.org. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5644439 Mon, 30 Jan 2012 05:00:00 +0100 5644439 http://www.medworm.com/index.php?rid=5636053&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F15 Conclusions: The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at http://cubique.concordia.ca/enzymedb/index.html under the GNU GPLv3 licence. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5636053 Thu, 26 Jan 2012 05:00:00 +0100 5636053 http://www.medworm.com/index.php?rid=5625337&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F14 Conclusions: CAT3 is a powerful tool that is a clear improvement over existing similar tools, especially in reducing the false positive rate. Human proteome screening, using CAT3, indicate the presence of a large number of possible caspase-3 substrates that exceed the anticipated figure. In addition to their involvement in various expected functions such as cytoskeleton organization, nuclear integrity and adhesion, a large number of the predicted substrates are remarkably associated with the development of nerve tissues. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5625337 Mon, 23 Jan 2012 05:00:00 +0100 5625337 http://www.medworm.com/index.php?rid=5617659&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F13 Conclusions: We have developed an extension of the TDT statistic (TDT-HET) that allows for locus heterogeneity among coded trios. Benefits of our method include: estimates of parameters in the presence of heterogeneity, and reasonable power even when the proportion of linked trios is small. Also, we have extended multi-locus methods to TDT-HET and have demonstrated that the empirical power may be high to detect linkage. Last, given that we obtain PPBs, we conjecture that the TDT-HET may be a useful method for correctly identifying linked trios. We anticipate that researchers will find this property increasingly useful as they apply next-generation sequencing data in family based studies. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5617659 Fri, 20 Jan 2012 05:00:00 +0100 5617659 http://www.medworm.com/index.php?rid=5604894&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F12 Conclusions: COMBINER can efficiently and robustly identify disease core module genes and construct their associated regulatory network. In the same way, it is potentially applicable in the characterization of any disease that can be probed with microarrays. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5604894 Wed, 18 Jan 2012 05:00:00 +0100 5604894 http://www.medworm.com/index.php?rid=5594136&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F11 Conclusions: Cross profile analysis reveals the polyphyletic and convergent evolution of beta-hairpin-like structures, which were verified both experimentally and computationally. The results presented here give us new insights into the evolution of short protein segments. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5594136 Mon, 16 Jan 2012 05:00:00 +0100 5594136 http://www.medworm.com/index.php?rid=5594138&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F9 Conclusions: PyElph decreases the effort and time spent processing data from gel images by providing an automatic step-by-step gel image analysis system with a friendly Graphical User Interface. The proposed free software tool is suitable for researchers and students which do not have access to expensive commercial software and image acquisition devices. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5594138 Fri, 13 Jan 2012 05:00:00 +0100 5594138 http://www.medworm.com/index.php?rid=5594137&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F10 Conclusions: Results demonstrate MIPHENO offers substantial benefit in improving the ability to detect putative mutant phenotypes from post-hoc analysis of large data sets. Additionally, it facilitates data interpretation and permits cross-dataset comparison where group-based controls are missing. MIPHENO is applicable to a wide range of high throughput screenings and the code is freely available as Additional file 1 as well as through an R package in CRAN. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5594137 Fri, 13 Jan 2012 05:00:00 +0100 5594137 http://www.medworm.com/index.php?rid=5594139&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F8 The Atlas2 is an analysis suite for variant calling in whole exome sequencing that combines regression models and user-adjustable cutoffs in order to separate true SNPs and INDELs from sequencing and mapping errors, with high sensitivity (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5594139 Thu, 12 Jan 2012 05:00:00 +0100 5594139 http://www.medworm.com/index.php?rid=5594142&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F5 Conclusions: With proTRAC we provide a reliable tool for detection, visualization and analysis of piRNA clusters. Detected clusters are well supported by comprehensible probabilistic parameters and retain a maximum amount of information, thus overcoming the present conflict of sensitivity and specificity in piRNA cluster detection. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5594142 Tue, 10 Jan 2012 05:00:00 +0100 5594142 http://www.medworm.com/index.php?rid=5594141&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F6 Conclusions: The standardization in description allows for the direct comparison of the metabolite and reaction content between metabolic models and databases and the exhaustive prospecting of pathways for biotechnological production. This ever-growing dataset currently consists of over 76,000 metabolites participating in more than 72,000 reactions (including unresolved entries). MetRxn is hosted on a web-based platform that uses relational database models (MySQL). (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5594141 Tue, 10 Jan 2012 05:00:00 +0100 5594141 http://www.medworm.com/index.php?rid=5594140&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F7 Conclusion: We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5594140 Tue, 10 Jan 2012 05:00:00 +0100 5594140 http://www.medworm.com/index.php?rid=5569808&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F4 Conclusions: Experimental results show that the structural features are differentially correlated with promoters. Specifically, DNA-bending stiffness, DNA denaturation and energy-related features are highly correlated with promoters. The predictive power for promoter sequences differentiates greatly among different structural features. Selecting the relevant features can significantly improve the accuracy of promoter prediction. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5569808 Sat, 07 Jan 2012 05:00:00 +0100 5569808 http://www.medworm.com/index.php?rid=5569809&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F3 Conclusions: We conclude that the proposed methodology can ease the burden of chemical data annotators and dramatically increase their productivity. We anticipate that the use of formal logic in our proposed framework will make chemical classification criteria more transparent to humans and machines alike and will thus facilitate predictive and integrative bioactivity model development. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5569809 Fri, 06 Jan 2012 05:00:00 +0100 5569809 http://www.medworm.com/index.php?rid=5569810&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F2 Conclusions: ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5569810 Thu, 05 Jan 2012 05:00:00 +0100 5569810 http://www.medworm.com/index.php?rid=5569811&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F13%2F1 Conclusions: GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The latest version of the software available as an executable (for PC) at www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5569811 Tue, 03 Jan 2012 05:00:00 +0100 5569811 http://www.medworm.com/index.php?rid=5557052&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F493 Conclusions: With more and more reference genomes available, our strategy will be useful to improve qualities of genome assemblies from very short reads. Some scripts are provided to make our strategy applicable at http://code.google.com/p/cd-hybrid/. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5557052 Fri, 30 Dec 2011 05:00:00 +0100 5557052 http://www.medworm.com/index.php?rid=5557051&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F494 Conclusions: The defined track types are shown to capture relevant distinctions between genomic annotation tracks, resulting in varying representational needs and analysis possibilities. The proposed formats, GTrack 1.0 and BioXSD 1.1, cater to the identified track distinctions and emphasize preciseness, flexibility and parsing convenience. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5557051 Fri, 30 Dec 2011 05:00:00 +0100 5557051 http://www.medworm.com/index.php?rid=5557050&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F495 Conclusions: MotifMap and its integration with other data provide a foundation for analyzing gene regulation on a genome-wide scale, and for automatically generating regulatory pathways and hypotheses.The power of this approach is demonstrated and discussed using the P53 apoptotic pathway and the Gli hedgehog pathway as examples. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5557050 Fri, 30 Dec 2011 05:00:00 +0100 5557050 http://www.medworm.com/index.php?rid=5557049&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F496 Conclusions: We propose an additive mixture model of a sample for feature extraction using, in principle, sparseness constrained factorization on a sample-by-sample basis. As opposed to that, existing methods factorize complete dataset simultaneously. The sample model is composed of a reference sample representing control and/or case (disease) groups and a test sample. Each sample is decomposed into two or more components that are selected automatically (without using label information) as control specific, case specific and not differentially expressed (neutral). The number of components is determined by cross-validation. Automatic assignment of features (m/z ratios or genes) to particular component is based on thresholds estimated from each sample directly. Due to the locality of decompo... BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5557049 Fri, 30 Dec 2011 05:00:00 +0100 5557049 http://www.medworm.com/index.php?rid=5557048&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F497 Conclusions: We show that the PDM is a useful tool for the analysis of gene expression data from complex diseases, where phenotypes are not linearly separable and multi-gene effects are likely to play a role. Our results demonstrate that the PDM is able to distinguish cell types and treatments with higher accuracy than is obtained through other approaches, and that the Pathway-PDM application is a valuable technique for identifying disease--associated pathways. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5557048 Fri, 30 Dec 2011 05:00:00 +0100 5557048 http://www.medworm.com/index.php?rid=5534434&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F489 Conclusions: Our experiments with RPISeq demonstrate that RNA-protein interactions can be reliably predicted using only sequence-derived information. RPISeq offers an inexpensive method for computational construction of RNA-protein interaction networks, and should provide useful insights into the function of non-coding RNAs. RPISeq is freely available as a web-based server at http://pridb.gdcb.iastate.edu/RPISeq/. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5534434 Thu, 22 Dec 2011 05:00:00 +0100 5534434 http://www.medworm.com/index.php?rid=5534433&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F490 Conclusions: We illustrate the advantages of Antelope when (a) modeling incomplete networks and environment interaction, (b) exhibiting the set of all states having a given property, and (c) representing Boolean GRN properties with hybrid CTL. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5534433 Thu, 22 Dec 2011 05:00:00 +0100 5534433 http://www.medworm.com/index.php?rid=5534432&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F491 Conclusions: MAKER2 is the first annotation engine specifically designed for second-generation genome projects. MAKER2 scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality. It can also update and manage legacy genome annotation datasets. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5534432 Thu, 22 Dec 2011 05:00:00 +0100 5534432 http://www.medworm.com/index.php?rid=5534436&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F487 Conclusions: Organizing metadata for cell imaging experiments under a framework of rules that include highly reused root terms will facilitate the addition of new terms into a vocabulary hierarchy and encourage the reuse of terms. These vocabulary hierarchies can be converted into XML schema or RDF graphs for displaying and querying, but this is not necessary for using it to annotate cell images. Vocabulary data trees from multiple experiments or laboratories can be aligned at the root terms to facilitate query development. This approach of developing vocabularies is compatible with the major advances in database technology and could be used for building the Semantic Web. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5534436 Wed, 21 Dec 2011 05:00:00 +0100 5534436 http://www.medworm.com/index.php?rid=5534435&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F488 Conclusions: Fusion of mRNA and miRNA expression data into one prediction model improves clinical outcome prediction in terms of prediction error and stable feature selection. The R source code of the proposed method is available in the supplement. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5534435 Wed, 21 Dec 2011 05:00:00 +0100 5534435 http://www.medworm.com/index.php?rid=5534437&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F486 Conclusions: While interannotator agreement in the practice phase confirms that conceptual annotation is a challenging task, the increasing agreement in the main annotation phase points out that an acceptable level of agreement can be achieved in multiple iterations, by setting stricter guidelines and establishing semantic equivalence criteria. Mapping text to ontological concepts emerges as the main challenge in conceptual annotation. Annotating predications involving biomolecular entities and processes is particularly challenging. While the resulting gold standard is mainly intended to serve as a test collection for our semantic interpreter, we believe that the lessons learned are applicable generally. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5534437 Tue, 20 Dec 2011 05:00:00 +0100 5534437 http://www.medworm.com/index.php?rid=5521007&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F484 Conclusion: While subtyping is often performed with genome-wide molecular data, we have shown that it can also be applied to categorizing histology sections. Accordingly, we have identified a subtype that is a predictor of the outcome as a result of a therapeutic regime. Computed representation has become publicly available through our Web site. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5521007 Tue, 20 Dec 2011 05:00:00 +0100 5521007 http://www.medworm.com/index.php?rid=5521006&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F485 Conclusions: Using a cell-based analysis and normalization for population context, we achieve improved sensitivity and specificity not only on a individual protein level, but especially also on a pathway level. This leads to the identification of new host dependency factors of the hepatitis C and dengue viruses and higher reproducibility of results. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5521006 Tue, 20 Dec 2011 05:00:00 +0100 5521006 http://www.medworm.com/index.php?rid=5521008&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F483 Conclusions: The classifier performance in the SRCCA space was found to be statistically significantly higher compared to the fused data representations obtained, not only from CCA and RCCA, but also two other statistical techniques called Principal Component Analysis and Partial Least Squares Regression. These results suggest that SRCCA is a computationally efficient and a highly accurate scheme for representing multimodal (histologic and proteomic) data in a metaspace and that it could be used to construct fused biomarkers for predicting disease recurrence and prognosis. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5521008 Mon, 19 Dec 2011 05:00:00 +0100 5521008 http://www.medworm.com/index.php?rid=5521009&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F481 Conclusions: While individual event extraction systems themselves provide useful features for bio text mining, the U-Compare meta-service is expected to improve the accessibility to the individual systems, and to enable meta-level uses over multiple event extraction systems such as comparison and ensemble. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5521009 Sun, 18 Dec 2011 05:00:00 +0100 5521009 http://www.medworm.com/index.php?rid=5513094&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F480 The combination of three different strategies for GC-content normalization of RNA-seq data leads to more accurate estimations of gene expression levels and fold-changes, making statistical inference of differential expression less prone to false discoveries. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5513094 Sat, 17 Dec 2011 05:00:00 +0100 5513094 http://www.medworm.com/index.php?rid=5513096&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F478 Conclusions: The preclustering information enables a more detailed analysis of the biological meaning of covariates selected in the final models. Compared to models built only with single genes there is additional functional information contained in the GO annotation, and compared to models using GO groups as covariates the preclustering yields coherent representative gene expression profiles. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5513096 Fri, 16 Dec 2011 05:00:00 +0100 5513096 http://www.medworm.com/index.php?rid=5513095&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F479 Conclusion: NanoStriDE allows biologists to take raw data produced by a NanoString nCounter analysis system and easily interpret differential expression analysis of this data represented through a heatmap. NanoStriDE is freely accessible to use on the NanoStriDE website and is available to use under the GPL v2 license. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5513095 Fri, 16 Dec 2011 05:00:00 +0100 5513095 http://www.medworm.com/index.php?rid=5513100&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F474 Conclusions: This method provides a simple, unambiguous mapping to allow assessment of the expression levels of specific genes of interest. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5513100 Thu, 15 Dec 2011 05:00:00 +0100 5513100 http://www.medworm.com/index.php?rid=5513099&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F475 Conclusions: None of selected methods is perfect in all scenarios and each has its own merits and limitations. In terms of detection power, AntEpiSeeker performs best on detecting epistasis displaying marginal effects (eME) and BOOST performs best on identifying epistasis displaying no marginal effects (eNME). In terms of robustness, AntEpiSeeker is robust to all types of noise on eME models, BOOST is robust to genotyping error and phenocopy on eNME models, and SNPRuler is robust to phenocopy on eME models and missing data on eNME models. In terms of sensitivity, AntEpiSeeker is the winner on eME models and both SNPRuler and BOOST perform well on eNME models. In terms of computational complexity, BOOST is the fastest among the methods. In terms of overall performance, AntEpiSeeker and BOOS... BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5513099 Thu, 15 Dec 2011 05:00:00 +0100 5513099 http://www.medworm.com/index.php?rid=5513098&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F476 Conclusion: Balanced profiles are superior to the raw profiles employed by traditional methods of phylogenetic profiling in searching for high order gene sets. Gene triplets can provide valuable information in detection of biological network organization and identification of key genes at different levels of cellular interaction. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5513098 Thu, 15 Dec 2011 05:00:00 +0100 5513098 http://www.medworm.com/index.php?rid=5513097&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F477 Conclusion: Rather than characterizing HIV-1 susceptibility toward each PI individually, our study offers a unique perspective on the phenomenon of PI class resistance by uncovering major multidrug-resistant phenotypic patterns and their often diverse genotypic determinants, providing a methodology that can be applied to understand clinically-relevant phenotypic patterns to aid in the design of novel inhibitors that target other rapidly evolving molecular targets as well. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5513097 Thu, 15 Dec 2011 05:00:00 +0100 5513097 http://www.medworm.com/index.php?rid=5501857&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F471 Conclusion: The previous version, MeInfoText, was developed by using association rules, whereas MeInfoText 2.0 is based on a new framework that combines machine learning, dictionary lookup and pattern matching for epigenetics information extraction. The results of experiments show that MeInfoText 2.0 outperforms existing tools in many respects. To the best of our knowledge, this is the first study that uses a hybrid approach to extract gene methylation-cancer relations. It is also the first attempt to develop a gene methylation and cancer relation corpus. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5501857 Wed, 14 Dec 2011 05:00:00 +0100 5501857 http://www.medworm.com/index.php?rid=5501856&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F472 Conclusion: MSACompro is an efficient and reliable multiple protein sequence alignment tool that can effectively incorporate predicted protein structural information into multiple sequence alignment. The software is available at http://sysbio.rnet.missouri.edu/multicom_toolbox/. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5501856 Wed, 14 Dec 2011 05:00:00 +0100 5501856 http://www.medworm.com/index.php?rid=5501855&cid=s_34020_79_f&fid=34020&url=%24%7Bitem.link%7D Conclusions: When estimating bacterial diversity, ESPRIT as well as the web-based workflow, RDP pyrosequencing pipeline, produced good results in all circumstances, however, its computational requirements can make method-combination workflows more attractive, depending on sequence variability, number and length. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5501855 Wed, 14 Dec 2011 05:00:00 +0100 5501855 http://www.medworm.com/index.php?rid=5501858&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F470 Conclusions: We address three major issues pertaining to large scale tree reconstruction under maximum likelihood and propose respective solutions. Respective proof-of-concept/production-level implementations of our ideas are made available as open-source code. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5501858 Tue, 13 Dec 2011 05:00:00 +0100 5501858 http://www.medworm.com/index.php?rid=5501859&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F469 Conclusions: SNPInterForest, offering an efficient means to detect epistatic interactions without statistical analyses, is promising for practical use as a way to reveal the epistatic interactions involved in common complex diseases. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5501859 Mon, 12 Dec 2011 05:00:00 +0100 5501859 http://www.medworm.com/index.php?rid=5493054&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F468 Conclusions: openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, flexibility to handle any biological data type and extensibility to the needs of any research domain. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5493054 Thu, 08 Dec 2011 05:00:00 +0100 5493054 http://www.medworm.com/index.php?rid=5474080&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F465 Conclusions: We use two different models to analyze the accuracy and eight experiments to investigate the speed of the threealgorithms. We find that they havesimilar accuracy and that EXPM is the slowestmethod. Furthermore we find that UNI isusually faster than EVD. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5474080 Mon, 05 Dec 2011 05:00:00 +0100 5474080 http://www.medworm.com/index.php?rid=5465870&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F464 Conclusions: Converting probe intensities to estimates of target concentrations prior to the statistical analysis, AffyILM(medianpolish) is one of the best performing strategy currently available. Using hybridization theory, probe-level estimates of target concentrations should be identically distributed. In the future, a probe-level multivariate analysis of the concentrations should be compared to the univariate analysis of probe-set summarized expression data. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5465870 Fri, 02 Dec 2011 05:00:00 +0100 5465870 http://www.medworm.com/index.php?rid=5465871&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F463 Conclusions: We found sufficiently large and strong predictive signatures only for distinguishing ER-positive from ER-negative cancers, there were no strong signatures for more subtle prediction problems. Current statistical methods efficiently identify highly informative features in gene expression data if such features exist and accurate models can be built with as few as 10 highly informative features. Features can be considered highly informative if at least 2-fold expression difference exists between comparison groups but such features do not appear to be common for many clinically relevant prediction problems in human data sets. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5465871 Thu, 01 Dec 2011 05:00:00 +0100 5465871 http://www.medworm.com/index.php?rid=5465872&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F462 Conclusions: The presented method adjusts for signal saturation at the segmentation stage that identifies a pixel as part of the foreground, background or other. The cluster membership of a pixel can be altered versus treating saturated values as truly observed. Thus, the resulting spot intensity estimates may be more accurate than those obtained from existing methods that correct for saturation based on already segmented data. As a model-based segmentation method, our procedure is able to identify inner holes, fuzzy edges and blank spots that are common in microarray images. The approach is independent of microarray platform and applicable to both single- and dual-channel microarrays. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5465872 Wed, 30 Nov 2011 05:00:00 +0100 5465872 http://www.medworm.com/index.php?rid=5465873&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F461 Conclusions: The SPF provides a unified framework to effectively manage provenance of translational research data during pre and post-publication phases. This framework is underpinned by an upper-level provenance ontology called Provenir that is extended to create domain-specific provenance ontologies to facilitate provenance interoperability, seamless propagation of provenance, automated querying, and analysis. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5465873 Tue, 29 Nov 2011 05:00:00 +0100 5465873 http://www.medworm.com/index.php?rid=5454545&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F460 Conclusions: To the best of our knowledge, a corpus that details such a wide range of biological concepts has never been presented to the text mining community. The inter-annotator agreement statistics provide evidence of the importance of a consolidated background when dealing with such complex descriptions, the ambiguities naturally arising from the terminology and their impact for modelling purposes.Availability is granted for the full-text corpora of 130 freely accessible documents, the annotation scheme and the annotation guidelines. Also, we include a corpus of 340 abstracts. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5454545 Mon, 28 Nov 2011 05:00:00 +0100 5454545 http://www.medworm.com/index.php?rid=5448080&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F458 Conclusions: Integrating causal information into gene selection algorithms is effective both in terms of prediction accuracy and biological interpretation. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5448080 Fri, 25 Nov 2011 05:00:00 +0100 5448080 http://www.medworm.com/index.php?rid=5448079&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F459 Conclusions: In this work we show that consideration of data from multiple platforms, in conjunction with summarization via a priori pathway information, leads to increased power in detection of genomic associations with phenotypes. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5448079 Fri, 25 Nov 2011 05:00:00 +0100 5448079 http://www.medworm.com/index.php?rid=5448084&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F454 Conclusion: The coupling of two parts: a sensitive Ab-Initio module and a selective machine learning part capable of recognizing the false positives, leads to an improved balance between sensitivity and specificity. miREE obtains a reasonable trade-off between filtering false positives and identifying targets.miREE tool is available online at http://didattica-online.polito.it/eda/miREE/ (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5448084 Thu, 24 Nov 2011 05:00:00 +0100 5448084 http://www.medworm.com/index.php?rid=5448083&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F455 Conclusions: The package allows the user to control how these issues are dealt with and communicate them via an R-script written using the iRefR package - this will facilitate communication of methods, reproducibility of network analyses and further modification and comparison of methods by researchers. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5448083 Thu, 24 Nov 2011 05:00:00 +0100 5448083 http://www.medworm.com/index.php?rid=5448082&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F456 Conclusions: The current OWL releases of OBO Foundry (and Foundry candidate) ontologies contain numerous assertions which do not properly describe the underlying biological reality, or are ambiguous and difficult to interpret. The solution is a better anchoring in upper ontologies and a restriction to relatively few, well defined relation types with given domain and range constraints. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5448082 Thu, 24 Nov 2011 05:00:00 +0100 5448082 http://www.medworm.com/index.php?rid=5448081&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F457 Conclusions: We show in this paper that well-fitted matrices can improve the predictions of orthologous and homologous relationships among proteins with a similar compositional bias. With the ever-increasing number of sequenced genomes, our approach could prove valuable in numerous comparative studies focusing on atypical genomes. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5448081 Thu, 24 Nov 2011 05:00:00 +0100 5448081 http://www.medworm.com/index.php?rid=5437824&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F453 Conclusion: We compared performances of iAssembler and several other de novo EST assembly programs using both Roche-454 and Sanger EST datasets. It demonstrated that iAssembler generated significantly more accurate consensus sequences than other assembly programs. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5437824 Wed, 23 Nov 2011 05:00:00 +0100 5437824 http://www.medworm.com/index.php?rid=5437826&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F451 Conclusions: Systematic errors can easily be mistaken for heterozygous sites in individuals, or for SNPs in population analyses. Systematic errors are particularly problematic in low coverage experiments, or in estimates of allele-specific expression from RNA-Seq data. Our characterization of systematic error has allowed us to develop a program, called SysCall, for identifying and correcting such errors. We conclude that correction of systematic errors is important to consider in the design and interpretation of high-throughput sequencing experiments. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5437826 Mon, 21 Nov 2011 05:00:00 +0100 5437826 http://www.medworm.com/index.php?rid=5437825&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F452 Conclusion: The web-based framework eXframe offers structured annotation of experiments as well as uniform processing and storage of molecular data from microarray and next generation sequencing platforms. The framework allows users to query and integrate information across species, technologies, measurement types and experimental conditions. Our framework is reusable and freely modifiable - other groups or institutions can deploy their own custom web-based repositories based on this software. It is interoperable with the most important data formats in this domain. We hope that other groups will not only use eXframe, but also contribute their own useful modifications. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5437825 Mon, 21 Nov 2011 05:00:00 +0100 5437825 http://www.medworm.com/index.php?rid=5418661&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F450 Conclusions: Given the superiority of Random KNN in classification performance when compared with Random Forests, RKNN-FS's simplicity and ease of implementation, and its superiority in speed and stability, we propose RKNN-FS as a faster and more stable alternative to Random Forests in classification problems involving feature selection for high-dimensional datasets. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5418661 Fri, 18 Nov 2011 05:00:00 +0100 5418661 http://www.medworm.com/index.php?rid=5418662&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F449 Conclusions: By combining datasets from many studies and providing data that has already been processed from .fastq format into ready-to-use .RData and .txt files, ReCount facilitates analysis and methods development for RNA-seq count data. We anticipate that ReCount will also be useful for investigators who wish to consider cross-study comparisons and alternative normalization strategies for RNA-seq. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5418662 Wed, 16 Nov 2011 05:00:00 +0100 5418662 http://www.medworm.com/index.php?rid=5418665&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F446 Conclusions: A computational method POPISK is proposed to predict immunogenicity with scores which are useful for predicting immunogenicity changes made by single-residue modifications. The web server of POPISK is freely available at http://iclab.life.nctu.edu.tw/POPISK. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5418665 Tue, 15 Nov 2011 05:00:00 +0100 5418665 http://www.medworm.com/index.php?rid=5418664&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F447 Conclusions: OmniMapFree provides a unified, versatile and easy-to-use software tool for studying a single genome in association with all the other datasets and data types available for the organism. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5418664 Tue, 15 Nov 2011 05:00:00 +0100 5418664 http://www.medworm.com/index.php?rid=5418663&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F448 Conclusion: Sparse simultaneous component analysis is a useful method for data integration: First, simultaneous analyses of multiple blocks offer advantages over sequential and separate analyses and second, interpretation of the results is highly facilitated by their sparseness. The approach offered is flexible and allows to take the block structure in different ways into account. As such, structures can be found that are exclusively tied to one data platform (group lasso approach) as well as structures that involve all data platforms (Elitist lasso approach).AvailabilityThe additional file contains a MATLAB implementation of the sparse simultaneous component method. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5418663 Tue, 15 Nov 2011 05:00:00 +0100 5418663 http://www.medworm.com/index.php?rid=5418666&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F445 Conclusions: We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the first to utilize model polymers to rigorously test the utility of clustering algorithms for studying biopolymers. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5418666 Mon, 14 Nov 2011 05:00:00 +0100 5418666 http://www.medworm.com/index.php?rid=5404983&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F442 Conclusions: We have successfully developed an accurate prediction system for screening effectors on a genome-wide scale. We confirmed the accuracy of our system by external validation using known effectors of Salmonella and obtained the accurate list of putative effectors of the organism. The level of accuracy was sufficient to yield candidates for gene-directed experimental verification. Furthermore, new features of effectors were revealed: non-optimal codon usage and instability of the N-terminal region. From these findings, a new working hypothesis is proposed regarding mechanisms controlling the translocation of virulence effectors and determining the substrate specificity encoded in the secretion system. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5404983 Mon, 14 Nov 2011 05:00:00 +0100 5404983 http://www.medworm.com/index.php?rid=5404982&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F443 Conclusions: SIGNATURE is available for public use at http://genepattern.genome.duke.edu/signature/. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5404982 Mon, 14 Nov 2011 05:00:00 +0100 5404982 http://www.medworm.com/index.php?rid=5404981&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F444 Conclusions: A novel method is presented, which uses regularized multinomialregression in order to obtain correlated mutations from protein multiple sequencealignments.AvailabilityR-code of our implementation is available via www.ab.wur.nl/rmrcmContact: aaltjan.vandijk@wur.nl (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5404981 Mon, 14 Nov 2011 05:00:00 +0100 5404981 http://www.medworm.com/index.php?rid=5404985&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F439 Conclusions: SCFIA can be used for accurate corresponding feature identification in LC-MS. We have shown that peak shape correlation can be used effectively for improving the accuracy. SCFIA provides high coverage in corresponding feature identification in multiple datasets, which serves the basis for integrating multiple LC-MS measurements for accurate peptide quantification. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5404985 Fri, 11 Nov 2011 05:00:00 +0100 5404985 http://www.medworm.com/index.php?rid=5404984&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F440 Conclusion: Thus, we have proposed a methodology that can identify potential statistically significant phenotype-related functional modules. The functional module is modeled as an (alpha,beta)-clique, where alpha and beta are two criteria introduced in this work. We also propose a novel network model, called the two-typed, divided network. The new network model and the criteria make the problem tractable even while very large networks are being compared. The code can be downloaded from http://www.freescience.org/cs/ABClique/ (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5404984 Fri, 11 Nov 2011 05:00:00 +0100 5404984 http://www.medworm.com/index.php?rid=5397622&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F438 Conclusions: CDEP is a flexible approach that borrows information from each dataset in a meta-analysis in order to identify genes being differentially expressed consistently. We have shown that CDEP can gain higher statistical power than other existing approaches under a variety of settings considered in the simulation study, suggesting its robustness and insensitivity to data variation commonly associated with microarray experiments.AvailabilityCDEP is implemented in R and freely available at: http://genomebioinfo.musc.edu/CDEP/Contact: zhengw@musc.edu (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5397622 Fri, 11 Nov 2011 05:00:00 +0100 5397622 http://www.medworm.com/index.php?rid=5397623&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F437 Conclusions: The iterative approach is more likely to reflect the real biological nature between proteins when predicting functions. A proper definition of protein similarity from protein functions is the key to predicting functions iteratively. The evaluation results demonstrated that in most cases, the iterative approach outperformed non-iterative ones with higher prediction quality in terms of prediction precision, recall and F-value. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5397623 Thu, 10 Nov 2011 05:00:00 +0100 5397623 http://www.medworm.com/index.php?rid=5397626&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F434 Conclusion: ProPhylo results show universal markers of methanogenesis, a new DNA phosphorothioation-dependent restriction enzyme, and efficacy in guiding protein family construction. The software and the associated databases are freely available under the open source Perl Artistic License from ftp://ftp.jcvi.org/pub/data/ppp/. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5397626 Wed, 09 Nov 2011 05:00:00 +0100 5397626 http://www.medworm.com/index.php?rid=5397625&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F435 Conclusions: PESCADOR is a platform independent web resource available at: http://cbdm.mdc-berlin.de/tools/pescador/ (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5397625 Wed, 09 Nov 2011 05:00:00 +0100 5397625 http://www.medworm.com/index.php?rid=5397624&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F436 Conclusions: The Cytoscape plugin clusterMaker provides a number of clustering algorithms and visualizations that can be used independently or in combination for analysis and visualization of biological data sets, and for confirming or generating hypotheses about biological function. Several of these visualizations and algorithms are only available to Cytoscape users through the clusterMaker plugin. clusterMaker is available via the Cytoscape plugin manager. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5397624 Wed, 09 Nov 2011 05:00:00 +0100 5397624 http://www.medworm.com/index.php?rid=5397627&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F433 Conclusions: The two-component EB model is a very useful for large-scale hypothesis testing. In proteomic analysis, the theoretical null density is often not appropriate. We demonstrate how to implement a two-component EB model for analyzing a set of 2D gel images. We show that it is necessary to estimate the mixture density and empirical null component simultaneously. The proposed constrained estimation method always yields valid estimates and more stable results. The proposed estimation approach proposed can be applied to other contexts where large-scale hypothesis testing occurs. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5397627 Tue, 08 Nov 2011 05:00:00 +0100 5397627 http://www.medworm.com/index.php?rid=5397628&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F432 Conclusion: We describe implementation of a parallel method for generating mass distributions of all theoretically possible amino acid compositions. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5397628 Mon, 07 Nov 2011 05:00:00 +0100 5397628 http://www.medworm.com/index.php?rid=5376941&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F429 Conclusions: We find that search space granularity affects the computed shape probabilities less than the over- or underapproximation of free energy by a simplified energy model.Still, the approximations perform similar enough to implementations of the full model to justify their continued use in settings where computational constraints call for simpler algorithms.On the side, we observe that the rarely used level 2 shapes, which predict the complete arrangement of helices, multiloops, internal loops and bulges, include the "true" shape in a rather small number of predicted high probability shapes.This calls for an investigation of new strategies to extract high probability members from the (very large) level 2 shape space of an RNA sequence.We provide implementations of all four models, w... BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5376941 Thu, 03 Nov 2011 04:00:00 +0100 5376941 http://www.medworm.com/index.php?rid=5376940&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F430 Conclusions: We demonstrated that periodic signals can be estimated using cross-correlation. In addition, discrete wavelet transform (DWT) can minimise noise while maintaining the signal. The proposed algorithm, which combines cross-correlation and DWT, significantly increases the accuracy of exonic region identification. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5376940 Thu, 03 Nov 2011 04:00:00 +0100 5376940 http://www.medworm.com/index.php?rid=5376939&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F431 Conclusions: This work is a step toward developing a unified framework for the systematic study of GO functional annotations. This framework has been designed so that new metrics on GO functional annotations can be added in a very straightforward way. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5376939 Thu, 03 Nov 2011 04:00:00 +0100 5376939 http://www.medworm.com/index.php?rid=5376942&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F428 Conclusions: We test our approximate sampling method on simulated and biological ArrayCGH datasets and high-density SNP arrays, and demonstrate a speed-up of 10 to 60 respectively 90 while achieving competitive results with the state-of-the art Bayesian approaches.AvailabilityAn implementation of our method will be made available as part of the open source GHMM library from http://ghmm.org. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5376942 Wed, 02 Nov 2011 04:00:00 +0100 5376942 http://www.medworm.com/index.php?rid=5376944&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F426 Conclusions: Compared to the maximum likelihood method, the Bayesian approach can produce more accurate estimates of the parameters in the birth and death model. In addition, the Bayesian hypothesis test is able to identify unlikely gene families based on Bayesian posterior p-values. As a powerful statistical technique, the Bayesian approach can effectively extract information from gene family data and thereby provide useful information regarding the evolutionary process of gene families across genomes. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5376944 Tue, 01 Nov 2011 04:00:00 +0100 5376944 http://www.medworm.com/index.php?rid=5376943&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F427 Conclusions: The F-like test statistic that uses the proposed flexible shrinkage error estimator considering both types of gene heteroscedasticity and unrestricted residual permutation can provide a statistically valid and powerful test. Therefore, we recommended that it should always applied in the analysis of real gene expression data analysis to test an interaction term. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5376943 Tue, 01 Nov 2011 04:00:00 +0100 5376943 http://www.medworm.com/index.php?rid=5376945&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F425 Conclusions: MolabIS is designed for small-to-medium sized labs conducting Sanger sequencing and microsatellite genotyping to store and efficiently handle a relative large amount of data. MolabIS not only helps to avoid time consuming tasks but also ensures the availability of data for further analyses. The software is packaged as a virtual appliance which can run on different platforms (e.g. Linux, Windows). MolabIS can be distributed to a wide range of molecular genetics labs since it was developed according to a general data model. Released under GPL, MolabIS is freely available at http://www.molabis.org. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5376945 Mon, 31 Oct 2011 04:00:00 +0100 5376945 http://www.medworm.com/index.php?rid=5376948&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F422 Conclusions: Our method renders a more cost-efficient classifier that is at least as good, and sometimes better, than one based on clinical or molecular data alone. Hence our approach is not just a classifier that minimizes a particular loss function. Instead, it aims to be cost-efficient by avoiding molecular tests for a potentially large subgroup of individuals; moreover, for these individuals a test result would be quickly available, which may lead to reduced waiting times (for diagnosis) and hence lower the patients distress. Stepwise classification is implemented in R-package stepwiseCM and available at the Bioconductor website. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5376948 Fri, 28 Oct 2011 04:00:00 +0100 5376948 http://www.medworm.com/index.php?rid=5376947&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F423 Conclusions: We proposed a novel statistical method, Q-FISH, for accurately identifying protein species and simultaneously quantifying the expression levels of identified peptides from mass spectrometry data. Q-FISH analysis on human HCC and liver tissue samples identified many protein biomarkers that are highly relevant to HCC. Q-FISH can be a useful tool both for peptide identification and quantification on mass spectrometry data analysis. It may also prove to be more effective in discovering novel protein biomarkers than SEQUEST and other standard methods. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5376947 Fri, 28 Oct 2011 04:00:00 +0100 5376947 http://www.medworm.com/index.php?rid=5376946&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F424 Conclusions: We have combined AL with class balancing to yield a general training strategy applicable to most supervised classification problems where the dataset is expensive to obtain and which suffers from the minority class problem. An intelligent training strategy is a critical component of supervised classification, but the integration of AL and intelligent choice of class ratios, as well as the application of a general cost model, will help researchers to plan the training process more quickly and effectively. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5376946 Fri, 28 Oct 2011 04:00:00 +0100 5376946 http://www.medworm.com/index.php?rid=5356098&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F417 Conclusions: We demonstrate that the method in most cases successfully predicts the holo conforma-tion given only an apo structure. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5356098 Thu, 27 Oct 2011 04:00:00 +0100 5356098 http://www.medworm.com/index.php?rid=5356097&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F418 Conclusions: Logical definitions of terms from biomedical ontologies provide a powerful way of error- and disagreement-detection. GULO gives ontology curators a fast and simple tool for validation of their work. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5356097 Thu, 27 Oct 2011 04:00:00 +0100 5356097 http://www.medworm.com/index.php?rid=5356096&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F419 Conclusions: The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others). (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5356096 Thu, 27 Oct 2011 04:00:00 +0100 5356096 http://www.medworm.com/index.php?rid=5356095&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F420 Conclusions: The BioNOT database can be a useful resource for biomedical researchers. BioNOT is freely available at http://bionot.askhermes.org/. In future work, we will develop semantic web related technologies to enrich BioNOT. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5356095 Thu, 27 Oct 2011 04:00:00 +0100 5356095 http://www.medworm.com/index.php?rid=5356094&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F421 Conclusions: NESSY is easy to use open source software to analyze NMR relaxation data. The robustness and standard procedures are demonstrated in this article. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5356094 Thu, 27 Oct 2011 04:00:00 +0100 5356094 http://www.medworm.com/index.php?rid=5356100&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F415 Conclusions: Segtools provides a convenient, powerful means of interpreting a genomic segmentation. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5356100 Wed, 26 Oct 2011 04:00:00 +0100 5356100 http://www.medworm.com/index.php?rid=5356099&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F416 Conclusions: Compared to the available data analysis systems, SegMine offers improved hypothesis generation and data interpretation for bioinformatics in an easy-to-use integrated workflow environment. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5356099 Wed, 26 Oct 2011 04:00:00 +0100 5356099 http://www.medworm.com/index.php?rid=5356103&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F412 Conclusions: The proposed two-step method showed good results on all four CoEPrA regression tasks. Thus, it may be useful for many other biological prediction problems where for training only a small number of molecules are available, which are described by thousands of descriptors. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5356103 Tue, 25 Oct 2011 04:00:00 +0100 5356103 http://www.medworm.com/index.php?rid=5356102&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F413 Conclusion: As both fold-change magnitudes and p-values are important in the context of microarray class comparison studies, we therefore recommend to combine the Edwards correction with a hybrid transformation method that uses the log2 transformation to estimate fold-change magnitudes and the glog transformation to estimate p-values. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5356102 Tue, 25 Oct 2011 04:00:00 +0100 5356102 http://www.medworm.com/index.php?rid=5356101&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F414 Conclusions: We believe that tools like MCMC5C are essential for the reliable analysis of data from the 3C-derived techniques such as 5C and Hi-C. By integrating complex, high-dimensional and noisy datasets into an easy to interpret ensemble of three-dimensional conformations, MCMC5C allows researchers to reliably interpret the result of their assay and contrast conformations under different conditions.Availabilityhttp://Dostielab.biochem.mcgill.ca (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5356101 Tue, 25 Oct 2011 04:00:00 +0100 5356101 http://www.medworm.com/index.php?rid=5344141&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F407 Conclusions: This algorithm provides a novel way to efficiently combine co-occurrence and correlation components in biological images, thereby generating an accurate measure of co-localization. This approach of rank weighting of intensities also eliminates the need for manual thresholding of the image, which is often a cause of error in co-localization quantification. We envisage that this tool will facilitate the quantitative analysis of a wide range of biological data sets, including high resolution confocal images, live cell time-lapse recordings, and high-throughput screening data sets. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5344141 Fri, 21 Oct 2011 04:00:00 +0100 5344141 http://www.medworm.com/index.php?rid=5344140&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F408 Conclusions: Our method provides a unified framework for quantifying DNA sequence specificity and serves as a guide for development of sequence-based prediction models. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5344140 Fri, 21 Oct 2011 04:00:00 +0100 5344140 http://www.medworm.com/index.php?rid=5344143&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F405 Conclusions: The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear improvements in comparison to other methods, and the down-to-earth quantitative analysis works well for the CluPA-aligned spectra. The whole workflow is embedded into a modular and statistically sound framework that is implemented as an R package called "speaq" ("spectrum alignment and quantitation"), which is freely available from http://code.google.com/p/speaq/. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5344143 Thu, 20 Oct 2011 04:00:00 +0100 5344143 http://www.medworm.com/index.php?rid=5344142&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F406 Conclusions: Using entropy reduction as an objective criterion gives a natural way to tackle both issues of detection and localization simultaneously and to integrate intermediate phenotypic data. We foresee entropy-based strategies as a fruitful research direction for selective phenotyping. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5344142 Thu, 20 Oct 2011 04:00:00 +0100 5344142 http://www.medworm.com/index.php?rid=5331506&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F404 Conclusions: pcrEfficiency provides an easy-to-use web interface predicting PCR efficiencies prior to web lab experiments thus easing quantitative real-time PCR set-up. A web-based service as well the source code are provided freely at http://srvgen.upct.es/efficiency.html under the GPL v2 license. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5331506 Thu, 20 Oct 2011 04:00:00 +0100 5331506 http://www.medworm.com/index.php?rid=5331508&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F402 Conclusions: Affymetrix MitoChip v2.0 analysis using our optimized MitoChip Filtering Protocol (MFP) bioinformatics pipeline now offers the high sensitivity and accuracy needed for reliable, high-throughput and cost-efficient whole mitochondrial genome sequencing. This approach provides a viable alternative of potential utility for both clinical diagnostic and research applications to traditional Sanger and other emerging sequencing technologies for whole mitochondrial genome analysis. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5331508 Wed, 19 Oct 2011 04:00:00 +0100 5331508 http://www.medworm.com/index.php?rid=5331507&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F403 Conclusions: Evaluating the consistency of prior information of pathway databases in molecular tumour profiles may substantial improve the subsequent inference of pathway activity in clinical tumour specimens. This denoising strategy should be incorporated in approaches which attempt to infer pathway activity from prior pathway models. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5331507 Wed, 19 Oct 2011 04:00:00 +0100 5331507 http://www.medworm.com/index.php?rid=5321992&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F401 Conclusions: The method provides an inferential basis for deciding whether two lists are functionally different. For global comparisons it is preferable to the global chi-square test of homogeneity. Furthermore, it may provide additional information if used in conjunction with class-by-class methods. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5321992 Sun, 16 Oct 2011 04:00:00 +0100 5321992 http://www.medworm.com/index.php?rid=5321993&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F400 Conclusions: MetaboHunter is a freely accessible, easy to use and user friendly 1H-NMR-based web server application that provides efficient data input and pre-processing, flexible parameter settings, fast and automatic metabolite fingerprinting and results visualization via intuitive plotting and compound peak hit maps. Compared to other published and freely accessible metabolomics tools, MetaboHunter implements three efficient methods to search for metabolites in manually curated data from two reference libraries.Availabilityhttp://www.nrcbioinformatics.ca/metabohunter/ (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5321993 Fri, 14 Oct 2011 04:00:00 +0100 5321993 http://www.medworm.com/index.php?rid=5311687&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F398 Conclusions: The updated SCOWLP has new functionalities that allow both, detection and comparison of protein regions recognizing different types of ligands, which include other proteins, peptides, nucleic acids and saccharides, within a solvated environment. Currently, SCOWLP allows the analysis of predicted protein binding regions based on structure-base inferences across fold space. These predictions may have a unique potential in assisting protein docking, in providing insights into protein interaction networks, and in guiding rational engineering of protein ligands. The newly designed SCOWLP web application has an improved user-friendly interface that facilitates its usage, and is available at www.scowlp.org. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5311687 Thu, 13 Oct 2011 04:00:00 +0100 5311687 http://www.medworm.com/index.php?rid=5311686&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F399 Conclusions: By incorporating outlier measurements and replicate values, this clustering algorithm for time series microarray data provides a step towards a better treatment of the noise inherent in measurements from high-throughput genomic technologies. Timeseries BHC is available as part of the R package `BHC' (version 1.5), which is available for download from Bioconductor (version 2.9 and above) via http://www.bioconductor.org/packages/release/bioc/html/BHC.html?pagewanted=all. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5311686 Thu, 13 Oct 2011 04:00:00 +0100 5311686 http://www.medworm.com/index.php?rid=5311690&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F395 Conclusions: :Phamerator represents a useful tool for comparative genomic analysis and comparative representative of bacteriophage genomes. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5311690 Wed, 12 Oct 2011 04:00:00 +0100 5311690 http://www.medworm.com/index.php?rid=5311689&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F396 Conclusions: PCFs and QHs together provide an effective means of characterising emergent patterns of differentiation in planar multicellular aggregates. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5311689 Wed, 12 Oct 2011 04:00:00 +0100 5311689 http://www.medworm.com/index.php?rid=5311688&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F397 Conclusions: The BioLexicon contains over 2.2M lexical entries and over 1.8M terminological variants, as well as over 3.3M semantic relations, including over 2M synonymy relations. Its exploitation can benefit both application developers and users. We demonstrate some such benefits by describing integration of the resource into a number of different tools, and evaluating improvements in performance that this can bring. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5311688 Wed, 12 Oct 2011 04:00:00 +0100 5311688 http://www.medworm.com/index.php?rid=5311691&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F394 Conclusions: Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5311691 Mon, 10 Oct 2011 04:00:00 +0100 5311691 http://www.medworm.com/index.php?rid=5302101&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F392 Conclusions: We developed an empirical Bayes model for metabolite identification and validated the method through a mixture of metabolite standards and rat plasma. The results show that our hierarchical model improves identification accuracy as compared with methods that do not structurally model the involved variables. The improvement in identification accuracy is likely to facilitate downstream analysis such as peak alignment and biomarker identification. Raw data and result matrices can be found at http://www.biostat.iupui.edu/~ChangyuShen/index.htmTrial Registration: 2123938128573429 (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5302101 Mon, 10 Oct 2011 04:00:00 +0100 5302101 http://www.medworm.com/index.php?rid=5302100&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F393 Conclusion: By augmenting event annotations with meta-knowledge, more sophisticated IE systems can be trained, which allow interpretative information to be specified as part of the search criteria. This can assist in a number of important tasks, e.g., finding new experimental knowledge to facilitate database curation, enabling textual inference to detect entailments and contradictions, etc. To our knowledge, our scheme is unique within the field with regards to the diversity of meta-knowledge aspects annotated for each event. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5302100 Mon, 10 Oct 2011 04:00:00 +0100 5302100 http://www.medworm.com/index.php?rid=5294133&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F390 Conclusion: Support Vector Machines with a radial basis kernel, linear kernel or polynomial kernel of degree 2 all performed consistently well across data sets. We show that there is a synergistic relationship between these methods and gene selection based on the T-test and the selection of a relatively high number of genes. Also, we find that these methods benefit significantly from using normalized data, although it is hard to draw general conclusions about the relative performance of different normalization procedures. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5294133 Fri, 07 Oct 2011 04:00:00 +0100 5294133 http://www.medworm.com/index.php?rid=5294132&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F391 Conclusions: For most of the datasets examined, the single-gene classification methods appear to work as well as more standard methods, suggesting that simple models could perform well in microarray-based cancer prediction. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5294132 Fri, 07 Oct 2011 04:00:00 +0100 5294132 http://www.medworm.com/index.php?rid=5294134&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F389 Conclusions: ProDiGe implements a new machine learning paradigm for gene prioritization, which could help the identification of new disease genes. It is freely available at http://cbio.ensmp.fr/prodige . (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5294134 Thu, 06 Oct 2011 04:00:00 +0100 5294134 http://www.medworm.com/index.php?rid=5294136&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F387 Conclusions: Literature-based automated network reconstruction is still far from providing complete reconstructions of molecular networks. However, its value as an auxiliary tool is high and it will increase as standards for reporting biological entities and relationships become more widely accepted and enforced. Biblio-MetReS is an application that can be downloaded from http://metres.udl.cat/. It provides an easy to use environment for researchers to reconstruct their networks of interest from an always up to date set of scientific documents. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5294136 Wed, 05 Oct 2011 04:00:00 +0100 5294136 http://www.medworm.com/index.php?rid=5294135&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F388 Conclusions: The iRefScape plug-in will be of interest to advanced users of interaction data. The plug-in provides access to a consolidated data set in a uniform accession space while remaining faithful to the underlying source data. Tools are provided to facilitate a range of tasks from a simple search to knowledge discovery. The plug-in uses a number of strategies that will be of interest to other plug-in developers. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5294135 Wed, 05 Oct 2011 04:00:00 +0100 5294135 http://www.medworm.com/index.php?rid=5282229&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F386 Conclusions: We successfully identified and validated novel NNRTI resistance associated mutations by developing parsimonious resistance prediction models in which repeated cross-validation within the stepwise regression was applied. Our model selection technique is computationally feasible for large data sets and provides an approach to the continued identification of resistance-causing mutations. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5282229 Mon, 03 Oct 2011 04:00:00 +0100 5282229 http://www.medworm.com/index.php?rid=5269868&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F385 Conclusions: Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5269868 Fri, 30 Sep 2011 04:00:00 +0100 5269868 http://www.medworm.com/index.php?rid=5269870&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F383 Conclusions: caCORRECT is shown to improve the accuracy of gene expression, and the reproducibility of experimental results in clinical application. This study suggests that caCORRECT will be useful to clean up possible artifacts in new as well as archived microarray data. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5269870 Thu, 29 Sep 2011 04:00:00 +0100 5269870 http://www.medworm.com/index.php?rid=5269869&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F384 Conclusions: Our method can automatically combine genetic information in local genomic regions and allow for linkage disequilibrium between SNPs. It can overcome some defects of the scan statistics approach and will be very promising in genome-wide case-control association studies. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5269869 Thu, 29 Sep 2011 04:00:00 +0100 5269869 http://www.medworm.com/index.php?rid=5269871&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F382 Conclusions: The Mulcom package provides a powerful tool for the identification of differentially expressed genes when several experimental conditions are compared against a common reference. The results of the practical example presented here show that lists of differentially expressed genes generated by Mulcom are particularly consistent across microarray platforms and enriched in genes belonging to functionally significant groups. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5269871 Wed, 28 Sep 2011 04:00:00 +0100 5269871 http://www.medworm.com/index.php?rid=5269872&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F381 Conclusions: openSESAME is a tool for leveraging the growing body of publicly available microarray data to discover relationships between different biological states based on common patterns of differential gene expression. These relationships may serve to generate hypotheses about the causes and consequences of specific patterns of observed differential gene expression. To encourage others to explore the utility of this approach, we have made a website for performing openSESAME queries freely available at http://opensesame.bu.edu. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5269872 Tue, 27 Sep 2011 04:00:00 +0100 5269872 http://www.medworm.com/index.php?rid=5257833&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F377 Conclusion: Simulation studies and a real data example indicate that GT, WT and GBST tend to have high power, whereas GSEA1 and GSEA2 have lower power. We also found that the power of the five tests is much higher when genes are correlated than when genes are independent, when survival is positively associated with genes. It seems that there is a synergistic effect in detecting significant gene sets when significant genes have within-class correlation and the association between survival and genes is positive or negative (i.e., one-direction correlation). (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5257833 Mon, 26 Sep 2011 04:00:00 +0100 5257833 http://www.medworm.com/index.php?rid=5257832&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F378 Conclusions: The network-based representation of protein structures can be used to identify protein-protein binding regions and to efficiently score docking poses, complementing energy-based approaches. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5257832 Mon, 26 Sep 2011 04:00:00 +0100 5257832 http://www.medworm.com/index.php?rid=5257831&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F379 Conclusions: GOmotif is a web-based tool designed to assist researchers in investigating the biological role of novel protein motifs. GOmotif can be freely accessed at http://www.gomotif.ca (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5257831 Mon, 26 Sep 2011 04:00:00 +0100 5257831 http://www.medworm.com/index.php?rid=5257830&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F380 Conclusions: iCTNet provides a user-friendly interface to search, integrate, visualize, and analyze genome-scale biological networks for human complex traits. We argue this tool is a key instrument that facilitates systematic integration of disparate large-scale data through network visualization, ultimately allowing the identification of disease similarities and the design of novel therapeutic approaches.The online database and Cytoscape plugin are freely available for academic use at: http://www.cs.queensu.ca/ictnet. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5257830 Mon, 26 Sep 2011 04:00:00 +0100 5257830 http://www.medworm.com/index.php?rid=5247023&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F375 Conclusions: The k-TSP ranking algorithm can be used as a computationally efficient, multivariate filter method for feature selection in machine learning. SVM in combination with k-TSP ranking algorithm outperforms k-TSP and SVM alone in simulated datasets and in some cancer prognosis datasets. Simulation studies suggest that as a feature selector, it is better tuned to certain data characteristics, i.e. correlations among informative genes, which is potentially interesting as an alternative feature ranking method in pathway analysis. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5247023 Fri, 23 Sep 2011 04:00:00 +0100 5247023 http://www.medworm.com/index.php?rid=5247022&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F376 Conclusions: EnzymeDetector provides a fast and comprehensive overview of the available enzyme function annotations for a genome of interest. The web interface allows the user to work with customisable weighting schemes and cut-offs for the different prediction methods. These customised quality criteria can easily be applied, and the resulting annotation can be downloaded. The summarised view of all used annotation sources provides up-to-date information. Annotation errors that occur in only one of the databases can be recognised (because of their low relevance score). The results are stored in a database and can be accessed at http://enzymedetector.tu-bs.de. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5247022 Fri, 23 Sep 2011 04:00:00 +0100 5247022 http://www.medworm.com/index.php?rid=5247024&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F374 Conclusions: The performance sweet spot occurs when using a number of threads per MPI process that allows the working sets of the corresponding MPI processes running on the multicore to fit within the machine cache. Hence, we suggest that practitioners follow this principle in selecting the appropriate number of MPI processes and threads within each MPI process for their cluster configurations. We believe that the principles of this hierarchical approach to parallelization can be utilized in the parallelization of other computationally demanding kernels. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5247024 Wed, 21 Sep 2011 04:00:00 +0100 5247024 http://www.medworm.com/index.php?rid=5234381&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F370 Conclusions: New descriptors for the intensity distribution profiles were found to be more discriminative, i.e. more significant, than those used in previous research publications for the translocation quantification. The slow manual calculation can be substituted by the fast and unbiased automated method. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5234381 Mon, 19 Sep 2011 04:00:00 +0100 5234381 http://www.medworm.com/index.php?rid=5234380&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F371 Conclusion: PRO is a unique database resource for species-specific protein complexes. PRO facilitates robust annotation of variations in composition and function contexts for protein complexes within and between species. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5234380 Mon, 19 Sep 2011 04:00:00 +0100 5234380 http://www.medworm.com/index.php?rid=5234379&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F372 Conclusions: The proposed test is a useful alternative to a permutation test for the estimation of the significance of ridge regression coefficients, at a much-reduced computational cost. The p-value trace is an informative graphical tool for evaluating the results of a test of significance of ridge regression coefficients as the shrinkage parameter increases, and the proposed test makes its production computationally feasible. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5234379 Mon, 19 Sep 2011 04:00:00 +0100 5234379 http://www.medworm.com/index.php?rid=5234378&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F373 Conclusion: We have developed two scores which quantify the functional coherence of sets of proteins. The scores reflect the actual associations of GO terms observed either in protein annotations or in literature. It has been shown that they have the ability to accurately distinguish biologically relevant groups of proteins from random ones as well as a good discriminative power for detecting interacting pairs of proteins. The scores were further successfully applied for assigning proteins to pathways. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5234378 Mon, 19 Sep 2011 04:00:00 +0100 5234378 http://www.medworm.com/index.php?rid=5234382&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F369 Conclusions: By allowing the user to easily create his or her own fRMA implementation, the frmaTools package greatly increases the applicability of the fRMA algorithm. The frmaTools package is freely available as part of the Bioconductor project. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5234382 Fri, 16 Sep 2011 04:00:00 +0100 5234382 http://www.medworm.com/index.php?rid=5234383&cid=s_34020_79_f&fid=34020&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2105%2F12%2F368 Conclusions: Our function demonstrates an unmatched combination of accuracy, speed, and simplicity and shows excellent promise for protein structure prediction. Broader applications may include protein-protein interactions and protein design. (Source: BMC Bioinformatics - Latest articles) BMC Bioinformatics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5234383 Thu, 15 Sep 2011 04:00:00 +0100 5234383