共查询到20条相似文献,搜索用时 31 毫秒
1.
Contact: anne.kupczok{at}univie.ac.at
Associate Editor: Martin Bishop 相似文献
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Asare Adam L.; Gao Zhong; Carey Vincent J.; Wang Richard; Seyfert-Margolis Vicki 《Bioinformatics (Oxford, England)》2009,25(1):48-53
Motivation: As the use of microarrays in human studies continuesto increase, stringent quality assurance is necessary to ensureaccurate experimental interpretation. We present a formal approachfor microarray quality assessment that is based on dimensionreduction of established measures of signal and noise componentsof expression followed by parametric multivariate outlier testing. Results: We applied our approach to several data resources.First, as a negative control, we found that the Affymetrix andIllumina contributions to MAQC data were free from outliersat a nominal outlier flagging rate of =0.01. Second, we createda tunable framework for artificially corrupting intensity datafrom the Affymetrix Latin Square spike-in experiment to allowinvestigation of sensitivity and specificity of quality assurance(QA) criteria. Third, we applied the procedure to 507 Affymetrixmicroarray GeneChips processed with RNA from human peripheralblood samples. We show that exclusion of arrays by this approachsubstantially increases inferential power, or the ability todetect differential expression, in large clinical studies. Availability: http://bioconductor.org/packages/2.3/bioc/html/arrayMvout.htmland http://bioconductor.org/packages/2.3/bioc/html/affyContam.htmlaffyContam (credentials: readonly/readonly) Contact: aasare{at}immunetolerance.org; stvjc{at}channing.harvard.edu
The authors wish it to be known that, in their opinion, thefirst two authors should be regarded as joint First Authors.
Associate Editor: Trey Ideker 相似文献
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Contact: nagarajanradhakrish{at}uams.edu
Associate Editor: Martin Bishop 相似文献
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Contact: ihh{at}berkeley.edu
Associate Editor: Alex Bateman 相似文献
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de Vienne Damien M.; Giraud Tatiana; Martin Olivier C. 《Bioinformatics (Oxford, England)》2009,25(1):150-151
Contact: damien.de-vienne{at}lri.fr
Associate Editor: Martin Bishop 相似文献
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Summary: FAMHAP is an established software for haplotype associationanalysis of nuclear families. We have released a major updatethat comprises various new features for case-control data. Furthermore,weprovide an additional program runFamhap that allows usersto start the same method repeatedly for varying sets of geneticmarkers. In addition, a platform-independent graphical userinterface (GUI) was developed to simplify the usage of bothFAMHAP and runFamhap. The runFamhap program greatly facilitatesthe application of FAMHAP to genome-wide association studies(GWAS) and supports flexible genome-wide haplotype analysis.As an example, we describe application to HapMap data. Availability: The software is available at http://famhap.meb.uni-bonn.de Contact: herold{at}imbie.meb.uni-bonn.de; becker{at}imbie.meb.uni-bonn.de Supplementary information: Supplementary data are availableat Bioinformatics online.
Associate Editor: Alex Bateman 相似文献
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Summary: We present a large-scale implementation of the RANKPROPprotein homology ranking algorithm in the form of an openlyaccessible web server. We use the NRDB40 PSI-BLAST all-versus-allprotein similarity network of 1.1 million proteins to constructthe graph for the RANKPROP algorithm, whereas previously, resultswere only reported for a database of 108 000 proteins. We alsodescribe two algorithmic improvements to the original algorithm,including propagation from multiple homologs of the query andbetter normalization of ranking scores, that lead to higheraccuracy and to scores with a probabilistic interpretation. Availability: The RANKPROP web server and source code are availableat http://rankprop.gs.washington.edu Contact: iain{at}nec-labs.com; noble{at}gs.washington.edu
Associate Editor: Burkhard Rost 相似文献
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Carver T Thomson N Bleasby A Berriman M Parkhill J 《Bioinformatics (Oxford, England)》2009,25(1):119-120
Summary: DNAPlotter is an interactive Java application for generatingcircular and linear representations of genomes. Making use ofthe Artemis libraries to provide a user-friendly method of loadingin sequence files (EMBL, GenBank, GFF) as well as data fromrelational databases, it filters features of interest to displayon separate user-definable tracks. It can be used to producepublication quality images for papers or web pages. Availability: DNAPlotter is freely available (under a GPL licence)for download (for MacOSX, UNIX and Windows) at the WellcomeTrust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/circular/ Contact: artemis{at}sanger.ac.uk
Associate Editor: John Quackenbush 相似文献
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Summary: Three dimensional structures of proteins contain errorswhich often originate from limitations of the experimental techniquesemployed. Such errors frequently result in unfavorable atomicinteractions. Here we present a new web service, called InteractionViewer, for the visualization and correction of such errors.We show how the Interaction Viewer is used in combination withthe NQ-Flipper service to spot strained asparagine and glutaminerotamers and we emphasize the convenience of this service incorrecting such errors. Availability: The web service is integrated with the NQ-Flipperservice and accessible at http://flipper.services.came.sbg.ac.at Contact: sippl{at}came.sbg.ac.at
Associate Editor: Anna Tramontano 相似文献
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Lunter G 《Bioinformatics (Oxford, England)》2007,23(18):2485-2487
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Webb-Robertson BJ Peterson ES Singhal M Klicker KR Oehmen CS Adkins JN Havre SL 《Bioinformatics (Oxford, England)》2007,23(13):1705-1707
Summary: The visual Platform for Proteomics Peptide and Proteindata exploration (PQuad) is a multi-resolution environment thatvisually integrates genomic and proteomic data for prokaryoticsystems, overlays categorical annotation and compares differentialexpression experiments. PQuad requires Java 1.5 and has beentested to run across different operating systems. Availability: http://ncrr.pnl.gov/software Contact: bobbie-jo.webb-robertson{at}pnl.gov
Associate Editor: Thomas Lengauer 相似文献
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Summary: Malaria, one of the world's most common diseases, iscaused by the intracellular protozoan parasite known as Plasmodium.Recently, with the arrival of several malaria parasite genomes,we established an integrated system named PlasmoGF for comparativegenomics and phylogenetic analysis of Plasmodium gene families.Gene families were clustered using the Markov Cluster algorithmimplemented in TribeMCL program and could be searched usingkeywords, gene-family information, domain composition, GeneOntology and BLAST. Moreover, a number of useful bioinformaticstools were implemented to facilitate the analysis of these putativePlasmodium gene families, including gene retrieval, annotation,sequence alignment, phylogeny construction and visualization.In the current version, PlasmoGF contained 8980 sets of genefamilies derived from six malaria parasite genomes: Plasmodium.falciparum, P. berghei, P. knowlesi, P. chabaudi, P. vivax andP. yoelii. The availability of such a highly integrated systemwould be of great interest for the community of researchersworking on malaria parasite phylogenomics. Availability: PlasmoGF is freely available at http://bioinformatics.zj.cn/pgf/ Contact: xiaokunli{at}163.net; baoqy{at}genomics.org.cn; fuz3{at}psu.edu
Associate Editor: Jonathan Wren
The authors wish it to be known that, in their opinion, thefirst two authors should be regarded as joint First Authors. 相似文献
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Summary: BLISS 2.0 is a web-based application for identifyingconserved regulatory modules in distantly related orthologoussequences. Unlike existing approaches, it performs the cross-genomecomparison at the binding site level. Experimental results onsimulated and real world data indicate that BLISS 2.0 can identifyconserved regulatory modules from sequences with little overallsimilarity at the DNA sequence level. Availability: http://www.blisstool.org/ Contact: leizhou{at}ufl.edu
Associate Editor: Olga Troyanskaya 相似文献
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Motivation: To enable a new way of submitting sequence informationto the EMBL nucleotide database through the WWW. This processof data submission is long and complex, and calls for efficientand user-friendly mechanisms for collection and validation ofinformation. Results: Described here is a generic, object-oriented data-submissionsystem that is being used for the EMBL database, but can easilybe tailored to serve several data-submission schemes with arelatively short development and implementation time. The programprovides the user with a friendly interface that breaks thecomplex task into smaller, more manageable tasks and, on theother hand, acts as a pre-filter, scanning errors online. Availability: The program is accessible through the EMBL-EBlWWW server at the URL: http: //www.ebi.ac.uk/subs/ emblsubs.html Contact: E-mail: bshomer{at}ebi.ac.uk 相似文献
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A multivariate test of association 总被引:1,自引:0,他引:1
Summary: Although genetic association studies often test multiple,related phenotypes, few formal multivariate tests of associationare available. We describe a test of association that can beefficiently applied to large population-based designs. Availability: A C++ implementation can be obtained from theauthors. Contact: manuel.ferreira{at}qimr.edu.au Supplementary information: Supplementary figures are availableat Bioinformatics online.
Associate Editor: Alex Bateman 相似文献
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Summary: Automated analysis of flow cytometry (FCM) data isessential for it to become successful as a high throughput technology.We believe that the principles of Trellis graphics can be adaptedto provide useful visualizations that can aid such automation.In this article, we describe the R/Bioconductor package flowVizthat implements such visualizations. Availability: flowViz is available as an R package from theBioconductor project: http://bioconductor.org Contact: dsarkar{at}fhcrc.org
Associate Editor: Olga Troyanskaya 相似文献
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The ability to rank proteins by their likely success in crystallizationis useful in current Structural Biology efforts and in particularin high-throughput Structural Genomics initiatives. We presentParCrys, a Parzen Window approach to estimate a protein's propensityto produce diffraction-quality crystals. The Protein Data Bank(PDB) provided training data whilst the databases TargetDB andPepcDB were used to define feature selection data as well astest data independent of feature selection and training. ParCrysoutperforms the OB-Score, SECRET and CRYSTALP on the data examined,with accuracy and Matthews correlation coefficient values of79.1% and 0.582, respectively (74.0% and 0.227, respectively,on data with a real-world ratio of positive:negativeexamples). ParCrys predictions and associated data are availablefrom www.compbio.dundee.ac.uk/parcrys. Contact: geoff{at}compbio.dundee.ac.uk Supplementary information: Supplementary data are availableat Bioinformatics online.
Associate Editor: John Quackenbush 相似文献