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Search Results: 1 - 10 of 314 matches for " Cara Woodwark "
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Meeting Review: Intelligent Systems for Molecular Biology 2002 (ISMB02)
K. Cara Woodwark
Comparative and Functional Genomics , 2002, DOI: 10.1002/cfg.215
Abstract: This report profiles the keynote talks given at ISMB02 in Edmonton, Canada, by Michael Ashburner, Barry Honig, Isidore Rigoutsos, Ford Doolittle, Stephen Altschul, Terry Gaasterland, John Reinitz, and the Overton Prize winner, David Baker.
The Characterisation of Three Types of Genes that Overlie Copy Number Variable Regions
Cara Woodwark,Alex Bateman
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0014814
Abstract: Due to the increased accuracy of Copy Number Variable region (CNV) break point mapping, it is now possible to say with a reasonable degree of confidence whether a gene (i) falls entirely within a CNV; (ii) overlaps the CNV or (iii) actually contains the CNV. We classify these as type I, II and III CNV genes respectively.
Meeting Review: The Intelligent Systems in Bioinformatics Conference 2001 (ISMB2001)
K. Cara Woodwark
Comparative and Functional Genomics , 2001, DOI: 10.1002/cfg.108
Meeting Review: The Bioinformatics Open Source Conference 2001 (BOSC 2001)
K. Cara Woodwark
Comparative and Functional Genomics , 2001, DOI: 10.1002/cfg.107
Sequence Search Algorithms for Single Pass Sequence Identification: Does One Size Fit All?
K. Cara Woodwark,Simon J. Hubbard,Stephen G. Oliver
Comparative and Functional Genomics , 2001, DOI: 10.1002/cfg.61
Abstract: Bioinformatic tools have become essential to biologists in their quest to understand the vast quantities of sequence data, and now whole genomes, which are being produced at an ever increasing rate. Much of these sequence data are single-pass sequences, such as sample sequences from organisms closely related to other organisms of interest which have already been sequenced, or cDNAs or expressed sequence tags (ESTs). These single-pass sequences often contain errors, including frameshifts, which complicate the identification of homologues, especially at the protein level. Therefore, sequence searches with this type of data are often performed at the nucleotide level. The most commonly used sequence search algorithms for the identification of homologues are Washington University’s and the National Center for Biotechnology Information’s (NCBI) versions of the BLAST suites of tools, which are to be found on websites all over the world. The work reported here examines the use of these tools for comparing sample sequence datasets to a known genome. It shows that care must be taken when choosing the parameters to use with the BLAST algorithms. NCBI’s version of gapped BLASTn gives much shorter, and sometimes different, top alignments to those found using Washington University’s version of BLASTn (which also allows for gaps), when both are used with their default parameters. Most of the differences in performance were found to be due to the choices of default parameters rather than underlying differences between the two algorithms. Washington University’s version, used with defaults, compares very favourably with the results obtained using the accurate but computationally intensive Smith–Waterman algorithm.
Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing
Johanna de Gruijter, Oscar Lao, Mark Vermeulen, Yali Xue, Cara Woodwark, Christopher J Gillson, Alison J Coffey, Qasim Ayub, S Qasim Mehdi, Manfred Kayser, Chris Tyler-Smith
Investigative Genetics , 2011, DOI: 10.1186/2041-2223-2-24
Abstract: Applying all commonly used neutrality-test statistics for allele frequency distribution to the newly generated sequence data provided conflicting results regarding evidence for positive selection. Previous haplotype-based findings could not be clearly confirmed. Although some tests were marginally significant for some populations and genes, none of them were significant after multiple-testing correction. Combined P values for each gene-population pair did not improve these results. Application of Approximate Bayesian Computation Markov chain Monte Carlo based to these sequence data using a simple forward simulator revealed broad posterior distributions of the selective parameters for all four genes, providing no support for positive selection. However, when we applied this approach to published sequence data on SLC45A2, another human pigmentation candidate gene, we could readily confirm evidence for positive selection, as previously detected with sequence-based and some haplotype-based tests.Overall, our data indicate that even genes that are strong biological candidates for positive selection and show reproducible signatures of positive selection in SNP scans do not always show the same replicability of selection signals in other tests, which should be considered in future studies on detecting positive selection in genetic data.Large-scale genotyping projects using genome-wide single-nucleotide polymorphisms (SNPs) have provided large amounts of data describing the genetic diversity of human populations [1-6]. Several statistical methods have been developed and used for detection of signatures of selective processes from genome-wide SNP data, which we refer to as 'SNP scans' [7]. All these approaches try to recover fingerprints of selective sweeps by detecting signals in the haplotypic variation of a genomic region and/or the spectrum of the variation of the genetic diversity [8-15]. However, the results obtained with the different test statistics usually show limi
Phylogenetics in the Bioinformatics Culture of Understanding
Robin G. Allaby,Mathew Woodwark
Comparative and Functional Genomics , 2004, DOI: 10.1002/cfg.381
Abstract: Bioinformatics, as a relatively young discipline, has grown up in a world of high-throughput large volume data that requires automatic analysis to enable us to stay on top of it all. As a response, the bioinformatics discipline has developed strategies to find patterns in a ‘low signal : noise ratio’ environment. While the need to process large amounts of information and extract hypotheses is both laudable and inescapable, the pressures that such requirements have introduced can lead to short cuts and misapprehensions. This is particularly the case with reference to assumptions about the underlying evolutionary theories that are implicitly invoked by the algorithms utilised in the analysis pipelines. The classic example is the misuse of the term ‘homologous’ to mean ‘similar’ or even ‘functionally similar’, rather than the correct definition of ‘having the same evolutionary origin’, which may or may not imply similarity of function. In this review, we outline some of the common phylogenetic questions from a bioinformatics perspective that can be better addressed with a deeper understanding of evolutionary principles and show, with examples from the amidohydrolase and Toll families, that quite different conclusions can be drawn if such approaches are taken. This review focuses on the importance of the underlying evolutionary biology, rather than assessing the merits of different phylogenetic techniques. The relative merits of a priori and a posteriori inclusion of biological information are discussed.
Phylogenomic Analysis Reveals Extensive Phylogenetic Mosaicism in the Human GPCR Superfamily
Robin G. Allaby,Mathew Woodwark
Evolutionary Bioinformatics , 2007,
Abstract: A novel high throughput phylogenomic analysis (HTP) was applied to the rhodopsin G-protein coupled receptor (GPCR) family. Instances of phylogenetic mosaicism between receptors were found to be frequent, often as instances of correlated mosaicism and repeated mosaicism. A null data set was constructed with the same phylogenetic topology as the rhodopsin GPCRs. Comparison of the two data sets revealed that mosaicism was found in GPCRs in a higher frequency than would be expected by homoplasy or the effects of topology alone. Various evolutionary models of differential conservation, recombination and homoplasy are explored which could result in the patterns observed in this analysis. We find that the results are most consistent with frequent recombination events. A complex evolutionary history is illustrated in which it is likely frequent recombination has endowed GPCRs with new functions. The pattern of mosaicism is shown to be informative for functional prediction for orphan receptors. HTP analysis is complementary to conventional phylogenomic analyses revealing mosaicism that would not otherwise have been detectable through conventional phylogenetics.
A falta na comunica o
Mariane Cara
Galáxia , 2010,
Abstract: O domínio discursivo é o enfoque do livro Margens da Comunica o: discurso e mídias. Como este é o território onde s o formados os la os sociais, que carregam consigo informa es do consciente e do inconsciente, inicia-se um processo de busca dos elementos que est o à margem e nas bordas de um discurso. é na falta, ou no elemento impossível de ser simbolizado, que podem ser encontradas novas perspectivas sobre a comunica o.
L'esperienza del Dipartimento della Protezione Civile sulle specifiche RNDT
Pierluigi Cara
GEOmedia , 2012,
Abstract: Il Comitato per le regole tecniche sui dati territoriali delle pubbliche amministrazioni ha approvato un provvedimento con il quale si definiscono le regole tecniche per la formazione e l’alimentazione del RepertorioNazionale dei Dati Territoriali (RNDT), le quali tengono anche conto del Regolamento (CE) recante attuazione della Direttiva Inspire sui metadati. In questo articolo viene descritta l’esperienza svolta dal Dipartimento della protezione civile nell’applicazione di queste specifiche tecniche. RNDT Specifications being tested at Civil Protection Department The Committee for technical regulation on the spatial data of the government, approved a measure to define the technical rules for the formation and feeding of the Repertorio Nazion-ale Dati Territoriali, which also take account of Regulation (EC) implementing INSPIRE Directive on metadata. This article de-scribes the experience carried out by the Department of Civil Protection in the application of these technical specifications.
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