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  • 1
    Publication Date: 2015-04-25
    Description: Over the past two decades, comparative sequence analysis using codon-substitution models has been honed into a powerful and popular approach for detecting signatures of natural selection from molecular data. A substantial body of work has focused on developing a class of "branch-site" models which permit selective pressures on sequences, quantified by the ratio, to vary among both codon sites and individual branches in the phylogeny. We develop and present a method in this class, adaptive branch-site random effects likelihood (aBSREL), whose key innovation is variable parametric complexity chosen with an information theoretic criterion. By applying models of different complexity to different branches in the phylogeny, aBSREL delivers statistical performance matching or exceeding best-in-class existing approaches, while running an order of magnitude faster. Based on simulated data analysis, we offer guidelines for what extent and strength of diversifying positive selection can be detected reliably and suggest that there is a natural limit on the optimal parametric complexity for "branch-site" models. An aBSREL analysis of 8,893 Euteleostomes gene alignments demonstrates that over 80% of branches in typical gene phylogenies can be adequately modeled with a single ratio model, that is, current models are unnecessarily complicated. However, there are a relatively small number of key branches, whose identities are derived from the data using a model selection procedure, for which it is essential to accurately model evolutionary complexity.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 2
    Publication Date: 2015-04-25
    Description: We present BUSTED, a new approach to identifying gene-wide evidence of episodic positive selection, where the non-synonymous substitution rate is transiently greater than the synonymous rate. BUSTED can be used either on an entire phylogeny (without requiring an a priori hypothesis regarding which branches are under positive selection) or on a pre-specified subset of foreground lineages (if a suitable a priori hypothesis is available). Selection is modeled as varying stochastically over branches and sites, and we propose a computationally inexpensive evidence metric for identifying sites subject to episodic positive selection on any foreground branches. We compare BUSTED with existing models on simulated and empirical data. An implementation is available on www.datamonkey.org/busted , with a widget allowing the interactive specification of foreground branches.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 3
    Publication Date: 2012-11-11
    Description: Motivation: Current methods in diagnostic microbiology typically focus on the detection of a single genomic locus or protein in a candidate agent. The presence of the entire microbe is then inferred from this isolated result. Problematically, the presence of recombination in microbial genomes would go undetected unless other genomic loci or protein components were specifically assayed. Microarrays lend themselves well to the detection of multiple loci from a given microbe; furthermore, the inherent nature of microarrays facilitates highly parallel interrogation of multiple microbes. However, none of the existing methods for analyzing diagnostic microarray data has the capacity to specifically identify recombinant microbes. In previous work, we developed a novel algorithm, VIPR, for analyzing diagnostic microarray data. Results: We have expanded upon our previous implementation of VIPR by incorporating a hidden Markov model (HMM) to detect recombinant genomes. We trained our HMM on a set of non-recombinant parental viruses and applied our method to 11 recombinant alphaviruses and 4 recombinant flaviviruses hybridized to a diagnostic microarray in order to evaluate performance of the HMM. VIPR HMM correctly identified 95% of the 62 inter-species recombination breakpoints in the validation set and only two false-positive breakpoints were predicted. This study represents the first description and validation of an algorithm capable of detecting recombinant viruses based on diagnostic microarray hybridization patterns. Availability: VIPR HMM is freely available for academic use and can be downloaded from http://ibridgenetwork.org/wustl/vipr . Contact: davewang@borcim.wustl.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 4
    Publication Date: 2014-08-07
    Description: The study, using 20 individual instruments of one model of recreational-grade Global Positioning Systems (GPS) receiver, was conducted in a mature predominantly deciduous forest in the southern United States. The true area was delineated from the eight test points that were very accurately located from monuments using survey-grade instrument and protocols, within the Whitehall Forest GPS Test Site in northeast Georgia. These same eight test points were used as controls during the dynamic horizontal accuracy assessments of GPS technology conducted within the forest. The test points are very precise compared with recent published literature. Our hypotheses were that the areas determined with the 20 receivers were not significantly different from the true areas, and the percentage of the area of agreement and the variation of the vertices around the true boundary were not different in winter and summer seasons. Also, based on the distribution of the vertices around the true boundary, we conducted simulations for larger areas. The average area of agreement was ~93 per cent during the winter season, and ~84 per cent during the summer season. The variation in sample areas was also greater for data collected during the summer, and data from the winter had higher association as measured by area of agreement with the true study area than data from the summer. A ranking of receivers by average area during each season did not reveal significant problems within the set of receivers tested. In conclusion, data collected during each season were not significantly different. Given the distribution of vertices around the true boundary of the study area, simulations of larger land areas revealed that there would be a 2 per cent or less error for mature, deciduous forests of greater than ~25 ha in size in both winter and summer seasons.
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 5
    Publication Date: 2014-06-28
    Description: The results of a Caltech Submillimeter Observatory (CSO) search for l -C 3 H + , first detected by Pety et al. in observations towards the Horsehead photodissociation region (PDR), are presented. A total of 39 sources were observed in the 1 mm window. Evidence of emission from l -C 3 H + is found in only a single source – the Orion Bar PDR region – which shows a rotational temperature of 178(13) K and a column density of 7(2) 10 11  cm –2 . In the remaining sources, upper limits of ~10 11 –10 13  cm –2 are found. These results are discussed in the context of guiding future observational searches for this species.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2018-03-06
    Description: Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of modern comparative sequence analysis. Advances in sequence generation and increased statistical sophistication of relevant methods now allow researchers to extract ever more evolutionary signal from the data, albeit at an increased computational cost. Here, we announce the release of Datamonkey 2.0, a completely re-engineered version of the Datamonkey web-server for analyzing evolutionary signatures in sequence data. For this endeavor, we leveraged recent developments in open-source libraries that facilitate interactive, robust, and scalable web application development. Datamonkey 2.0 provides a carefully curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application. To complement Datamonkey 2.0, we additionally release HyPhy Vision, an accompanying JavaScript application for visualizing analysis results. HyPhy Vision can also be used separately from Datamonkey 2.0 to visualize locally executed HyPhy analyses. Together, Datamonkey 2.0 and HyPhy Vision showcase how scientific software development can benefit from general-purpose open-source frameworks. Datamonkey 2.0 is freely and publicly available at http://www.datamonkey.org , and the underlying codebase is available from https://github.com/veg/datamonkey-js .
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 7
  • 8
    Publication Date: 2014-05-29
    Print ISSN: 0015-752X
    Electronic ISSN: 1464-3626
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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