| 1. |
- Benson, Mikael, 1954, et al.
(författare)
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A network-based analysis of allergen-challenged CD4+T cells from patients with allergic rhinitis
- 2006
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Ingår i: Genes and Immunity. - : Springer Science and Business Media LLC. - 1466-4879 .- 1476-5470. ; 7:6, s. 514-521
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Tidskriftsartikel (refereegranskat)abstract
- We performed a network-based analysis of DNA microarray data from allergen-challenged CD4 + T cells from patients with seasonal allergic rhinitis. Differentially expressed genes were organized into a functionally annotated network using the Ingenuity Knowledge Database, which is based on manual review of more than 200000 publications. The main function of this network is the regulation of lymphocyte apoptosis, a role associated with several genes of the tuber necrosis factor superfamily. The expression of TNFRSF4, one of the genes in this family, was found to be 48 times higher in allergen-challenged cells than in diluent-challenged cells. TNFRSF4 is known to inhibit apoptosis and to enhance Th2 proliferation. Examination of a different material of allergen-stimulated peripheral blood mononuclear cells showed a higher number of interleukin-4 + type 2 CD4 + T (Th2) cells in patients than in controls (P
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| 2. |
- Guillot, Gilles, 1972, et al.
(författare)
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Correcting for ascertainment bias in the inference of population structure
- 2009
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 25:4, s. 552-554
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Tidskriftsartikel (refereegranskat)abstract
- Background: The ascertainment process of molecular markers amounts to disregard loci carrying alleles with low frequencies. This can result in strong biases in inferences under population genetics models if not properly taken into account by the inference algorithm. Attempting to model this censoring process in view of making inference of population structure (i.e. identifying clusters of individuals) brings up challenging numerical difficulties. Method: These difficulties are related to the presence of intractable normalizing constants in Metropolis-Hastings acceptance ratios. This can be solved via an Markov chain Monte Carlo (MCMC) algorithm known as single variable exchange algorithm (SVEA). Result: We show how this general solution can be implemented for a class of clustering models of broad interest in population genetics that includes the models underlying the computer programs STRUCTURE, GENELAND and GESTE. We also implement the method proposed for a simple example and show that it allows us to reduce the bias substantially.
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| 3. |
- Guillot, Gilles, 1972
(författare)
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On the inference of spatial structure from population genetics data
- 2009
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 25:14, s. 1796-1801
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: In a series of recent papers, Tess, a computer program based on the concept of hidden Markov random field, has been proposed to infer the number and locations of panmictic population units from the genotypes and spatial locations of these individuals. The method seems to be of broad appeal as it is conceptually much simpler than other competing methods and it has been reported by its authors to be fast and accurate. However, this methodology is not grounded in a formal statistical inference method and seems to rely to a large extent on arbitrary choices regarding the parameters used. The present article is an investigation of the accuracy of this method and an attempt to assess whether recent results reported on the basis of this method are genuine features of the genetic process or artefacts of the method. Method: I analyse simulated data consisting of populations at Hardy-Weinberg and linkage equilibrium and also data simulated under a scenario of isolation-by-distance at mutation-migration-drift equilibrium. Arabidopsis thaliana data previously analysed with this method are also reconsidered. Results: Using the Tess program under the no-admixture model to analyse data consisting of several genuine HWLE populations with individuals of pure ancestries leads to highly inaccurate results; Using the Tess program under the admixture model to analyse data consisting of a continuous isolation-by-distance population leads to the inference of spurious HWLE populations whose number and features depend on the parameters used. Results previously reported about the A. thaliana using Tess seem to a large extent to be artefacts of the statistical methodology used. The findings go beyond population clustering models and can be an help to design more efficient algorithms based on graphs.
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| 4. |
- Guillot, Gilles, 1972, et al.
(författare)
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Spatial prediction of weed intensities from exact count data and image-based estimates
- 2009
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Ingår i: Journal of the Royal Statistical Society Series C-Applied Statistics. - : Oxford University Press (OUP). - 0035-9254 .- 1467-9876. ; 58, s. 525-542
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Tidskriftsartikel (refereegranskat)abstract
- Collecting weed exact counts in an agricultural field is easy but extremely time consuming. Image analysis algorithms for object extraction applied to pictures of agricultural fields may be used to estimate the weed content with a high resolution (about 1 m(2)), and pictures that are acquired at a large number of sites can be used to obtain maps of weed content over a whole field at a reasonably low cost. However, these image-based estimates are not perfect and acquiring exact weed counts also is highly useful both for assessing the accuracy of the image-based algorithms and for improving the estimates by use of the combined data. We propose and compare various models for image index and exact weed count and we use them to assess how such data should be combined to obtain reliable maps. The method is applied to a real data set from a 30-ha field. We show that using image estimates in addition to exact counts allows us to improve the accuracy of maps significantly. We also show that the relative performances of the methods depend on the size of the data set and on the specific methodology (full Bayes versus plug-in) that is implemented.
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