| 1. |
- Beier, Sebastian, et al.
(författare)
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Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
- 2017
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. â € Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
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| 2. |
- Bull, Philip, et al.
(författare)
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Beyond ΛCDM : Problems, solutions, and the road ahead
- 2016
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Ingår i: Physics of the Dark Universe. - : Elsevier BV. - 2212-6864. ; 12, s. 56-99
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Tidskriftsartikel (refereegranskat)abstract
- Despite its continued observational successes, there is a persistent (and growing) interest in extending cosmology beyond the standard model, Lambda CDM. This is motivated by a range of apparently serious theoretical issues, involving such questions as the cosmological constant problem, the particle nature of dark matter, the validity of general relativity on large scales, the existence of anomalies in the CMB and on small scales, and the predictivity and testability of the inflationary paradigm. In this paper, we summarize the current status of Lambda CDM as a physical theory, and review investigations into possible alternatives along a number of different lines, with a particular focus on highlighting the most promising directions. While the fundamental problems are proving reluctant to yield, the study of alternative cosmologies has led to considerable progress, with much more to come if hopes about forthcoming high-precision observations and new theoretical ideas are fulfilled.
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| 3. |
- Leclercq, Florent, et al.
(författare)
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Primordial power spectrum and cosmology from black-box galaxy surveys
- 2019
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 490:3, s. 4237-4253
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Tidskriftsartikel (refereegranskat)abstract
- We propose a new, likelihood-free approach to inferring the primordial matter power spectrum and cosmological parameters from arbitrarily complex forward models of galaxy surveys where all relevant statistics can be determined from numerical simulations, i.e. black boxes. Our approach, which we call simulator expansion for likelihood-free inference (SELFI), builds upon approximate Bayesian computation using a novel effective likelihood, and upon the linearization of black-box models around an expansion point. Consequently, we obtain simple 'filter equations' for an effective posterior of the primordial power spectrum, and a straightforward scheme for cosmological parameter inference. We demonstrate that the workload is computationally tractable, fixed a priori, and perfectly parallel. As a proof of concept, we apply our framework to a realistic synthetic galaxy survey, with a data model accounting for physical structure formation and incomplete and noisy galaxy observations. In doing so, we show that the use of non-linear numerical models allows the galaxy power spectrum to be safely fitted up to at least k(max) = 0.5 h Mpc(-1), outperforming state-of-the-art backward-modelling techniques by a factor of similar to 5 in the number of modes used. The result is an unbiased inference of the primordial matter power spectrum across the entire range of scales considered, including a high-fidelity reconstruction of baryon acoustic oscillations. It translates into an unbiased and robust inference of cosmological parameters. Our results pave the path towards easy applications of likelihood-free simulation-based inference in cosmology.
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| 4. |
- Mascher, Martin, et al.
(författare)
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A chromosome conformation capture ordered sequence of the barley genome
- 2017
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 544:7651, s. 427-433
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Tidskriftsartikel (refereegranskat)abstract
- Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
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| 5. |
- Porqueres, Natalia, et al.
(författare)
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Bayesian forward modelling of cosmic shear data
- 2021
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 502:2, s. 3035-3044
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Tidskriftsartikel (refereegranskat)abstract
- We present a Bayesian hierarchical modelling approach to infer the cosmic matter density field, and the lensing and the matter power spectra, from cosmic shear data. This method uses a physical model of cosmic structure formation to infer physically plausible cosmic structures, which accounts for the non-Gaussian features of the gravitationally evolved matter distribution and light-cone effects. We test and validate our framework with realistic simulated shear data, demonstrating that the method recovers the unbiased matter distribution and the correct lensing and matter power spectrum. While the cosmology is fixed in this test, and the method employs a prior power spectrum, we demonstrate that the lensing results are sensitive to the true power spectrum when this differs from the prior. In this case, the density field samples are generated with a power spectrum that deviates from the prior, and the method recovers the true lensing power spectrum. The method also recovers the matter power spectrum across the sky, but as currently implemented, it cannot determine the radial power since isotropy is not imposed. In summary, our method provides physically plausible inference of the dark matter distribution from cosmic shear data, allowing us to extract information beyond the two-point statistics and exploiting the full information content of the cosmological fields.
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| 6. |
- Porqueres, Natalia, et al.
(författare)
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Lifting weak lensing degeneracies with a field-based likelihood
- 2021
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 509:3, s. 3194-3202
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Tidskriftsartikel (refereegranskat)abstract
- We present a field-based approach to the analysis of cosmic shear data to infer jointly cosmological parameters and the dark matter distribution. This forward modelling approach samples the cosmological parameters and the initial matter fluctuations, using a physical gravity model to link the primordial fluctuations to the non-linear matter distribution. Cosmological parameters are sampled and updated consistently through the forward model, varying (1) the initial matter power spectrum, (2) the geometry through the distance-redshift relationship, and (3) the growth of structure and light-cone effects. Our approach extracts more information from the data than methods based on two-point statistics. We find that this field-based approach lifts the strong degeneracy between the cosmological matter density, Ωm, and the fluctuation amplitude, σ8, providing tight constraints on these parameters from weak lensing data alone. In the simulated four-bin tomographic experiment we consider, the field-based likelihood yields marginal uncertainties on σ8 and Ωm that are, respectively, a factor of 3 and 5 smaller than those from a two-point power spectrum analysis applied to the same underlying data.
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| 7. |
- Prideaux-Ghee, James, et al.
(författare)
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Field-based physical inference from peculiar velocity tracers
- 2022
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 518:3, s. 4191-4213
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Tidskriftsartikel (refereegranskat)abstract
- We present a proof-of-concept Bayesian hierarchical modelling approach to reconstruct the initial cosmic matter density field constrained by peculiar velocity observations. Using a model for the gravitational evolution of dark matter to connect the initial conditions to late-time observations, it reconstructs the late-time density and velocity fields as natural byproducts. We implement this field-based physical inference approach by adapting the Bayesian Origin Reconstruction from Galaxies (BORG) algorithm, which explores the high-dimensional posterior through the use of Hamiltonian Monte Carlo sampling. We test the self-consistency of the method using random sets of tracers, and assess its accuracy in a more complex scenario where peculiar velocity tracers are mock haloes drawn from GADGET2 N-body simulations. We find that our framework self-consistently infers the initial conditions, density and velocity fields, and shows some robustness to model mis-specification. Compared with the approach of constrained Gaussian random fields/Wiener filtering, the hierarchical model produces more accurate final density and velocity field reconstructions. It also allows us to constrain the initial conditions by peculiar velocity observations, complementing in this aspect other field-based approaches based on alternative cosmological observables such as galaxy clustering or weak lensing.
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