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  • 1
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    VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research (2016)
    Oxford University Press
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    Publication Date: 2016-06-21
    Description: Accurate variant calling in next generation sequencing (NGS) is critical to understand cancer genomes better. Here we present VarDict, a novel and versatile variant caller for both DNA- and RNA-sequencing data. VarDict simultaneously calls SNV, MNV, InDels, complex and structural variants, expanding the detected genetic driver landscape of tumors. It performs local realignments on the fly for more accurate allele frequency estimation. VarDict performance scales linearly to sequencing depth, enabling ultra-deep sequencing used to explore tumor evolution or detect tumor DNA circulating in blood. In addition, VarDict performs amplicon aware variant calling for polymerase chain reaction (PCR)-based targeted sequencing often used in diagnostic settings, and is able to detect PCR artifacts. Finally, VarDict also detects differences in somatic and loss of heterozygosity variants between paired samples. VarDict reprocessing of The Cancer Genome Atlas (TCGA) Lung Adenocarcinoma dataset called known driver mutations in KRAS, EGFR, BRAF, PIK3CA and MET in 16% more patients than previously published variant calls. We believe VarDict will greatly facilitate application of NGS in clinical cancer research.
    Keywords: Polymorphism/mutation detection
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    A framework for testing isotropy with the cosmic microwave background (2016)
    Oxford University Press
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    Publication Date: 2016-08-21
    Description: We present a new framework for testing the isotropy of the Universe using cosmic microwave background data, building on the nested-sampling anicosmo code. Uniquely, we are able to constrain the scalar, vector and tensor degrees of freedom alike; previous studies only considered the vector mode (linked to vorticity). We employ Bianchi type VII h cosmologies to model the anisotropic Universe, from which other types may be obtained by taking suitable limits. In a separate development, we improve the statistical analysis by including the effect of Bianchi power in the high-, as well as the low-, likelihood. To understand the effect of all these changes, we apply our new techniques to Wilkinson Microwave Anisotropy Probe data. We find no evidence for anisotropy, constraining shear in the vector mode to ( V / H ) 0 〈 1.7 x 10 –10 (95 per cent confidence level). For the first time, we place limits on the tensor mode; unlike other modes, the tensor shear can grow from a near-isotropic early Universe. The limit on this type of shear is ( T , reg /H) 0 〈 2.4 x 10 – 7 (95 per cent confidence level).
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    SILC: a new Planck internal linear combination CMB temperature map using directional wavelets (2016)
    Oxford University Press
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    Publication Date: 2016-06-18
    Description: We present new clean maps of the cosmic microwave background (CMB) temperature anisotropies (as measured by Planck ) constructed with a novel internal linear combination (ILC) algorithm using directional, scale-discretized wavelets – scale-discretized, directional wavelet ILC or Scale-discretised, directional wavelet Internal Linear Combination (SILC). Directional wavelets, when convolved with signals on the sphere, can separate the anisotropic filamentary structures which are characteristic of both the CMB and foregrounds. Extending previous component separation methods, which use the frequency, spatial and harmonic signatures of foregrounds to separate them from the cosmological background signal, SILC can additionally use morphological information in the foregrounds and CMB to better localize the cleaning algorithm. We test the method on Planck data and simulations, demonstrating consistency with existing component separation algorithms, and discuss how to optimize the use of morphological information by varying the number of directional wavelets as a function of spatial scale. We find that combining the use of directional and axisymmetric wavelets depending on scale could yield higher quality CMB temperature maps. Our results set the stage for the application of SILC to polarization anisotropies through an extension to spin wavelets.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques (2012)
    Oxford University Press
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    Publication Date: 2012-03-14
    Description: Determining the underlying haplotypes of individual human genomes is an essential, but currently difficult, step toward a complete understanding of genome function. Fosmid pool-based next-generation sequencing allows genome-wide generation of 40-kb haploid DNA segments, which can be phased into contiguous molecular haplotypes computationally by Single Individual Haplotyping (SIH). Many SIH algorithms have been proposed, but the accuracy of such methods has been difficult to assess due to the lack of real benchmark data. To address this problem, we generated whole genome fosmid sequence data from a HapMap trio child, NA12878, for which reliable haplotypes have already been produced. We assembled haplotypes using eight algorithms for SIH and carried out direct comparisons of their accuracy, completeness and efficiency. Our comparisons indicate that fosmid-based haplotyping can deliver highly accurate results even at low coverage and that our SIH algorithm, ReFHap, is able to efficiently produce high-quality haplotypes. We expanded the haplotypes for NA12878 by combining the current haplotypes with our fosmid-based haplotypes, producing near-to-complete new gold-standard haplotypes containing almost 98% of heterozygous SNPs. This improvement includes notable fractions of disease-related and GWA SNPs. Integrated with other molecular biological data sets, this phase information will advance the emerging field of diploid genomics.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Characterization of behavioral and neuromuscular junction phenotypes in a novel allelic series of SMA mouse models (2012)
    Oxford University Press
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    Publication Date: 2012-09-28
    Description: A number of mouse models for spinal muscular atrophy (SMA) have been genetically engineered to recapitulate the severity of human SMA by using a targeted null mutation at the mouse Smn1 locus coupled with the transgenic addition of varying copy numbers of human SMN2 genes. Although this approach has been useful in modeling severe SMA and very mild SMA, a mouse model of the intermediate form of the disease would provide an additional research tool amenable for drug discovery. In addition, many of the previously engineered SMA strains are multi-allelic by design, containing a combination of transgenes and targeted mutations in the homozygous state, making further genetic manipulation difficult. A new genetic engineering approach was developed whereby variable numbers of SMN2 sequences were incorporated directly into the murine Smn1 locus. Using combinations of these alleles, we generated an allelic series of SMA mouse strains harboring no, one, two, three, four, five, six or eight copies of SMN2. We report here the characterization of SMA mutants in this series that displayed a range in disease severity from embryonic lethal to viable with mild neuromuscular deficits.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Probabilistic image reconstruction for radio interferometers (2014)
    Oxford University Press
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    Publication Date: 2014-01-16
    Description: We present a novel, general-purpose method for deconvolving and denoizing images from gridded radio interferometric visibilities using Bayesian inference based on a Gaussian process model. The method automatically takes into account incomplete coverage of the uv -plane, signal mode coupling due to the primary beam and noise mode coupling due to uv sampling. Our method uses Gibbs sampling to efficiently explore the full posterior distribution of the underlying signal image given the data. We use a set of widely diverse mock images with a realistic interferometer set-up and level of noise to assess the method. Compared to results from a proxy for point source-based clean method we find that in terms of rms error and signal-to-noise ratio our approach performs better than traditional deconvolution techniques, regardless of the structure of the source image in our test suite. Our implementation scales as $\mathcal {O}(n_{\rm p} \log n_{\rm p})$ provides full statistical and uncertainty information of the reconstructed image, requires no supervision and provides a robust, consistent framework for incorporating noise and parameter marginalizations and foreground removal.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 7
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    PURIFY: a new approach to radio-interferometric imaging (2014)
    Oxford University Press
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    Publication Date: 2014-03-25
    Description: In a recent paper series, the authors have promoted convex optimization algorithms for radio-interferometric imaging in the framework of compressed sensing, which leverages sparsity regularization priors for the associated inverse problem and defines a minimization problem for image reconstruction. This approach was shown, in theory and through simulations in a simple discrete visibility setting, to have the potential to outperform significantly clean and its evolutions. In this work, we leverage the versatility of convex optimization in solving minimization problems to both handle realistic continuous visibilities and offer a highly parallelizable structure paving the way to significant acceleration of the reconstruction and high-dimensional data scalability. The new algorithmic structure promoted relies on the simultaneous-direction method of multipliers (SDMM) and contrasts with the current major–minor cycle structure of clean and its evolutions, which in particular cannot handle the state-of-the-art minimization problems under consideration where neither the regularization term nor the data term are differentiable functions. We release a beta version of an SDMM-based imaging software written in c and dubbed purify ( http://basp-group.github.io/purify/ ) that handles various sparsity priors, including our recent average sparsity approach sparsity averaging reweighted analysis (SARA). We evaluate the performance of different priors through simulations in the continuous visibility setting, confirming the superiority of SARA.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Revisiting the spread spectrum effect in radio interferometric imaging: a sparse variant of the w-projection algorithm (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-17
    Description: Next-generation radio interferometric telescopes will exhibit non-coplanar baseline configurations and wide field of views, inducing a w -modulation of the sky image, which induces the spread spectrum effect. We revisit the impact of this effect on the imaging quality and study a new algorithmic strategy to deal with the associated operator. In previous studies, it has been shown that image recovery in the framework of compressed sensing is improved due to this effect, where the w -modulation can increase the incoherence between measurement and sparsifying signal representations. For the purpose of computational efficiency, idealized experiments with a constant baseline component w were performed. We extend this analysis to the more realistic setting where the w -component varies for each visibility measurement. First, incorporating varying w -components into imaging algorithms is a computational demanding task. We propose a variant of the w -projection algorithm, which is based on an adaptive sparsification procedure, and incorporate it in compressed sensing imaging methods. Secondly, we show that for varying w -components, the reconstruction quality is significantly improved compared to no w -modulation, reaching levels comparable to a constant, maximal w -component. This finding confirms that one may seek to optimize future telescope configurations to promote large w -components, thus enhancing the fidelity of image reconstruction.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Scalable splitting algorithms for big-data interferometric imaging in the SKA era (2016)
    Oxford University Press
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    Publication Date: 2016-09-07
    Description: In the context of next-generation radio telescopes, like the Square Kilometre Array (SKA), the efficient processing of large-scale data sets is extremely important. Convex optimization tasks under the compressive sensing framework have recently emerged and provide both enhanced image reconstruction quality and scalability to increasingly larger data sets. We focus herein mainly on scalability and propose two new convex optimization algorithmic structures able to solve the convex optimization tasks arising in radio-interferometric imaging. They rely on proximal splitting and forward-backward iterations and can be seen, by analogy, with the clean major-minor cycle, as running sophisticated clean -like iterations in parallel in multiple data, prior, and image spaces. Both methods support any convex regularization function, in particular, the well-studied 1 priors promoting image sparsity in an adequate domain. Tailored for big-data, they employ parallel and distributed computations to achieve scalability, in terms of memory and computational requirements. One of them also exploits randomization, over data blocks at each iteration, offering further flexibility. We present simulation results showing the feasibility of the proposed methods as well as their advantages compared to state-of-the-art algorithmic solvers. Our matlab code is available online on GitHub.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Spin-SILC: CMB polarization component separation with spin wavelets (2016)
    Oxford University Press
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    Publication Date: 2016-10-08
    Description: We present Spin-SILC, a new foreground component separation method that accurately extracts the cosmic microwave background (CMB) polarization E and B modes from raw multifrequency Stokes Q and U measurements of the microwave sky. Spin-SILC is an internal linear combination method that uses spin wavelets to analyse the spin-2 polarization signal P  =  Q  + i U . The wavelets are additionally directional (non-axisymmetric). This allows different morphologies of signals to be separated and therefore the cleaning algorithm is localized using an additional domain of information. The advantage of spin wavelets over standard scalar wavelets is to simultaneously and self-consistently probe scales and directions in the polarization signal P  =  Q  + i U and in the underlying E and B modes, therefore providing the ability to perform component separation and E – B decomposition concurrently for the first time. We test Spin-SILC on full-mission Planck simulations and data and show the capacity to correctly recover the underlying cosmological E and B modes. We also demonstrate a strong consistency of our CMB maps with those derived from existing component separation methods. Spin-SILC can be combined with the pseudo- and pure E – B spin wavelet estimators presented in a companion paper to reliably extract the cosmological signal in the presence of complicated sky cuts and noise. Therefore, it will provide a computationally efficient method to accurately extract the CMB E and B modes for future polarization experiments.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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