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  • Articles  (21,219)
  • Oxford University Press  (18,043)
  • Public Library of Science
  • 2015-2019  (21,219)
  • Computer Science  (11,623)
  • Geosciences  (9,596)
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  • Articles  (21,219)
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  • 1
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    AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-08
    Description: : As sequencing becomes cheaper and more widely available, there is a greater need to quickly and effectively analyze large-scale genomic data. While the functionality of AVIA v1.0, whose implementation was based on ANNOVAR, was comparable with other annotation web servers, AVIA v2.0 represents an enhanced web-based server that extends genomic annotations to cell-specific transcripts and protein-level functional annotations. With AVIA’s improved interface, users can better visualize their data, perform comprehensive searches and categorize both coding and non-coding variants. Availability and implementation : AVIA is freely available through the web at http://avia.abcc.ncifcrf.gov . Contact : Hue.Vuong@fnlcr.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-08
    Description: : As new methods for multivariate analysis of genome wide association studies become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance-based method for meta-analysis, generalized to an n -dimensional setting. Availability and implementation: The R package MultiMeta can be downloaded from CRAN. Contact: dragana.vuckovic@burlo.trieste.it ; vi1@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    Slip rates and locking depth variation along central and easternmost segments of North Anatolian Fault (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-30
    Description: While the kinematics of Anatolia plate and the North Anatolian Fault System (NAFS) has been studied extensively, the slip rate and locking depth along the NAFS are usually assumed constant in the analyses due to the lack of sufficient data. This is also partly due to the reasonably good fit of Euler small circle and partly due to the lack of spatial resolution of observations to determine slip rates independently from locking depths. On the other hand, recent geodetic studies show a contrast for locking depth between Marmara and other parts of the NAFS, implying a non-uniform locking depth across the NAFS. In this study, we analyse new GPS data and homogenously combine available data sets covering the eastern part of the NAFS to form the most complete data set. In particular, we incorporate the first results of Turkish Real-Time Kinematic GPS Network (CORS-TR) into our data set. A detailed analysis of three profiles within the NAFS reveals an increase of locking depth in the middle profile to 19.1 ± 3.4 km from 11.9 ± 3.5 km in the easternmost profile while the slip rate is nearly constant (20–22 mm yr –1 ), which implies a variation of strain rate of ~100 nanostrain yr –1 . Assuming a constant locking depth throughout whole NAFS gives an average locking depth of 14.3 ± 1.7 km. Our best estimates of slip rates in block modelling which takes the variation of locking depths into account are in the range between 22.5 and 22.8 mm yr –1 over eastern part of the NAFS.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 4
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    Quasi-geostrophic modes in the Earth's fluid core with an outer stably stratified layer (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-30
    Description: Seismic waves sensitive to the outermost part of the Earth's liquid core seem to be affected by a stably stratified layer at the core–mantle boundary. Such a layer could have an observable signature in both long-term and short-term variations of the magnetic field of the Earth, which are used to probe the flow at the top of the core. Indeed, with the recent SWARM mission, it seems reasonable to be able to identify waves propagating in the core with period of several months, which may play an important role in the large-scale dynamics. In this paper, we characterize the influence of a stratified layer at the top of the core on deep quasi-geostrophic (Rossby) waves. We compute numerically the quasi-geostrophic eigenmodes of a rapidly rotating spherical shell, with a stably stratified layer near the outer boundary. Two simple models of stratification are taken into account, which are scaled with commonly adopted values of the Brunt–Väisälä frequency in the Earth's core. In the absence of magnetic field, we find that both azimuthal wavelength and frequency of the eigenmodes control their penetration into the stratified layer: the higher the phase speed, the higher the permeability of the stratified layer to the wave motion. We also show that the theory developed by Takehiro & Lister for thermal convection extends to the whole family of Rossby waves in the core. Adding a magnetic field, the penetrative behaviour of the quasi-geostrophic modes (the so-called fast branch) is insensitive to the imposed magnetic field and only weakly sensitive to the precise shape of the stratification. Based on these results, the large-scale and high-frequency modes (1–2 month periods) may be detectable in the geomagnetic data measured at the Earth's surface, especially in the equatorial area where the modes can be trapped.
    Keywords: Geomagnetism, Rock Magnetism and Palaeomagnetism
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 5
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    Attenuation of sonic waves in water-saturated alluvial sediments due to wave-induced fluid flow at microscopic, mesoscopic and macroscopic scales (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-08
    Description: The attenuation and velocity dispersion of sonic waves contain valuable information on the mechanical and hydraulic properties of the probed medium. An inherent complication arising in the interpretation of corresponding measurements is, however, that there are multiple physical mechanisms contributing to the energy dissipation and that the relative importance of the various contributions is difficult to unravel. To address this problem for the practically relevant case of terrestrial alluvial sediments, we analyse the attenuation and velocity dispersion characteristics of broad-band multifrequency sonic logs with dominant source frequencies ranging between 1 and 30 kHz. To adequately compensate for the effects of geometrical spreading, which is critical for reliable attenuation estimates, we simulate our experimental setup using a correspondingly targeted numerical solution of the poroelastic equations. After having applied the thus inferred corrections, the broad-band sonic log data set, in conjunction with a comprehensive suite of complementary logging data, allows for assessing the relative importance of a range of pertinent attenuation mechanisms. In doing so, we focus on the effects of wave-induced fluid flow over a wide range of scales. Our results indicate that the levels of attenuation due to the presence of mesoscopic heterogeneities in unconsolidated clastic sediments fully saturated with water are expected to be largely negligible. Conversely, Monte-Carlo-type inversions indicate that Biot's classical model permits to explain most of the considered data. Refinements with regard to the fitting of the observed attenuation and velocity dispersion characteristics are locally provided by accounting for energy dissipation at the microscopic scale, although the nature of the underlying physical mechanism remains speculative.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 6
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    Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-08
    Description: Motivation: Stem cell differentiation is largely guided by master transcriptional regulators, but it also depends on the expression of other types of genes, such as cell cycle genes, signaling genes, metabolic genes, trafficking genes, etc. Traditional approaches to understanding gene expression patterns across multiple conditions, such as principal components analysis or K-means clustering, can group cell types based on gene expression, but they do so without knowledge of the differentiation hierarchy. Hierarchical clustering can organize cell types into a tree, but in general this tree is different from the differentiation hierarchy itself. Methods: Given the differentiation hierarchy and gene expression data at each node, we construct a weighted Euclidean distance metric such that the minimum spanning tree with respect to that metric is precisely the given differentiation hierarchy. We provide a set of linear constraints that are provably sufficient for the desired construction and a linear programming approach to identify sparse sets of weights, effectively identifying genes that are most relevant for discriminating different parts of the tree. Results: We apply our method to microarray gene expression data describing 38 cell types in the hematopoiesis hierarchy, constructing a weighted Euclidean metric that uses just 175 genes. However, we find that there are many alternative sets of weights that satisfy the linear constraints. Thus, in the style of random-forest training, we also construct metrics based on random subsets of the genes and compare them to the metric of 175 genes. We then report on the selected genes and their biological functions. Our approach offers a new way to identify genes that may have important roles in stem cell differentiation. Contact: tperkins@ohri.ca Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    Applying stability selection to consistently estimate sparse principal components in high-dimensional molecular data (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-08
    Description: Motivation: Principal component analysis (PCA) is a basic tool often used in bioinformatics for visualization and dimension reduction. However, it is known that PCA may not consistently estimate the true direction of maximal variability in high-dimensional, low sample size settings, which are typical for molecular data. Assuming that the underlying signal is sparse, i.e. that only a fraction of features contribute to a principal component (PC), this estimation consistency can be retained. Most existing sparse PCA methods use L1-penalization, i.e. the lasso , to perform feature selection. But, the lasso is known to lack variable selection consistency in high dimensions and therefore a subsequent interpretation of selected features can give misleading results. Results: We present S4VDPCA, a sparse PCA method that incorporates a subsampling approach, namely stability selection. S4VDPCA can consistently select the truly relevant variables contributing to a sparse PC while also consistently estimate the direction of maximal variability. The performance of the S4VDPCA is assessed in a simulation study and compared to other PCA approaches, as well as to a hypothetical oracle PCA that ‘knows’ the truly relevant features in advance and thus finds optimal, unbiased sparse PCs. S4VDPCA is computationally efficient and performs best in simulations regarding parameter estimation consistency and feature selection consistency. Furthermore, S4VDPCA is applied to a publicly available gene expression data set of medulloblastoma brain tumors. Features contributing to the first two estimated sparse PCs represent genes significantly over-represented in pathways typically deregulated between molecular subgroups of medulloblastoma. Availability and implementation: Software is available at https://github.com/mwsill/s4vdpca . Contact: m.sill@dkfz.de Supplementary information: Supplementary data are available at Bioinformatics online.
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    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 8
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    GS-align for glycan structure alignment and similarity measurement (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-08
    Description: Motivation: Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. Comparative structural studies of biological molecules provide useful insight into their biological relationships. However, most computational tools are designed for protein structure, and despite their importance, there is no currently available tool for comparing glycan structures in a sequence order- and size-independent manner. Results: A novel method, GS-align, is developed for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition. The optimal alignment is then determined by the maximum structural similarity score, GS-score, which is size-independent. Benchmark tests against the Protein Data Bank (PDB) N -linked glycan library and PDB homologous/non-homologous N -glycoprotein sets indicate that GS-align is a robust computational tool to align glycan structures and quantify their structural similarity. GS-align is also applied to template-based glycan structure prediction and monosaccharide substitution matrix generation to illustrate its utility. Availability and implementation: http://www.glycanstructure.org/gsalign . Contact: wonpil@ku.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 9
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    Analysis of impedance-based cellular growth assays (2015)
    Oxford University Press
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    Publication Date: 2015-08-08
    Description: Motivation: Impedance-based technologies are advancing methods for measuring proliferation of adherent cell cultures non-invasively and in real time. The analysis of the resulting data has so far been hampered by inappropriate computational methods and the lack of systematic data to evaluate the characteristics of the assay. Results: We used a commercially available system for impedance-based growth measurement (xCELLigence) and compared the reported cell index with data from microscopy. We found that the measured signal correlates linearly with the cell number throughout the time of an experiment with sufficient accuracy in subconfluent cell cultures. The resulting growth curves for various colon cancer cells could be well described with the empirical Richards growth model, which allows for extracting quantitative parameters (such as characteristic cycle times). We found that frequently used readouts like the cell index at a specific time or the area under the growth curve cannot be used to faithfully characterize growth inhibition. We propose to calculate the average growth rate of selected time intervals to accurately estimate time-dependent IC50 values of drugs from growth curves. Contact: nils.bluethgen@charite.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    Data-dependent bucketing improves reference-free compression of sequencing reads (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-25
    Description: Motivation: The storage and transmission of high-throughput sequencing data consumes significant resources. As our capacity to produce such data continues to increase, this burden will only grow. One approach to reduce storage and transmission requirements is to compress this sequencing data. Results: We present a novel technique to boost the compression of sequencing that is based on the concept of bucketing similar reads so that they appear nearby in the file. We demonstrate that, by adopting a data-dependent bucketing scheme and employing a number of encoding ideas, we can achieve substantially better compression ratios than existing de novo sequence compression tools, including other bucketing and reordering schemes. Our method, Mince, achieves up to a 45% reduction in file sizes (28% on average) compared with existing state-of-the-art de novo compression schemes. Availability and implementation : Mince is written in C++11, is open source and has been made available under the GPLv3 license. It is available at http://www.cs.cmu.edu/~ckingsf/software/mince . Contact: carlk@cs.cmu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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