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  • 1
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    Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation (2013)
    Oxford University Press
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    Publication Date: 2013-02-02
    Description: Structural variation is an important class of genetic variation in mammals. High-throughput sequencing (HTS) technologies promise to revolutionize copy-number variation (CNV) detection but present substantial analytic challenges. Converging evidence suggests that multiple types of CNV-informative data (e.g. read-depth, read-pair, split-read) need be considered, and that sophisticated methods are needed for more accurate CNV detection. We observed that various sources of experimental biases in HTS confound read-depth estimation, and note that bias correction has not been adequately addressed by existing methods. We present a novel read-depth–based method, GENSENG, which uses a hidden Markov model and negative binomial regression framework to identify regions of discrete copy-number changes while simultaneously accounting for the effects of multiple confounders. Based on extensive calibration using multiple HTS data sets, we conclude that our method outperforms existing read-depth–based CNV detection algorithms. The concept of simultaneous bias correction and CNV detection can serve as a basis for combining read-depth with other types of information such as read-pair or split-read in a single analysis. A user-friendly and computationally efficient implementation of our method is freely available.
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Allele-specific copy-number discovery from whole-genome and whole-exome sequencing (2015)
    Oxford University Press
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    Publication Date: 2015-08-18
    Description: Copy-number variants (CNVs) are a major form of genetic variation and a risk factor for various human diseases, so it is crucial to accurately detect and characterize them. It is conceivable that allele-specific reads from high-throughput sequencing data could be leveraged to both enhance CNV detection and produce allele-specific copy number (ASCN) calls. Although statistical methods have been developed to detect CNVs using whole-genome sequence (WGS) and/or whole-exome sequence (WES) data, information from allele-specific read counts has not yet been adequately exploited. In this paper, we develop an integrated method, called AS-GENSENG, which incorporates allele-specific read counts in CNV detection and estimates ASCN using either WGS or WES data. To evaluate the performance of AS-GENSENG, we conducted extensive simulations, generated empirical data using existing WGS and WES data sets and validated predicted CNVs using an independent methodology. We conclude that AS-GENSENG not only predicts accurate ASCN calls but also improves the accuracy of total copy number calls, owing to its unique ability to exploit information from both total and allele-specific read counts while accounting for various experimental biases in sequence data. Our novel, user-friendly and computationally efficient method and a complete analytic protocol is freely available at https://sourceforge.net/projects/asgenseng/ .
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    QPOs and Orbital elements of X-ray binary 4U 0115+63 during the 2017 outburst observed by Insight-HXMT (2021)
    Oxford University Press
    Details
    Publication Date: 2021-03-24
    Description: In this paper, we presented a detailed timing analysis of a prominent outburst of 4U 0115+63 detected by Insight-HXMT in 2017 August. The spin period of the neutron star was determined to be 3.61398 ± 0.00002 s at MJD 57978. We measured the period variability and extract the orbital elements of the binary system. The angle of periastron evolved with a rate of $0.048^circ pm 0.003^circ m , yr^{-1}$. The light curves are folded to sketch the pulse profiles in different energy ranges. A multi-peak structure in 1-10 keV is clearly illustrated. We introduced wavelet analysis into our data analysis procedures to study QPO signals and perform a detailed wavelet analysis in many different energy ranges. Through the wavelet spectra, we report the discovery of a QPO at the frequency ∼10 mHz. In addition, the X-ray light curves showed multiple QPOs in the period of ∼16 − 32 s and ∼67 − 200 s. We found that the ∼100 s QPO was significant in most of the observations and energies. There exist positive relations between X-ray luminosity and their Q-factors and S-factors, while the QPO periods have no correlation with X-ray luminosity. In wavelet phase maps, we found that the pulse phase of ∼67 − 200 s QPO drifting frequently while the ∼16 − 32 s QPO scarcely drifting. The dissipation of oscillations from high energy to low energy was also observed. These features of QPOs in 4U 0115+63 provide new challenge to our understanding of their physical origins.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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  • 4
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    Planes of satellite galaxies: when exceptions are the rule (2015)
    Oxford University Press
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    Publication Date: 2015-08-08
    Description: The detection of planar structures within the satellite systems of both the Milky Way (MW) and Andromeda (M31) has been reported as being in stark contradiction to the predictions of the standard cosmological model ( cold dark matter – CDM). Given the ambiguity in defining a planar configuration, it is unclear how to interpret the low incidence of the MW and M31 planes in CDM. We investigate the prevalence of satellite planes around galactic mass haloes identified in high-resolution cosmological simulations. We find that planar structures are very common, and that ~10 per cent of CDM haloes have even more prominent planes than those present in the Local Group. While ubiquitous, the planes of satellite galaxies show a large diversity in their properties. This precludes using one or two systems as small-scale probes of cosmology, since a large sample of satellite systems is needed to obtain a good measure of the object-to-object variation. This very diversity has been misinterpreted as a discrepancy between the satellite planes observed in the Local Group and CDM predictions. In fact, ~10 per cent of CDM galactic haloes have planes of satellites that are as infrequent as the MW and M31 planes. The look-elsewhere effect plays an important role in assessing the detection significance of satellite planes and accounting for it leads to overestimating the significance level by a factor of 30 and 100 for the MW and M31 systems, respectively.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Estimating the dark matter halo mass of our Milky Way using dynamical tracers (2015)
    Oxford University Press
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    Publication Date: 2015-08-15
    Description: The mass of the dark matter halo of the Milky Way can be estimated by fitting analytical models to the phase-space distribution of dynamical tracers. We test this approach using realistic mock stellar haloes constructed from the Aquarius N -body simulations of dark matter haloes in the cold dark matter cosmology. We extend the standard treatment to include a Navarro–Frenk–White potential and use a maximum likelihood method to recover the parameters describing the simulated haloes from the positions and velocities of their mock halo stars. We find that the estimate of halo mass is highly correlated with the estimate of halo concentration. The best-fitting halo masses within the virial radius, R 200 , are biased, ranging from a 40 per cent underestimate to a 5 per cent overestimate in the best case (when the tangential velocities of the tracers are included). There are several sources of bias. Deviations from dynamical equilibrium can potentially cause significant bias; deviations from spherical symmetry are relatively less important. Fits to stars at different galactocentric radii can give different mass estimates. By contrast, the model gives good constraints on the mass within the half-mass radius of tracers even when restricted to tracers within 60 kpc. The recovered velocity anisotropies of tracers, β, are biased systematically, but this does not affect other parameters if tangential velocity data are used as constraints.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-29
    Description: The RNA-directed DNA methylation (RdDM) pathway can be divided into three phases: 1) small interfering RNA biogenesis, 2) de novo methylation, and 3) chromatin modification. To determine the degree of conservation of this pathway we searched for key genes among land plants. We used OrthoMCL and the OrthoMCL Viridiplantae database to analyze proteomes of species in bryophytes, lycophytes, monilophytes, gymnosperms, and angiosperms. We also analyzed small RNA size categories and, in two gymnosperms, cytosine methylation in ribosomal DNA. Six proteins were restricted to angiosperms, these being NRPD4/NRPE4, RDM1, DMS3 (defective in meristem silencing 3), SHH1 (SAWADEE homeodomain homolog 1), KTF1, and SUVR2, although we failed to find the latter three proteins in Fritillaria persica , a species with a giant genome. Small RNAs of 24 nt in length were abundant only in angiosperms. Phylogenetic analyses of Dicer-like (DCL) proteins showed that DCL2 was restricted to seed plants, although it was absent in Gnetum gnemon and Welwitschia mirabilis . The data suggest that phases (1) and (2) of the RdDM pathway, described for model angiosperms, evolved with angiosperms. The absence of some features of RdDM in F. persica may be associated with its large genome. Phase (3) is probably the most conserved part of the pathway across land plants. DCL2, involved in virus defense and interaction with the canonical RdDM pathway to facilitate methylation of CHH, is absent outside seed plants. Its absence in G. gnemon , and W. mirabilis coupled with distinctive patterns of CHH methylation, suggest a secondary loss of DCL2 following the divergence of Gnetales.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Seismological investigation of the 2016 January 6 North Korean underground nuclear test (2016)
    Oxford University Press
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    Publication Date: 2016-07-13
    Description: Seismology plays an important role in characterizing potential underground nuclear tests. Using broad-band digital seismic data from Northeast China, South Korea and Japan, we investigated the properties of the recent seismic event occurred in North Korea on 2016 January 6. Using a relative location method and choosing the previous 2006 explosion as the master event, the 2016 event was located within the North Korean nuclear test site, with its epicentre at latitude 41.3003°N and longitude 129.0678°E, approximately 900 m north and 500 m west of the previous event on 2013 February 12. Based on the error ellipse, the relocation uncertainty was approximately 70 m. Using the P / S spectral ratios, including Pg/Lg, Pn/Lg and Pn/Sn, as the discriminants, we identify the 2016 event as an explosion rather than an earthquake. The body-wave magnitude calculated from regional wave Lg is m b (Lg) equal to 4.7 ± 0.2. Adopting an empirical magnitude–yield relation, and assuming that the explosion is fully coupled and detonated at a normally scaled depth, we find that the seismic yield is about 4 kt, with the uncertainties allowing a range from 2 to 8 kt.
    Keywords: Express Letters, 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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  • 8
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    RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-28
    Description: DNA Topoisomerases are essential to resolve topological problems during DNA metabolism in all species. However, the prevalence and function of RNA topoisomerases remain uncertain. Here, we show that RNA topoisomerase activity is prevalent in Type IA topoisomerases from bacteria, archaea, and eukarya. Moreover, this activity always requires the conserved Type IA core domains and the same catalytic residue used in DNA topoisomerase reaction; however, it does not absolutely require the non-conserved carboxyl-terminal domain (CTD), which is necessary for relaxation reactions of supercoiled DNA. The RNA topoisomerase activity of human Top3β differs from that of Escherichia coli topoisomerase I in that the former but not the latter requires the CTD, indicating that topoisomerases have developed distinct mechanisms during evolution to catalyze RNA topoisomerase reactions. Notably, Top3β proteins from several animals associate with polyribosomes, which are units of mRNA translation, whereas the Top3 homologs from E. coli and yeast lack the association. The Top3β-polyribosome association requires TDRD3, which directly interacts with Top3β and is present in animals but not bacteria or yeast. We propose that RNA topoisomerases arose in the early RNA world, and that they are retained through all domains of DNA-based life, where they mediate mRNA translation as part of polyribosomes in animals.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Mutations of charged amino acids at the cytoplasmic end of transmembrane helix 2 affect transport activity of the budding yeast multidrug resistance protein Pdr5p (2016)
    Oxford University Press
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    Publication Date: 2016-05-11
    Description: Pdr5p is a major ATP-binding cassette (ABC) transporter in Saccharomyces cerevisiae. It displays a sequence and functional homology to the pathogenic Candida albicans multidrug resistance protein Cdr1p. The transmembrane helices of Pdr5p act in substrate recognition, binding, translocation and eventual removal of toxic substances out of the plasma membrane via the formation of a binding pocket. In this study, we identify two novel Pdr5 mutants (E574K and E580K), which exhibit impaired substrate efflux functions. Both mutants remained hypersensitive to all tested Pdr5p substrates without affecting their protein expression levels, localization or ATPase activities. As E574 and E580 are both located adjacent to the predicted cytoplasmic end of transmembrane helix 2, this implies that such charged residues are functionally essential for Pdr5p. Molecular docking studies suggest the possibility that oppositely charged substitution at residue E574 may disturb the interaction between the substrates and Pdr5p, resulting in impaired transport activity. Our results present new evidence, suggesting that transmembrane helix 2 plays an important role for the efflux function of Pdr5p.
    Print ISSN: 1567-1356
    Electronic ISSN: 1567-1364
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution (2016)
    Oxford University Press
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    Publication Date: 2016-05-06
    Description: RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous ‘synthetic nucleic acid substitution’ strategy has been successfully applied in dissecting the function of nucleic acid moieties in pol II transcription. However, how the triphosphate moiety of substrate influences the rate of P-O bond cleavage and formation during nucleotide incorporation is still unclear. Here, by employing β, -bridging atom-‘substituted’ NTPs, we elucidate how the methylene substitution in the pyrophosphate leaving group affects cognate and non-cognate nucleotide incorporation. Intriguingly, the effect of the β, -methylene substitution on the non-cognate UTP/dT scaffold (~3-fold decrease in k pol ) is significantly different from that of the cognate ATP/dT scaffold (~130-fold decrease in k pol ). Removal of the wobble hydrogen bonds in U:dT recovers a strong response to methylene substitution of UTP. Our kinetic and modeling studies are consistent with a unique altered transition state for bond formation and cleavage for UTP/dT incorporation compared with ATP/dT incorporation. Collectively, our data reveals the functional interplay between NTP triphosphate moiety and base pair hydrogen bonding recognition during nucleotide incorporation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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