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  • Oxford University Press  (157)
  • American Physical Society (APS)  (45)
  • 2020-2023
  • 2010-2014  (173)
  • 2000-2004  (21)
  • 1980-1984  (6)
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  • 11
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    A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data (2013)
    Oxford University Press
    Details
    Publication Date: 2013-01-17
    Description: Motivation: The Illumina Infinium 450 k DNA Methylation Beadchip is a prime candidate technology for Epigenome-Wide Association Studies (EWAS). However, a difficulty associated with these beadarrays is that probes come in two different designs, characterized by widely different DNA methylation distributions and dynamic range, which may bias downstream analyses. A key statistical issue is therefore how best to adjust for the two different probe designs. Results: Here we propose a novel model-based intra-array normalization strategy for 450 k data, called BMIQ (Beta MIxture Quantile dilation), to adjust the beta-values of type2 design probes into a statistical distribution characteristic of type1 probes. The strategy involves application of a three-state beta-mixture model to assign probes to methylation states, subsequent transformation of probabilities into quantiles and finally a methylation-dependent dilation transformation to preserve the monotonicity and continuity of the data. We validate our method on cell-line data, fresh frozen and paraffin-embedded tumour tissue samples and demonstrate that BMIQ compares favourably with two competing methods. Specifically, we show that BMIQ improves the robustness of the normalization procedure, reduces the technical variation and bias of type2 probe values and successfully eliminates the type1 enrichment bias caused by the lower dynamic range of type2 probes. BMIQ will be useful as a preprocessing step for any study using the Illumina Infinium 450 k platform. Availability: BMIQ is freely available from http://code.google.com/p/bmiq/ . Contact: a.teschendorff@ucl.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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  • 12
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    PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-14
    Description: Pan-genome ortholog clustering tool ( PanOCT ) is a tool for pan-genomic analysis of closely related prokaryotic species or strains. PanOCT uses conserved gene neighborhood information to separate recently diverged paralogs into orthologous clusters where homology-only clustering methods cannot. The results from PanOCT and three commonly used graph-based ortholog-finding programs were compared using a set of four publicly available strains of the same bacterial species. All four methods agreed on ~70% of the clusters and ~86% of the proteins. The clusters that did not agree were inspected for evidence of correctness resulting in 85 high-confidence manually curated clusters that were used to compare all four methods.
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 13
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    Reinforcement learning for Golog programs with first-order state-abstraction (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-25
    Description: A special feature of programs in the action language Golog are non-deterministic constructs such as non-deterministic choice of actions or arguments. It has been shown that in the presence of stochastic actions and rewards reinforcement learning techniques can be applied to obtain optimal choices for those choice-points. In order to avoid an explosion of the state space, an abstraction mechanism is employed that computes first-order state descriptions for the given program. Intuitively, the idea is to generate abstract descriptions that group together states for which the expected reward of executing the program is the same. A current limitation is that a non-deterministic choice of arguments can be handled only if the possible candidates are known in advance. In this article we show how this restriction can be lifted. We also show how a first-order variant of binary decision diagrams can be used to efficiently compute first-order state abstractions. Moreover, we give a completely declarative specification of a learning Golog interpreter that incorporates the presented state-abstraction mechanisms.
    Print ISSN: 1367-0751
    Electronic ISSN: 1368-9894
    Topics: Mathematics
    Published by Oxford University Press
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  • 14
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    Signal analysis for genome-wide maps of histone modifications measured by ChIP-seq (2012)
    Oxford University Press
    Details
    Publication Date: 2012-04-08
    Description: Motivation: Chromatin structure, including post-translational modifications of histones, regulates gene expression, alternative splicing and cell identity. ChIP-seq is an increasingly used assay to study chromatin function. However, tools for downstream bioinformatics analysis are limited and are only based on the evaluation of signal intensities. We reasoned that new methods taking into account other signal characteristics such as peak shape, location and frequencies might reveal new insights into chromatin function, particularly in situation where differences in read intensities are subtle. Results: We introduced an analysis pipeline, based on linear predictive coding (LPC), which allows the capture and comparison of ChIP-seq histone profiles. First, we show that the modeled signal profiles distinguish differentially expressed genes with comparable accuracy to signal intensities. The method was robust against parameter variations and performed well up to a signal-to-noise ratio of 0.55. Additionally, we show that LPC profiles of activating and repressive histone marks cluster into distinct groups and can be used to predict their function. Availability and implementation: http://www.cancerresearch.unsw.edu.au/crcweb.nsf/page/LPCHP A Matlab implementation along with usage instructions and an example input file are available from: http://www.cancerresearch.unsw.edu.au/crcweb.nsf/page/LPCHP Contact: d.beck@student.unsw.edu.au ; jpimanda@unsw.edu.au ; jason.wong@unsw.edu.au 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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  • 15
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    Deficiency of FRAS1-related extracellular matrix 1 (FREM1) causes congenital diaphragmatic hernia in humans and mice (2013)
    Oxford University Press
    Details
    Publication Date: 2013-02-02
    Description: Congenital diaphragmatic hernia (CDH) is a common life-threatening birth defect. Recessive mutations in the FRAS1-related extracellular matrix 1 ( FREM1 ) gene have been shown to cause bifid nose with or without anorectal and renal anomalies (BNAR) syndrome and Manitoba oculotrichoanal (MOTA) syndrome, but have not been previously implicated in the development of CDH. We have identified a female child with an isolated left-sided posterolateral CDH covered by a membranous sac who had no features suggestive of BNAR or MOTA syndromes. This child carries a maternally-inherited ~86 kb FREM1 deletion that affects the expression of FREM1 's full-length transcripts and a paternally-inherited splice site mutation that causes activation of a cryptic splice site, leading to a shift in the reading frame and premature termination of all forms of the FREM1 protein. This suggests that recessive FREM1 mutations can cause isolated CDH in humans. Further evidence for the role of FREM1 in the development of CDH comes from an N -ethyl- N -nitrosourea -derived mouse strain, eyes2 , which has a homozygous truncating mutation in Frem1. Frem1 eyes2 mice have eye defects, renal agenesis and develop retrosternal diaphragmatic hernias which are covered by a membranous sac. We confirmed that Frem1 is expressed in the anterior portion of the developing diaphragm and found that Frem1 eyes2 embryos had decreased levels of cell proliferation in their developing diaphragms when compared to wild-type embryos. We conclude that FREM1 plays a critical role in the development of the diaphragm and that FREM1 deficiency can cause CDH in both humans and mice.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 16
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    Open borders for system-on-a-chip buses: A wire format for connecting large physics controls (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-08-24
    Description: Author(s): M. Kreider, R. Bär, D. Beck, W. Terpstra, J. Davies, V. Grout, J. Lewis, J. Serrano, and T. Wlostowski System-on-a-chip (SoC) bus systems are typically confined on-chip and rely on higher level components to communicate with the outside world. The idea behind the EtherBone (EB) protocol is to extend the reach of the SoC bus to remote field-programmable gate arrays or processors. The EtherBone core im... [Phys. Rev. ST Accel. Beams 15, 082801] Published Thu Aug 23, 2012
    Keywords: Beam Control, Diagnostics, and Feedback
    Electronic ISSN: 1098-4402
    Topics: Physics
    Published by American Physical Society (APS)
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  • 17
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    Mouse model reveals the role of SOX7 in the development of congenital diaphragmatic hernia associated with recurrent deletions of 8p23.1 (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-28
    Description: Recurrent microdeletions of 8p23.1 that include GATA4 and SOX7 confer a high risk of both congenital diaphragmatic hernia (CDH) and cardiac defects. Although GATA4-deficient mice have both CDH and cardiac defects, no humans with cardiac defects attributed to GATA4 mutations have been reported to have CDH. We were also unable to identify deleterious GATA4 sequence changes in a CDH cohort. This suggested that haploinsufficiency of another 8p23.1 gene may contribute, along with GATA4 , to the development of CDH. To determine if haploinsufficiency of SOX7 —another transcription factor encoding gene—contributes to the development of CDH, we generated mice with a deletion of the second exon of Sox7 . A portion of these Sox7 ex2/+ mice developed retrosternal diaphragmatic hernias located in the anterior muscular portion of the diaphragm. Anterior CDH is also seen in Gata4 +/– mice and has been described in association with 8p23.1 deletions in humans. Immunohistochemistry revealed that SOX7 is expressed in the vascular endothelial cells of the developing diaphragm and may be weakly expressed in some diaphragmatic muscle cells. Sox7 ex2/ex2 embryos die prior to diaphragm development with dilated pericardial sacs and failure of yolk sac remodeling suggestive of cardiovascular failure. Similar to our experience screening GATA4 , no clearly deleterious SOX7 sequence changes were identified in our CDH cohort. We conclude that haploinsufficiency of Sox7 or Gata4 is sufficient to produce anterior CDH in mice and that haploinsufficiency of SOX7 and GATA4 may each contribute to the development of CDH in individuals with 8p23.1 deletions.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 18
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    Surveying the N=40 island of inversion with new manganese masses (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-07-21
    Description: Author(s): S. Naimi, G. Audi, D. Beck, K. Blaum, Ch. Böhm, Ch. Borgmann, M. Breitenfeldt, S. George, F. Herfurth, A. Herlert, A. Kellerbauer, M. Kowalska, D. Lunney, E. Minaya Ramirez, D. Neidherr, M. Rosenbusch, L. Schweikhard, R. N. Wolf, and K. Zuber High-precision mass measurements of neutron-rich 57−66 Mn and 61−63 Fe isotopes are reported. The new mass surface shows no shell closure at N =40 . In contrast, there is an increase of the two-neutron separation energy at N =38 . This behavior is consistent with the onset of collectivity due to the occup... [Phys. Rev. C 86, 014325] Published Fri Jul 20, 2012
    Keywords: Nuclear Structure
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
    Published by American Physical Society (APS)
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  • 19
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    Mapping of Electron-Hole Excitations in the Charge-Density-Wave System 1T-TiSe_{2} Using Resonant Inelastic X-Ray Scattering (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-07-25
    Description: Author(s): C. Monney, K. J. Zhou, H. Cercellier, Z. Vydrova, M. G. Garnier, G. Monney, V. N. Strocov, H. Berger, H. Beck, T. Schmitt, and P. Aebi In high-resolution resonant inelastic x-ray scattering at the Ti L edge of the charge-density-wave system 1 T -TiSe 2 , we observe sharp low energy loss peaks from electron-hole pair excitations developing at low temperature. These excitations are strongly dispersing as a function of the transferred mom... [Phys. Rev. Lett. 109, 047401] Published Tue Jul 24, 2012
    Keywords: Condensed Matter: Electronic Properties, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 20
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    Decadal-scale changes in southern California sciaenids under different levels of harvesting pressure (2011)
    Oxford University Press
    Details
    Publication Date: 2011-11-24
    Description: Miller, E. F., Pondella II, D. J., Beck, D. S., and Herbinson, K. T. 2011. Decadal-scale changes in southern California sciaenids under different levels of harvesting pressure. – ICES Journal of Marine Science, 68: 2123–2133. A unique 38-year time-series of power-plant entrapment data collected across ~170 km of the southern California coastline was examined to describe the decadal-scale trends in common Southern California Bight sciaenid abundance in relation to oceanographic conditions. Adult catches for five of seven species declined at differing rates and severity. Declines of up to 94% were detected in historically common species such as Genyonemus lineatus , whereas historically less abundant species have increased dramatically, e.g. Umbrina roncador (2626%). Over time, the entrapped community became increasingly influenced by species with more southerly distributions, indicated by a significant decline in the average latitudinal midpoint of the community. This shift was significantly related to rising ocean temperature and took place in the early to mid-1980s. The observed species-specific abundance changes in all species except Atractoscion nobilis were significantly correlated with sea surface temperature, nearshore plankton volumetric biomass, G. lineatus or Seriphus politus nearshore larval density, or a combination of these. Patterns in A. nobilis abundance were the most isolated, likely reflecting its standing as an intensively fished species, unlike the other six species evaluated. The consistent relationship with environmental indices strongly supported the notion of a faunal shift driven by bottom-up forcing.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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