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  • Oxford University Press (OUP)  (3)
  • 2005-2009  (3)
  • 1
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2009
    In:  Bioinformatics Vol. 25, No. 9 ( 2009-05-01), p. 1099-1104
    In: Bioinformatics, Oxford University Press (OUP), Vol. 25, No. 9 ( 2009-05-01), p. 1099-1104
    Abstract: Motivation: Many high-resolution array comparative genomic hybridization tumor profiles contain a wave bias, which makes accurate detection of breakpoints in such profiles more difficult. Results: An efficient and highly effective algorithm that largely removes the wave bias from tumor profiles by regressing the tumor profile data on data of profiles from the clinical genetics practice. Results are illustrated on two independent datasets. The algorithm is shown to be robust against the presence of true copy number aberrations. Moreover, the smoothed profiles are able to recapitulate the aberration location and signal for simulated tumor profiles. Availability: Easy-to-use R scripts, user instructions and data are available from http://www.few.vu.nl/~mavdwiel/nowaves.html. Contact:  mark.vdwiel@vumc.nl Supplementary information:  Supplementary information are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2009
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2007
    In:  Microscopy Today Vol. 15, No. 5 ( 2007-09-01), p. 16-21
    In: Microscopy Today, Oxford University Press (OUP), Vol. 15, No. 5 ( 2007-09-01), p. 16-21
    Abstract: Most of the specimens for high-resolution electron microscopy have amorphous surface layers due to contamination during observation and/or damaged surface layers during specimen preparation. Moreover, many specimens are radiation sensitive, and a part of the specimen easily becomes amorphous during the observation. These amorphous materials make clear observation of crystal structure difficult. A periodic structure may be extracted by simply using a periodic mask in Fourier space. However, this kind of mask often introduces a periodic feature in addition to the crystal structure. To reduce such artifacts a Wiener filter or an average background subtraction filter has been discussed. However, these filters do not work for non-ideal crystals, such as cylindrical crystals and nano-crystals, where a translational periodicity is limited to the order of nano-meter. In this report we improve these filters by introducing new ways to estimate a contribution from the amorphous materials.
    Type of Medium: Online Resource
    ISSN: 2150-3583 , 1551-9295
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2007
    detail.hit.zdb_id: 2139756-9
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  • 3
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2005
    In:  Bioinformatics Vol. 21, No. 7 ( 2005-04-01), p. 1146-1153
    In: Bioinformatics, Oxford University Press (OUP), Vol. 21, No. 7 ( 2005-04-01), p. 1146-1153
    Abstract: Motivation: Plots of array Comparative Genomic Hybridization (CGH) data often show special patterns: stretches of constant level (copy number) with sharp jumps between them. There can also be much noise. Classic smoothing algorithms do not work well, because they introduce too much rounding. To remedy this, we introduce a fast and effective smoothing algorithm based on penalized quantile regression. It can compute arbitrary quantile curves, but we concentrate on the median to show the trend and the lower and upper quartile curves showing the spread of the data. Two-fold cross-validation is used for optimizing the weight of the penalties. Results: Simulated data and a published dataset are used to show the capabilities of the method to detect the segments of changed copy numbers in array CGH data. Availability: Software for R and Matlab is available. Contact:  p.eilers@lumc.nl
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2005
    detail.hit.zdb_id: 1468345-3
    SSG: 12
    Location Call Number Limitation Availability
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