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    Characterization of phenotypes by gene expression patterns and classification of samples based thereon
    1.
    发明授权
    Characterization of phenotypes by gene expression patterns and classification of samples based thereon 失效
    通过基因表达模式表征表型并基于样品的分类

    公开(公告)号：US07860660B2

    公开(公告)日：2010-12-28

    申请号：US12574195

    申请日：2009-10-06

    申请人： Andrea Califano ,  Gustavo A. Stolovitzky ,  Yuhai Tu

    发明人： Andrea Califano ,  Gustavo A. Stolovitzky ,  Yuhai Tu

    IPC分类号： G06F19/00 ,  G06F17/18 ,  G01N31/00

    CPC分类号： G06F19/24 ,  G06F19/20

    摘要： Generally, the present invention applies a transformation to convert a probability distribution of gene expression signals in control samples to a uniform distribution. The uniform distribution allows better comparisons between expression levels for genes. The transformation is derived from gene expression signals of control data, and is applied to gene expression signals of phenotype data. The phenotype data can be represented in a matrix format. A number of gene expression patterns may be determined (in the form of submatrices) that will characterize the phenotype. The uniform distribution helps in this regard, as it allows better comparisons of patterns. The gene expression patterns can then be used to classify samples as belonging to the phenotype set. Preferably, a discriminant function is used to compare a sample with the gene expression patterns that characterize the phenotype. The discriminant function can determine a score that can be used to determine whether the sample belongs to the phenotype.

    摘要翻译： 通常，本发明应用将对照样品中的基因表达信号的概率分布转换为均匀分布的转化。 均匀分布可以更好地比较基因的表达水平。 转化源自对照数据的基因表达信号，并应用于表型数据的基因表达信号。 表型数据可以以矩阵格式表示。 可以确定将以表型为特征的许多基因表达模式（以子矩阵的形式）。 统一分配在这方面有所帮助，因为它可以更好地比较模式。 然后可以将基因表达模式用于将样品分类为属于表型集。 优选地，使用判别函数将样品与表征表型的基因表达模式进行比较。 判别函数可以确定可用于确定样本是否属于表型的分数。

    Characterization of Phenotypes by Gene Expression Patterns and Classification of Samples Based Thereon
    2.
    发明申请
    Characterization of Phenotypes by Gene Expression Patterns and Classification of Samples Based Thereon 失效
    通过基因表达模式表征表型和样本分类

    公开(公告)号：US20100023273A1

    公开(公告)日：2010-01-28

    申请号：US12574195

    申请日：2009-10-06

    申请人： Andrea Califano ,  Gustavo A. Stolovitzky ,  Yuhai Tu

    发明人： Andrea Califano ,  Gustavo A. Stolovitzky ,  Yuhai Tu

    IPC分类号： G06F19/00

    CPC分类号： G06F19/24 ,  G06F19/20

    摘要： Generally, the present invention applies a transformation to convert a probability distribution of gene expression signals in control samples to a uniform distribution. The uniform distribution allows better comparisons between expression levels for genes. The transformation is derived from gene expression signals of control data, and is applied to gene expression signals of phenotype data. The phenotype data can be represented in a matrix format. A number of gene expression patterns may be determined (in the form of submatrices) that will characterize the phenotype. The uniform distribution helps in this regard, as it allows better comparisons of patterns. The gene expression patterns can then be used to classify samples as belonging to the phenotype set. Preferably, a discriminant function is used to compare a sample with the gene expression patterns that characterize the phenotype. The discriminant function can determine a score that can be used to determine whether the sample belongs to the phenotype.

    摘要翻译： 通常，本发明应用将对照样品中的基因表达信号的概率分布转换为均匀分布的转化。 均匀分布可以更好地比较基因的表达水平。 转化源自对照数据的基因表达信号，并应用于表型数据的基因表达信号。 表型数据可以以矩阵格式表示。 可以确定将以表型为特征的许多基因表达模式（以子矩阵的形式）。 统一分配在这方面有所帮助，因为它可以更好地比较模式。 然后可以将基因表达模式用于将样品分类为属于表型集。 优选地，使用判别函数将样品与表征表型的基因表达模式进行比较。 判别函数可以确定可用于确定样本是否属于表型的分数。

    Method and apparatus for determining gene expression levels
    3.
    发明授权
    Method and apparatus for determining gene expression levels 失效
    用于确定基因表达水平的方法和装置

    公开(公告)号：US06816790B2

    公开(公告)日：2004-11-09

    申请号：US10365891

    申请日：2003-02-13

    申请人： Geoffrey Grinstein ,  Glenn Allen Held ,  Yuhai Tu

    发明人： Geoffrey Grinstein ,  Glenn Allen Held ,  Yuhai Tu

    IPC分类号： G06F1900

    CPC分类号： G06F19/20

    摘要： Techniques for analyzing gene expression levels are provided. In one aspect of the invention, the technique provides a method for determining a concentration level of a target nucleic acid, the target nucleic acid comprising at least one target oligonucleotide. The method determines (i) a measure of affinity value of the target oligonucleotide with a probe oligonucleotide; and (ii) a hybridization intensity value for the target oligonucleotide and the probe oligonucleotide at a probe spot. The measure of affinity value and the hybridization intensity value are used to determine the concentration level of the target nucleic acid.

    Techniques for reconstructing synthetic networks using pair-wise correlation analysis
    6.
    发明申请
    Techniques for reconstructing synthetic networks using pair-wise correlation analysis 有权
    使用成对相关分析重建合成网络的技术

    公开(公告)号：US20050096887A1

    公开(公告)日：2005-05-05

    申请号：US10699283

    申请日：2003-10-31

    申请人： J. Rice ,  Gustavo Stolovitzky ,  Yuhai Tu

    发明人： J. Rice ,  Gustavo Stolovitzky ,  Yuhai Tu

    IPC分类号： G06F17/10 ,  G06F19/00

    CPC分类号： G06F19/12

    摘要： Techniques for reconstructing networks are provided. In one aspect, a method for reconstructing a synthetic network, such as a synthetic biological network, is provided. In another aspect, a method for reconstructing a supply chain network is provided. Exemplary supply chain networks include supply chains for petroleum distribution.

    摘要翻译： 提供了重建网络的技术。 一方面，提供了一种用于重建诸如合成生物网络的合成网络的方法。 另一方面，提供一种重建供应链网络的方法。 示例性供应链网络包括石油分销供应链。

    Techniques for reconstructing synthetic networks using pair-wise correlation analysis
    7.
    发明授权
    Techniques for reconstructing synthetic networks using pair-wise correlation analysis 有权
    使用成对相关分析重建合成网络的技术

    公开(公告)号：US07496550B2

    公开(公告)日：2009-02-24

    申请号：US10699283

    申请日：2003-10-31

    申请人： J. Jeremy Rice ,  Gustavo Stolovitzky ,  Yuhai Tu

    发明人： J. Jeremy Rice ,  Gustavo Stolovitzky ,  Yuhai Tu

    IPC分类号： G06F17/00 ,  G06N5/02

    CPC分类号： G06F19/12

    摘要： Techniques for reconstructing networks are provided. In one aspect, a method for reconstructing a synthetic network, such as a synthetic biological network, is provided. In another aspect, a method for reconstructing a supply chain network is provided. Exemplary supply chain networks include supply chains for petroleum distribution.

    摘要翻译： 提供了重建网络的技术。 一方面，提供了一种用于重建诸如合成生物网络的合成网络的方法。 另一方面，提供一种重建供应链网络的方法。 示例性供应链网络包括石油分销供应链。