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    NON-RANDOM CONTROL DATA SET GENERATION FOR FACILITATING GENOMIC DATA PROCESSING
    1.
    发明申请
    NON-RANDOM CONTROL DATA SET GENERATION FOR FACILITATING GENOMIC DATA PROCESSING 审中-公开
    非随机控制数据集生成促进基因数据处理

    公开(公告)号：US20080281819A1

    公开(公告)日：2008-11-13

    申请号：US12026051

    申请日：2008-02-05

    申请人： Scott A. TENENBAUM ,  Christopher ZALESKI ,  Francis DOYLE ,  Ajish GEORGE

    发明人： Scott A. TENENBAUM ,  Christopher ZALESKI ,  Francis DOYLE ,  Ajish GEORGE

    IPC分类号： G06F7/06 ,  G06F17/30

    CPC分类号： G16B40/00 ,  G16B20/00

    摘要： Processing of genomic data is facilitated by providing a control data set generation system wherein a control generator tool or process creates matched data sets for facilitating informatics analysis. These matched data sets may include genomic loci or genomic sequences, or both. The data is taken from a database of actual genomic data, including sequence and annotation data, as opposed to ad-hoc generation, sequence scrambling or the like. This produces biologically relevant and accurate results which allow for stronger controls. The controls are matched against a user-provided data set via a number of parameters.

    摘要翻译： 通过提供控制数据集生成系统来促进基因组数据的处理，其中控制生成器工具或过程创建用于促进信息分析的匹配数据集。 这些匹配的数据集可以包括基因组基因座或基因组序列，或两者。 数据来自实际基因组数据的数据库，包括序列和注释数据，而不是自组织生成，序列加扰等。 这产生了生物相关和准确的结果，允许更强的控制。 控件通过多个参数与用户提供的数据集进行匹配。

    Methods for Isolating and Characterizing Endogenous mRNA-Protein (mRNP) Complexes
    2.
    发明申请
    Methods for Isolating and Characterizing Endogenous mRNA-Protein (mRNP) Complexes 有权
    分离和表征内源性mRNA蛋白（mRNP）复合物的方法

    公开(公告)号：US20080248479A1

    公开(公告)日：2008-10-09

    申请号：US12049862

    申请日：2008-03-17

    申请人： Jack D. Keene ,  Scott A. Tenenbaum ,  Craig C. Carson

    发明人： Jack D. Keene ,  Scott A. Tenenbaum ,  Craig C. Carson

    IPC分类号： C12Q1/68

    CPC分类号： G01N33/5008 ,  C07H21/02 ,  C12Q1/6804 ,  C12Q1/6809 ,  C12Q2600/158 ,  G01N33/5023 ,  G01N33/5308 ,  G01N33/68 ,  G01N33/6803 ,  G01N33/6845 ,  C12Q2522/101

    摘要： Cellular mRNA-protein (mRNP) complexes are partitioned in vivo by contacting a biological sample with at least one ligand that specifically binds at least one component of a mRNP complex. Suitable biological samples comprise at least one mRNA-protein (mRNP) complex and include cell cultures, cell extracts, and whole tissue, including tumor tissue. Ligands include antibodies that specifically bind RNA-binding or RNA-associated proteins present in the mRNP complex. The mRNP complex is separated by binding the ligand with a binding molecule specific for the ligand, where the binding molecule is attached to a solid support. The mRNP complex is collected by removing the mRNP complex from the solid support. After collecting the mRNP complex, the mRNA bound within the complex may be characterized and identified. Subsets of the total mRNA population of a cell may accordingly be characterized, and a gene expression profile of the cell obtained.

    摘要翻译： 通过使生物样品与至少一种特异性结合mRNP复合物的至少一种组分的配体接触，在体内分配细胞mRNA-蛋白（mRNP）复合物。 合适的生物样品包含至少一种mRNA-蛋白（mRNP）复合物，并且包括细胞培养物，细胞提取物和包括肿瘤组织的整个组织。 配体包括特异性结合存在于mRNP复合物中的RNA结合或RNA相关蛋白的抗体。 通过将配体与对配体特异性的结合分子结合来分离mRNP复合物，其中结合分子连接到固体支持物上。 通过从固体支持物上除去mRNP复合物来收集mRNP复合物。 在收集mRNP复合物后，可以鉴定和鉴定复合物内结合的mRNA。 因此可以对细胞的总mRNA群体的亚群进行表征，并获得所获得的细胞的基因表达谱。

    Trans-acting RNA switches
    4.
    发明授权
    Trans-acting RNA switches 有权
    反式RNA开关

    公开(公告)号：US08841438B2

    公开(公告)日：2014-09-23

    申请号：US13321816

    申请日：2010-05-21

    申请人： Scott A. Tenenbaum ,  Francis J. Doyle, II ,  Ajish George ,  Christopher Zaleski

    发明人： Scott A. Tenenbaum ,  Francis J. Doyle, II ,  Ajish George ,  Christopher Zaleski

    IPC分类号： C07H21/04 ,  C07H21/02 ,  C12N15/63 ,  C12N15/85

    CPC分类号： C12N15/113 ,  C12N15/111 ,  C12N2310/113 ,  C12N2310/141 ,  C12N2310/531 ,  C12N2320/50 ,  C12N2330/51 ,  G01N33/5005 ,  G01N33/5308

    摘要： Disclosed are RNA constructs which function to activate or inactivate a biological process, e.g., may be designed for attachment to a polypeptide coding region. Such RNA constructs modulate translation of a polypeptide from the coding region in response to the presence of a target polynucleotide in an expression environment. Such RNA constructs include a weakened stem-loop structure which, when bound to the target polynucleotide, assumes stem-loop secondary structure and associates with an RNA binding protein. Association with the RNA binding protein modulates translation of the polypeptide coding region. Such RNA constructs also have three-way junction joining regions 3′ and 5′ of the stem-loop structure.

    摘要翻译： 公开了用于激活或灭活生物过程的RNA构建体，例如可以设计用于附着到多肽编码区。 响应于表达环境中靶多核苷酸的存在，这样的RNA构建体调节来自编码区的多肽的翻译。 这样的RNA构建体包括弱化的茎 - 环结构，其当与靶多核苷酸结合时，其呈现茎环二级结构并与RNA结合蛋白缔合。 与RNA结合蛋白的结合调节多肽编码区的翻译。 这样的RNA构建体也具有茎 - 环结构的三通连接区域3'和5'。

    Methods for isolating and characterizing endogenous mRNA-protein (mRNP) complexes
    6.
    发明授权
    Methods for isolating and characterizing endogenous mRNA-protein (mRNP) complexes 有权
    分离和表征内源性mRNA - 蛋白（mRNP）复合物的方法

    公开(公告)号：US08143002B2

    公开(公告)日：2012-03-27

    申请号：US12049862

    申请日：2008-03-17

    申请人： Jack D. Keene ,  Scott A. Tenenbaum ,  Craig C. Carson

    发明人： Jack D. Keene ,  Scott A. Tenenbaum ,  Craig C. Carson

    IPC分类号： C12Q1/68 ,  G01N33/53 ,  G01N33/536 ,  G01N33/543 ,  C12N15/00

    CPC分类号： G01N33/5008 ,  C07H21/02 ,  C12Q1/6804 ,  C12Q1/6809 ,  C12Q2600/158 ,  G01N33/5023 ,  G01N33/5308 ,  G01N33/68 ,  G01N33/6803 ,  G01N33/6845 ,  C12Q2522/101

    摘要： Cellular mRNA-protein (mRNP) complexes are partitioned in vivo by contacting a biological sample with at least one ligand that specifically binds at least one component of a mRNP complex. Suitable biological samples comprise at least one mRNA-protein (mRNP) complex and include cell cultures, cell extracts, and whole tissue, including tumor tissue. Ligands include antibodies that specifically bind RNA-binding or RNA-associated proteins present in the mRNP complex. The mRNP complex is separated by binding the ligand with a binding molecule specific for the ligand, where the binding molecule is attached to a solid support. The mRNP complex is collected by removing the mRNP complex from the solid support. After collecting the mRNP complex, the mRNA bound within the complex may be characterized and identified. Subsets of the total mRNA population of a cell may accordingly be characterized, and a gene expression profile of the cell obtained.

    摘要翻译： 通过使生物样品与至少一种特异性结合mRNP复合物的至少一种组分的配体接触，在体内分配细胞mRNA-蛋白（mRNP）复合物。 合适的生物样品包含至少一种mRNA-蛋白（mRNP）复合物，并且包括细胞培养物，细胞提取物和包括肿瘤组织的整个组织。 配体包括特异性结合存在于mRNP复合物中的RNA结合或RNA相关蛋白的抗体。 通过将配体与对配体特异性的结合分子结合来分离mRNP复合物，其中结合分子连接到固体支持物上。 通过从固体支持物上除去mRNP复合物来收集mRNP复合物。 在收集mRNP复合物后，可以鉴定和鉴定复合物内结合的mRNA。 因此可以对细胞的总mRNA群体的亚群进行表征，并获得所获得的细胞的基因表达谱。

    GENOMIC DATA PROCESSING UTILIZING CORRELATION ANALYSIS OF NUCLEOTIDE LOCI
    7.
    发明申请
    GENOMIC DATA PROCESSING UTILIZING CORRELATION ANALYSIS OF NUCLEOTIDE LOCI 审中-公开
    基因数据处理利用核苷酸位点的相关分析

    公开(公告)号：US20080281530A1

    公开(公告)日：2008-11-13

    申请号：US12026035

    申请日：2008-02-05

    申请人： Scott A. TENENBAUM ,  Christopher ZALESKI ,  Francis DOYLE ,  Ajish GEORGE

    发明人： Scott A. TENENBAUM ,  Christopher ZALESKI ,  Francis DOYLE ,  Ajish GEORGE

    IPC分类号： G06F19/00 ,  G01N33/48

    CPC分类号： G16B40/00 ,  G16B20/00

    摘要： Processing of genomic data is provided utilizing correlation analysis of first and second nucleotide loci employing a selected comparison type and value. The comparison type is either intersection or proximity type, and the comparison value is either a number (n) of nucleotide positions, wherein n≧1, or a percent number (pn) of nucleotide positions, wherein pn≧0, to be employed in comparing the loci. When intersection type is selected, correlation is defined by the loci overlapping with at least the number (n) of nucleotide positions in common, or by the loci overlapping with at least the percent number (pn) of nucleotide positions in common relative to a smaller one of the first and second loci, or when proximity type is selected, correlation is defined by the first and second loci being within at least the number (n) of nucleotide positions.

    摘要翻译： 使用选择的比较类型和值的第一和第二核苷酸位点的相关性分析来提供基因组数据的处理。 比较类型是交叉点或邻近类型，并且比较值是核苷酸位置的数目（n），其中n> = 1或核苷酸位置的百分数（pn），其中pn> = 0，为 用于比较基因座。 当选择交叉路口类型时，相关性由与至少共同的核苷酸位置的数目（n）重叠的位点定位，或者与至少相对于较小的核苷酸位置的百分数（pn）重叠的位点重叠 第一和第二位点之一，或者当选择邻近类型时，相关性由位于至少核苷酸位置数目（n）内的第一和第二位点定义。

    GENOMIC DATA PROCESSING UTILIZING CORRELATION ANALYSIS OF NUCLEOTIDE LOCI OF MULTIPLE DATA SETS
    8.
    发明申请
    GENOMIC DATA PROCESSING UTILIZING CORRELATION ANALYSIS OF NUCLEOTIDE LOCI OF MULTIPLE DATA SETS 审中-公开
    基因数据处理利用多数据集核心位置的相关分析

    公开(公告)号：US20080281529A1

    公开(公告)日：2008-11-13

    申请号：US12026042

    申请日：2008-02-05

    申请人： Scott A. TENENBAUM ,  Christopher ZALESKI ,  Francis DOYLE ,  Ajish GEORGE

    发明人： Scott A. TENENBAUM ,  Christopher ZALESKI ,  Francis DOYLE ,  Ajish GEORGE

    IPC分类号： G06F19/00 ,  G01N33/48

    CPC分类号： G16B40/00 ,  G16B20/00

    摘要： Processing of genomic data is facilitated utilizing correlation analysis of mapped data sets, each data set including genomic data mapped and ordered relative to a genomic coordinate system. Correlation analysis identifies at a nucleotide level nucleotide positions wherein at least one nucleotide locus of each data set correlate. The analysis includes for each data set, selecting a nucleotide locus thereof closest to one end of the coordinate system, comparing the selected nucleotide loci for correlation, and if so, outputting results of the comparing, and updating the selected nucleotide loci by identifying the data set having a next nucleotide locus closest to the one end of the coordinate system, and inserting that next locus into the group of selected loci, and repeating the comparing for the newly selected loci. The process is repeated until nucleotide loci of the mapped data sets are compared and results of the comparison are output.

    摘要翻译： 利用映射数据集的相关分析来促进基因组数据的处理，每个数据集包括相对于基因组坐标系映射和排序的基因组数据。 相关分析在核苷酸水平的核苷酸位置鉴别其中每个数据集的至少一个核苷酸位点相关联。 分析包括对于每个数据集，选择最靠近坐标系一端的核苷酸位点，比较所选择的核苷酸位点进行相关，如果是，则输出比较结果，并通过识别数据来更新所选择的核苷酸位点 设置具有最靠近坐标系的一端的下一个核苷酸位点，并将该下一个轨迹插入到所选择的位点组中，并重复对新选择的位点的比较。 重复该过程，直到比较映射数据集的核苷酸位点并输出比较结果。