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51. 发明申请

US20070185656A1 Computer systems and methods for identifying surrogate markers 有权
标题翻译：用于识别替代标记的计算机系统和方法
公开(公告)号：US20070185656A1
公开(公告)日：2007-08-09
申请号：US10558928
申请日：2004-05-28
申请人： Eric Schadt
发明人： Eric Schadt
IPC分类号： G06F19/00
CPC分类号： G01N33/5023 , G01N33/5082 , G01N33/6803 , G01N2500/00
摘要： Methods, computer program products and systems for identifying cellular constituents in a secondary tissue that serve as surrogate markers for a target gene expressed in a primary tissue of a species are provided. A classifier is constructed using cellular constituent abundances of cellular constituents in a first plurality of cellular constituents measured in the secondary tissue in a population. This population comprises a first and second subgroup. The classifier is based on a second plurality of cellular constituents that comprises all or a portion of the first plurality of cellular constituents. Abundance levels of each cellular constituent in the second plurality of cellular constituents varies between the first and second subgroup. All or portion of the population is classified into a plurality of subtypes using the classifier. Then, one or more cellular constituents that can discriminate members of the population between a first subtype and a second subtype in the plurality of subtypes are identified.
摘要翻译：提供了用于鉴定作为在物种的初级组织中表达的靶基因的替代标记物的次级组织中的细胞成分的计算机程序产品和系统。在群体中的次级组织中测量的第一多个细胞成分中，使用细胞组分的细胞组成丰度构建分类器。该群体包括第一和第二子群。分类器基于包含第一多个细胞成分的全部或一部分的第二多个细胞成分。第二多个细胞组分中每个细胞成分的丰度水平在第一和第二亚组之间变化。使用分类器将全部或部分群体分类为多个亚型。然后，识别可以区分多个亚型中的第一亚型和第二亚型之间的群体成员的一个或多个细胞组分。

52. 发明申请

US20070134660A1 Methods for identifying modulators of kinesin activity 审中-公开
标题翻译：识别驱动蛋白活性调节剂的方法
公开(公告)号：US20070134660A1
公开(公告)日：2007-06-14
申请号：US10558463
申请日：2004-05-28
申请人： Mao Mao , Peter Linsley , Carolyn Buser , Christopher Marshall
发明人： Mao Mao , Peter Linsley , Carolyn Buser , Christopher Marshall
IPC分类号： C12Q1/68 , G01N33/574 , A61K31/175
CPC分类号： G01N33/5011 , A61K31/175 , A61K38/00 , C12Q1/34 , G01N33/573 , G01N33/57415
摘要： In a first aspect, the invention provides methods for screening for modulators of a target protein, comprising the steps of contacting a target protein with a candidate agent and determining whether the candidate agent modulates the activity of the target protein, wherein the target protein comprises a sequence that has more than 80% amino acid sequence identity to KIF14 (SEQ ID NO:2) or the KIF14 motor domain (SEQ ID NO:3). In a second aspect, the invention provides methods for modulating cell proliferation comprising administering to a cell an effective amount of a modulator of the activity of a target protein. Some embodiments of this aspect provide methods for treating a subject with a cellular hyperproliferation disorder, such as cancer. In a third aspect, the invention provides methods for identifying candidate subjects for treatment with an inhibitor of the activity of a target protein.
摘要翻译：在第一方面，本发明提供了筛选靶蛋白的调节剂的方法，包括以下步骤：使靶蛋白与候选试剂接触并确定候选试剂是否调节靶蛋白的活性，其中靶蛋白包含与KIF14（SEQ ID NO：2）或KIF14运动结构域（SEQ ID NO：3）具有80％以上氨基酸序列同一性的序列。在第二方面，本发明提供了调节细胞增殖的方法，包括向细胞施用有效量的靶蛋白活性的调节剂。该方面的一些实施方案提供了用细胞过度增殖病症如癌症治疗受试者的方法。在第三方面，本发明提供用于鉴定候选受试者用靶蛋白活性抑制剂治疗的方法。

53. 发明授权

US07150969B2 Alternatively spliced isoform of acetyl-CoA carboxylase 2 (ACC2) 有权
标题翻译：乙酰辅酶A羧化酶2（ACC2）的可选剪接同种型
公开(公告)号：US07150969B2
公开(公告)日：2006-12-19
申请号：US11144368
申请日：2005-06-03
申请人： Zhengyan Kan , Philip W. Garrett-Engele , Christopher D. Armour , Christopher K. Raymond , John C. Castle
发明人： Zhengyan Kan , Philip W. Garrett-Engele , Christopher D. Armour , Christopher K. Raymond , John C. Castle
IPC分类号： C12Q1/48 , C12Q1/68 , C12N15/70 , C12N9/10 , C12N5/16 , C07H21/04
CPC分类号： C12N9/93
摘要： The present invention features nucleic acids and polypeptides encoding novel splice variant isoforms of acetyl-CoA carboxylase 2 (ACC2). The polynucleotide sequence of ACC2sv1 is provided by SEQ ID NO 3. The amino acid sequence of ACC2sv1 is provided by SEQ ID NO 4. The present invention also provides methods for using ACC2sv1 polynucleotides and proteins to screen for compounds that bind to ACC2sv1.
摘要翻译：本发明的特征在于编码乙酰辅酶A羧化酶2（ACC2）的剪接变异体亚型的核酸和多肽。 ACC2sv1的多核苷酸序列由SEQ ID NO 3提供。ACC2sv1的氨基酸序列由SEQ ID NO 4提供。本发明还提供了使用ACC2sv1多核苷酸和蛋白质筛选结合ACC2sv1的化合物的方法。

54. 发明授权

US07141398B2 Methods for recycling mRNA for linear cRNA amplification 有权
标题翻译：回收mRNA用于线性cRNA扩增的方法
公开(公告)号：US07141398B2
公开(公告)日：2006-11-28
申请号：US10745462
申请日：2003-12-23
申请人： Mingjie Zhou , Sven Duenwald , Mark Parrish
发明人： Mingjie Zhou , Sven Duenwald , Mark Parrish
IPC分类号： C12P19/34 , C12Q1/68 , C12N9/00 , C12N9/96
CPC分类号： C12Q1/6865 , C12Q2521/107
摘要： In one aspect, the present invention provides methods for synthesizing multiple copies of antisense cDNA molecules from an RNA molecule, comprising using an RNA molecule as a template for synthesizing multiple copies of antisense cDNA molecules. In some embodiments of the methods, the RNA molecule is incubated with a primer and with an enzyme possessing reverse transcriptase activity under suitable conditions for synthesizing multiple copies of antisense cDNA molecules. In some embodiments, the methods produce multiple copies of double-stranded cDNA from a template RNA molecule. In further embodiments, the methods produce multiple copies of cRNA from a template RNA molecule.
摘要翻译：一方面，本发明提供从RNA分子合成多个拷贝的反义cDNA分子的方法，其包括使用RNA分子作为合成多个反义cDNA分子拷贝的模板。在该方法的一些实施方案中，将RNA分子与引物和具有逆转录酶活性的酶在合适的条件下温育以合成多个反义cDNA分子拷贝。在一些实施方案中，该方法从模板RNA分子产生双链cDNA的多拷贝。在另外的实施方案中，该方法从模板RNA分子产生cRNA的多拷贝。

55. 发明授权

US07130746B2 Computer systems and computer programs for determining protein activity levels using gene expression profiles 失效
标题翻译：使用基因表达谱测定蛋白质活性水平的计算机系统和计算机程序
公开(公告)号：US07130746B2
公开(公告)日：2006-10-31
申请号：US09975843
申请日：2001-10-12
申请人： Stephen H. Friend , Roland Stoughton
发明人： Stephen H. Friend , Roland Stoughton
IPC分类号： G01N33/48 , G06F19/00 , G06G7/48
CPC分类号： C07K14/4702 , A61K38/00
摘要： The present invention provides methods for determining the level of protein activity in a cell by: (i) measuring abundances of cellular constituents in a cell in which the activity of a specific protein is to be determined so that a diagnostic profile is thus obtained; (ii) measuring abundances of cellular constituents that occur in a cell in response to perturbations in the activity of said protein to obtain response profiles and interpolating said response profiles to generate response curves; and (iii) determining a protein activity level at which the response profile extracted from the response curves best fits the measured diagnostic profile, according to some objective measure. In alternative embodiments, the present invention also provides methods for identifying individuals having genetic mutations or polymorphisms that disrupt protein activity, and methods for identifying drug activity in vivo by determining the activity levels of proteins which interact with said drugs.
摘要翻译：本发明提供了通过以下步骤确定细胞中蛋白质活性水平的方法：（i）测量要确定特定蛋白质的活性的细胞中细胞成分的丰度，从而获得诊断特征; （ii）测量在细胞中发生的细胞成分的丰度以响应所述蛋白质的活动中的扰动以获得反应谱并内插所述响应谱以产生响应曲线; 和（iii）根据一些客观的测定，确定从响应曲线提取的反应曲线最适合测量的诊断谱的蛋白质活性水平。在替代实施方案中，本发明还提供了用于鉴定具有破坏蛋白质活性的遗传突变或多态性的个体的方法，以及通过测定与所述药物相互作用的蛋白质的活性水平来鉴定体内药物活性的方法。

56. 发明授权

US06950752B1 Methods for removing artifact from biological profiles 失效
标题翻译：从生物学特征中去除人造物的方法
公开(公告)号：US06950752B1
公开(公告)日：2005-09-27
申请号：US09220275
申请日：1998-12-23
申请人： Stephen H. Friend , Roland Stoughton , Yudong He
发明人： Stephen H. Friend , Roland Stoughton , Yudong He
IPC分类号： G01N33/50 , C12M1/00 , C12N15/09 , C12P21/04 , C12Q1/68 , C40B30/02 , C40B30/04 , C40B40/02 , C40B50/02 , C40B50/06 , C40B60/12 , G01N33/15 , G01N33/68 , G06F17/10 , G06F17/16 , G06F17/18 , G06F17/30 , G06F19/20 , G06F19/24 , G01N33/48 , C12P21/06 , G06G7/48
CPC分类号： C12Q1/6834 , C12Q1/6809 , G01N33/6803 , G06F19/20 , G06F19/24
摘要： The invention provides methods for removing unwanted response components (i.e., “artifacts”) from a measured biological profile comprising measurements of a plurality of cellular constituents of a cell or organism in response to a perturbation. The methods involve subtracting from the measured biological profile one or more artifact patterns, each of which comprises measurements of changes in cellular constituents as a result of deviation of one or more experimental variables, such as cell culture density and temperature, hybridization temperature, as well as concentrations of total RNA and/or hybridization reagents, from desired values.
摘要翻译：本发明提供了用于从测量的生物谱中去除不需要的反应成分（即，“伪像”）的方法，其包括响应于扰动的细胞或生物体的多个细胞成分的测量。所述方法包括从所测量的生物学概况中减去一个或多个伪影图案，其中每一个包括由于一个或多个实验变量如细胞培养物密度和温度，杂交温度的偏差而导致的细胞组分变化的测量作为总RNA和/或杂交试剂的浓度，从所需值。

57. 发明申请

US20050176125A1 Alternatively spliced isoform of CDC25A phosphatase and methods of use 审中-公开
标题翻译： CDC25A磷酸酶的剪接异构体及其使用方法
公开(公告)号：US20050176125A1
公开(公告)日：2005-08-11
申请号：US11022042
申请日：2004-12-22
申请人： John Castle , Christopher Armour , Philip Garrett-Engele , Zhengyan Kan , Christopher Raymond , Nicholas Tsinoremas
发明人： John Castle , Christopher Armour , Philip Garrett-Engele , Zhengyan Kan , Christopher Raymond , Nicholas Tsinoremas
IPC分类号： C07H21/04 , C12N9/16
CPC分类号： C12N9/16 , C07H21/04
摘要： The present invention features nucleic acids and polypeptides encoding a novel splice variant isoform of cell division cycle 25A (Cdc25A) phosphatase. The polynucleotide sequence of Cdc25Asv1 is provided by SEQ ID NO:2. The amino acid sequence for Cdc25Asv1 is provided by SEQ ID NO:3. The present invention also provides methods for using Cdc25Asv1 polynucleotides and proteins to screen for compounds that bind to Cdc25Asv1.
摘要翻译：本发明的特征在于编码细胞分裂周期25A（Cdc25A）磷酸酶的新型剪接变体同种型的核酸和多肽。 Cdc25Asv1的多核苷酸序列由SEQ ID NO：2提供。 Cdc25Asv1的氨基酸序列由SEQ ID NO：3提供。本发明还提供了使用Cdc25Asv1多核苷酸和蛋白质筛选结合Cdc25Asv1的化合物的方法。

58. 发明授权

US06847897B1 Method and system for analyzing biological response signal data 失效
标题翻译：分析生物反应信号数据的方法和系统
公开(公告)号：US06847897B1
公开(公告)日：2005-01-25
申请号：US09469360
申请日：1999-12-22
申请人： Douglas Bassett, Jr. , Andrey Bondarenko
发明人： Douglas Bassett, Jr. , Andrey Bondarenko
IPC分类号： G01N33/48 , G06F3/048 , G06F17/30 , G06F19/20 , G06F19/24 , G06F19/26 , G06F19/28 , G06Q50/00 , G06F19/00
CPC分类号： G06F19/26 , G06F19/20 , G06F19/24 , G06F19/28 , G06F2221/2145
摘要： A system, method, and computer program product for enhanced computer-aided analysis of biological response data is disclosed. In a preferred embodiment, biological datasets are graphically selected by a user from a first active biological viewer window on a user computer display and projected onto one or more other active biological viewers on the display. The selected data is highlighted in the destination biological viewers using contrast or color differentiation from other data appearing in the destination windows. In another preferred embodiment, hierarchical cluster trees from biological signal profiles are presented in a hyperbolic display fashion. In another preferred embodiment, biological menu and submenu items utilized by the user computer are not stored in the user computer, but rather are stored a central biological response database. Biological menus and submenus are generated at startup time based on queries to the central biological response database, allowing for increased flexibility, changeability, and customization of the biological menus. In another preferred embodiment, correlation data between biological signal profile data is precomputed when the experiments are added to the central biological response database, eliminating the need for real time computation of correlation coefficients by the user computer.
摘要翻译：公开了一种用于增强生物反应数据计算机辅助分析的系统，方法和计算机程序产品。在优选实施例中，生物数据集由用户从用户计算机显示器上的第一活动生物观察者窗口图形地选择并投影到显示器上的一个或多个其他活跃生物观察者上。所选数据在目的地生物观察者中使用与出现在目的地窗口中的其他数据进行对比或颜色分化来突出显示。在另一个优选实施例中，来自生物信号轮廓的分层丛树以双曲显示方式呈现。在另一个优选实施例中，由用户计算机使用的生物菜单和子菜单项不存储在用户计算机中，而是存储在中央生物反应数据库中。基于对中央生物反应数据库的查询，生物菜单和子菜单在启动时生成，允许提高生物菜单的灵活性，可变性和定制性。在另一个优选实施例中，当将实验添加到中心生物反应数据库时，生物信号特征数据之间的相关数据被预先计算，消除了用户计算机对相关系数的实时计算的需要。

59. 发明授权

US06839635B2 Method and system for analyzing biological response signal data 失效
标题翻译：分析生物反应信号数据的方法和系统
公开(公告)号：US06839635B2
公开(公告)日：2005-01-04
申请号：US10186383
申请日：2002-06-28
申请人： Douglas Bassett, Jr. , Stewart Buskirk , Andrey Bondarenko
发明人： Douglas Bassett, Jr. , Stewart Buskirk , Andrey Bondarenko
IPC分类号： G01N33/48 , G06F3/048 , G06F17/30 , G06F19/20 , G06F19/24 , G06F19/26 , G06F19/28 , G06Q50/00 , G06F19/00 , G05B15/00 , G11C17/00
CPC分类号： G06F19/26 , G06F19/20 , G06F19/24 , G06F19/28 , G06F2221/2145
摘要： Systems, methods, and computer program products for analysis of biological response data are disclosed. Biological datasets are selected from an active biological viewer window on a computer display and projected onto one or more other active biological viewers on the display. The selected data is highlighted in the destination biological viewers using contrast or color differentiation from other data appearing in the destination windows. Systems, methods, and computer program products for displaying hierarchical cluster trees from biological signal profiles in a hyperbolic display fashion are disclosed. Systems, methods, and computer program products are disclosed for precomputing correlation data between biological signal profile data when the experiments are added to a biological response database, thereby eliminating the need for real time computation of correlation coefficients by a user computer.
摘要翻译：公开了用于分析生物反应数据的系统，方法和计算机程序产品。生物数据集从计算机显示器上的活跃生物观察者窗口中选择并投影到显示器上的一个或多个其他活跃的生物观察者上。所选数据在目的地生物观察者中使用与出现在目的地窗口中的其他数据进行对比或颜色分化来突出显示。公开了用于以双曲显示方式从生物信号轮廓显示分层聚类树的系统，方法和计算机程序产品。公开了系统，方法和计算机程序产品，用于在将实验添加到生物反应数据库之前预生成生物信号简档数据之间的相关数据，从而消除了用户计算机对相关系数的实时计算的需要。

60. 发明申请

US20040259146A1 Method for making populations of defined nucleic acid molecules 有权
标题翻译：确定核酸分子群体的方法
公开(公告)号：US20040259146A1
公开(公告)日：2004-12-23
申请号：US10860559
申请日：2004-06-02
申请人： Rosetta Inpharmatics LLC , Cold Spring Harbor Laboratory
发明人： Stephen H. Friend , Michele A. Cleary , Kristopher A. Kilian , Ernest M. Coffey , Gregory J. Hannon
IPC分类号： C12Q001/68 , C12P019/34
CPC分类号： C12Q1/6837 , Y10S977/792 , C12Q2565/513 , C12Q2531/113 , C12Q2525/161
摘要： The present invention provides methods of making a population of nucleic acid molecules, wherein each nucleic acid molecule comprises a predetermined nucleic acid sequence, each of said methods comprising the steps of: (a) synthesizing, on a substrate, a population of nucleic acid molecules wherein: i) each synthesized nucleic acid molecule comprises a predetermined nucleic acid sequence; and ii) each synthesized nucleic acid molecule is localized to a defined area of said substrate; (b) harvesting said population of synthesized nucleic acid molecules from said substrate to yield harvested nucleic acid molecules; and (c) introducing said harvested nucleic acid molecules into vector molecules.
摘要翻译：本发明提供了制备核酸分子群体的方法，其中每个核酸分子包含预定的核酸序列，所述方法中的每一种包括以下步骤：（a）在底物上合成核酸分子群体其中：i）每个合成的核酸分子包含预定的核酸序列; 和ii）每个合成的核酸分子定位于所述基质的限定区域; （b）从所述底物收获所述合成核酸分子群体以产生收获的核酸分子; 和（c）将所述收获的核酸分子引入载体分子。

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