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11. 发明申请

US20110173201A1 METHOD OF DETERMINING A RELIABILITY INDICATOR FOR SIGNATURES OBTAINED FROM CLINICAL DATA AND USE OF THE RELIABILITY INDICATOR FOR FAVORING ONE SIGNATURE OVER THE OTHER 有权
标题翻译：确定从临床数据中获取的标志的可靠性指标的方法和使用可靠性指标，以便在其他人身上获得一个签名
公开(公告)号：US20110173201A1
公开(公告)日：2011-07-14
申请号：US13119742
申请日：2009-09-24
申请人： Angel Janevski , Nilanjana Banerjee , Yasser Alsafadi , Vinay Varadan
发明人： Angel Janevski , Nilanjana Banerjee , Yasser Alsafadi , Vinay Varadan
IPC分类号： G06F17/30
CPC分类号： G06F19/24 , G06F19/00 , G16H50/20 , G16H50/70
摘要： This invention relates to a method and an apparatus for determining a reliability indicator for at least one set of signatures obtained from clinical data collected from a group of samples. The signatures are obtained by detecting characteristics in the clinical data from the group of sample sand each of the signatures generate a first set of stratification values that stratify the group of samples. At least one additional and parallel stratification source to the signatures obtained from group of sample sis provided, the at least one additional and parallel stratification source to the signatures being independent from the signatures and generates a second set of stratification values. A comparison is done for each respective sample, where the first stratification values are compared with a true reference stratification values, and where the second stratification values are compared with the true reference stratification values. The signatures are assigned with similarity measure indicators indicating whether the first and the second stratification values match with the true reference stratification values. These are then implementing as input in determining the reliability of the signatures.
摘要翻译：本发明涉及一种用于确定从从一组样本收集的临床数据中获得的至少一组签名的可靠性指标的方法和装置。通过检测来自样品组的临床数据的特征来获得这些特征，每个签名产生分层样本的第一组分层值。至少一个附加和平行分层源提供从样本组提供的签名，所述签名的至少一个附加和平行分层源独立于签名并产生第二组分层值。对每个相应的样本进行比较，其中将第一分层值与真实的参考分层值进行比较，并且将第二分层值与真实的参考分层值进行比较。赋予签名的相似性度量指示符指示第一和第二分层值是否与真实的参考分层值相匹配。然后在确定签名的可靠性时，将其作为输入。

12. 发明授权

US11348662B2 Biomarkers based on sets of molecular signatures 有权
公开(公告)号：US11348662B2
公开(公告)日：2022-05-31
申请号：US13321723
申请日：2010-05-18
申请人： Angel Janevski , Vinay Varadan , Nilanjana Banerjee
发明人： Angel Janevski , Vinay Varadan , Nilanjana Banerjee
IPC分类号： G16B40/00 , G16B25/10 , G16B25/00
摘要： A method (10) for forming novel signatures of biological data is provided. The method comprises ranking features based on a trend value, which is created based on multiple signatures identified by a pattern discovery method. Furthermore, a device (30) and a computer program product (40), performing the steps according to the method (10) is provided. Uses of the method, for statistically analyzing clinical data, designing assays based on multiple molecular signatures and interpreting assays based on multiple molecular signatures are also provided.

13. 发明申请

US20120290218A1 Computational Analysis of the Synergy Among Multiple Interacting Factors 审中-公开
标题翻译：多重交互因子之间协同作用的计算分析
公开(公告)号：US20120290218A1
公开(公告)日：2012-11-15
申请号：US13534578
申请日：2012-06-27
申请人： Dimitris Anastassiou , Vinay Varadan
发明人： Dimitris Anastassiou , Vinay Varadan
IPC分类号： G06F19/22 , G06F15/00
CPC分类号： C12Q1/6883 , C12Q2600/158
摘要： A method is provided for selecting two or more genes from gene expression data. In the method, gene expression data for a plurality of genes is provided, where the gene expression data include expression levels for each of the plurality of genes. The gene expression data is discretized. Based on the discretized gene expression data, the synergy among the plurality of genes with respect to a phenotype, for example, presence or absence of a disease in a tissue, is evaluated. Two or more genes whose synergy exceeds a predetermined threshold are selected. A system implementing the method is also provided.
摘要翻译：提供从基因表达数据中选择两个或多个基因的方法。在该方法中，提供了多个基因的基因表达数据，其中基因表达数据包括多个基因中的每一个的表达水平。基因表达数据离散化。基于离散化的基因表达数据，评估了多个基因相对于表型的协同作用，例如组织中存在或不存在疾病。选择两个或更多个协同作用超过预定阈值的基因。还提供了一种实现该方法的系统。

14. 发明授权

US08290715B2 System and method for multiple-factor selection 有权
标题翻译：多因素选择的系统和方法
公开(公告)号：US08290715B2
公开(公告)日：2012-10-16
申请号：US12133045
申请日：2008-06-04
申请人： Dimitris Anastassiou , Vinay Varadan
发明人： Dimitris Anastassiou , Vinay Varadan
IPC分类号： A61B5/00 , G01N33/48 , G01N33/00 , G06F19/00
CPC分类号： G06F19/24 , G06F19/20
摘要： The disclosed subject matter provides techniques for multiple-factor selection. The factors can be features or elements that are jointly associated with one or more outcomes by their joint presence or absence. There may be a non-causative correlation between the factors, features, or elements and the outcomes. In some embodiments, Entropy Minimization and Boolean Parsimony (EMBP) is used to identify modules of genes jointly associated with disease from gene expression data, and a logic function is provided to connect the combined expression levels in each gene module with the presence of disease. The smallest module of genes whose joint expression levels can predict the presence of disease can be identified.
摘要翻译：所公开的主题提供了多因素选择的技术。这些因素可以是通过其联合存在或不存在与一个或多个结果共同相关联的特征或元件。因素，特征或要素与结果之间可能存在非因果关系。在一些实施方案中，使用熵最小化和布尔参数（EMBP）来鉴定与基因表达数据共同与疾病相关联的基因的模块，并且提供逻辑功能以将每个基因模块中的组合表达水平与疾病的存在相关联。可以确定其联合表达水平可以预测疾病存在的最小的基因组。

15. 发明申请

US20120253686A1 SYSTEM AND METHOD FOR MULTIPLE-FACTOR SELECTION 审中-公开
标题翻译：多因素选择的系统与方法
公开(公告)号：US20120253686A1
公开(公告)日：2012-10-04
申请号：US13489334
申请日：2012-06-05
申请人： Dimitris Anastassiou , Vinay Varadan
发明人： Dimitris Anastassiou , Vinay Varadan
IPC分类号： G06F19/24
CPC分类号： G16B40/00 , G16B25/00
摘要： The disclosed subject matter provides techniques for multiple-factor selection. The factors can be features or elements that are jointly associated with one or more outcomes by their joint presence or absence. There may be a non-causative correlation between the factors, features, or elements and the outcomes. In some embodiments, Entropy Minimization and Boolean Parsimony (EMBP) is used to identify modules of genes jointly associated with disease from gene expression data, and a logic function is provided to connect the combined expression levels in each gene module with the presence of disease. The smallest module of genes whose joint expression levels can predict the presence of disease can be identified.
摘要翻译：所公开的主题提供了多因素选择的技术。这些因素可以是通过其联合存在或不存在与一个或多个结果共同相关联的特征或元件。因素，特征或要素与结果之间可能存在非因果关系。在一些实施方案中，使用熵最小化和布尔参数（EMBP）来鉴定与基因表达数据共同与疾病相关联的基因的模块，并且提供逻辑功能以将每个基因模块中的组合表达水平与疾病的存在相关联。可以确定其联合表达水平可以预测疾病存在的最小的基因组。

16. 发明申请

US20120004855A1 METHYLATION BIOMARKERS FOR PREDICTING RELAPSE FREE SURVIVAL 审中-公开
标题翻译：用于预测免费生存的甲基生物标志物
公开(公告)号：US20120004855A1
公开(公告)日：2012-01-05
申请号：US13141343
申请日：2009-12-22
申请人： Sitharthan Kamalakaran , Vinay Varadan , James B. Hicks
发明人： Sitharthan Kamalakaran , Vinay Varadan , James B. Hicks
IPC分类号： G06F19/00 , C40B40/06
CPC分类号： C12Q1/6886 , C12Q2600/118 , C12Q2600/154 , C12Q2600/156
摘要： A methylation classification list comprising loci DNA, for which loci the methylation status of the DNA is indicative of likelihood of recurrence of cancer, is provided. Furthermore, a method, apparatus and use for predicting probability of relapse free survival of a subject diagnosed with cancer, are provided.
摘要翻译：提供了包含基因座的甲基化分类表，其中DNA位点的甲基化状态表示癌症复发的可能性。此外，提供了用于预测诊断为癌症的受试者的无复发生存概率的方法，装置和用途。

17. 发明申请

US20120109678A1 DEVICE AND METHOD FOR COMPARING MOLECULAR SIGNATURES 有权
标题翻译：用于比较分子信号的装置和方法
公开(公告)号：US20120109678A1
公开(公告)日：2012-05-03
申请号：US13319567
申请日：2010-05-05
申请人： Yasser H. Alsafadi , Nilanjana Banerjee , Vinay Varadan , Angel J. Janevski
发明人： Yasser H. Alsafadi , Nilanjana Banerjee , Vinay Varadan , Angel J. Janevski
IPC分类号： G06Q50/24
CPC分类号： G06F19/18 , G06Q50/22
摘要： A method (10) for clinical decision support by comparison of multiple molecular signatures of biological data is provided. The method comprises comparing at least two of said molecular signatures are different kinds of molecular signatures. Furthermore, a device (70), a system (100), and a computer program product (200) and a use for clinical decision support, performing the steps according to the method (10) is provided.
摘要翻译：提供了一种用于通过比较生物数据的多个分子特征的临床决定支持的方法（10）。所述方法包括比较所述分子特征中的至少两个是不同种类的分子标记。此外，提供了根据方法（10）的设备（70），系统（100）和计算机程序产品（200）和用于临床决策支持的用途，执行步骤。

18. 发明申请

US20080300799A1 System And Method For Multiple-Factor Selection 有权
标题翻译：多因素选择的系统和方法
公开(公告)号：US20080300799A1
公开(公告)日：2008-12-04
申请号：US12133045
申请日：2008-06-04
申请人： Dimitris Anastassiou , Vinay Varadan
发明人： Dimitris Anastassiou , Vinay Varadan
IPC分类号： G06F19/00 , G06F15/00
CPC分类号： G06F19/24 , G06F19/20
摘要： The disclosed subject matter provides techniques for multiple-factor selection. The factors can be features or elements that are jointly associated with one or more outcomes by their joint presence or absence. There may be a non-causative correlation between the factors, features, or elements and the outcomes. In some embodiments, Entropy Minimization and Boolean Parsimony (EMBP) is used to identify modules of genes jointly associated with disease from gene expression data, and a logic function is provided to connect the combined expression levels in each gene module with the presence of disease. The smallest module of genes whose joint expression levels can predict the presence of disease can be identified.
摘要翻译：所公开的主题提供了多因素选择的技术。这些因素可以是通过其联合存在或不存在与一个或多个结果共同相关联的特征或元件。因素，特征或要素与结果之间可能存在非因果关系。在一些实施方案中，使用熵最小化和布尔参数（EMBP）来鉴定与基因表达数据共同与疾病相关联的基因的模块，并且提供逻辑功能以将每个基因模块中的组合表达水平与疾病的存在相关联。可以确定其联合表达水平可以预测疾病存在的最小的基因组。

19. 发明授权

US08924232B2 Device and method for comparing molecular signatures 有权
标题翻译：用于比较分子标记的装置和方法
公开(公告)号：US08924232B2
公开(公告)日：2014-12-30
申请号：US13319567
申请日：2010-05-05
申请人： Yasser H. Alsafadi , Nilanjana Banerjee , Vinay Varadan , Angel J. Janevski
发明人： Yasser H. Alsafadi , Nilanjana Banerjee , Vinay Varadan , Angel J. Janevski
IPC分类号： G06Q50/24 , G06F19/18 , G06Q50/22
CPC分类号： G06F19/18 , G06Q50/22
摘要： A method (10) for clinical decision support by comparison of multiple molecular signatures of biological data is provided. The method comprises comparing at least two of said molecular signatures are different kinds of molecular signatures. Furthermore, a device (70), a system (100), and a computer program product (200) and a use for clinical decision support, performing the steps according to the method (10) is provided.
摘要翻译：提供了一种用于通过比较生物数据的多个分子特征的临床决定支持的方法（10）。所述方法包括比较所述分子特征中的至少两个是不同种类的分子标记。此外，提供了根据方法（10）的设备（70），系统（100）和计算机程序产品（200）和用于临床决策支持的用途，执行步骤。

20. 发明授权

US08234077B2 Method of selecting genes from gene expression data based on synergistic interactions among the genes 有权
标题翻译：基于基因之间的协同相互作用从基因表达数据中选择基因的方法
公开(公告)号：US08234077B2
公开(公告)日：2012-07-31
申请号：US12307694
申请日：2007-05-10
申请人： Dimitris Anastassiou , Vinay Varadan
发明人： Dimitris Anastassiou , Vinay Varadan
IPC分类号： G01N33/48 , C12Q1/68 , G06F7/60 , G06G7/58
CPC分类号： C12Q1/6883 , C12Q2600/158
摘要： A method is provided for selecting two or more genes from gene expression data. In the method, gene expression data for a plurality of genes is provided, where the gene expression data include expression levels for each of the plurality of genes. The gene expression data is discretized. Based on the discretized gene expression data, the synergy among the plurality of genes with respect to a phenotype, for example, presence or absence of a disease in a tissue, is evaluated. Two or more genes whose synergy exceeds a predetermined threshold are selected. A system implementing the method is also provided.
摘要翻译：提供从基因表达数据中选择两个或多个基因的方法。在该方法中，提供了多个基因的基因表达数据，其中基因表达数据包括多个基因中的每一个的表达水平。基因表达数据离散化。基于离散化的基因表达数据，评价了多个基因相对于表型的协同作用，例如组织中存在或不存在疾病。选择两个或更多个协同作用超过预定阈值的基因。还提供了一种实现该方法的系统。

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