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21. 发明申请

US20060190191A1 Systems and methods for evaluating the significance of differences in biological measurements 失效
公开(公告)号：US20060190191A1
公开(公告)日：2006-08-24
申请号：US11303121
申请日：2005-12-12
申请人： Roland Stoughton , Hongyue Dai
发明人： Roland Stoughton , Hongyue Dai
IPC分类号： G06F19/00
CPC分类号： G06F19/20 , C12Q1/6837 , Y10T436/10
摘要： A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

22. 发明授权

US06859735B1 Computer systems for identifying pathways of drug action 失效
标题翻译：用于识别药物作用途径的计算机系统
公开(公告)号：US06859735B1
公开(公告)日：2005-02-22
申请号：US09374565
申请日：1999-08-13
申请人： Roland Stoughton , Stephen H. Friend
发明人： Roland Stoughton , Stephen H. Friend
IPC分类号： G01N33/53 , C12N15/09 , C12Q1/02 , C12Q1/04 , C12Q1/68 , G06F19/12 , G01N33/48 , C12P21/06 , G06G7/48
CPC分类号： G06F19/12 , C12Q1/025 , G01N33/5041
摘要： The present invention provides methods and computer systems for identifying and representing the biological pathways of drug action on a cell The present invention also provides methods and computer systems for assessing the significance of the identified representation and for verifying that the identified pathways are actual pathway of drug action. The present invention also provides methods and computer systems for drug development based on the methods for identifying biological pathways of drug action, and methods and computer systems for representing the biological pathways involved in the effect of an environmental change upon a cell.
摘要翻译：本发明提供用于鉴定和表示药物作用于细胞的生物学途径的方法和计算机系统本发明还提供了用于评估所鉴定的表现的重要性并用于验证所鉴定的途径是药物的实际途径的方法和计算机系统行动。本发明还提供了用于鉴定药物作用的生物学途径的方法的用于药物开发的方法和计算机系统，以及用于表示涉及环境变化对细胞的影响的生物学途径的方法和计算机系统。

23. 发明授权

US06132969A Methods for testing biological network models 失效
标题翻译：生物网络模型测试方法
公开(公告)号：US06132969A
公开(公告)日：2000-10-17
申请号：US99722
申请日：1998-06-19
申请人： Roland Stoughton , Richard M. Karp
发明人： Roland Stoughton , Richard M. Karp
IPC分类号： G01N33/50 , C12N15/09 , C12Q1/06 , C12Q1/68 , C12R1/865 , G01N33/15 , G06F19/12 , C12Q1/00 , G01N33/53 , G06F17/00
CPC分类号： G06F19/12
摘要： The present invention provides methods and systems for testing and confirming how well a network model represents a biological pathway in a biological system. The network model comprises a network of logical operators relating input cellular constituents (e.g., mRNA or protein abundances) to output classes of cellular constituents, which are affected by the pathway in the biological system. The methods of this invention provide, first, for choosing complete and efficient experiments for testing the network model which compare relative changes in the biological system in response to perturbations of the network. The methods also provide for determining an overall goodness of fit of the network model to biological system by: predicting from the network model how output classes behave in response to the chosen experiments, finding measures of relative change of cellular constituents actually observed in the chosen experiments, finding goodnesses of fit of each observed cellular constituent to an output class with which the cellular constituent has the strongest correlation, and determining an overall goodness of fit of the network model from the individual goodnesses of fit of each observed cellular constituent. Additionally, these methods provide for testing the significance of the overall goodness of fit according to a nonparametric statistical test using an empirically determined distribution of possible goodnesses of fit. This invention also provides for computer systems for carrying out the computational steps of these methods.
摘要翻译：本发明提供用于测试和确认网络模型在生物系统中代表生物学途径的方式和系统。网络模型包括将输入细胞成分（例如，mRNA或蛋白质丰度）与输出生物系统中途径影响的细胞成分类型相关联的逻辑运算器网络。本发明的方法首先提供用于选择用于测试网络模型的完整和有效的实验，该网络模型响应于网络的扰动来比较生物系统中的相对变化。该方法还提供了通过以下方式来确定网络模型对生物系统的整体拟合度：从网络模型预测输出类型如何响应于所选择的实验而行为，找到在所选实验中实际观察到的细胞成分的相对变化的度量将每个观察到的细胞成分适合于细胞成分具有最强相关性的输出类别，并根据每个观察到的细胞成分的拟合优度确定网络模型的整体拟合度。此外，这些方法提供了使用经验确定的可能的适合度的分布来根据非参数统计检验测试整体拟合度的重要性。本发明还提供了用于执行这些方法的计算步骤的计算机系统。

24. 发明申请

US20130302797A1 METHODS FOR DIAGNOSING, PROGNOSING, OR THERANOSING A CONDITION USING RARE CELLS 审中-公开
公开(公告)号：US20130302797A1
公开(公告)日：2013-11-14
申请号：US13803741
申请日：2013-03-14
申请人： Anne R. Kopf-Sill , Lena Wu , Roland Stoughton
发明人： Anne R. Kopf-Sill , Lena Wu , Roland Stoughton
IPC分类号： G01N33/50
CPC分类号： G01N33/57488 , C12Q1/6883 , C12Q1/6886 , C12Q2600/118 , C12Q2600/156 , G01N1/31 , G01N33/5091 , G01N33/57484 , G01N33/57492 , G01N2333/705 , G01N2333/71 , G01N2333/912 , G01N2333/96433
摘要： The invention encompasses methods for diagnosing, theranosing, or prognosing a condition in a patient based on the results of one or more analysis methods. The methods can comprise enriching a sample obtained from the patient for one or more rare cells. The analysis methods can include performing enumeration of the one or more rare cells or cell subtypes, performing nucleic acid analysis, or detecting a serum marker.

25. 发明授权

US08521441B2 Method and computer program product for reducing fluorophore-specific bias 失效
标题翻译：减少荧光团特异性偏倚的方法和计算机程序产品
公开(公告)号：US08521441B2
公开(公告)日：2013-08-27
申请号：US11042654
申请日：2005-01-24
申请人： Roland Stoughton , Hongyue Dai
发明人： Roland Stoughton , Hongyue Dai
IPC分类号： G06F19/00
CPC分类号： G06F19/20 , C12Q1/6837 , Y10T436/10
摘要： A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.
摘要翻译：用于微阵列实验对中的荧光团的微阵列实验中的荧光团偏置去除方法是相反的。此外，一种用于计算与名义上重复的微阵列实验中进行的每个测量相关联的各个错误的方法。该误差测量可选地与基于秩的方法耦合，以便确定响应于扰动的细胞成分向上或向下调节的概率。最后，在名义上重复的微阵列实验中确定细胞成分的表达水平的加权平均的置信度的方法。

26. 发明申请

US20110251081A1 METHODS AND COMPOSITIONS FOR DETERMINING GENE FUNCTION 有权
标题翻译：用于确定基因功能的方法和组合物
公开(公告)号：US20110251081A1
公开(公告)日：2011-10-13
申请号：US12686311
申请日：2010-01-12
申请人： Roland Stoughton , Timothy R. Hughes
发明人： Roland Stoughton , Timothy R. Hughes
IPC分类号： C40B30/04 , G06F19/00 , C12Q1/68
CPC分类号： G06F19/18 , C12Q1/6809 , C12Q1/6837 , C40B30/04 , G01N33/5005 , G01N2500/00 , G06F19/20 , G06F19/24 , C12Q2545/114 , C12Q2521/107 , C12Q2539/113
摘要： The invention relates to methods and systems (e.g., computer systems and computer program products) for characterizing cellular constituents, particularly genes and gene products. In particular, the invention provides methods for assigning or determining the biological function of uncharacterized genes and gene products by using “response profiles,” i.e., measurements of pluralities of cellular constituents in cells having a modified gene or gene product, as phenotypic markers for the gene or gene product. Methods are provided for clustering such response profiles so that similar or correlated response profiles are organized into the same cluster. The invention also provides databases or “compendiums” of response profiles to which the response profile of an uncharacterized gene or gene product can compared.
摘要翻译：本发明涉及用于表征细胞组分，特别是基因和基因产物的方法和系统（例如，计算机系统和计算机程序产品）。特别地，本发明提供了通过使用“响应曲线”来分配或确定未表征的基因和基因产物的生物学功能的方法，即，具有修饰的基因或基因产物的细胞中多种细胞成分的测量作为表型标记物基因或基因产物。提供了用于聚类这种响应简档的方法，使得相似或相关的响应简档被组织到相同的集群中。本发明还提供了可以比较非特异性基因或基因产物的响应特征的响应概况的数据库或“纲要”。

27. 发明授权

US07966130B2 Systems and methods for determining a weighted mean intensity 失效
标题翻译：用于确定加权平均强度的系统和方法
公开(公告)号：US07966130B2
公开(公告)日：2011-06-21
申请号：US10287130
申请日：2002-11-04
申请人： Roland Stoughton , Hongyue Dai
发明人： Roland Stoughton , Hongyue Dai
IPC分类号： G06F19/00 , G06F7/38 , G01N33/48
CPC分类号： G06F19/20 , C12Q1/6837 , Y10T436/10
摘要： A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.
摘要翻译：用于微阵列实验对中的荧光团的微阵列实验中的荧光团偏置去除方法是相反的。此外，一种用于计算与名义上重复的微阵列实验中进行的每个测量相关联的各个错误的方法。该误差测量可选地与基于秩的方法耦合，以便确定响应于扰动的细胞成分向上或向下调节的概率。最后，在名义上重复的微阵列实验中确定细胞成分的表达水平的加权平均的置信度的方法。

28. 发明授权

US06801859B1 Methods of characterizing drug activities using consensus profiles 有权
标题翻译：使用共识的形式表征药物活动的方法
公开(公告)号：US06801859B1
公开(公告)日：2004-10-05
申请号：US09220142
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： G01N3348
CPC分类号： G06F19/24 , G06F19/20
摘要： The present invention provides methods for enhanced detection of biological response profiles. In particular, the methods of this invention allow for the detection of biological response patterns, such as gene expression patterns, in response to different drug treatments. The methods of the invention also allow the determination of a “consensus profile” which describes a particular class or type of biological response. In certain embodiments the consensus profile may describe the biological response of a particular group or class of drugs. In other embodiments, the consensus profile may describe an “ideal” biological response such as one associated with a desired therapeutic effect. The methods of the present invention also allow for the comparison of different biological responses. Thus, the methods of the invention may be used, e.g., to identify and/or study new drugs.
摘要翻译：本发明提供用于增强生物反应曲线检测的方法。特别地，本发明的方法允许响应于不同的药物治疗来检测生物反应模式，如基因表达模式。本发明的方法还允许确定描述特定类别或类型的生物反应的“共有概况”。在某些实施方案中，共有概况可以描述特定组或一类药物的生物反应。在其它实施方案中，共有概况可以描述“理想”生物反应，例如与期望的治疗效果相关联的生物反应。本发明的方法还允许比较不同的生物反应。因此，本发明的方法可以用于例如鉴定和/或研究新的药物。

29. 发明授权

US06673536B1 Methods of ranking oligonucleotides for specificity using wash dissociation histories 失效
标题翻译：使用洗涤解离历史对特异性的寡核苷酸进行排序的方法
公开(公告)号：US06673536B1
公开(公告)日：2004-01-06
申请号：US09408582
申请日：1999-09-29
申请人： Roland Stoughton , Julja Burchard , Stephen H. Friend
发明人： Roland Stoughton , Julja Burchard , Stephen H. Friend
IPC分类号： C12Q168
CPC分类号： G06F19/22 , C12Q1/6832 , C12Q2565/107
摘要： The present invention provides methods and systems, particularly computer systems, for determining the relative specificity with which a particular polynucleotide molecule hybridizes to a polynucleotide probe. For example, the methods and systems of the invention enable a user to compare the specificity with which different polynucleotides hybridize to a given probe and/or rank these polynucleotides according to their specificity to that probe. The methods and systems of the invention also enable a user to compare the specificity with which a particular polynucleotide hybridizes to different probes, and/or rank those different probes according to their specificity for that particular polynucleotide.
摘要翻译：本发明提供了用于确定特定多核苷酸分子与多核苷酸探针杂交的相对特异性的方法和系统，特别是计算机系统。例如，本发明的方法和系统使用户能够根据其对该探针的特异性，比较不同多核苷酸与给定探针杂交的特异性和/或对这些多核苷酸进行排序。本发明的方法和系统还使用户能够根据其对特定多核苷酸的特异性，比较特定多核苷酸与不同探针杂交的特异性和/或对这些不同探针进行排序。

30. 发明授权

US06351712B1 Statistical combining of cell expression profiles 失效
公开(公告)号：US06351712B1
公开(公告)日：2002-02-26
申请号：US09222596
申请日：1998-12-28
申请人： Roland Stoughton , Hongyue Dai
发明人： Roland Stoughton , Hongyue Dai
IPC分类号： G01N3348
CPC分类号： G06F19/20 , C12Q1/6837 , Y10T436/10
摘要： A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

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