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1. 发明申请

WO2006037025A2 MOLECULAR TOXICITY MODELS FROM ISOLATED HEPATOCYTES 审中-公开
标题翻译：分离的肝细胞分子毒性模型
公开(公告)号：WO2006037025A2
公开(公告)日：2006-04-06
申请号：PCT/US2005034780
申请日：2005-09-28
申请人： GENE LOGIC INC , HIGGS BRANDON , ELASHOFF MICHAEL , MENDRICK DONNA L , PORTER MARK W , CASTLE ARTHUR L , JOHNSON KORY R
发明人： HIGGS BRANDON , ELASHOFF MICHAEL , MENDRICK DONNA L , PORTER MARK W , CASTLE ARTHUR L , JOHNSON KORY R
IPC分类号： C12Q1/00
CPC分类号： C12Q1/6876 , C12Q2600/142 , G01N33/5014 , G01N33/5023 , G01N33/5067 , G06F19/18 , G06F19/20
摘要： The present invention includes methods of predicting hepatotoxicity of test agents and methods of generating hepatotoxicity prediction models using algorithms for analyzing quantitative gene expression information. The invention also includes microarrays, computer systems comprising the toxicity prediction models, as well as methods of using the computer systems by remote users for determining the toxicity of test agents.
摘要翻译：本发明包括使用用于分析定量基因表达信息的算法来预测测试剂的肝毒性的方法和产生肝毒性预测模型的方法。本发明还包括微阵列，包括毒性预测模型的计算机系统，以及由远程用户使用计算机系统来确定测试剂的毒性的方法。

2. 发明申请

WO2005052181A2 METHODS FOR MOLECULAR TOXICOLOGY MODELING 审中-公开
标题翻译：分子毒理学建模方法
公开(公告)号：WO2005052181A2
公开(公告)日：2005-06-09
申请号：PCT/US2004039593
申请日：2004-11-24
申请人： GENE LOGIC INC , DIGGANS JAMES C , ELASHOFF MICHAEL
发明人： DIGGANS JAMES C , ELASHOFF MICHAEL
IPC分类号： C12Q20060101 , G06F19/18 , G06F19/20 , C12Q
CPC分类号： G06F19/20 , G06F19/18
摘要： The present invention is based on methods of predicting toxicity of test agents and methods of generating toxicity prediction models using algorithms for analyzing quantitative gene expression information. The invention also includes computer systems comprising the toxicity prediction models, as well as methods of using the computer systems by remote users for determining the toxicity of test agents.
摘要翻译：本发明是基于预测试剂的毒性的方法和使用用于分析定量基因表达信息的算法产生毒性预测模型的方法。本发明还包括包含毒性预测模型的计算机系统，以及由远程用户使用计算机系统来确定测试剂的毒性的方法。

3. 发明申请

WO0210453A3 MOLECULAR TOXICOLOGY MODELING 审中-公开
标题翻译：分子毒理学建模
公开(公告)号：WO0210453A3
公开(公告)日：2003-08-14
申请号：PCT/US0123872
申请日：2001-07-30
申请人： GENE LOGIC INC , MENDRICK DONNA , PORTER MARK W , JOHNSON KORY R , CASTLE ARTHUR L , ELASHOFF MICHAEL R
发明人： MENDRICK DONNA , PORTER MARK W , JOHNSON KORY R , CASTLE ARTHUR L , ELASHOFF MICHAEL R
IPC分类号： C12N15/09 , C12Q1/02 , C12Q1/68 , G06F19/28 , G06F19/00
CPC分类号： C12Q1/6876 , C12Q1/6837 , C12Q1/6883 , C12Q2600/142 , C12Q2600/158 , G06F19/20 , G06F19/28
摘要： The present invention is based on the elucidation of the global changes in gene expression and the identification of toxicity markers in tissues or cells exposed to a known toxin. The genes may be used as toxicity markers in drug screening and toxicity assays. The invention includes a database of genes characterized by toxin-induced differential expression that is designed for use with microarrays and other solid-phase probes.
摘要翻译：本发明基于阐明基因表达的全面变化以及暴露于已知毒素的组织或细胞中毒性标志物的鉴定。这些基因可用作药物筛选和毒性测定中的毒性标记。本发明包括以毒素诱导的差异表达为特征的基因数据库，其设计用于与微阵列和其它固相探针一起使用。

4. 发明申请

WO2003064624A3 MOLECULAR HEPATOTOXICOLOGY MODELING 审中-公开
公开(公告)号：WO2003064624A3
公开(公告)日：2003-08-07
申请号：PCT/US2003/003194
申请日：2003-01-31
申请人： GENE LOGIC, INC. , MENDRICK, Donna , PORTER, Mark , JOHNSON, Kory , HIGGS, Brandon , CASTLE, Arthur , ELASHOFF, Michael
发明人： MENDRICK, Donna , PORTER, Mark , JOHNSON, Kory , HIGGS, Brandon , CASTLE, Arthur , ELASHOFF, Michael
IPC分类号： G01N33/48
摘要： The present invention is based on the elucidation of the global changes in gene expression and the identification of toxicity markers in liver tissues or cells exposed to a known toxin. The genes may be used as toxicity markers in drug screening and toxicity assays. The invention includes a database of genes characterized by liver toxin-induced differential expression that is designed for use with microarrays and other solid-phase probes.

5. 发明申请

WO2009049257A2 PREDICTIVE MODELS AND METHODS FOR DIAGNOSING AND ASSESSING CORONARY ARTERY DISEASE 审中-公开
标题翻译：预测模型和方法诊断和评估冠状动脉疾病
公开(公告)号：WO2009049257A2
公开(公告)日：2009-04-16
申请号：PCT/US2008/079646
申请日：2008-10-10
申请人： CARDIO DX, INC. , ROSENBERG, Steve , DANIELS, Susan , ELASHOFF, Michael, R. , WINGROVE, James, A. , TINGLEY, Whittemore, G. , SEHNEERT, Amy, J. , PAONI, Nicholas, F.
发明人： ROSENBERG, Steve , DANIELS, Susan , ELASHOFF, Michael, R. , WINGROVE, James, A. , TINGLEY, Whittemore, G. , SEHNEERT, Amy, J. , PAONI, Nicholas, F.
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , C12Q2600/112 , C12Q2600/158
摘要： Biomarkers useful for diagnosing and assessing the extent of coronary artery disease (CAD) are provided, along with kits for measuring their expression. The invention also provides predictive models, based on the biomarkers, as well as computer systems, and software embodiments of the models for scoring and optionally classifying samples. In a preferred embodiment, the biomarkers are organized into clustered groups. The expression level of the biomarkers within a group are highly correlated to each other in normal and disease states. Expression values of genes chosen from each of two, three, four or five of the clustered gene groups, A, B, C, D, E may be used. Alternatively, expression values of genes chosen from the groups are combined into a metagene. Preferred biomarkers include S100A12, S100A8, S100A9, BCL2A1, and F5 (group A); XK, P62, and FECH (group B); TUBB2 (group C); IFNG, PDGFB, VSIG4, and TNF (group D); CSF3R, TLR5, CD46, and NCFl (group E); S100A12, S100A9, BCL2A1, TXN and CSTA (group I); OLIGl, 0LIG2, AD0RA3, CLC, and SLC29A1 (group II); and CBS and ARGl (group IV).
摘要翻译：提供用于诊断和评估冠状动脉疾病（CAD）程度的生物标志物，以及用于测量其表达的试剂盒。本发明还提供了基于生物标志物的预测模型以及计算机系统和用于对样品进行评分和任选分类的模型的软件实施例。在一个优选的实施方案中，生物标志物被组织成群集。组内生物标志物的表达水平在正常和疾病状态下彼此高度相关。可以使用从2,3,4或5个群集基因组A，B，C，D，E中的每一个中选择的基因的表达值。或者，将选自这些基因的基因的表达值组合成一种变应原。优选的生物标志物包括S100A12，S100A8，S100A9，BCL2A1和F5（A组）; XK，P62和FECH（B组）; TUBB2（C组）; IFNG，PDGFB，VSIG4和TNF（D组）; CSF3R，TLR5，CD46和NCF1（E组）; S100A12，S100A9，BCL2A1，TXN和CSTA（组I）; OLIG1，0LIG2，AD0RA3，CLC和SLC29A1（组II）; 和CBS和ARG1（第IV组）。

6. 发明申请

WO03065993A8 PRIMARY RAT HEPATOCYTE TOXICITY MODELING 审中-公开
标题翻译：原发性肝细胞毒性建模
公开(公告)号：WO03065993A8
公开(公告)日：2006-04-27
申请号：PCT/US0303482
申请日：2003-02-04
申请人： GENE LOGIC INC , MENDRICK DONNA , PORTER MARK , JOHNSON KORY , HIGGS BRANDON , CASTLE ARTHUR , ORR MICHAEL , ELASHOFF MICHAEL
发明人： MENDRICK DONNA , PORTER MARK , JOHNSON KORY , HIGGS BRANDON , CASTLE ARTHUR , ORR MICHAEL , ELASHOFF MICHAEL
IPC分类号： A61K20060101 , A61K9/00 , C12Q1/02 , C12Q1/68 , G06F19/00 , A61K
CPC分类号： C12Q1/6883 , C12Q1/6837 , C12Q2600/142 , C12Q2600/158

7. 发明申请

WO2004063334A2 MOLECULAR CARDIOTOXICOLOGY MODELING 审中-公开
标题翻译：分子心理学建模
公开(公告)号：WO2004063334A2
公开(公告)日：2004-07-29
申请号：PCT/US2004/000240
申请日：2004-01-08
申请人： GENE LOGIC, INC. , MENDRICK, Donna, L. , PORTER, Mark, W. , JOHNSON, Kory, R. , HIGGS, Brandon , CASTLE, Arthur , ELASHOFF, Michael
发明人： MENDRICK, Donna, L. , PORTER, Mark, W. , JOHNSON, Kory, R. , HIGGS, Brandon , CASTLE, Arthur , ELASHOFF, Michael
IPC分类号： C12N
CPC分类号： C12Q1/6883 , C12Q1/6837 , C12Q2600/142 , C12Q2600/158 , G01N2500/00 , Y10S707/99945 , Y10S707/99948
摘要： The present invention is based on the elucidation of the global changes in gene expression and the identification of toxicity markers in tissues or cells exposed to a known cardiotoxin. The genes may be used as toxicity markers in drug screening and toxicity assays. The invention includes a database of genes characterized by toxin-induced differential expression that is designed for use with microarrays and other solid-phase probes.
摘要翻译：本发明基于阐明基因表达的全面变化以及暴露于已知心脏毒素的组织或细胞中毒性标志物的鉴定。这些基因可用作药物筛选和毒性测定中的毒性标记。本发明包括以毒素诱导的差异表达为特征的基因数据库，其设计用于与微阵列和其它固相探针一起使用。

8. 发明申请

WO2003042780A3 SYSTEM AND METHOD FOR STORAGE AND ANALYSIS OF GENE EXPRESSION DATA 审中-公开
公开(公告)号：WO2003042780A3
公开(公告)日：2003-05-22
申请号：PCT/US2002/035454
申请日：2002-11-04
申请人： GENE LOGIC INC. , DIGGANS, James, C. , DOLGINOW, Doug , ELASHOFF, Michael , HUANG, Da, Wei , MENEZES, Supriya , MERTZ, Larry , NADIMPALLI, Ramgopal
发明人： DIGGANS, James, C. , DOLGINOW, Doug , ELASHOFF, Michael , HUANG, Da, Wei , MENEZES, Supriya , MERTZ, Larry , NADIMPALLI, Ramgopal
IPC分类号： G01N33/48
摘要： In a computer system for analysis of gene expression data, a gene expression database is organized in a hierarchical b-tree according to the descriptive and clinical sample attributes stored in the database. A user submits a query for searching the database and defines attributes on which to filter for each level of the b-tree. A simple search can be employed to arbitrarily group together leaf nodes depending on their attributes. The grouped leaf nodes are used as "control" and "experimental" sample sets. A t-test can be performed to test for statistically significant regulation between the control and experimental sample sets. In one embodiment, the results of the b-tree analysis are organized as a table of information which may be part of a relational database. The data in the database are encoded according to a three-state scheme based on regulation behavior. A similarity search algorithm can be performed on the encoded data to identify genes or gene fragments that show regulation profiles similar to the query gene or gene fragment, ranking the genes according to the level of similarity.

9. 发明申请

WO03042780A2 SYSTEM AND METHOD FOR STORAGE AND ANALYSIS OF GENE EXPRESSION DATA 审中-公开
标题翻译：用于存储和分析基因表达数据的系统和方法
公开(公告)号：WO03042780A2
公开(公告)日：2003-05-22
申请号：PCT/US0235454
申请日：2002-11-04
申请人： GENE LOGIC INC , DIGGANS JAMES C , DOLGINOW DOUG , ELASHOFF MICHAEL , HUANG DA WEI , MENEZES SUPRIYA , MERTZ LARRY , NADIMPALLI RAMGOPAL
发明人： DIGGANS JAMES C , DOLGINOW DOUG , ELASHOFF MICHAEL , HUANG DA WEI , MENEZES SUPRIYA , MERTZ LARRY , NADIMPALLI RAMGOPAL
IPC分类号： G06F17/30 , G06F19/20 , G06F19/28 , G06F
CPC分类号： G06F19/28 , G06F19/20
摘要： In a computer system for analysis of gene expression data, a gene expression database is organized in a hierarchical b-tree according to the descriptive and clinical sample attributes stored in the database. A user submits a query for searching the database and defines attributes on which to filter for each level of the b-tree. A simple search can be employed to arbitrarily group together leaf nodes depending on their attributes. The grouped leaf nodes are used as "control" and "experimental" sample sets. A t-test can be performed to test for statistically significant regulation between the control and experimental sample sets. In one embodiment, the results of the b-tree analysis are organized as a table of information which may be part of a relational database. The data in the database are encoded according to a three-state scheme based on regulation behavior. A similarity search algorithm can be performed on the encoded data to identify genes or gene fragments that show regulation profiles similar to the query gene or gene fragment, ranking the genes according to the level of similarity.
摘要翻译：在用于分析基因表达数据的计算机系统中，根据存储在数据库中的描述性和临床样本属性，将基因表达数据库组织在分层b树中。用户提交查询以搜索数据库，并定义要为每个级别的b树过滤的属性。可以使用简单的搜索来根据其属性任意地将叶节点组合在一起。分组叶节点用作“对照”和“实验”样本集。可以进行t检验以测试对照和实验样品组之间的统计学显着性调节。在一个实施例中，b-tree分析的结果被组织为可以是关系数据库的一部分的信息表。数据库中的数据根据调节行为的三态方案进行编码。可以对编码数据执行相似性搜索算法，以识别显示与查询基因或基因片段类似的调节特征的基因或基因片段，根据相似性等级对基因进行排序。

10. 发明申请

WO2002095000A3 MOLECULAR TOXICOLOGY MODELING 审中-公开
公开(公告)号：WO2002095000A3
公开(公告)日：2002-11-28
申请号：PCT/US2002/016173
申请日：2002-05-22
申请人： GENE LOGIC, INC. , MENDRICK, Donna , PORTER, Mark , JOHNSON, Kory , HIGGS, Brandon , CASTLE, Arthur , ELASHOFF, Michael
发明人： MENDRICK, Donna , PORTER, Mark , JOHNSON, Kory , HIGGS, Brandon , CASTLE, Arthur , ELASHOFF, Michael
IPC分类号： C12Q1/68
摘要： The present invention is based on the elucidation of the global changes in gene expression and the identification of toxicity markers in tissues or cells exposed to a known renal toxin. The genes may be used as toxicity markers in drug screening and toxicity assays. The invention includes a database of genes characterized by toxin-induced differential expression that is designed for use with microarrays and other solid-phase probes.

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