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1. 发明专利

CA2462099A1 COMPOSITIONS AND METHODS FOR MODELING SACCHAROMYCES CEREVISIAE METABOLISM 未知
公开(公告)号：CA2462099A1
公开(公告)日：2003-05-01
申请号：CA2462099
申请日：2002-10-24
申请人： NIELSEN JENS B , UNIV CALIFORNIA , FORSTER JOCHEN
发明人： NIELSEN JENS B , FAMILI IMANDOKHT , FORSTER JOCHEN , FU PENGCHENG , PALSSON BERNHARD O
IPC分类号： G06F17/30 , G06F19/12 , G06F19/18 , G06F19/00 , C12Q1/02 , C12N1/18 , G01N33/48
摘要： The invention provides an in silica model for determining a S. cerevisiae physiological function. The model includes a data structure relating a plurality of S. cerevisiae reactants to a plurality of S. cerevisiae reactions, a constraint set for the plurality of S. cerevisiae reactions, and commands for determining a distribution of flux through the reactions that is predictive ofa s. cerevisiae physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. The invention further provides methods for making an in silica S. cerevisiae model and methods for determining a S. cerevisiae physiological function using a model of the invention.

2. 发明专利

CA2462099C COMPOSITIONS AND METHODS FOR MODELING SACCHAROMYCES CEREVISIAE METABOLISM 未知
公开(公告)号：CA2462099C
公开(公告)日：2013-01-08
申请号：CA2462099
申请日：2002-10-24
申请人： UNIV CALIFORNIA , NIELSEN JENS B , FORSTER JOCHEN
发明人： PALSSON BERNHARD O , FAMILI IMANDOKHT , FU PENGCHENG , NIELSEN JENS B , FORSTER JOCHEN
IPC分类号： C40B30/02 , C12N1/16 , C12Q1/02 , C12Q1/68 , C40B50/02 , G01N33/48 , G06F17/30 , G06F19/12 , G06F19/18
摘要： The invention provides an in silica model for determining a S. cerevisiae physiological function. The model includes a data structure relating a plurality of S. cerevisiae reactants to a plurality of S. cerevisiae reactions, a constraint set for the plurality of S. cerevisiae reactions, and commands for determining a distribution of flux through the reactions that is predictive ofa s. cerevisiae physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. The invention further provides methods for making an in silica S. cerevisiae model and methods for determining a S. cerevisiae physiological function using a model of the invention.

3. 发明申请

WO03036296A9 COMPOSITIONS AND METHODS FOR MODELING SACCHAROMYCES CEREVISIAE METABOLISM 审中-公开
标题翻译：组合物和方法用于建模细胞因子代谢
公开(公告)号：WO03036296A9
公开(公告)日：2004-05-13
申请号：PCT/US0234394
申请日：2002-10-24
申请人： UNIV CALIFORNIA , PALSSON BERNHARD O , FAMILI IMANDOKHT , FU PENGCHENG , NIELSEN JENS B , FORSTER JOCHEN
发明人： PALSSON BERNHARD O , FAMILI IMANDOKHT , FU PENGCHENG , NIELSEN JENS B , FORSTER JOCHEN
IPC分类号： G06F17/30 , G06F19/12 , G06F19/18 , G01N33/48
CPC分类号： G06F19/12 , G06F19/18 , Y02A90/26 , Y02E50/343
摘要： The invention provides an in silica model for determining a S. cerevisiae physiological function. The model includes a data structure relating a plurality of S. cerevisiae reactants to a plurality of S. cerevisiae reactions, a constraint set for the plurality of S. cerevisiae reactions, and commands for determining a distribution of flux through the reactions that is predictive ofa s. cerevisiae physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. The invention further provides methods for making an in silica S. cerevisiae model and methods for determining a S. cerevisiae physiological function using a model of the invention.
摘要翻译：本发明提供了用于确定酿酒酵母生理功能的二氧化硅模型。该模型包括将多个酿酒酵母反应物与多个酿酒酵母反应相关联的数据结构，针对多个酿酒酵母反应的约束集，以及用于确定通过预测的反应的通量分布的命令秒。酿酒酵母生理功能。本发明的模型还可以包括含有表征相关基因或基因的信息的基因数据库。本发明还提供了使用本发明的模型制备二氧化硅酿酒酵母模型和确定酿酒酵母生理功能的方法的方法。

4. 发明专利

JP2010225171A METHOD AND SYSTEM TO IDENTIFY OPERATIONAL REACTION PATHWAY 审中-公开
公开(公告)号：JP2010225171A
公开(公告)日：2010-10-07
申请号：JP2010122236
申请日：2010-05-28
申请人： UNIV CALIFORNIA
发明人： PALSSON BERNHARD O , COVERT MARKUS W , HERRGARD MARKUS
IPC分类号： G01N33/50 , G06F19/12 , G06F19/24
摘要： PROBLEM TO BE SOLVED: To provide a method of identifying an operational reaction pathway of a biosystem. SOLUTION: The method includes (a) a step for providing a set of systemic reaction pathways though a reaction network representing the biosystem, (b) a step for providing a set of phenomenological reaction pathways of the biosystem, and (c) a step for comparing the set of systemic reaction pathways with the set of phenomenological reaction pathways, and further includes a step in which a pathway common to the sets is an operational reaction pathway of the biosystem. The method includes a method of refining a biosystem reaction network; a method of measuring effect of a genetic polymorphism on whole cell functions; and a method of diagnosing a genetic polymorphism-mediated pathology. COPYRIGHT: (C)2011,JPO&INPIT

5. 发明公开

EP1552472A4 METHODS AND SYSTEMS TO IDENTIFY OPERATIONAL REACTION PATHWAYS 审中-公开
标题翻译： VERFAHREN UND SYSTEME ZUM IDENTIFIZIEREN VON OPERATIONEN REAKTIONSWEGEN
公开(公告)号：EP1552472A4
公开(公告)日：2008-02-20
申请号：EP03717893
申请日：2003-02-14
申请人： UNIV CALIFORNIA
发明人： PALSSON BERNHARD O , COVERT MARKUS W , HERRGARD MARKUS
IPC分类号： G01N33/50 , G06F19/12 , G06F19/24 , G06F19/00 , G06N3/00
CPC分类号： G01N33/5005 , G06F19/12 , G06F19/20 , G06F19/24
摘要： The present invention provides a method for identifying an operational reaction pathway of a biosystem. The method includes (a) providing a set of systemic reaction pathways though a reaction network representing said biosystem, (b) providing a set of phenomenological reaction pathways of said biosystem, and (c) comparing said set of systemic reaction pathways with said set of phenomenological reaction pathways, wherein a pathway common to said sets is an operational reaction pathway of said biosystem. Also described is a method of refining a biosystem reaction network; a method of reconciling biosystem data sets; a method of determining the effect of a genetic polymorphism on whole cell function; and a method of diagnosing a genetic polymorphism-mediated pathology.
摘要翻译：本发明提供了一种用于鉴定生物系统的操作反应路径的方法。该方法包括：（a）通过代表所述生物系统的反应网络提供一组系统反应途径，（b）提供所述生物系统的一组现象学反应途径，以及（c）将所述系统反应途径组与所述现象学反应路径，其中所述组共同的路径是所述生物系统的操作反应路径。还描述了精制生物系统反应网络的方法; 协调生物系统数据集的方法; 确定遗传多态性对全细胞功能影响的方法; 以及诊断基因多态性介导的病理学的方法。

6. 发明公开

EP1438580A4 COMPOSITIONS AND METHODS FOR MODELING SACCHAROMYCES CEREVISIAE METABOLISM 审中-公开
标题翻译：组合物和方法建模酿酒酵母的代谢的影响
公开(公告)号：EP1438580A4
公开(公告)日：2007-11-14
申请号：EP02784306
申请日：2002-10-24
申请人： UNIV CALIFORNIA
发明人： PALSSON BERNHARD O , FAMILI IMANDOKHT , FU PENGCHENG , NIELSEN JENS B , FORSTER JOCHEN
IPC分类号： G06F17/30 , G06F19/12 , G06F19/18 , G01N33/48
CPC分类号： G06F19/12 , G06F19/18 , Y02A90/26 , Y02E50/343
摘要： The invention provides an in silica model for determining a S. cerevisiae physiological function. The model includes a data structure relating a plurality of S. cerevisiae reactants to a plurality of S. cerevisiae reactions, a constraint set for the plurality of S. cerevisiae reactions, and commands for determining a distribution of flux through the reactions that is predictive of a S. cerevisiae physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. The invention further provides methods for making an in silica S. cerevisiae model and methods for determining a S. cerevisiae physiological function using a model of the invention. The invention provides an in silica model for determining a S. cerevisiae physiological function. The model includes a data structure relating a plurality of S. cerevisiae reactants to a plurality of S. cerevisiae reactions, a constraint set for the plurality of S. cerevisiae reactions, and commands for determining a distribution of flux through the reactions that is predictive of a S. cerevisiae physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. The invention further provides methods for making an in silica S. cerevisiae model and methods for determining a S. cerevisiae physiological function using a model of the invention.

7. 发明公开

EP1377901A4 METHOD FOR THE EVOLUTIONARY DESIGN OF BIOCHEMICAL REACTION NETWORKS 审中-公开
标题翻译：程序对生化反应网络进化设计
公开(公告)号：EP1377901A4
公开(公告)日：2007-10-03
申请号：EP02709271
申请日：2002-01-31
申请人： UNIV CALIFORNIA
发明人： PALSSON BERNHARD O , EDWARDS JEREMY S
IPC分类号： C12N15/09 , C12N1/15 , C12N1/19 , C12N1/20 , C12N1/21 , C12N5/10 , G06F17/30 , G06F19/12 , G06F19/18 , G06G7/58 , G06G7/60
CPC分类号： G06F19/12 , G06F19/18

8. 发明申请

WO2004035009A3 METHODS AND SYSTEMS TO IDENTIFY OPERATIONAL REACTION PATHWAYS 审中-公开
标题翻译：识别操作反应路径的方法和系统
公开(公告)号：WO2004035009A3
公开(公告)日：2004-09-30
申请号：PCT/US0304486
申请日：2003-02-14
申请人： UNIV CALIFORNIA , PALSSON BERNHARD O , COVERT MARKUS W , HERRGARD MARKUS
发明人： PALSSON BERNHARD O , COVERT MARKUS W , HERRGARD MARKUS
IPC分类号： G01N33/50 , G06F19/12 , G06F19/24 , G06N3/00
CPC分类号： G01N33/5005 , G06F19/12 , G06F19/20 , G06F19/24
摘要： The present invention provides a method for identifying an operational reaction pathway of a biosystem. The method includes (a) providing a set of systemic reaction pathways though a reaction network representing said biosystem, (b) providing a set of phenomenological reaction pathways of said biosystem, and (c) comparing said set of systemic reaction pathways with said set of phenomenological reaction pathways, wherein a pathway common to said sets is an operational reaction pathway of said biosystem. Also described is a method of refining a biosystem reaction network; a method of reconciling biosystem data sets; a method of determining the effect of a genetic polymorphism on whole cell function; and a method of diagnosing a genetic polymorphism-mediated pathology.
摘要翻译：本发明提供了用于鉴定生物系统的操作反应途径的方法。该方法包括（a）通过代表所述生物系统的反应网络提供一组全身反应途径，（b）提供所述生物系统的一组现象学反应途径，和（c）将所述一组全身反应途径与所述一组现象学反应途径，其中所述组共同的途径是所述生物系统的操作反应途径。还描述了一种精制生物系统反应网络的方法; 调和生物系统数据集的方法; 确定遗传多态性对全细胞功能的影响的方法; 以及诊断遗传多态性介导的病理学的方法。

9. 发明申请

WO2008045306A3 COMPOSITIONS AND METHODS FOR MODELING HUMAN METABOLISM 审中-公开
标题翻译：用于建立人类代谢的组合物和方法
公开(公告)号：WO2008045306A3
公开(公告)日：2008-12-18
申请号：PCT/US2007021369
申请日：2007-10-03
申请人： UNIV CALIFORNIA , PALSSON BERNHARD O , DUARTE NATALIE , BECKER SCOTT , JAMSHIDI NEEMA
发明人： PALSSON BERNHARD O , DUARTE NATALIE , BECKER SCOTT , JAMSHIDI NEEMA
IPC分类号： G06F19/00 , G01N33/50
CPC分类号： G06F19/12 , G06F19/18 , G06F19/28
摘要： The present invention provides Homo sapiens Recon 1, a manually assembled, functionally validated, bottom-up reconstruction of human metabolism. Recon l's 1496 genes, 2004 proteins, 2766 metabolites, and 3311 biochemical and transport reactions were extracted from more than 50 years of legacy biochemical knowledge and Build 35 of the human genome sequence.
摘要翻译：本发明提供了智人Recon 1，其是人类代谢的手动组装的功能验证的自下而上的重建。从50多年的遗传生物化学知识和人类基因组序列构建中提取了1496个基因，2004年蛋白质，2766个代谢物和3311个生物化学和转运反应。

10. 发明公开

EP1381860A4 MODELS AND METHODS FOR DETERMINING SYSTEMIC PROPERTIES OF REGULATED REACTION NETWORKS 审中-公开
标题翻译：模型与分析方法用于确定系统性特点反应监管网络
公开(公告)号：EP1381860A4
公开(公告)日：2008-10-15
申请号：EP02748376
申请日：2002-03-01
申请人： UNIV CALIFORNIA , GENOMATICA INC
发明人： PALSSON BERNHARD O , COVERT MARKUS W , SCHILLING CHRISTOPHE H
IPC分类号： G01N33/48 , C12N15/10 , C12Q1/02 , C12Q1/25 , C12Q1/68 , G01N33/53 , G01N33/68 , G06F19/12 , G06F19/18 , G06G7/48 , G06G7/58
CPC分类号： G06F19/12 , C12N15/1089 , G06F19/18
摘要： The invention provides a model of a reaction network integrated with regulatory controls related to the reactions. A method is provided for determining a systemic property of a reaction network using a model of the invention. Also provided is a method for modeling changes that occur in a reaction network at various time points due to regulatory events.
摘要翻译：本发明提供了与相关的反应监管控制集成在反应网络的模型。提供了一种用于确定性采矿的方法，使用本发明的模型的反应网络的全身属性。因此，提供了用于建模变化的方法确实发生在由于监管事件的不同时间点的反应网络。

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