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1. 发明申请

WO2002070730A2 MODELS AND METHODS FOR DETERMINING SYSTEMIC PROPERTIES OF REGULATED REACTION NETWORKS 审中-公开
标题翻译：用于确定调节反应网络系统特性的模型和方法
公开(公告)号：WO2002070730A2
公开(公告)日：2002-09-12
申请号：PCT/US2002/006276
申请日：2002-03-01
申请人： THE REGENTS OF THE UNIVERSITY OF CALIFORNIA , GENOMATICA, INC. , PALSSON, Bernhard, O. , COVERT, Markus, W. , SCHILLING, Christophe, H.
发明人： PALSSON, Bernhard, O. , COVERT, Markus, W. , SCHILLING, Christophe, H.
IPC分类号： C12Q
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：本发明提供了与反应相关的调节控制整合的反应网络的模型。提供了使用本发明的模型来确定反应网络的系统性质的方法。还提供了一种用于对由于调节事件在不同时间点发生在反应网络中的变化进行建模的方法。

2. 发明申请

WO2012027533A1 SELECTABLE MARKERS AND RELATED METHODS 审中-公开
标题翻译：可选标记及相关方法
公开(公告)号：WO2012027533A1
公开(公告)日：2012-03-01
申请号：PCT/US2011/049070
申请日：2011-08-25
申请人： GT LIFE SCIENCES, INC. , GENOMATICA, INC. , FAMILI, Imandokht , USAITE BLACK, Renata , SCHILLING, Christophe, H.
发明人： FAMILI, Imandokht , USAITE BLACK, Renata , SCHILLING, Christophe, H.
IPC分类号： C12N5/07
CPC分类号： C12N15/85 , C12N9/0071 , C12Y114/16001
摘要： The invention relates to newly identified selectable marker systems, cells for use in a selectable marker system, and methods for using the selectable marker systems.
摘要翻译：本发明涉及新鉴定的选择性标记系统，用于选择性标记系统的细胞以及使用可选标记系统的方法。

3. 发明申请

WO2002070730A3 MODELS AND METHODS FOR DETERMINING SYSTEMIC PROPERTIES OF REGULATED REACTION NETWORKS 审中-公开
公开(公告)号：WO2002070730A3
公开(公告)日：2002-09-12
申请号：PCT/US2002/006276
申请日：2002-03-01
申请人： THE REGENTS OF THE UNIVERSITY OF CALIFORNIA , GENOMATICA, INC. , PALSSON, Bernhard, O. , COVERT, Markus, W. , SCHILLING, Christophe, H.
发明人： PALSSON, Bernhard, O. , COVERT, Markus, W. , SCHILLING, Christophe, H.
IPC分类号： G01N33/48
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.

4. 发明申请

WO2003106998A1 SYSTEMS AND METHODS FOR CONSTRUCTING GENOMIC-BASED PHENOTYPIC MODELS 审中-公开
标题翻译：用于构建基于基因的相位模型的系统和方法
公开(公告)号：WO2003106998A1
公开(公告)日：2003-12-24
申请号：PCT/US2003/018838
申请日：2003-06-13
申请人： GENOMATICA INC. , SCHILLING, Christophe, H.
发明人： SCHILLING, Christophe, H.
IPC分类号： G01N33/48
CPC分类号： G06F19/12
摘要： The invention provides a computer implemented process for constructing a scalable output network model for a bioparticle. The process includes computer implemented steps of: (a) accessing a database of network gene components including an annotated network set of open reading frames (ORFs) of a bioparticle genome, (b) forming a data structure associating the network gene components with network reaction components, the data structure establishing a data set specifying a network model of connectivity and flow of the network reaction components, and (c) transforming the data set into a mathematical description of reactant fluxes defining the network model of connectivity and flow, wherein the mathematical description defines a scalable output network model of a bioparticle.
摘要翻译：本发明提供了一种用于构建用于生物颗粒的可伸缩输出网络模型的计算机实现过程。该过程包括计算机实现的步骤：（a）访问网络基因组件的数据库，包括生物粒子基因组的开放阅读框（ORF）的注释网络集合，（b）形成将网络基因组分与网络反应相关联的数据结构组件，建立指定网络反应组件的连接性和流量的网络模型的数据集的数据结构，以及（c）将数据集转换为定义连通性和流程的网络模型的反应物通量的数学描述，其中数学描述定义了生物颗粒的可扩展输出网络模型。

5. 发明申请

WO2003081207A3 COMPOSITIONS AND METHODS FOR MODELING BACILLUS SUBTILIS METABOLISM 审中-公开
公开(公告)号：WO2003081207A3
公开(公告)日：2003-10-02
申请号：PCT/US2003/008326
申请日：2003-03-18
申请人： GENOMATICA, INC. , PARK, Sung, M. , SCHILLING, Christophe, H. , PALSSON, Bernhard, O.
发明人： PARK, Sung, M. , SCHILLING, Christophe, H. , PALSSON, Bernhard, O.
IPC分类号： G01N33/48
摘要： The invention provides an in silico model for determining a Bacillus subtilis physiological function. The model includes a data structure relating a plurality of B. subtilis reactants to a plurality of B. subtilis reactions, a constraint set for the plurality of B. subtilis reactions, and commands for determining a distribution of flux through the reactions that is predictive of a B. subtilis physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. A regulated B. subtilis reaction can be represented in a model of the invention by including a variable constraint for the regulated reaction. The invention further provides methods for making an in silico B. subtilis model and methods for determining a B. subtilis physiological function using a model of the invention.

6. 发明申请

WO2006099220A2 COMPOSITIONS AND METHODS FOR BIOELECTRICITY PRODUCTION 审中-公开
标题翻译：用于生物生产的组合物和方法
公开(公告)号：WO2006099220A2
公开(公告)日：2006-09-21
申请号：PCT/US2006/008760
申请日：2006-03-10
申请人： GENOMATICA, INC. , SCHILLING, Christophe, H.
发明人： SCHILLING, Christophe, H.
IPC分类号： C12N9/02
CPC分类号： H01M8/16 , H01M4/86 , H01M2004/8684 , Y02E60/527 , Y02P70/56
摘要： The invention provides a microbial fuel cell having a dissimilatory metal-reducing microbe expressing exogenous or native ATPase subunits, the ATPase subunits assembling into an active ATP synthase and consuming ATP in a futile cycle. The dissimilatory metal-reducing microbe can include an organism selected from the organisms set forth in Table 1. The one or more exogenous ATPase subunits can include a subunit selected from the ATPase subunits set forth in Tables 2 or 3. Also provided is a microbial fuel cell having a dissimilatory metal-reducing microbe expressing one or more exogenous genes encoding a gene product that promotes ATP consumption, the gene products of the one or more exogenous genes having an activity that reduces ATP synthesis, increases ATP consumption or both. The one or more gene products can increase ATP consumption through a futile cycle or through altering a metabolic reaction directly involved in ATP synthesis. Further provided is a microbial fuel cell having a dissimilatory metal-reducing microbe expressing one or more exogenous genes encoding a gene products that increases the electron/mole ratio compared to an unmodified microbe, wherein the increased ratio enhances electron transfer to an electrode. A method of producing electricity from an microbial organism is further provided. The method includes: (a) culturing a microbial fuel cell under anaerobic conditions sufficient for growth, the microbial fuel cell comprising a dissimilatory metal-reducing microbe expressing exogenous ATPase subunits, the ATPase subunits assembling into an active ATP synthase and consuming ATP in a futile cycle when grown under anaerobic conditions, and (b) capturing electrons produced by an increased ATP demand with an electron acceptor.
摘要翻译：本发明提供了一种微生物燃料电池，其具有表达外源或天然ATP酶亚基的异构金属还原微生物，ATP酶亚基组装成活性ATP合酶并在无效循环中消耗ATP。异构金属还原微生物可以包括选自表1所示的生物体的生物体。一种或多种外源性ATP酶亚基可以包括选自表2或3所示的ATP酶亚基的亚基。还提供了微生物燃料具有表达编码促进ATP消耗的基因产物的一种或多种外源基因的异构金属还原微生物的细胞，具有降低ATP合成的活性的一种或多种外源基因的基因产物增加ATP消耗或两者。一种或多种基因产物可以通过无效循环或通过改变直接参与ATP合成的代谢反应来增加ATP消耗。还提供了具有异构金属还原微生物的微生物燃料电池，其表达一种或多种编码与未修饰微生物相比增加电子/摩尔比的基因产物的外源基因，其中增加的比例增强了电子传递到电极。还提供了从微生物生物发电的方法。该方法包括：（a）在足够生长的厌氧条件下培养微生物燃料电池，所述微生物燃料电池包含表达外源ATP酶亚基的异构金属还原微生物，组装成活性ATP合酶的ATP酶亚基，并消耗无效的ATP 在无氧条件下生长的循环，以及（b）用电子受体捕获由ATP需求增加产生的电子。

7. 发明申请

WO2003082214A3 HUMAN METABOLIC MODELS AND METHODS 审中-公开
公开(公告)号：WO2003082214A3
公开(公告)日：2003-10-09
申请号：PCT/US2003/009751
申请日：2003-03-27
申请人： GENOMATICA, INC. , PALSSON, Bernhard, O. , FAMILI, Imandokht , COVERT, Markus, W. , SCHILLING, Christophe, H.
发明人： PALSSON, Bernhard, O. , FAMILI, Imandokht , COVERT, Markus, W. , SCHILLING, Christophe, H.
IPC分类号： G01N33/48
摘要： The invention provides in silico models for determining the physiological function of human cells, including human skeletal muscle cells. The models include a data structure relating a plurality of Homo sapiens reactions, a constraint set for the plurality of Homo sapiens reactions, and commands for determining a distribution of flux through the reactions that is predictive of a Homo sapiens physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. A regulated Homo sapiens reaction can be represented in a model of the invention by including a variable constraint for the regulated reaction. The invention further provides methods for making an in silico Homo sapiens physiological function using a model of the invention.

8. 发明申请

WO2009094485A1 METHODS AND ORGANISMS FOR UTILIZING SYNTHESIS GAS OR OTHER GASEOUS CARBON SOURCES AND METHANOL 审中-公开
标题翻译：使用合成气或其他气体碳源和甲醇的方法和有机体
公开(公告)号：WO2009094485A1
公开(公告)日：2009-07-30
申请号：PCT/US2009/031737
申请日：2009-01-22
申请人： GENOMATICA, INC. , BURK, Mark , SCHILLING, Christophe, H. , BURGARD, Anthony , TRAWICK, John, D.
发明人： BURK, Mark , SCHILLING, Christophe, H. , BURGARD, Anthony , TRAWICK, John, D.
IPC分类号： C12N1/20 , C12P21/06 , C12P11/00
CPC分类号： C12P7/18 , C12N9/0008 , C12N9/0036 , C12N9/1007 , C12N9/93 , C12N15/70 , C12P19/32 , Y02E50/343
摘要： The invention provides a non-naturally occurring microbial organism having an acetyl- CoA pathway and the capability of utilizing syngas or syngas and methanol. In one embodiment, the invention provides a non-naturally occurring microorganism, comprising one or more exogenous proteins conferring to the microorganism a pathway to convert CO, CO 2 and/or H 2 to acetyl-coenzyme A (acetyl-CoA), methyl tetrahydro folate (methyl-THF) or other desired products, wherein the microorganism lacks the ability to convert CO or CO 2 and H 2 to acetyl- CoA or methyl-THF in the absence of the one or more exogenous proteins. For example, the microbial organism can contain at least one exogenous nucleic acid encoding an enzyme or protein in an acetyl-CoA pathway. The microbial organism is capable of utilizing synthesis gases comprising CO, CO 2 and/or H 2 , alone or in combination with methanol, to produce acetyl- CoA. The invention additionally provides a method for producing acetyl-CoA, for example, by culturing an acetyl-CoA producing microbial organism, where the microbial organism expresses at least one exogenous nucleic acid encoding an acetyl-CoA pathway enzyme or protein in a sufficient amount to produce acetyl-CoA, under conditions and for a sufficient period of time to produce acetyl-CoA.
摘要翻译：本发明提供了具有乙酰辅酶A途径和利用合成气或合成气和甲醇的能力的非天然存在的微生物。在一个实施方案中，本发明提供非天然存在的微生物，其包含一种或多种外源蛋白质，赋予微生物将CO，CO 2和/或H 2转化为乙酰辅酶A（乙酰辅酶A），甲基四氢叶酸（甲基-THF）或其它所需产物，其中微生物缺乏在不存在一种或多种外源蛋白的情况下将CO或CO 2和H 2转化为乙酰辅酶A或甲基-THF的能力。例如，微生物生物体可以含有至少一种编码乙酰辅酶A途径中的酶或蛋白质的外源核酸。微生物生物能够单独或与甲醇组合使用包含CO，CO 2和/或H 2的合成气体，以产生乙酰辅酶A。本发明另外提供了生产乙酰辅酶A的方法，例如通过培养产生乙酰辅酶A的微生物，其中微生物生物体表达至少一种编码乙酰辅酶A途径酶或蛋白质的外源核酸，其量足够在条件和足够的时间内产生乙酰辅酶A产生乙酰辅酶A。

9. 发明申请

WO2003082214A2 HUMAN METABOLIC MODELS AND METHODS 审中-公开
标题翻译：人类代谢模型和方法
公开(公告)号：WO2003082214A2
公开(公告)日：2003-10-09
申请号：PCT/US2003/009751
申请日：2003-03-27
申请人： GENOMATICA, INC. , PALSSON, Bernhard, O. , FAMILI, Imandokht , COVERT, Markus, W. , SCHILLING, Christophe, H.
发明人： PALSSON, Bernhard, O. , FAMILI, Imandokht , COVERT, Markus, W. , SCHILLING, Christophe, H.
IPC分类号： A61K
CPC分类号： G06F19/12 , G06F19/18 , G06F19/28
摘要： The invention provides in silico models for determining the physiological function of human cells, including human skeletal muscle cells. The models include a data structure relating a plurality of Homo sapiens reactions, a constraint set for the plurality of Homo sapiens reactions, and commands for determining a distribution of flux through the reactions that is predictive of a Homo sapiens physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. A regulated Homo sapiens reaction can be represented in a model of the invention by including a variable constraint for the regulated reaction. The invention further provides methods for making an in silico Homo sapiens physiological function using a model of the invention.
摘要翻译：本发明提供了用于确定人类细胞（包括人类骨骼肌细胞）的生理功能的计算机模型。这些模型包括涉及多个智人反应的数据结构，用于多个人类反应的约束集，以及用于确定通过预测人类生理功能的反应的通量分布的命令。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。调节的智人反应可以通过包括调节反应的可变约束在本发明的模型中表示。本发明进一步提供了使用本发明的模型制备计算机智人生理功能的方法。

10. 发明申请

WO2003081207A2 COMPOSITIONS AND METHODS FOR MODELING BACILLUS SUBTILIS METABOLISM 审中-公开
标题翻译：组合物和方法用于建立BACILLUS SUBTILIS代谢
公开(公告)号：WO2003081207A2
公开(公告)日：2003-10-02
申请号：PCT/US2003/008326
申请日：2003-03-18
申请人： GENOMATICA, INC. , PARK, Sung, M. , SCHILLING, Christophe, H. , PALSSON, Bernhard, O.
发明人： PARK, Sung, M. , SCHILLING, Christophe, H. , PALSSON, Bernhard, O.
IPC分类号： G01N
CPC分类号： G06F19/12 , G06F19/28 , Y02A90/26
摘要： The invention provides an in silico model for determining a Bacillus subtilis physiological function. The model includes a data structure relating a plurality of B. subtilis reactants to a plurality of B. subtilis reactions, a constraint set for the plurality of B. subtilis reactions, and commands for determining a distribution of flux through the reactions that is predictive of a B. subtilis physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. A regulated B. subtilis reaction can be represented in a model of the invention by including a variable constraint for the regulated reaction. The invention further provides methods for making an in silico B. subtilis model and methods for determining a B. subtilis physiological function using a model of the invention.
摘要翻译：本发明提供了一种用于测定枯草芽孢杆菌生理功能的计算机模型。该模型包括将多个枯草芽孢杆菌反应物与多个枯草芽孢杆菌反应相关联的数据结构，用于多个枯草芽孢杆菌反应的约束集，以及用于确定通过预测的反应的通量分布的命令枯草芽孢杆菌生理功能。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。经调节的枯草芽孢杆菌反应可以在本发明的模型中通过包括调节反应的可变约束来表示。本发明进一步提供了使用本发明的模型制备电脑枯草芽孢杆菌模型和确定枯草芽孢杆菌生理功能的方法的方法。

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