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1. 发明授权

US06713257B2 Gene discovery using microarrays 失效
公开(公告)号：US06713257B2
公开(公告)日：2004-03-30
申请号：US09781814
申请日：2001-02-12
申请人： Daniel D. Shoemaker , Stewart Scherer , Steven J. Altschuler , Lani F. Wu , Christopher D. Armour
发明人： Daniel D. Shoemaker , Stewart Scherer , Steven J. Altschuler , Lani F. Wu , Christopher D. Armour
IPC分类号： C12Q168
CPC分类号： G06F19/18 , B01J2219/00605 , B01J2219/0061 , B01J2219/00612 , B01J2219/00626 , B01J2219/00659 , B01J2219/00689 , B01J2219/00695 , B01J2219/00707 , B01J2219/00722 , B01J2219/00743 , C12Q1/6809 , C12Q1/6837 , C40B40/06 , G06F19/20
摘要： The invention relates to methods and systems (e.g., computer systems and computer program products) for identifying and characterizing genes using microarrays. In particular, the invention provides for improved, robust methods for detecting genes through the use of microarrays to analyze the expression state of the genome. Genes which are expressed can be mapped to their respective positions in the genome, and the structure of such genes can be determined.

2. 发明授权

US07432084B2 Methods for preparing nucleic acid samples 有权
标题翻译：制备用于筛选dna阵列的核酸样品的方法
公开(公告)号：US07432084B2
公开(公告)日：2008-10-07
申请号：US10485008
申请日：2002-07-17
申请人： Daniel D. Shoemaker , Christopher D. Armour , Philip W. Garrett-Engele
发明人： Daniel D. Shoemaker , Christopher D. Armour , Philip W. Garrett-Engele
IPC分类号： C12P19/34
CPC分类号： C12N15/1096 , C12Q1/6837 , C12Q1/6865 , C12Q2563/107
摘要： In one aspect the present invention provides methods of synthesizing a preparation of nucleic acid molecules, the methods comprising the steps of: (a) utilizing an RNA template to enzymatically synthesize a first DNA molecule that is complementary to at least 50 contiguous bases of the RNA template; (b) utilizing the first DNA molecule as a template to enzymatically synthesize a second DNA molecule, thereby forming a double-stranded DNA molecule wherein the first DNA molecule is hybridized to the second DNA molecule; (c) utilizing the first or second DNA molecule of the double-stranded DNA molecule as a template to enzymatically synthesize a first RNA molecule that is complementary to either the first DNA molecule or to the second DNA molecule; and (d) utilizing the first RNA molecule as a template to enzymatically synthesize a third DNA molecule that is complementary to the first RNA molecule. In another aspect, the present invention provides processed DNA samples prepared by a method of the invention for synthesizing a preparation of nucleic acid molecules. In another aspect, the present invention provides methods for hybridizing a processed DNA sample to a population of immobilized nucleic acid molecules.
摘要翻译：一方面，本发明提供了合成核酸分子制剂的方法，所述方法包括以下步骤：（a）利用RNA模板来酶促合成与RNA的至少50个连续碱基互补的第一DNA分子模板; （b）利用第一DNA分子作为模板来酶促合成第二DNA分子，从而形成双链DNA分子，其中第一DNA分子与第二DNA分子杂交; （c）利用双链DNA分子的第一或第二DNA分子作为模板来酶促合成与第一DNA分子或第二DNA分子互补的第一RNA分子; 和（d）利用第一RNA分子作为模板来酶促合成与第一RNA分子互补的第三DNA分子。另一方面，本发明提供了通过本发明的用于合成核酸分子制剂的方法制备的加工DNA样品。另一方面，本发明提供了将经处理的DNA样品与固定的核酸分子群杂交的方法。

3. 发明授权

US07807447B1 Compositions and methods for exon profiling 有权
标题翻译：外显子分析的组成和方法
公开(公告)号：US07807447B1
公开(公告)日：2010-10-05
申请号：US09724538
申请日：2000-11-28
申请人： Daniel D. Shoemaker , Stewart Scherer , Stephen H. Friend
发明人： Daniel D. Shoemaker , Stewart Scherer , Stephen H. Friend
IPC分类号： C12M1/34 , C12M3/00 , C12Q1/68 , C12P1/34 , C07H21/02 , C07H21/04
CPC分类号： C12Q1/6837 , B01J2219/00605 , B01J2219/00612 , B01J2219/00626 , B01J2219/00659 , B01J2219/00689 , B01J2219/00695 , B01J2219/00707 , B01J2219/00722 , B01J2219/00743 , C12Q1/6809 , C40B40/06
摘要： The present invention provides methods for analyzing exon expression profiles of a cell or type of cell. In the invention, the expression levels of a plurality of individual exons or multiexons for each of a plurality of genes in the genome of an organism are measured and analyzed to determine the biological state, such as the exon expression state or transcriptional state, of the cell or type of cell. The methods of the invention are useful for determination of alternative RNA splicing in a plurality of genes. The invention also provides nucleic acid probe arrays for determining in parallel the expression levels of a plurality of exons or multiexons for each of a plurality of genes in the genome of an organism. The invention further provides methods for determining the effects of perturbations, such as perturbations by drugs, on exon expression and alternative RNA splicing pathways.
摘要翻译：本发明提供了分析细胞或细胞类型的外显子表达谱的方法。在本发明中，对生物体基因组中的多个基因中的每一个的多个单独的外显子或多核苷酸的表达水平进行测定和分析，以确定生物学状态，例如外显子表达状态或转录状态细胞或细胞类型。本发明的方法可用于确定多个基因中的替代RNA剪接。本发明还提供用于平行测定生物体基因组中多个基因中的每一个的多个外显子或多核苷酸的表达水平的核酸探针阵列。本发明还提供了用于确定扰动（例如药物扰动）对外显子表达和替代RNA剪接途径的影响的方法。

4. 发明授权

US07930406B2 System and method for secure communication of mode of access information 有权
标题翻译：用于访问信息模式的安全通信的系统和方法
公开(公告)号：US07930406B2
公开(公告)日：2011-04-19
申请号：US11981425
申请日：2007-10-31
申请人： Daniel D. Shoemaker , Lee Thomas O'Donnell , James P. Broder , Scott D. Shoemaker
发明人： Daniel D. Shoemaker , Lee Thomas O'Donnell , James P. Broder , Scott D. Shoemaker
IPC分类号： G06F17/30
CPC分类号： G06F21/6218 , G06F3/0484 , G06F17/30312 , G06F17/30345 , G06F17/30575 , H04L63/08 , H04L67/1095 , H04L67/18
摘要： A system for transmission of mode of access information between a first device operated by a first user and a second device operated by a second user includes a database that is in network communication with the first device and the second device. The database stores a plurality of different modes of access for contacting the first user that are devoid of alpha-numeric identifiers specific to the first user. The database allows the first user to select one of the modes of access as a current mode of access of the first user. The current mode of access of the first user can be communicated to the second device once the second device queries the database. The current mode of access of the first user can be selected from the group consisting of mobile phone, text message and electronic mail. The current mode of access of the first user can change automatically over time according to a schedule input into the database by the first user. In some embodiments, at least one of the first device and the second device is a web-based mobile phone.
摘要翻译：用于在由第一用户操作的第一设备和由第二用户操作的第二设备之间传输访问信息模式的系统包括与第一设备和第二设备进行网络通信的数据库。数据库存储用于联系第一用户的多个不同模式的访问，该第一用户不具有第一用户特有的字母数字标识符。数据库允许第一用户选择访问模式之一作为第一用户的当前访问模式。一旦第二设备查询数据库，第一用户的当前访问模式可以被传送到第二设备。可以从由移动电话，短信和电子邮件组成的组中选择当前的第一用户的接入模式。第一用户的当前访问模式可以根据由第一用户输入到数据库中的日程表自动改变。在一些实施例中，第一设备和第二设备中的至少一个是基于web的移动电话。

5. 发明申请

US20080171364A1 Methods and compositions for amplification and capture of nucleic acid sequences 失效
标题翻译：扩增和捕获核酸序列的方法和组合物
公开(公告)号：US20080171364A1
公开(公告)日：2008-07-17
申请号：US11879966
申请日：2007-07-19
申请人： Daniel D. Shoemaker
发明人： Daniel D. Shoemaker
IPC分类号： C12P19/34
CPC分类号： C12Q1/6846 , C12Q2563/131 , C12Q2527/101 , C12Q2525/185
摘要： A method for amplification and capture of nucleic acid sequences can include the steps of annealing a forward primer to a DNA or RNA template in a first reaction vessel that includes fewer than four different dNTPs; extending the forward primer with the dNTPs to form an extended primer that terminates when an omitted dNTP is required for further extension of the forward primer; releasing the extended primer; exponentially amplifying the extended primer in a second reaction vessel that includes a reverse primer, four different dNTPs and a capture probe, the capture probe including n oligonucleotides, wherein fewer than n of the oligonucleotides are locking nucleic acids; and concurrently capturing one of the extended primers in the second reaction vessel with the capture probe while amplifying the extended primer. Further, in certain embodiments, the steps of annealing, extending and releasing occur at a first reaction temperature that is substantially isothermal and in the absence of a helicase. In addition, or alternatively, the steps of exponentially amplifying and capturing occur at a second reaction temperature that is substantially isothermal.
摘要翻译：扩增和捕获核酸序列的方法可以包括在包含少于四种不同dNTP的第一反应容器中将正向引物退火至DNA或RNA模板的步骤; 使用dNTP扩展正向引物以形成延长的引物，当需要省略dNTP以进一步延伸正向引物时终止; 释放延伸引物; 在包括反向引物，四种不同dNTP和捕获探针的第二反应容器中指数扩增扩增引物，捕获探针包括n个寡核苷酸，其中少于n个寡核苷酸是锁定核酸; 并在扩增引物的同时用捕获探针同时捕获第二反应容器中的一个延伸引物。此外，在某些实施方案中，退火，延伸和释放的步骤在基本上是等温的第一反应温度下和在没有解旋酶的情况下发生。另外或替代地，指数扩增和捕获的步骤在基本上是等温的第二反应温度下发生。

6. 发明授权

US5525300A Thermal cycler including a temperature gradient block 失效
公开(公告)号：US5525300A
公开(公告)日：1996-06-11
申请号：US139540
申请日：1993-10-20
申请人： John L. Danssaert , Robert J. Shopes , Daniel D. Shoemaker
发明人： John L. Danssaert , Robert J. Shopes , Daniel D. Shoemaker
IPC分类号： B01L7/00 , C12M1/00 , C12M1/02 , C12M1/38 , G01N35/00 , G01N35/02 , G01N35/04
CPC分类号： B01L7/52 , B01L7/525 , B01L7/54 , B01L2200/147 , B01L2300/0829 , B01L2300/1822 , B01L2300/1827 , B01L2300/1838 , B01L2300/1844 , B01L7/5255 , G01N2035/042 , G01N35/0099 , G01N35/028 , Y10S435/809 , Y10T436/25
摘要： A method in which a temperature gradient is generated across a "gradient" block, and an apparatus comprising a block across which a temperature gradient can be generated. By setting up such a gradient, multiple reaction mixtures held in wells on the gradient block can be simultaneously run at temperatures which differ only slightly, thereby permitting an optimum temperature for the reaction to be quickly identified. In a preferred embodiment the gradient block is integrated into a thermal cycler used for nucleic acid amplification reactions.

7. 发明授权

US07501254B2 Methods and compositions for amplification and capture of nucleic acid sequences 失效
标题翻译：扩增和捕获核酸序列的方法和组合物
公开(公告)号：US07501254B2
公开(公告)日：2009-03-10
申请号：US11879966
申请日：2007-07-19
申请人： Daniel D. Shoemaker
发明人： Daniel D. Shoemaker
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6846 , C12Q2563/131 , C12Q2527/101 , C12Q2525/185
摘要： Methods for amplification and capture of nucleic acid sequences include annealing a forward primer to a DNA or RNA template in a first reaction vessel including fewer than four different dNTPs; forming an extended primer that terminates when an omitted dNTP is required for further extension; releasing the extended primer; exponentially amplifying the extended primer in a second reaction vessel that includes a reverse primer, four different dNTPs and a capture probe that includes n oligonucleotides having fewer than n locking nucleic acids; and concurrently capturing one of the extended primers with the capture probe while amplifying the extended primer. The steps of annealing, extending and releasing can occur at a first reaction temperature that is substantially isothermal and in the absence of a helicase. The steps of exponentially amplifying and capturing can occur at a second reaction temperature that is substantially isothermal.
摘要翻译：用于扩增和捕获核酸序列的方法包括在包含少于四种不同dNTP的第一反应容器中将正向引物退火至DNA或RNA模板; 形成延伸引物，当需要省略dNTP进一步延长时终止; 释放延伸引物; 在包括反向引物，四种不同dNTP的第二反应容器中的延伸引物指数扩增，和包含具有少于n个锁定核酸的n个寡核苷酸的捕获探针; 并在扩增引物的同时用捕获探针同时捕获一个扩展的引物。退火，延伸和释放的步骤可以在基本上是等温的第一反应温度和不存在解旋酶的情况下发生。指数扩增和捕获的步骤可以在基本上是等温的第二反应温度下发生。

8. 发明授权

US06458530B1 Selecting tag nucleic acids 失效
标题翻译：选择标签核酸
公开(公告)号：US06458530B1
公开(公告)日：2002-10-01
申请号：US08626285
申请日：1996-04-04
申请人： Macdonald S. Morris , Daniel D. Shoemaker , Ronald W. Davis , Michael P. Mittmann
发明人： Macdonald S. Morris , Daniel D. Shoemaker , Ronald W. Davis , Michael P. Mittmann
IPC分类号： C12Q168
CPC分类号： C12Q1/6837 , B01J19/0046 , B01J2219/00529 , B01J2219/0054 , B01J2219/00542 , B01J2219/00608 , B01J2219/0061 , B01J2219/00612 , B01J2219/00621 , B01J2219/00626 , B01J2219/00637 , B01J2219/00639 , B01J2219/00659 , B01J2219/00695 , B01J2219/00702 , B01J2219/00722 , C40B40/06 , C40B70/00
摘要： Methods of selecting tag nucleic acids and VLSIPS™ arrays and the arrays made by the methods are used to label and track compositions, including cells and viruses, e.g., in libraries of cells or viruses. In addition to providing a way of tracking compositions in mixtures, the tags facilitate analysis of cell and viral phenotypes.
摘要翻译：选择标签核酸和VLSIPS TM阵列的方法以及通过该方法制备的阵列用于标记和跟踪组合物，包括细胞和病毒，例如在细胞或病毒的文库中。除了提供跟踪混合物中组合物的方式之外，标签有助于细胞和病毒表型的分析。

9. 发明授权

US07958144B2 System and method for secure reciprocal exchange of data 有权
标题翻译：用于安全的数据交换的系统和方法
公开(公告)号：US07958144B2
公开(公告)日：2011-06-07
申请号：US10651733
申请日：2003-08-29
申请人： Daniel D. Shoemaker , Lee Thomas O'Donnell , James P. Broder , Scott D. Shoemaker
发明人： Daniel D. Shoemaker , Lee Thomas O'Donnell , James P. Broder , Scott D. Shoemaker
IPC分类号： G06F17/30
CPC分类号： G06F21/6218 , G06F3/0484 , G06F17/30312 , G06F17/30345 , G06F17/30575 , H04L63/08 , H04L67/1095 , H04L67/18
摘要： A system for transmission of data between a first device operated by a first user and a second device includes a database that receives a first set of data input by the first user and a second set of data input by the second user. In one embodiment, the first set of data includes an immediate mode of access and/or one or more future modes of access of the first user which correlate to one or more specific time periods during which the future mode of access will become the immediate mode of access. Additionally, the first set of data can include a time-dependent schedule of the future mode of access of the first user.
摘要翻译：用于在由第一用户操作的第一设备和第二设备之间传输数据的系统包括接收由第一用户输入的第一组数据和由第二用户输入的第二组数据的数据库。在一个实施例中，第一组数据包括第一用户的即时访问模式和/或一个或多个未来访问模式，其与未来访问模式将成为即时模式的一个或多个特定时间段相关联的访问。此外，第一组数据可以包括第一用户的未来访问模式的时间相关调度。

10. 发明申请

US20080311628A1 Methods and compositions for rapid amplification and capture of nucleic acid sequences 审中-公开
标题翻译：用于快速扩增和捕获核酸序列的方法和组合物
公开(公告)号：US20080311628A1
公开(公告)日：2008-12-18
申请号：US11903014
申请日：2007-09-19
申请人： Daniel D. Shoemaker
发明人： Daniel D. Shoemaker
IPC分类号： C12P19/34
CPC分类号： C12Q1/686 , B01L7/54 , B01L2300/0832 , B01L2400/0442 , B01L2400/0475 , C12Q2549/119 , C12Q2521/531
摘要： A method for amplifying a nucleic acid sequence includes the steps of (i) providing a first pair of primers that include one or more uracil nucleotides, the primers being complementary to a portion of a genomic template, (ii) introducing the first pair of primers, the genomic template and a first polymerase into a reaction vessel, (iii) carrying out one or more polymerase chain reaction cycles in the reaction vessel to generate a plurality of first amplicons, and (iv) selectively degrading a portion each first amplicon with a Uracil-DNA Glycosylase to decrease the binding energy of each first amplicon. In one embodiment, the step of selectively degrading includes using a thermostable Uracil-DNA Glycosylase to decrease the binding energy of each first amplicon. In another embodiment, the method also includes the step of adding a second polymerase and a second pair of primers to the reaction vessel to generate a plurality of second amplicons that are different than the first amplicons. Generating the plurality of second amplicons can occur substantially isothermally or non-isothermally. Further, the second pair of primers can be nested primers.
摘要翻译：扩增核酸序列的方法包括以下步骤：（i）提供包含一个或多个尿嘧啶核苷酸的第一对引物，所述引物与基因组模板的一部分互补，（ii）引入第一对引物，基因组模板和第一聚合酶进入反应容器，（iii）在反应容器中进行一个或多个聚合酶链反应循环以产生多个第一扩增子，和（iv）选择性降解第一扩增子的部分，尿嘧啶-DNA糖基化酶降低每个第一扩增子的结合能。在一个实施方案中，选择性降解的步骤包括使用热稳定的尿嘧啶-DNA糖基酶降低每个第一扩增子的结合能。在另一个实施方案中，该方法还包括将第二聚合酶和第二对引物加入反应容器以产生不同于第一扩增子的多个第二扩增子的步骤。产生多个第二扩增子可以基本上等温或非等温发生。此外，第二对引物可以是嵌套引物。

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