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1. 发明授权

US08795960B2 Optimization of gene expression analysis using immobilized capture probes 有权
标题翻译：使用固定化捕获探针优化基因表达分析
公开(公告)号：US08795960B2
公开(公告)日：2014-08-05
申请号：US12480215
申请日：2009-06-08
申请人： Michael Seul , Sukanta Banerjee , Jiacheng Yang , Tatiana Vener
发明人： Michael Seul , Sukanta Banerjee , Jiacheng Yang , Tatiana Vener
IPC分类号： C12Q1/68 , C12P19/34 , C12M1/34 , C12M3/00 , C07H21/04
CPC分类号： C12Q1/6832 , B01J2219/00459 , B01J2219/00576 , B01J2219/00608 , B01J2219/00648 , B01J2219/00722 , C12Q1/6809 , C12Q1/6834 , C12Q1/6837 , C12Q2537/143 , C12Q2565/501 , C12Q2565/507 , C12Q2533/101 , C12Q2565/514 , C12Q2565/519
摘要： Disclosed are methods of multiplexed analysis of oligonucleotides in a sample, including: methods of probe and target “engineering”, as well as methods of assay signal analysis relating to the modulation of the probe-target affinity constant, K by a variety of factors including the elastic properties of target strands and layers of immobilized (“grafted”) probes; and assay methodologies relating to: the tuning of assay signal intensities including dynamic range compression and on-chip signal amplification; the combination of hybridization-mediated and elongation-mediated detection for the quantitative determination of abundance of messages displaying a high degree of sequence similarity, including, for example, the simultaneous determination of the relative expression levels, and identification of the specific class of, untranslated AU-rich subsequences located near the 3′ terminus of mRNA; and a new method of subtractive differential gene expression analysis which requires only a single color label.
摘要翻译：公开了样品中寡核苷酸多重分析的方法，包括：探针和靶标“工程”的方法，以及通过多种因素与探针 - 靶亲和常数K的调节相关的信号分析方法，包括目标链和固定（“接枝”）探针层的弹性性质; 以及与以下方法相关的测定方法：调整测定信号强度，包括动态范围压缩和片上信号放大; 杂交介导和延长介导检测的组合用于定量测定显示高度序列相似性的消息丰度，包括例如同时确定相对表达水平，以及鉴定特异性类别，未翻译位于mRNA的3'末端附近的富含子序列; 以及仅需要单一颜色标签的减法差分基因表达分析的新方法。

2. 发明申请

US20060035240A1 Optimization of gene expression analysis using immobilized capture probes 有权
公开(公告)号：US20060035240A1
公开(公告)日：2006-02-16
申请号：US10974036
申请日：2004-10-26
申请人： Michael Seul , Sukanta Banerjee , Jiacheng Yang , Tatiana Vener
发明人： Michael Seul , Sukanta Banerjee , Jiacheng Yang , Tatiana Vener
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6832 , B01J2219/00459 , B01J2219/00576 , B01J2219/00608 , B01J2219/00648 , B01J2219/00722 , C12Q1/6809 , C12Q1/6834 , C12Q1/6837 , C12Q2537/143 , C12Q2565/501 , C12Q2565/507 , C12Q2533/101 , C12Q2565/514 , C12Q2565/519
摘要： Disclosed are methods of multiplexed analysis of oligonucleotides in a sample, including: methods of probe and target “engineering”, as well as methods of assay signal analysis relating to the modulation of the probe-target affinity constant, K by a variety of factors including the elastic properties of target strands and layers of immobilized (“grafted”) probes; and assay methodologies relating to: the tuning of assay signal intensities including dynamic range compression and on-chip signal amplification; the combination of hybridization-mediated and elongation-mediated detection for the quantitative determination of abundance of messages displaying a high degree of sequence similarity, including, for example, the simultaneous determination of the relative expression levels, and identification of the specific class of, untranslated AU-rich subsequences located near the 3′ terminus of mRNA; and a new method of subtractive differential gene expression analysis which requires only a single color label.

3. 发明申请

US20090263820A1 Optimization of Gene Expression Analysis using Immobilized Capture Probes 有权
标题翻译：使用固定化捕获探针优化基因表达分析
公开(公告)号：US20090263820A1
公开(公告)日：2009-10-22
申请号：US12480215
申请日：2009-06-08
申请人： Michael Seul , Sukanta Banerjee , Jiacheng Yang , Tatiana Vener
发明人： Michael Seul , Sukanta Banerjee , Jiacheng Yang , Tatiana Vener
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6832 , B01J2219/00459 , B01J2219/00576 , B01J2219/00608 , B01J2219/00648 , B01J2219/00722 , C12Q1/6809 , C12Q1/6834 , C12Q1/6837 , C12Q2537/143 , C12Q2565/501 , C12Q2565/507 , C12Q2533/101 , C12Q2565/514 , C12Q2565/519
摘要： Disclosed are methods of multiplexed analysis of oligonucleotides in a sample, including: methods of probe and target “engineering”, as well as methods of assay signal analysis relating to the modulation of the probe-target affinity constant, K by a variety of factors including the elastic properties of target strands and layers of immobilized (“grafted”) probes; and assay methodologies relating to: the tuning of assay signal intensities including dynamic range compression and on-chip signal amplification; the combination of hybridization-mediated and elongation-mediated detection for the quantitative determination of abundance of messages displaying a high degree of sequence similarity, including, for example, the simultaneous determination of the relative expression levels, and identification of the specific class of, untranslated AU-rich subsequences located near the 3′ terminus of mRNA; and a new method of subtractive differential gene expression analysis which requires only a single color label.
摘要翻译：公开了样品中寡核苷酸多重分析的方法，包括：探针和靶标“工程”的方法，以及通过多种因素与探针 - 靶亲和常数K的调节相关的信号分析方法，包括目标链和固定（“接枝”）探针层的弹性性质; 以及与以下方法相关的测定方法：调整测定信号强度，包括动态范围压缩和片上信号放大; 杂交介导和延长介导检测的组合用于定量测定显示高度序列相似性的消息丰度，包括例如同时确定相对表达水平，以及鉴定特异性类别，未翻译位于mRNA的3'末端附近的富含子序列; 以及仅需要单一颜色标签的减法差分基因表达分析的新方法。

4. 发明授权

US07563569B2 Optimization of gene expression analysis using immobilized capture probes 有权
标题翻译：使用固定化捕获探针优化基因表达分析
公开(公告)号：US07563569B2
公开(公告)日：2009-07-21
申请号：US10974036
申请日：2004-10-26
申请人： Michael Seul , Sukanta Banerjee , Jiacheng Yang , Tatiana Vener
发明人： Michael Seul , Sukanta Banerjee , Jiacheng Yang , Tatiana Vener
IPC分类号： C12Q1/68 , C12P19/34 , C12M1/00 , C12M1/34 , C12M3/00 , C07H21/02 , C07H21/04
CPC分类号： C12Q1/6832 , B01J2219/00459 , B01J2219/00576 , B01J2219/00608 , B01J2219/00648 , B01J2219/00722 , C12Q1/6809 , C12Q1/6834 , C12Q1/6837 , C12Q2537/143 , C12Q2565/501 , C12Q2565/507 , C12Q2533/101 , C12Q2565/514 , C12Q2565/519
摘要： Disclosed are methods of multiplexed analysis of oligonucleotides in a sample, including: methods of probe and target “engineering”, as well as methods of assay signal analysis relating to the modulation of the probe-target affinity constant, K by a variety of factors including the elastic properties of target strands and layers of immobilized (“grafted”) probes; and assay methodologies relating to: the tuning of assay signal intensities including dynamic range compression and on-chip signal amplification; the combination of hybridization-mediated and elongation-mediated detection for the quantitative determination of abundance of messages displaying a high degree of sequence similarity, including, for example, the simultaneous determination of the relative expression levels, and identification of the specific class of, untranslated AU-rich subsequences located near the 3′ terminus of mRNA; and a new method of subtractive differential gene expression analysis which requires only a single color label.
摘要翻译：公开了样品中寡核苷酸多重分析的方法，包括：探针和靶标“工程”的方法，以及通过多种因素与探针 - 靶亲和常数K的调节相关的信号分析方法，包括目标链和固定（“接枝”）探针层的弹性性质; 以及与以下方法相关的测定方法：调整测定信号强度，包括动态范围压缩和片上信号放大; 杂交介导和延长介导检测的组合用于定量测定显示高度序列相似性的消息丰度，包括例如同时确定相对表达水平，以及鉴定特异性类别，未翻译位于mRNA的3'末端附近的富含子序列; 以及仅需要单一颜色标签的减法差分基因表达分析的新方法。

5. 发明申请

US20100021909A1 Concurrent Optimization In Selection of Primer and Capture Probe Sets for Nucleic Acid Analysis 有权
标题翻译：选择用于核酸分析的引物和捕获探针组的并行优化
公开(公告)号：US20100021909A1
公开(公告)日：2010-01-28
申请号：US12502725
申请日：2009-07-14
申请人： Michael Seul , Tatiana Vener , XiongWu Xia
发明人： Michael Seul , Tatiana Vener , XiongWu Xia
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6876 , C12Q2600/16 , G06F19/20 , G06F19/22
摘要： Disclosed is a method of iteratively optimizing two (or more) interrelated sets of probes for the multi-step analysis of sets of designated sequences, each such sequence requiring, for conversion, at least one conversion probe (“primer”), and each converted sequence requiring, for detection, at least one capture probe. The iterative method disclosed herein for the concurrent optimization of primer and probe selection invokes fast logical string matching functions to perform a complete cross-correlation of probe sequences and target sequences. The score function assigns to each probe-target alignment a “degree of matching” score on the basis of position-weighted Hamming distance functions introduced herein. Pairs of probes in the final selection may differ in several positions, while other pairs of probes may differ in only a single position. Not all such positions are of equal importance, and a score function is introduced, reflecting the position of the mismatch within the probe sequence.
摘要翻译：公开了一种迭代优化两个（或多个）相互关联的探针组的方法，用于多步分析指定序列组，每个这样的序列需要用于转化的至少一个转化探针（“引物”），并且每个转化用于检测至少一个捕获探针的序列。本文公开的用于并行优化引物和探针选择的迭代方法调用快速逻辑串匹配函数来执行探针序列和靶序列的完全互相关。得分函数根据本文介绍的位置加权汉明距离函数将每个探针 - 目标对准分配给“匹配度”得分。最终选择中的一对探针在几个位置可能有所不同，而其他探针对只能在一个位置上不同。并不是所有这样的位置都是同等重要的，并且引入了分数函数，反映了探针序列内不匹配的位置。

6. 发明授权

US07970553B2 Concurrent optimization in selection of primer and capture probe sets for nucleic acid analysis 有权
标题翻译：选择引物和捕获探针组进行核酸分析的并发优化
公开(公告)号：US07970553B2
公开(公告)日：2011-06-28
申请号：US12502725
申请日：2009-07-14
申请人： Michael Seul , Tatiana Vener , Xiongwu Xia
发明人： Michael Seul , Tatiana Vener , Xiongwu Xia
IPC分类号： G01N33/48
CPC分类号： C12Q1/6876 , C12Q2600/16 , G06F19/20 , G06F19/22
摘要： Disclosed is a method of iteratively optimizing two (or more) interrelated sets of probes for the multi-step analysis of sets of designated sequences, each such sequence requiring, for conversion, at least one conversion probe (“primer”), and each converted sequence requiring, for detection, at least one capture probe. The iterative method disclosed herein for the concurrent optimization of primer and probe selection invokes fast logical string matching functions to perform a complete cross-correlation of probe sequences and target sequences. The score function assigns to each probe-target alignment a “degree of matching” score on the basis of position-weighted Hamming distance functions introduced herein. Pairs of probes in the final selection may differ in several positions, while other pairs of probes may differ in only a single position. Not all such positions are of equal importance, and a score function is introduced, reflecting the position of the mismatch within the probe sequence.
摘要翻译：公开了一种迭代优化两个（或多个）相互关联的探针组的方法，用于多步分析指定序列集合，每个这样的序列需要转化至少一个转化探针（“引物”），并且每个转化用于检测至少一个捕获探针的序列。本文公开的用于并行优化引物和探针选择的迭代方法调用快速逻辑串匹配函数来执行探针序列和靶序列的完全互相关。得分函数根据本文介绍的位置加权汉明距离函数将每个探针 - 目标对准分配给“匹配度”得分。最终选择中的一对探针在几个位置可能有所不同，而其他探针对只能在一个位置上不同。并不是所有这样的位置都是同等重要的，并且引入了分数函数，反映了探针序列内不匹配的位置。

7. 发明申请

US20120190585A1 CONCURRENT OPTIMIZATION IN SELECTION OF PRIMER AND CAPTURE PROBE SETS FOR NUCLEIC ACID ANALYSIS 审中-公开
标题翻译：选择核酸分析初始化和捕获探针组的同时优化
公开(公告)号：US20120190585A1
公开(公告)日：2012-07-26
申请号：US13169201
申请日：2011-06-27
申请人： Michael Seul , Tatiana Vener , Xiongwu Xia
发明人： Michael Seul , Tatiana Vener , Xiongwu Xia
IPC分类号： C40B50/02
CPC分类号： C12Q1/6876 , C12Q2600/16 , G16B25/00 , G16B30/00
摘要： Disclosed is a method of iteratively optimizing two (or more) interrelated sets of probes for the multi-step analysis of sets of designated sequences, each such sequence requiring, for conversion, at least one conversion probe (“primer”), and each converted sequence requiring, for detection, at least one capture probe. The iterative method disclosed herein for the concurrent optimization of primer and probe selection invokes fast logical string matching functions to perform a complete cross-correlation of probe sequences and target sequences. The score function assigns to each probe-target alignment a “degree of matching” score on the basis of position-weighted Hamming distance functions introduced herein. Pairs of probes in the final selection may differ in several positions, while other pairs of probes may differ in only a single position. Not all such positions are of equal importance, and a score function is introduced, reflecting the position of the mismatch within the probe sequence.
摘要翻译：公开了一种迭代优化两个（或多个）相互关联的探针组的方法，用于多步分析指定序列集合，每个这样的序列需要转化至少一个转化探针（“引物”），并且每个转化用于检测至少一个捕获探针的序列。本文公开的用于并行优化引物和探针选择的迭代方法调用快速逻辑串匹配函数来执行探针序列和靶序列的完全互相关。得分函数根据本文介绍的位置加权汉明距离函数将每个探针 - 目标对准分配给“匹配度”得分。最终选择中的一对探针在几个位置可能有所不同，而其他探针对只能在一个位置上不同。并不是所有这样的位置都是同等重要的，并且引入了分数函数，反映了探针序列内不匹配的位置。

8. 发明授权

US07574305B2 Concurrent optimization in selection of primer and capture probe sets for nucleic acid analysis 有权
标题翻译：选择引物和捕获探针组进行核酸分析的并发优化
公开(公告)号：US07574305B2
公开(公告)日：2009-08-11
申请号：US10892514
申请日：2004-07-15
申请人： Michael Seul , Tatiana Vener , Xiongwu Xia
发明人： Michael Seul , Tatiana Vener , Xiongwu Xia
IPC分类号： G06F19/00
CPC分类号： C12Q1/6876 , C12Q2600/16 , G06F19/20 , G06F19/22
摘要： Disclosed is a method of iteratively optimizing two (or more) interrelated sets of probes for the multi-step analysis of sets of designated sequences, each such sequence requiring, for conversion, at least one conversion probe (“primer”), and each converted sequence requiring, for detection, at least one capture probe. The iterative method disclosed herein for the concurrent optimization of primer and probe selection invokes fast logical string matching functions to perform a complete cross-correlation of probe sequences and target sequences. The score function assigns to each probe-target alignment a “degree of matching” score on the basis of position-weighted Hamming distance functions introduced herein. Pairs of probes in the final selection may differ in several positions, while other pairs of probes may differ in only a single position. Not all such positions are of equal importance, and a score function is introduced, reflecting the position of the mismatch within the probe sequence.
摘要翻译：公开了一种迭代优化两个（或多个）相互关联的探针组的方法，用于多步分析指定序列集合，每个这样的序列需要转化至少一个转化探针（“引物”），并且每个转化用于检测至少一个捕获探针的序列。本文公开的用于并行优化引物和探针选择的迭代方法调用快速逻辑串匹配函数来执行探针序列和靶序列的完全互相关。得分函数根据本文介绍的位置加权汉明距离函数将每个探针 - 目标对准分配给“匹配度”得分。最终选择中的一对探针在几个位置可能有所不同，而其他探针对只能在一个位置上不同。并不是所有这样的位置都是同等重要的，并且引入了分数函数，反映了探针序列内不匹配的位置。

9. 发明申请

US20060127916A1 Concurrent optimization in selection of primer and capture probe sets for nucleic acid analysis 有权
公开(公告)号：US20060127916A1
公开(公告)日：2006-06-15
申请号：US10892514
申请日：2004-07-15
申请人： Michael Seul , Tatiana Vener , Xiongwu Xia
发明人： Michael Seul , Tatiana Vener , Xiongwu Xia
IPC分类号： C12Q1/68 , G06F19/00
CPC分类号： C12Q1/6876 , C12Q2600/16 , G06F19/20 , G06F19/22
摘要： Disclosed is a method of iteratively optimizing two (or more) interrelated sets of probes for the multi-step analysis of sets of designated sequences, each such sequence requiring, for conversion, at least one conversion probe (“primer”), and each converted sequence requiring, for detection, at least one capture probe. The iterative method disclosed herein for the concurrent optimization of primer and probe selection invokes fast logical string matching functions to perform a complete cross-correlation of probe sequences and target sequences. The score function assigns to each probe-target alignment a “degree of matching” score on the basis of position-weighted Hamming distance functions introduced herein. Pairs of probes in the final selection may differ in several positions, while other pairs of probes may differ in only a single position. Not all such positions are of equal importance, and a score function is introduced, reflecting the position of the mismatch within the probe sequence.

10. 发明申请

US20100081145A1 Detecting Prostate Cancer 审中-公开
标题翻译：检测前列腺癌
公开(公告)号：US20100081145A1
公开(公告)日：2010-04-01
申请号：US12628764
申请日：2009-12-01
申请人： Haiying Wang , Jonathan F. Baden , Tatiana Vener , Dondapati Chowdary , Abhijit Mazumder
发明人： Haiying Wang , Jonathan F. Baden , Tatiana Vener , Dondapati Chowdary , Abhijit Mazumder
IPC分类号： C12Q1/68
CPC分类号： G01N33/57434 , G01N2333/91171
摘要： Methods and kits for detecting prostate cancer in urine samples include detecting the methylation status of various genes.
摘要翻译：用于检测尿样中前列腺癌的方法和试剂盒包括检测各种基因的甲基化状态。

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