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1. 发明申请

US20090175520A1 METHOD AND APPARATUS FOR MATCHING OF BRACKETED PATTERNS IN TEST STRINGS 失效
标题翻译：用于匹配测试条中的包围图案的方法和装置
公开(公告)号：US20090175520A1
公开(公告)日：2009-07-09
申请号：US11969451
申请日：2008-01-04
申请人： Tien Huynh , Stanislav Polonsky , Isidore Rigoutsos
发明人： Tien Huynh , Stanislav Polonsky , Isidore Rigoutsos
IPC分类号： G06K9/00
CPC分类号： G06F17/30985
摘要： Disclose are a method of and system for matching input character sequences in a set of input patterns. The method comprises the steps of analyzing the set of input patterns, creating a pattern cluster look-up table (PCLT) based on said input patterns, and defining an offset value k. The PCLT is used to find, for each sequence s and offset k, a set of candidate patterns that can possibly match s, the set of candidate patterns is searched for patterns that match s, and all found matching patterns and sequences are reported.
摘要翻译： Disclose是在一组输入模式中匹配输入字符序列的方法和系统。该方法包括以下步骤：分析输入模式集，基于所述输入模式创建模式集群查找表（PCLT），并定义偏移值k。 PCLT用于针对每个序列s和偏移k找到一组可能匹配s的候选模式，搜索匹配s的模式的候选模式集合，并且报告所有找到的匹配模式和序列。

2. 发明授权

US08189931B2 Method and apparatus for matching of bracketed patterns in test strings 失效
标题翻译：用于匹配测试串中的括号图案的方法和装置
公开(公告)号：US08189931B2
公开(公告)日：2012-05-29
申请号：US11969451
申请日：2008-01-04
申请人： Tien Huynh , Stanislav Polonsky , Isidore Rigoutsos
发明人： Tien Huynh , Stanislav Polonsky , Isidore Rigoutsos
IPC分类号： G06K9/00 , G06F17/30
CPC分类号： G06F17/30985
摘要： A method and system are disclosed for matching input character sequences in a set of input patterns. The method comprises the steps of analyzing the set of input patterns, creating a pattern cluster look-up table (PCLT) based on said input patterns, and defining an offset value k. The PCLT is used to find, for each sequence s and offset k, a set of candidate patterns that can possibly match s, the set of candidate patterns is searched for patterns that match s, and all found matching patterns and sequences are reported.
摘要翻译：公开了一种用于在一组输入模式中匹配输入字符序列的方法和系统。该方法包括以下步骤：分析输入模式集，基于所述输入模式创建模式集群查找表（PCLT），并定义偏移值k。 PCLT用于针对每个序列s和偏移k找到一组可能匹配s的候选模式，搜索匹配s的模式的候选模式集合，并且报告所有找到的匹配模式和序列。

3. 发明申请

US20110178283A1 Ribonucleic acid interference molecules and binding sites derived by analyzing intergenic and intronic regions of genomes 有权
标题翻译：通过分析基因组的基因和内含子区域导致的核糖核酸干扰分子和结合位点
公开(公告)号：US20110178283A1
公开(公告)日：2011-07-21
申请号：US11408557
申请日：2006-04-21
申请人： Isidore Rigoutsos , Tien Huynh , Aristotelis Tsirigos , Alice Carolyn McHardy
发明人： Isidore Rigoutsos , Tien Huynh , Aristotelis Tsirigos , Alice Carolyn McHardy
IPC分类号： C07H21/02
CPC分类号： G06F19/22 , G06F19/18
摘要： Sequences that can be used in the context of controlled gene regulation are provided. In one aspect, at least one sequence comprising at least one of one or more sequences having SEQ ID NO: 1 through SEQ ID NO: 747,326 is provided. One or more of the provided sequences may be computationally predicted, e.g., from publicly available genomes, using a method based on pattern discovery. In another aspect, a method for regulating the expression of a transcript comprises the step of said transcript containing a region that corresponds to at least one of the provided sequences having SEQ ID NO: 1 through SEQ ID NO: 747,326, the region being targeted either by a naturally occurring, or appropriately designed, interfering RNA molecule that regulates the expression of said transcript through post-transcriptional silencing. In a third aspect, a method for regulating the expression of a transcript comprises the step of at least one of the provided sequences having SEQ ID NO: 1 through SEQ ID NO: 747,326 being used to design an interfering RNA molecule that contains a region that corresponds to the reverse complement of one or more of the one or more sequences having SEQ ID NO: 1 through SEQ ID NO: 747,326, the interfering molecule regulating, through post-transcriptional silencing, one or more transcripts that contain said sequence of the one or more sequences having SEQ ID NO: 1 through SEQ ID NO: 747,326, or a substantial fraction thereof.
摘要翻译：提供了可在受控基因调控环境中使用的序列。在一个方面，提供至少一个包含具有SEQ ID NO：1至SEQ ID NO：747,326的一个或多个序列中的至少一个的序列。所提供的序列中的一个或多个可以使用基于模式发现的方法从计算上预测，例如来自公众可获得的基因组。在另一方面，调节转录物表达的方法包括所述转录物的步骤，所述转录物含有对应于至少一个所提供的具有SEQ ID NO：1至SEQ ID NO：747,326的序列的区域，所述区域被靶向通过天然存在或适当设计的干扰RNA分子，其通过转录后沉默调节所述转录物的表达。在第三方面，用于调节转录物表达的方法包括提供的具有SEQ ID NO：1至SEQ ID NO：747,326的序列中的至少一个的步骤用于设计干扰RNA分子，所述干扰RNA分子含有对应于具有SEQ ID NO：1至SEQ ID NO：747,326的一个或多个一个或多个序列的反向互补序列，干扰分子通过转录后沉默调节一个或多个含有所述序列的所述序列的转录本或更多的具有SEQ ID NO：1至SEQ ID NO：747,326的序列，或其相当一部分。

4. 发明申请

US20080311661A1 RIBONUCLEIC ACID INTERFERENCE MOLECULES OF ARABIDOPSIS THALIANA 有权
标题翻译： ARIBIDOPSIS THALIANA的RIBONUCLEIC ACID INTERFERENCE MOLECULES
公开(公告)号：US20080311661A1
公开(公告)日：2008-12-18
申请号：US12183166
申请日：2008-07-31
申请人： Tien Huynh , Isidore Rigoutsos
发明人： Tien Huynh , Isidore Rigoutsos
IPC分类号： C12N15/82 , C12N15/11 , C12N15/00
CPC分类号： C12N15/8218 , G06F19/18 , G06F19/24 , Y10T436/143333
摘要： Sequences of ribonucleic acid interference molecules are provided. For example, in one aspect, at least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ_ID NO: 1 through SEQ_ID NO: 3,197 and one or more corresponding mature sequences having SEQ_ID NO: 3,198 through SEQ_ID NO: 6,565 is provided. Techniques are also provided for regulating gene expression.
摘要翻译：提供了核糖核酸干扰分子的序列。例如，在一个方面，至少一个核酸分子包含至少一个具有SEQ ID NO：1至SEQ ID NO：3,197的一个或多个前体序列的一个或多个具有SEQ ID NO：3,198至SEQ ID NO：6,565的相应成熟序列被提供。还提供了调节基因表达的技术。

5. 发明申请

US20080052008A1 Techniques for Linking Non-Coding and Gene-Coding Deoxyribonucleic Acid Sequences and Applications Thereof 有权
标题翻译：用于连接非编码和基因编码脱氧核糖核酸序列的技术及其应用
公开(公告)号：US20080052008A1
公开(公告)日：2008-02-28
申请号：US11928611
申请日：2007-10-30
申请人： Isidore Rigoutsos , Tien Huynh , Aristotelis Tsirigos , Alice McHardy , Kevin Miranda
发明人： Isidore Rigoutsos , Tien Huynh , Aristotelis Tsirigos , Alice McHardy , Kevin Miranda
IPC分类号： G06F19/00 , C07H21/04 , C12Q1/68
CPC分类号： G06F19/22 , G06F19/18
摘要： Techniques for linking non-coding and gene coding regions of a genome are provided. In one aspect, a method of determining associations between non-coding sequences and gene coding sequences in a genome of an organism comprises the following steps. At least one conserved region is identified from one or more non-coding sequences. Additional instances of the conserved region are located in the untranslated or amino acid coding regions of one or more genes in the organism under consideration, and the conserved region is associated with the one or more biological processes in which these one or more genes participate.
摘要翻译：提供了用于连接基因组的非编码区和基因编码区的技术。一方面，确定生物体基因组中非编码序列与基因编码序列之间的关联的方法包括以下步骤。从一个或多个非编码序列鉴定至少一个保守区。保守区域的另外的实例位于正在考虑的生物体中的一个或多个基因的非翻译区或氨基酸编码区，并且保守区与这些一个或多个基因参与的一个或多个生物学过程相关。

6. 发明申请

US20070042397A1 Techniques for linking non-coding and gene-coding deoxyribonucleic acid sequences and applications thereof 审中-公开
标题翻译：用于连接非编码和基因编码脱氧核糖核酸序列的技术及其应用
公开(公告)号：US20070042397A1
公开(公告)日：2007-02-22
申请号：US11367512
申请日：2006-03-03
申请人： Isidore Rigoutsos , Tien Huynh , Aristotelis Tsirigos , Alice McHardy , Kevin Miranda
发明人： Isidore Rigoutsos , Tien Huynh , Aristotelis Tsirigos , Alice McHardy , Kevin Miranda
IPC分类号： C12Q1/68 , G06F19/00
CPC分类号： G16B30/00 , G16B20/00
摘要： Techniques for linking non-coding and gene coding regions of a genome are provided. In one aspect, a method of determining associations between non-coding sequences and gene coding sequences in a genome of an organism comprises the following steps. At least one conserved region is identified from one or more non-coding sequences. Additional instances of the conserved region are located in the untranslated or amino acid coding regions of one or more genes in the organism under consideration, and the conserved region is associated with the one or more biological processes in which these one or more genes participate.
摘要翻译：提供了用于连接基因组的非编码区和基因编码区的技术。一方面，确定生物体基因组中非编码序列与基因编码序列之间的关联的方法包括以下步骤。从一个或多个非编码序列鉴定至少一个保守区。保守区域的另外的实例位于正在考虑的生物体中的一个或多个基因的非翻译区或氨基酸编码区，并且保守区与这些一个或多个基因参与的一个或多个生物学过程相关。

7. 发明申请

US20090012720A1 System and Method for Identification of MicroRNA Target Sites and Corresponding Targeting MicroRNA Sequences 失效
标题翻译：用于鉴定微小RNA靶位点的系统和方法以及相应的靶向性微RNA序列
公开(公告)号：US20090012720A1
公开(公告)日：2009-01-08
申请号：US12135551
申请日：2008-06-09
申请人： Tien Huynh , Kevin Charles Miranda , Isidore Rigoutsos
发明人： Tien Huynh , Kevin Charles Miranda , Isidore Rigoutsos
IPC分类号： G06F19/00
CPC分类号： G06F19/22 , C12N15/111 , C12N2310/14 , C12N2320/11 , C12N2330/10 , G06F19/16 , G06F19/18 , G06F19/24
摘要： A method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA will bind thereto is provided. For example, in one aspect of the invention, a method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto is comprised of the following steps. One or more patterns are generated by processing a collection of known mature microRNA sequences. The reverse complement of each generated patter is then computed. One or more attributes are then assigned to the reverse complement of the one or more generated patterns. The one or more patterns that correspond to a reverse complement having one or more assigned attributes that satisfy at least one criterion are thereafter subselected. Each subselected pattern is then used to analyze the nucleotide sequence, such that a determination is made whether the nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto.
摘要翻译：提供了确定核苷酸序列是否含有微小RNA结合位点以及哪个微小RNA将与其结合的方法。例如，在本发明的一个方面，确定核苷酸序列是否含有微小RNA结合位点以及哪个微小RNA序列将与其结合的方法包括以下步骤。通过处理已知的成熟microRNA序列的集合来产生一个或多个图案。然后计算每个生成的图案的反向补码。然后将一个或多个属性分配给一个或多个生成的模式的反向补码。对应于具有满足至少一个标准的一个或多个分配属性的反向补码的一个或多个模式随后被子选择。然后使用每个子选择图案来分析核苷酸序列，从而确定核苷酸序列是否含有微小RNA结合位点，哪个微小RNA序列将与其结合。

8. 发明申请

US20070154896A1 System and method for identification of MicroRNA target sites and corresponding targeting MicroRNA sequences 审中-公开
标题翻译：用于鉴定MicroRNA靶位点的系统和方法以及相应的靶向MicroRNA序列
公开(公告)号：US20070154896A1
公开(公告)日：2007-07-05
申请号：US11351821
申请日：2006-02-10
申请人： Tien Huynh , Kevin Miranda , Isidore Rigoutsos
发明人： Tien Huynh , Kevin Miranda , Isidore Rigoutsos
IPC分类号： C12Q1/68 , G06F19/00
CPC分类号： G16B30/00 , C12N15/111 , C12N2310/14 , C12N2320/11 , C12N2330/10 , G16B15/00 , G16B20/00 , G16B40/00
摘要： A method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA will bind thereto is provided. For example, in one aspect of the invention, a method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto is comprised of the following steps. One or more patterns are generated by processing a collection of known mature microRNA sequences. The reverse complement of each generated patter is then computed. One or more attributes are then assigned to the reverse complement of the one or more generated patterns. The one or more patterns that correspond to a reverse complement having one or more assigned attributes that satisfy at least one criterion are thereafter subselected. Each subselected pattern is then used to analyze the nucleotide sequence, such that a determination is made whether the nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto.
摘要翻译：提供了确定核苷酸序列是否含有微小RNA结合位点以及哪个微小RNA将与其结合的方法。例如，在本发明的一个方面，确定核苷酸序列是否含有微小RNA结合位点以及哪个微小RNA序列将与其结合的方法包括以下步骤。通过处理已知的成熟microRNA序列的集合来产生一个或多个图案。然后计算每个生成的图案的反向补码。然后将一个或多个属性分配给一个或多个生成的模式的反向补码。对应于具有满足至少一个标准的一个或多个分配属性的反向补码的一个或多个模式随后被子选择。然后使用每个子选择图案来分析核苷酸序列，从而确定核苷酸序列是否含有微小RNA结合位点，哪个微小RNA序列将与其结合。

9. 发明授权

US08912317B2 Ribonucleic acid interference molecules of Arabidopsis thaliana 有权
标题翻译：拟南芥的核糖核酸干扰分子
公开(公告)号：US08912317B2
公开(公告)日：2014-12-16
申请号：US12183166
申请日：2008-07-31
申请人： Tien Huynh , Isidore Rigoutsos
发明人： Tien Huynh , Isidore Rigoutsos
IPC分类号： C07H21/00 , C12P19/34 , G01N33/48 , C07H21/02 , C07H21/04
CPC分类号： C12N15/8218 , G06F19/18 , G06F19/24 , Y10T436/143333
摘要： Sequences of ribonucleic acid interference molecules are provided. For example, in one aspect, at least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ_ID NO: 1 through SEQ_ID NO: 3,197 and one or more corresponding mature sequences having SEQ_ID NO: 3,198 through SEQ_ID NO: 6,565 is provided. Techniques are also provided for regulating gene expression.
摘要翻译：提供了核糖核酸干扰分子的序列。例如，在一个方面，至少一个核酸分子包含至少一个具有SEQ ID NO：1至SEQ ID NO：3,197的一个或多个前体序列的一个或多个具有SEQ ID NO：3,198至SEQ ID NO：6,565的相应成熟序列被提供。还提供了调节基因表达的技术。

10. 发明授权

US08795987B2 Ribonucleic acid interference molecules of Oryza sativa 有权
标题翻译：水稻的核糖核酸干扰分子
公开(公告)号：US08795987B2
公开(公告)日：2014-08-05
申请号：US12183204
申请日：2008-07-31
申请人： Tien Huynh , Isidore Rigoutsos
发明人： Tien Huynh , Isidore Rigoutsos
IPC分类号： C12P19/34 , C07H21/04 , C07H21/02
CPC分类号： C12N15/8218 , G06F19/18 , G06F19/24
摘要： Sequences of ribonucleic acid interference molecules are provided. For example, in one aspect, at least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ_ID NO: 1 through SEQ_ID NO: 11,928 and one or more corresponding mature sequences having SEQ_ID NO: 11,929 through SEQ_ID NO: 24,555 is provided. Techniques are also provided for regulating gene expression.
摘要翻译：提供了核糖核酸干扰分子的序列。例如，一方面，至少一个核酸分子包含一个或多个具有SEQ ID NO：1至SEQ ID NO：11,928的前体序列中的至少一种，以及具有SEQ ID NO：11,929至SEQ ID NO：24,555的一个或多个相应的成熟序列被提供。还提供了调节基因表达的技术。

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