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1. 发明申请

WO2008051530A2 POLYMERASE ENZYMES AND REAGENTS FOR ENHANCED NUCLEIC ACID SEQUENCING 审中-公开
标题翻译：聚合酶和增强型核酸测序试剂
公开(公告)号：WO2008051530A2
公开(公告)日：2008-05-02
申请号：PCT/US2007/022459
申请日：2007-10-22
申请人： PACIFIC BIOSCIENCES OF CALIFORNIA, INC. , RANK, David, R. , BIBILLO, Arek , HANZEL, David, K. , PELUSO, Paul , WEGENER, Jeff
发明人： RANK, David, R. , BIBILLO, Arek , HANZEL, David, K. , PELUSO, Paul , WEGENER, Jeff
IPC分类号： C07H21/00 , C12N9/12 , C12P19/34 , C12Q1/68 , C40B30/00 , C40B50/06
CPC分类号： C12N9/1252 , C12P19/34
摘要： Compositions that include DNA polymerases having increased residence times for nucleotide analogues, particularly modified recombinant Φ29-type DNA polymerases with such increased residence times, are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA amplification are also provided. Compositions including α-thiophosphate nucleotide analogues with four or more phosphate groups are described, as are methods for determining the sequence of nucleic acid molecules using such analogues.
摘要翻译：提供了包含具有增加的核苷酸类似物停留时间的DNA聚合酶的组合物，特别是具有增加的停留时间的经修饰的重组Φ29型DNA聚合酶。还提供了在测序和DNA扩增中制备聚合酶和使用聚合酶的方法。描述了包含具有四个或更多个磷酸基团的α-硫代磷酸核苷酸类似物的组合物，以及使用此类类似物确定核酸分子序列的方法。

2. 发明申请

WO2007149724A2 SUBSTRATES FOR PERFORMING ANALYTICAL REACTIONS 审中-公开
标题翻译：执行分析反应的基质
公开(公告)号：WO2007149724A2
公开(公告)日：2007-12-27
申请号：PCT/US2007/070901
申请日：2007-06-11
申请人： PACIFIC BIOSCIENCES OF CALIFORNIA, INC. , FOQUET, Mathieu , PELUSO, Paul , TURNER, Stephen , ROITMAN, Daniel, Bernardo , OTTO, Geoffrey
发明人： FOQUET, Mathieu , PELUSO, Paul , TURNER, Stephen , ROITMAN, Daniel, Bernardo , OTTO, Geoffrey
IPC分类号： C12M3/00
CPC分类号： G02B6/10 , G01N21/648 , G01N2021/7713
摘要： Substrates, including zero mode waveguide substrates that have been fabricated to provide additional fυπclionai elements and/or components including increased volumes for positioning of active surfaces and or components for the mitigation of negative electrochemical properties of the underlying substrates.
摘要翻译：衬底，包括零模式波导衬底，其已经被制造以提供额外的光伏元件和/或组件，包括用于定位有源表面的增加的体积和/或用于减轻下面衬底的负电化学性质的组件。

3. 发明申请

WO2007147110A2 CONTROLLED INITIATION OF PRIMER EXTENSION 审中-公开
标题翻译：控制引擎扩展
公开(公告)号：WO2007147110A2
公开(公告)日：2007-12-21
申请号：PCT/US2007/071327
申请日：2007-06-15
申请人： PACIFIC BIOSCIENCES OF CALIFORNIA, INC. , LYLE, John , PELUSO, Paul , SHEN, Gene
发明人： LYLE, John , PELUSO, Paul , SHEN, Gene
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q2561/113 , C12Q2525/186 , C12Q2523/313
摘要： Controlled initiation of primer extension in determination of nucleic acid sequence information by incorporation of nucleotides or nucleotide analogs. Preferred aspects include photo-initiated extension through the use of photo-cleavable blocking groups on termini of primer sequences followed by non-terminating primer extension using nucleotides or nucleotide analogs that are not extension terminators.
摘要翻译：通过掺入核苷酸或核苷酸类似物来测定核酸序列信息中引物延伸的控制引发。优选的方面包括通过在引物序列的末端使用可光切割的封闭基团，然后使用不是延伸终止子的核苷酸或核苷酸类似物进行非终止引物延伸的光引发延伸。

4. 发明申请

WO2007076057A2 POLYMERASES FOR NUCLEOTIDE ANALOGUE INCORPORATION 审中-公开
标题翻译：用于核苷类似物合成的聚合物
公开(公告)号：WO2007076057A2
公开(公告)日：2007-07-05
申请号：PCT/US2006/049122
申请日：2006-12-21
申请人： PACIFIC BIOSCIENCES OF CALIFORNIA, INC. , HANZEL, David, K. , OTTO, Geoff , MURPHY, Devon , PELUSO, Paul , PHAM, Thang , RANK, David, R. , MITSIS, Paul
发明人： HANZEL, David, K. , OTTO, Geoff , MURPHY, Devon , PELUSO, Paul , PHAM, Thang , RANK, David, R. , MITSIS, Paul
IPC分类号： C12Q1/68
CPC分类号： C12N9/1252 , C07K2319/20 , C12P19/34 , C12Q1/6827 , C12Q1/6869 , C12Y207/07007 , Y02P20/52
摘要： Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.
摘要翻译：提供了包含具有改善核苷酸类似物进入活性位点区域并与活性位点区域中的核苷酸类似物配位的特征的聚合酶的组合物。还提供了制备聚合酶和在测序和DNA复制和扩增中使用聚合酶的方法以及聚合酶活性的动力学模型和使用该模型的计算机实现的方法。

5. 发明申请

WO2009145820A3 GENERATION OF MODIFIED POLYMERASES FOR IMPROVED ACCURACY IN SINGLE MOLECULE SEQUENCING 审中-公开
公开(公告)号：WO2009145820A3
公开(公告)日：2009-12-03
申请号：PCT/US2009/001974
申请日：2009-03-30
申请人： PACIFIC BIOSCIENCES OF CALIFORNIA, INC. , CLARK, Sonya , BIBILLO, Arek , PELUSO, Paul , CHRISTIANS, Fred , HE, Molly , PARK, Insil , LEE, Harold , BJORNSON, Keith , JIA, Lei , EMIG, Robin
发明人： CLARK, Sonya , BIBILLO, Arek , PELUSO, Paul , CHRISTIANS, Fred , HE, Molly , PARK, Insil , LEE, Harold , BJORNSON, Keith , JIA, Lei , EMIG, Robin
IPC分类号： C12N9/12 , C12N15/54 , C12N15/10
摘要： Provided are compositions comprising modified recombinant polymerases that exhibit branching fractions that are less than the branching fractions of the polymerases from which they were derived, or branching fractions that are less than about 25% for a phosphate-labeled nucleotide analog. Also provided are compositions comprising modified recombinant polymerases that exhibit closed polymerase/DNA complexes with increased stability relative to the parental polymerases. Also provided are compositions comprising modified recombinant polymerases that exhibit decreased rate constants relative to the parental polymerases. Provided are methods for generating polymerases with the aforementioned phenotypes. Provided are methods of using such polymerases to make a DNA or to sequence a DNA template.

6. 发明申请

WO2007075873A2 PROTEIN ENGINEERING STRATEGIES TO OPTIMIZE ACTIVITY OF SURFACE ATTACHED PROTEINS 审中-公开
标题翻译：蛋白质工程技术优化表面附着蛋白的活性
公开(公告)号：WO2007075873A2
公开(公告)日：2007-07-05
申请号：PCT/US2006/048764
申请日：2006-12-21
申请人： PACIFIC BIOSCIENCES OF CALIFORNIA, INC. , HANZEL, David , KORLACH, Jonas , PELUSO, Paul , OTTO, Geoff , PHAM, Thang , RANK, David , TURNER, Stephen
发明人： HANZEL, David , KORLACH, Jonas , PELUSO, Paul , OTTO, Geoff , PHAM, Thang , RANK, David , TURNER, Stephen
IPC分类号： C12N9/22
CPC分类号： C12N9/22 , C07K2319/21 , Y10T428/2991 , Y10T428/2993 , Y10T428/2996 , Y10T428/31663 , Y10T428/31768
摘要： Isolated and/or recombinant enzymes that include surface binding domains, surfaces with active enzymes bound to them and methods of coupling enzymes to surfaces are provided. Enzymes can include large and/or multiple surface coupling domains for surface coupling.
摘要翻译：提供了包括表面结合结构域，与其结合的活性酶的表面和将酶与表面偶联的方法的分离和/或重组酶。酶可以包括用于表面偶联的大的和/或多个表面耦合域。

7. 发明申请

WO2007041394A2 REACTIVE SURFACES, SUBSTRATES AND METHODS FOR PRODUCING AND USING SAME 审中-公开
标题翻译：反应性表面，基材及其制造方法和使用方法
公开(公告)号：WO2007041394A2
公开(公告)日：2007-04-12
申请号：PCT/US2006/038243
申请日：2006-09-29
申请人： PACIFIC BIOSCIENCES OF CALIFORNIA, INC. , ROITMAN, Daniel, Bernardo , PELUSO, Paul , FOQUET, Mathieu
发明人： ROITMAN, Daniel, Bernardo , PELUSO, Paul , FOQUET, Mathieu
IPC分类号： G01N33/53
CPC分类号： G01N33/54353 , G01N33/552
摘要： Reactive surfaces, substrates and methods of producing and using such substrates and surfaces are provided. The substrates and surfaces provide low density reactive groups preferably on an otherwise non-reactive surface for use in different applications including single molecule analyses.
摘要翻译：提供反应性表面，基材以及制造和使用这些基材和表面的方法。底物和表面提供低密度反应性基团，优选在其它非反应性表面上用于不同应用，包括单分子分析。

8. 发明申请

WO2016191380A1 DE NOVO DIPLOID GENOME ASSEMBLY AND HAPLOTYPE SEQUENCE RECONSTRUCTION 审中-公开
标题翻译： DE NOVO DIPLOID基因组大会和HAPLOTYPE序列重建
公开(公告)号：WO2016191380A1
公开(公告)日：2016-12-01
申请号：PCT/US2016/033798
申请日：2016-05-23
申请人： PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
发明人： CHIN, Chen-shan , PELUSO, Paul , RANK, David
IPC分类号： G06F19/22 , G06F19/18 , C12P19/34
CPC分类号： G06F19/22 , G06F19/18
摘要： Exemplary embodiments provide methods and systems for diploid genome assembly and haplotype sequence reconstruction. Aspects of the exemplary embodiment include generating a fused assembly graph from reads of both haplotypes, the fused assembly graph including identified primary contigs and associated contigs; generating haplotype-specific assembly graphs using phased reads and haplotype aware overlapping of the phased reads; merging the fused assembly graph and haplotype- specific assembly graphs to generate a merged assembly haplotype graph; removing cross-phasing edges from the merged assembly haplotype graph to generate a final haplotype-resolved assembly graph; and reconstructing haplotype-specific contigs from the final haplotype-resolved assembly graph resulting in haplotype-specific contigs.
摘要翻译：示例性实施方案提供了用于二倍体基因组装配和单倍型序列重建的方法和系统。示例性实施方案的方面包括从两个单倍型的读取产生融合组合图，所述融合组合图包括鉴定的原始重叠群和相关联的重叠群; 使用相位读取和相位读取的单倍型感知重叠来产生单倍型特异性组装图; 合并融合组合图和单倍型特异性组装图以生成合并的组合单倍型图; 从合并的组合单倍型图中去除交叉相位边缘以产生最终的单倍型分解组装图; 并从最终的单元型分解的组装图中重建单倍型特异性重叠群，得到单倍型特异性重叠群。

9. 发明申请

WO2011040971A9 GENERATION OF MODIFIED POLYMERASES FOR IMPROVED ACCURACY IN SINGLE MOLECULE SEQUENCING 审中-公开
公开(公告)号：WO2011040971A9
公开(公告)日：2011-04-07
申请号：PCT/US2010/002659
申请日：2010-09-30
申请人： PACIFIC BIOSCIENCES OF CALIFORNIA, INC. , CLARK, Sonya , BIBILLO, Arek , PELUSO, Paul , CHRISTIANS, Fred , HE, Molly , PARK, Insil , LEE, Harold , BJORNSON, Keith , JIA, Lei , EMIG, Robin
发明人： CLARK, Sonya , BIBILLO, Arek , PELUSO, Paul , CHRISTIANS, Fred , HE, Molly , PARK, Insil , LEE, Harold , BJORNSON, Keith , JIA, Lei , EMIG, Robin
IPC分类号： C12N9/12 , C12N15/54 , C12Q1/68
摘要： Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions and/or heterologous or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include reduced reaction rates at one or more steps of the polymerase kinetic cycle, increased closed polymerase/DNA complex stability, enhanced metal ion coordination, reduced exonuclease activity, decreased branching fractions, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.

10. 发明申请

WO2007123763A2 ARTICLES HAVING LOCALIZED MOLECULES DISPOSED THEREON AND METHODS OF PRODUCING SAME 审中-公开
标题翻译：具有本地化分子的制品及其生产方法
公开(公告)号：WO2007123763A2
公开(公告)日：2007-11-01
申请号：PCT/US2007/008019
申请日：2007-03-29
申请人： PACIFIC BIOSCIENCES OF CALIFORNIA, INC. , RANK, David, R. , WEGENER, Jeffery , KORLACH, Jonas , ROITMAN, Daniel , XU, Yue , LYLE, John , TURNER, Stephen , PELUSO, Paul , OTTO, Geoff
发明人： RANK, David, R. , WEGENER, Jeffery , KORLACH, Jonas , ROITMAN, Daniel , XU, Yue , LYLE, John , TURNER, Stephen , PELUSO, Paul , OTTO, Geoff
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , B01J19/0046 , B01J2219/00427 , B01J2219/0045 , B01J2219/00605 , B01J2219/0061 , B01J2219/00612 , B01J2219/00617 , B01J2219/00626 , B01J2219/00635 , B01J2219/00637 , B01J2219/00639 , B01J2219/00659 , B01J2219/00711 , B01J2219/00722 , B82Y20/00 , B82Y30/00 , C12Q1/6837 , Y10T29/49002 , C12Q2565/629 , C12Q2527/127
摘要： Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.
摘要翻译：通过使用底物的元素来辅助活性化学基团在基底的所需区域中的定位来制备具有选定的活性化学区域的基底的方法。所述方法可以包括用于沉积，去除，激活和/或去活衬底的选定区域中的化学基团的光学，化学和/或机械方法，以提供衬底的选择性活性区域。

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