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1. 发明申请

US20180023134A1 Methods and Compositions for Delivery of Molecules and Complexes to Reaction Sites 审中-公开
公开(公告)号：US20180023134A1
公开(公告)日：2018-01-25
申请号：US15656622
申请日：2017-07-21
申请人： Pacific Biosciences of California, Inc.
发明人： Jeremiah Hanes , Satwik Kamtekar , Yufeng Qian , Keith Bjornson , Thang Pham , David Rank , Paul Peluso , Erik Miller , Kristin Gleitsman , Leewin Chern , Steven Lin , Stephen Turner
IPC分类号： C12Q1/68 , G01N27/447 , G01N33/487
摘要： The present invention provides methods, compositions, and systems for distributing molecules and complexes into reaction sites. In particular, the methods, compositions, and systems of the present invention result in an active loading of molecules and complexes into reaction sites with improved efficiency over loading by passive diffusion methods alone.

2. 发明授权

US10655172B2 Articles having localized molecules disposed thereon and methods of producing same 有权
公开(公告)号：US10655172B2
公开(公告)日：2020-05-19
申请号：US14318324
申请日：2014-06-27
申请人： Pacific Biosciences of California, Inc.
发明人： David R. Rank , Jeffrey Wegener , Jonas Korlach , Daniel Roitman , Yue Xu , John Lyle , Stephen Turner , Paul Peluso , Geoff Otto , Ronald L. Cicero
IPC分类号： C12Q1/68 , C12Q1/6874 , B01J19/00 , B82Y20/00 , B82Y30/00 , C12Q1/6837
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.

3. 发明申请

US20150184239A1 Polymerases for Nucleotide Analogue Incorporation 审中-公开
标题翻译：核苷酸类似物掺入的聚合酶
公开(公告)号：US20150184239A1
公开(公告)日：2015-07-02
申请号：US14538653
申请日：2014-11-11
申请人： Pacific Biosciences of California, Inc.
发明人： David K. Hanzel , Geoff Otto , Paul Peluso , Thang Pham , David R. Rank , Paul Mitsis , Fred Christians , Arekadiusz Bibillo , Insil Park , Sonya Clark , John Lyle
IPC分类号： C12Q1/68 , C12P19/34
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。

4. 发明申请

US20140315756A1 Articles Having Localized Molecules Disposed Thereon and Methods of Producing Same 审中-公开
标题翻译：具有本地化分子的文章及其生产方法
公开(公告)号：US20140315756A1
公开(公告)日：2014-10-23
申请号：US14318324
申请日：2014-06-27
申请人： Pacific Biosciences of California, Inc.
发明人： David R. Rank , Jeffrey Wegener , Jonas Korlach , Daniel Roitman , Yue Xu , John Lyle , Stephen Turner , Paul Peluso , Geoff Otto , Ronald L. Cicero
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。

5. 发明授权

US11186871B2 Articles having localized molecules disposed thereon and methods of producing same 有权
公开(公告)号：US11186871B2
公开(公告)日：2021-11-30
申请号：US16848620
申请日：2020-04-14
申请人： Pacific Biosciences of California, Inc.
发明人： David R. Rank , Jeffery Wegener , Jonas Korlach , Daniel Roitman , Yue Xu , John Lyle , Stephen Turner , Paul Peluso , Geoff Otto , Ron L. Cicero
IPC分类号： C12Q1/6874 , B01J19/00 , B82Y20/00 , B82Y30/00 , C12Q1/6837
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.

6. 发明授权

US10783984B2 De novo diploid genome assembly and haplotype sequence reconstruction 有权
公开(公告)号：US10783984B2
公开(公告)日：2020-09-22
申请号：US15162315
申请日：2016-05-23
申请人： Pacific Biosciences of California, Inc.
发明人： Chen-Shan Chin , Paul Peluso , David Rank
IPC分类号： G16B30/00 , G16B20/00 , G16B30/20
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.

7. 发明申请

US20220098660A1 ARTICLES HAVING LOCALIZED MOLECULES DISPOSED THEREON AND METHODS OF PRODUCING SAME 有权
公开(公告)号：US20220098660A1
公开(公告)日：2022-03-31
申请号：US17504115
申请日：2021-10-18
申请人： Pacific Biosciences of California, Inc.
发明人： David R. Rank , Jeffery Wegener , Jonas Korlach , Daniel Roitman , Yue Xu , John Lyle , Stephen Turner , Paul Peluso , Geoff Otto , Ron L. Cicero
IPC分类号： C12Q1/6874 , B01J19/00 , B82Y20/00 , B82Y30/00 , C12Q1/6837
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.

8. 发明申请

US20200377940A1 ARTICLES HAVING LOCALIZED MOLECULES DISPOSED THEREON AND METHODS OF PRODUCING SAME 审中-公开
公开(公告)号：US20200377940A1
公开(公告)日：2020-12-03
申请号：US16848620
申请日：2020-04-14
申请人： Pacific Biosciences of California, Inc.
发明人： David R. Rank , Jeffery Wegener , Jonas Korlach , Daniel Roitman , Yue XU , John Lyle , Stephen Turner , Paul Peluso , Geoff Otto , Ron L. Cicero
IPC分类号： C12Q1/6874 , B01J19/00 , B82Y20/00 , B82Y30/00 , C12Q1/6837
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.

9. 发明授权

US09556479B2 Polymerases for nucleotide analogue incorporation 有权
标题翻译：用于核苷酸类似物掺入的聚合酶
公开(公告)号：US09556479B2
公开(公告)日：2017-01-31
申请号：US14538653
申请日：2014-11-11
申请人： Pacific Biosciences of California, Inc.
发明人： David K. Hanzel , Geoff Otto , Paul Peluso , Thang Pham , David R. Rank , Paul Mitsis , Fred Christians , Arekadiusz Bibillo , Insil Park , Sonya Clark , John Lyle
IPC分类号： C12P19/34 , C12Q1/68 , C12N9/12
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。

10. 发明申请

US20160350478A1 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：US20160350478A1
公开(公告)日：2016-12-01
申请号：US15162315
申请日：2016-05-23
申请人： Pacific Biosciences of California, Inc.
发明人： Chen-Shan Chin , Paul Peluso , David Rank
IPC分类号： G06F19/22
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。

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