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公开(公告)号：US20120330566A1
公开(公告)日：2012-12-27
申请号：US13334601
申请日：2011-12-22
Applicant: Mark Chaisson
Inventor： Mark Chaisson
Abstract: Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof. In particularly preferred embodiments, nucleic acid sequences generated by such methods are subjected to de novo assembly and/or consensus sequence determination.
Abstract translation: 计算机实现的方法和执行这种方法的系统用于处理来自分析操作和系统的信号数据，特别是处理来自逐个引入过程的信号数据，以鉴定模板核酸和较大核酸分子的核苷酸序列，例如基因组或 片段。 在特别优选的实施方案中，通过这些方法产生的核酸序列经受从头组装和/或共有序列测定。
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公开(公告)号：US08911972B2
公开(公告)日：2014-12-16
申请号：US12967507
申请日：2010-12-14
Applicant: Mark Chaisson , Sonya Clark , Christopher Silk , John Lyle , Lei Jia , Keith Bjornson
Inventor： Mark Chaisson , Sonya Clark , Christopher Silk , John Lyle , Lei Jia , Keith Bjornson
CPC classification number: C12Q1/6869 , C12Q2521/101 , C12Q2561/113 , C12Q2563/107
Abstract: Systems and methods are provided for single-molecule sequencing of template nucleic acids in which the signal from a label attached to a polymerase enzyme is used to monitor conformational changes in the polymerase which occur while labeled nucleotides or nucleotide analogs are added to a growing nucleic acid chain which is complementary to the template nucleic acid. The signal indicative of the conformational state of the enzyme is used to determine with higher confidence when true nucleotide or nucleotide analog incorporation events occur, allowing for the improved quality of base calls and sequence determination.
Abstract translation: 提供了用于模板核酸的单分子测序的系统和方法，其中来自连接到聚合酶的标记的信号用于监测聚合酶中的构象变化，同时将标记的核苷酸或核苷酸类似物加入生长的核酸 与模板核酸互补的链。 当发生真核苷酸或核苷酸类似物并入事件时，使用指示酶构象状态的信号来确定更高的置信度，从而提高碱基调用质量和序列测定。
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公开(公告)号：US08383369B2
公开(公告)日：2013-02-26
申请号：US12561221
申请日：2009-09-16
Applicant: Kenneth Mark Maxham , Jon Sorenson , John Eid , Patrick Marks , Kevin Travers , Donald Gray , Robin Emig , Mark Chaisson , Benjamin Flusberg
Inventor： Kenneth Mark Maxham , Jon Sorenson , John Eid , Patrick Marks , Kevin Travers , Donald Gray , Robin Emig , Mark Chaisson , Benjamin Flusberg
CPC classification number: G01N21/6452 , C12Q1/6869 , G01N21/6428 , G01N2201/0635 , Y10T436/143333 , C12Q2525/119 , C12Q2521/125 , C12Q2537/149
Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
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公开(公告)号：US20100075327A1
公开(公告)日：2010-03-25
申请号：US12561221
申请日：2009-09-16
Applicant: Kenneth Mark Maxham , Jon Sorenson , John Eid , Patrick Marks , Kevin Travers , Donald Gray , Robin Emig , Mark Chaisson , Benjamin Flusberg
Inventor： Kenneth Mark Maxham , Jon Sorenson , John Eid , Patrick Marks , Kevin Travers , Donald Gray , Robin Emig , Mark Chaisson , Benjamin Flusberg
CPC classification number: G01N21/6452 , C12Q1/6869 , G01N21/6428 , G01N2201/0635 , Y10T436/143333 , C12Q2525/119 , C12Q2521/125 , C12Q2537/149
Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
Abstract translation: 提供了在分析反应期间执行间歇检测的方法，装置和系统。 这种方法有助于从不同的反应时间收集反应数据。 此外，这样的方法可用于在给定的反应时间下降低照明分析反应中一种或多种反应物的光诱导损伤。 在优选的实施方案中，将反应混合物经受至少一个照明和非照射期，并允许进行，使得反应混合物被照射的时间小于光诱导的损伤阈值期。
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Patent Agency Ranking
公开(公告)号：US20110257889A1
公开(公告)日：2011-10-20
申请号：US13034233
申请日：2011-02-24
Applicant: Aaron Klammer , Susan Tang , Mark Chaisson , Jon Sorenson , Chen-Shan Chin
Inventor： Aaron Klammer , Susan Tang , Mark Chaisson , Jon Sorenson , Chen-Shan Chin
IPC: G06F19/00
CPC classification number: G16B30/00
Abstract: Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof. In particularly preferred embodiments, nucleic acid sequences generated by such methods are subjected to de novo assembly and/or consensus sequence determination.
Abstract translation: 计算机实现的方法和执行这种方法的系统用于处理来自分析操作和系统的信号数据，特别是处理来自逐个引入过程的信号数据，以鉴定模板核酸和较大核酸分子的核苷酸序列，例如基因组或 片段。 在特别优选的实施方案中，通过这些方法产生的核酸序列经受从头组装和/或共有序列测定。
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公开(公告)号：US20110160077A1
公开(公告)日：2011-06-30
申请号：US12967507
申请日：2010-12-14
Applicant: Mark Chaisson , Sonya Clark , Christopher Silk , John Lyle , Lei Jia , Keith Bjornson
Inventor： Mark Chaisson , Sonya Clark , Christopher Silk , John Lyle , Lei Jia , Keith Bjornson
CPC classification number: C12Q1/6869 , C12Q2521/101 , C12Q2561/113 , C12Q2563/107
Abstract: Systems and methods are provided for single-molecule sequencing of template nucleic acids in which the signal from a label attached to a polymerase enzyme is used to monitor conformational changes in the polymerase which occur while labeled nucleotides or nucleotide analogs are added to a growing nucleic acid chain which is complementary to the template nucleic acid. The signal indicative of the conformational state of the enzyme is used to determine with higher confidence when true nucleotide or nucleotide analog incorporation events occur, allowing for the improved quality of base calls and sequence determination.
Abstract translation: 提供了用于模板核酸的单分子测序的系统和方法，其中来自连接到聚合酶的标记的信号用于监测聚合酶中的构象变化，同时将标记的核苷酸或核苷酸类似物加入生长的核酸 与模板核酸互补的链。 当发生真核苷酸或核苷酸类似物并入事件时，使用指示酶构象状态的信号来确定更高的置信度，从而提高碱基调用质量和序列测定。
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公开(公告)号：US09165109B2
公开(公告)日：2015-10-20
申请号：US13334601
申请日：2011-12-22
Applicant: Mark Chaisson
Inventor： Mark Chaisson
Abstract: Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof. In particularly preferred embodiments, nucleic acid sequences generated by such methods are subjected to de novo assembly and/or consensus sequence determination.
Abstract translation: 计算机实现的方法和执行这种方法的系统用于处理来自分析操作和系统的信号数据，特别是处理来自逐个引入过程的信号数据，以鉴定模板核酸和较大核酸分子的核苷酸序列，例如基因组或 片段。 在特别优选的实施方案中，通过这些方法产生的核酸序列经受从头组装和/或共有序列测定。
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公开(公告)号：US09063156B2
公开(公告)日：2015-06-23
申请号：US12814075
申请日：2010-06-11
Applicant: Jonas Korlach , Stephen Turner , Benjamin Flusberg , Mark Chaisson , Eric Schadt , Jeffrey Wegener
Inventor： Jonas Korlach , Stephen Turner , Benjamin Flusberg , Mark Chaisson , Eric Schadt , Jeffrey Wegener
IPC: C12Q1/68 , G01N33/53 , G01N33/68 , G01N33/542 , G01N33/543
CPC classification number: G01N33/68 , C12Q1/6825 , C12Q1/6827 , C12Q1/6869 , G01N33/542 , G01N33/54306 , G01N33/54373 , G01N33/582 , G01N33/6875 , G01N2333/705 , G01N2458/10 , C12Q2563/107 , C12Q2522/101 , C12Q2561/113 , C12Q2537/164 , C12Q2523/125
Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions, and for determining various characteristics of the different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to stimulate, enhance, or inhibit such reactions.
Abstract translation: 本发明一般涉及用于进行各种不同生物反应的单分子实时分析以及用于确定不同生物反应的各种特征的组合物，方法和系统。 分析这些反应的能力提供研究这些反应的机会，并且潜在地鉴定影响这些反应的因素和/或方法，例如刺激，增强或抑制这些反应。
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公开(公告)号：US20100323912A1
公开(公告)日：2010-12-23
申请号：US12814075
申请日：2010-06-11
Applicant: Jonas Korlach , Stephen Turner , Benjamin Flusberg , Mark Chaisson , Eric Schadt , Jeffrey Wegener
Inventor： Jonas Korlach , Stephen Turner , Benjamin Flusberg , Mark Chaisson , Eric Schadt , Jeffrey Wegener
IPC: C40B30/04 , C12Q1/68 , G01N33/566 , C40B50/14
CPC classification number: G01N33/68 , C12Q1/6825 , C12Q1/6827 , C12Q1/6869 , G01N33/542 , G01N33/54306 , G01N33/54373 , G01N33/582 , G01N33/6875 , G01N2333/705 , G01N2458/10 , C12Q2563/107 , C12Q2522/101 , C12Q2561/113 , C12Q2537/164 , C12Q2523/125
Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions, and for determining various characteristics of the different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to stimulate, enhance, or inhibit such reactions.
Abstract translation: 本发明一般涉及用于进行各种不同生物反应的单分子实时分析以及用于确定不同生物反应的各种特征的组合物，方法和系统。 分析这些反应的能力提供研究这些反应的机会，并且潜在地鉴定影响这些反应的因素和/或方法，例如刺激，增强或抑制这些反应。
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