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1. 发明授权

US09175338B2 Methods for identifying nucleic acid modifications 有权
标题翻译：识别核酸修饰的方法
公开(公告)号：US09175338B2
公开(公告)日：2015-11-03
申请号：US12945767
申请日：2010-11-12
申请人： Benjamin Flusberg , Jonas Korlach , Jeffrey Wegener , Tyson A. Clark , Igor Vilfan , Andrey Kislyuk , Stephen Turner , Jon Sorenson , Kevin Travers , Cheryl Heiner , Austin B. Tomaney , Patrick Marks , Jessica Lee , Lei Jia , Dale Webster , John Lyle , Jeremiah Hanes , Joseph Puglisi
发明人： Benjamin Flusberg , Jonas Korlach , Jeffrey Wegener , Tyson A. Clark , Igor Vilfan , Andrey Kislyuk , Stephen Turner , Jon Sorenson , Kevin Travers , Cheryl Heiner , Austin B. Tomaney , Patrick Marks , Jessica Lee , Lei Jia , Dale Webster , John Lyle , Jeremiah Hanes , Joseph Puglisi
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , C12Q1/6837 , C12Q1/6858 , C12Q1/6874 , C12Q1/689 , C12Q2600/154 , C12Q2537/164 , C12Q2527/113 , C12Q2521/101 , C12Q2525/307 , C12Q2525/117
摘要： Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
摘要翻译：提供了方法，组合物和系统用于表征修饰的核酸。在某些优选实施方案中，提供单分子测序方法用于鉴定核酸序列内的修饰的核苷酸。通过本文提供的方法可检测的修饰物包括化学修饰的碱基，酶修饰的碱基，脱碱基位点，非天然碱基，二级结构和与模板核酸结合的试剂。

2. 发明申请

US20110183320A1 CLASSIFICATION OF NUCLEIC ACID TEMPLATES 有权
标题翻译：核酸模板分类
公开(公告)号：US20110183320A1
公开(公告)日：2011-07-28
申请号：US12945767
申请日：2010-11-12
申请人： Benjamin Flusberg , Jonas Korlach , Jeffrey Wegener , Tyson A. Clark , Igor Vilfan , Andrey Kislyuk , Stephen Turner , Jon Sorenson , Kevin Travers , Cheryl Heiner , Austin B. Tomaney , Patrick Marks , Jessica Lee , Lei Jia , Dale Webster , John Lyle , Jeremiah Hanes , Joseph Puglisi
发明人： Benjamin Flusberg , Jonas Korlach , Jeffrey Wegener , Tyson A. Clark , Igor Vilfan , Andrey Kislyuk , Stephen Turner , Jon Sorenson , Kevin Travers , Cheryl Heiner , Austin B. Tomaney , Patrick Marks , Jessica Lee , Lei Jia , Dale Webster , John Lyle , Jeremiah Hanes , Joseph Puglisi
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , C12Q1/6837 , C12Q1/6858 , C12Q1/6874 , C12Q1/689 , C12Q2600/154 , C12Q2537/164 , C12Q2527/113 , C12Q2521/101 , C12Q2525/307 , C12Q2525/117
摘要： Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
摘要翻译：提供了方法，组合物和系统用于表征修饰的核酸。在某些优选实施方案中，提供单分子测序方法用于鉴定核酸序列内的修饰的核苷酸。通过本文提供的方法可检测的修饰物包括化学修饰的碱基，酶修饰的碱基，脱碱基位点，非天然碱基，二级结构和与模板核酸结合的试剂。

3. 发明申请

US20090024331A1 METHODS AND PROCESSES FOR CALLING BASES IN SEQUENCE BY INCORPORATION METHODS 有权
标题翻译：通过并入方法对序列进行呼叫的方法和过程
公开(公告)号：US20090024331A1
公开(公告)日：2009-01-22
申请号：US12134186
申请日：2008-06-05
申请人： Austin B. Tomaney , Kenneth Mark Maxham , David Holden , Kevin Hester , Devon Murphy , Patrick Marks
发明人： Austin B. Tomaney , Kenneth Mark Maxham , David Holden , Kevin Hester , Devon Murphy , Patrick Marks
IPC分类号： G01N33/68 , G01J3/28
CPC分类号： C12Q1/6869 , G06F19/22 , C12Q2563/107
摘要： 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.
摘要翻译：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。

4. 发明授权

US08182993B2 Methods and processes for calling bases in sequence by incorporation methods 有权
标题翻译：通过并入方法顺序调用碱基的方法和方法
公开(公告)号：US08182993B2
公开(公告)日：2012-05-22
申请号：US12134186
申请日：2008-06-05
申请人： Austin B. Tomaney , Kenneth Mark Maxham , David Holden , Kevin Hester , Devon Murphy , Patrick Marks
发明人： Austin B. Tomaney , Kenneth Mark Maxham , David Holden , Kevin Hester , Devon Murphy , Patrick Marks
IPC分类号： C12Q1/68 , C12P19/34 , C07H21/04
CPC分类号： C12Q1/6869 , G06F19/22 , C12Q2563/107
摘要： 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.
摘要翻译：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。

5. 发明申请

US20120015825A1 ANALYTICAL SYSTEMS AND METHODS WITH SOFTWARE MASK 审中-公开
标题翻译：分析系统和方法与软件掩蔽
公开(公告)号：US20120015825A1
公开(公告)日：2012-01-19
申请号：US13174089
申请日：2011-06-30
申请人： Cheng Frank Zhong , Austin B. Tomaney , Patrick Marks , Stuart George Johnson , James N. LaBrenz , Paul Lundquist
发明人： Cheng Frank Zhong , Austin B. Tomaney , Patrick Marks , Stuart George Johnson , James N. LaBrenz , Paul Lundquist
IPC分类号： C40B30/10 , C40B20/08 , C40B40/00 , C40B30/04
CPC分类号： G01N21/6428 , G01N21/6452
摘要： Methods and systems for obtaining and processing optical signal data from analytical reactions, and in processing signal data from arrays of sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof are described. Defining and applying a 2-dimensional software mask allows for obtaining signal data from arrays with higher signal to noise than where the mask is not applied.
摘要翻译：描述了用于从分析反应获得和处理光信号数据的方法和系统，以及处理来自逐个并入过程的阵列的信号数据以识别模板核酸和较大核酸分子（例如基因组或其片段）的核苷酸序列。定义和应用二维软件掩码允许从没有应用掩码的阵列获得具有更高信噪比的阵列的信号数据。

6. 发明授权

US08274650B2 Signal noise reduction for imaging in biological analysis 有权
标题翻译：生物分析中成像信号降噪
公开(公告)号：US08274650B2
公开(公告)日：2012-09-25
申请号：US12775391
申请日：2010-05-06
申请人： Austin B. Tomaney , Mark F. Oldham
发明人： Austin B. Tomaney , Mark F. Oldham
IPC分类号： G01J1/42
CPC分类号： G01N21/6486 , G01N21/6428 , G01N2201/06113 , G01N2201/062 , G01N2201/08 , G01N2201/121 , H04N5/225 , H04N5/357 , H04N5/361 , H04N5/367
摘要： A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.
摘要翻译：用于表征与适用于生物分析的电荷耦合器件相关的信号噪声的贡献的系统和方法。暗电流贡献，读出偏移贡献，光响应不均匀性和杂散电荷贡献可以由本教导的方法确定并用于本教导的系统的信号校正。

7. 发明申请

US20120214246A1 System and Method for Extending Dynamic Range for a Detector 审中-公开
标题翻译：用于扩展检测器动态范围的系统和方法
公开(公告)号：US20120214246A1
公开(公告)日：2012-08-23
申请号：US13361875
申请日：2012-01-30
申请人： Mark F. Oldham , Austin B. Tomaney
发明人： Mark F. Oldham , Austin B. Tomaney
IPC分类号： G01N21/75
CPC分类号： G01J1/42 , G01J2001/4406 , Y10T436/143333
摘要： A system and method for measuring signals having a wide range of intensity components using detectors adapted for use in biological analysis devices. In certain biological analysis applications, signals emitted by a sample may have intensity components that vary over several orders of magnitude. Measurement of such a signal may yield an acceptable quality for one intensity component at the expense of another component. For example, a detector configured to measure a relatively weak intensity component may cause it to overflow when subjected to a relatively strong intensity component. The detector can be adapted to be operated at different configurations to allow measurements of different components of the signal, and the results can be combined to yield an accurate representation of the signal.
摘要翻译：一种用于使用适用于生物分析装置的检测器来测量具有宽范围的强度分量的信号的系统和方法。在某些生物分析应用中，由样品发射的信号可以具有在几个数量级上变化的强度分量。这种信号的测量可以以另一个组件为代价产生一个强度分量的可接受的质量。例如，被配置为测量相对弱的强度分量的检测器可以在经受相对强的强度分量时使其溢出。检测器可以适于以不同的配置操作，以允许对信号的不同部件进行测量，并且可以将结果组合以产生信号的精确表示。

8. 发明申请

US20120319008A1 Signal Noise Reduction for Imaging in Biological Analysis 有权
标题翻译：信号降噪用于生物分析中的成像
公开(公告)号：US20120319008A1
公开(公告)日：2012-12-20
申请号：US13593945
申请日：2012-08-24
申请人： Austin B. Tomaney , Mark F. Oldham
发明人： Austin B. Tomaney , Mark F. Oldham
IPC分类号： G01N21/64
CPC分类号： G01N21/6486 , G01N21/6428 , G01N2201/06113 , G01N2201/062 , G01N2201/08 , G01N2201/121 , H04N5/225 , H04N5/357 , H04N5/361 , H04N5/367
摘要： A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.
摘要翻译：用于表征与适用于生物分析的电荷耦合器件相关的信号噪声的贡献的系统和方法。暗电流贡献，读出偏移贡献，光响应不均匀性和杂散电荷贡献可以由本教导的方法确定并用于本教导的系统的信号校正。

9. 发明申请

US20110079705A1 Signal Noise Reduction for Imaging in Biological Analysis 有权
标题翻译：信号降噪用于生物分析中的成像
公开(公告)号：US20110079705A1
公开(公告)日：2011-04-07
申请号：US12775391
申请日：2010-05-06
申请人： Austin B. Tomaney , Mark F. Oldham
发明人： Austin B. Tomaney , Mark F. Oldham
IPC分类号： H01L27/146
CPC分类号： G01N21/6486 , G01N21/6428 , G01N2201/06113 , G01N2201/062 , G01N2201/08 , G01N2201/121 , H04N5/225 , H04N5/357 , H04N5/361 , H04N5/367
摘要： A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.
摘要翻译：用于表征与适用于生物分析的电荷耦合器件相关的信号噪声的贡献的系统和方法。暗电流贡献，读出偏移贡献，光响应不均匀性和杂散电荷贡献可以由本教导的方法确定并用于本教导的系统的信号校正。

10. 发明申请

US20080290283A1 Signal noise reduction for imaging in biological analysis 有权
标题翻译：生物分析中成像信号降噪
公开(公告)号：US20080290283A1
公开(公告)日：2008-11-27
申请号：US12220763
申请日：2008-07-28
申请人： Austin B. Tomaney , Mark F. Oldham
发明人： Austin B. Tomaney , Mark F. Oldham
IPC分类号： H01L27/148
CPC分类号： G01N21/6486 , G01N21/6428 , G01N2201/06113 , G01N2201/062 , G01N2201/08 , G01N2201/121 , H04N5/225 , H04N5/357 , H04N5/361 , H04N5/367
摘要： A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.
摘要翻译：用于表征与适用于生物分析的电荷耦合器件相关的信号噪声的贡献的系统和方法。暗电流贡献，读出偏移贡献，光响应不均匀性和杂散电荷贡献可以由本教导的方法确定并用于本教导的系统的信号校正。

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