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1. 发明申请

WO2015069713A3 SYSTEMS AND METHODS FOR AUTOMATED MULTIPLEX ASSAY DESIGN 审中-公开
标题翻译：用于自动化多重分析设计的系统和方法
公开(公告)号：WO2015069713A3
公开(公告)日：2015-11-12
申请号：PCT/US2014064050
申请日：2014-11-05
申请人： FIREFLY BIOWORKS INC
发明人： MARINI DAVIDE , RAFFERTY CONOR , TYTELL JESSICA DAWN , WINDEMUTH ANDREAS
IPC分类号： G01N33/531
CPC分类号： G06F19/28 , C12Q1/6837 , C12Q2537/165
摘要： Described herein, in certain embodiments, are systems and methods for automated multiplex assay design. For example, a statistically significant (and/or biologically meaningful) cluster of probes resulting from an experiment are identified, then analyzed for association with additional probes (different from the experimentally identified probes) by performing a query of one or more databases. In some embodiments, mapping is performed between multiple types of probes, such that an experimentally observed probe is mapped into a database to identify associations with a different kind of probe, thereby designing a multiplex assay.
摘要翻译：在某些实施方案中，本文描述了用于自动化多重测定设计的系统和方法。例如，鉴定来自实验的统计学显着的（和/或生物学有意义的）探针簇，然后通过执行一个或多个数据库的查询来分析与另外的探针（不同于实验鉴定的探针）的关联。在一些实施方案中，在多种类型的探针之间进行作图，使得实验观察的探针被映射到数据库中以识别与不同种类的探针的关联，由此设计多重化验。

2. 发明申请

WO2011156432A3 SCANNING MULTIFUNCTIONAL PARTICLES 审中-公开
标题翻译：扫描多功能颗粒
公开(公告)号：WO2011156432A3
公开(公告)日：2012-04-26
申请号：PCT/US2011039529
申请日：2011-06-07
申请人： FIREFLY BIOWORKS INC , PREGIBON DANIEL C , MARINI DAVIDE M , STONER ISAAC , WINDEMUTH ANDREAS , ERPS TIMOTHY
发明人： PREGIBON DANIEL C , MARINI DAVIDE M , STONER ISAAC , WINDEMUTH ANDREAS , ERPS TIMOTHY
IPC分类号： G01N33/483 , C12Q1/02 , C12Q1/68 , G01N15/14 , G01N21/47
CPC分类号： C12Q1/6825 , C12Q1/6809 , C12Q1/6813 , C12Q1/6816 , C12Q1/6834 , C12Q1/6888 , C12Q1/689 , C12Q1/6895 , C12Q1/70 , G01N15/14 , G01N21/47 , G01N21/6428 , G01N33/6803 , C12Q2565/626 , C12Q2525/161 , C12Q2525/191 , C12Q2533/107
摘要： The present invention provides, among other things, methods and systems for characterizing multifunctional objects using a flow-through device, such as, a flow cytometer. In some embodiments, an inventive method according to the present invention includes one more steps of (a) interrogating a plurality of objects (e.g., particles), wherein each individual object (e.g., particle) comprises one or more interrogation regions detectable as a sequence of events; (b) recording multiple events, wherein each individual event corresponds to each individual interrogation region detectable above a pre-determined triggering threshold; (c) grouping the recorded multiple events, and (d) characterizing the plurality of objects based on the grouped events.
摘要翻译：本发明尤其提供了使用流通装置如流式细胞仪来表征多功能物体的方法和系统。在一些实施例中，根据本发明的发明方法包括以下步骤：（a）询问多个对象（例如，粒子），其中每个单个对象（例如，粒子）包括可检测为序列的一个或多个询问区域的事件; （b）记录多个事件，其中每个单独的事件对应于在预先确定的触发阈值之上可检测的每个个别询问区域; （c）对记录的多个事件进行分组，以及（d）基于分组的事件来表征多个对象。

3. 发明申请

WO2011156432A2 SCANNING MULTIFUNCTIONAL PARTICLES 审中-公开
标题翻译：扫描多功能颗粒
公开(公告)号：WO2011156432A2
公开(公告)日：2011-12-15
申请号：PCT/US2011/039529
申请日：2011-06-07
申请人： FIREFLY BIOWORKS, INC. , PREGIBON, Daniel, C. , MARINI, Davide, M. , STONER, Isaac , WINDEMUTH, Andreas , ERPS, Timothy
发明人： PREGIBON, Daniel, C. , MARINI, Davide, M. , STONER, Isaac , WINDEMUTH, Andreas , ERPS, Timothy
IPC分类号： G01N33/483 , G01N15/14 , C12Q1/68 , C12Q1/02 , G01N21/47
CPC分类号： C12Q1/6825 , C12Q1/6809 , C12Q1/6813 , C12Q1/6816 , C12Q1/6834 , C12Q1/6888 , C12Q1/689 , C12Q1/6895 , C12Q1/70 , G01N15/14 , G01N21/47 , G01N21/6428 , G01N33/6803 , C12Q2565/626 , C12Q2525/161 , C12Q2525/191 , C12Q2533/107
摘要： The present invention provides, among other things, methods and systems for characterizing multifunctional objects using a flow-through device, such as, a flow cytometer. In some embodiments, an inventive method according to the present invention includes one more steps of (a) interrogating a plurality of objects (e.g., particles), wherein each individual object (e.g., particle) comprises one or more interrogation regions detectable as a sequence of events; (b) recording multiple events, wherein each individual event corresponds to each individual interrogation region detectable above a pre-determined triggering threshold; (c) grouping the recorded multiple events, and (d) characterizing the plurality of objects based on the grouped events.
摘要翻译：本发明尤其提供了使用流通装置如流式细胞仪来表征多功能物体的方法和系统。在一些实施例中，根据本发明的发明方法包括以下步骤：（a）询问多个对象（例如，粒子），其中每个单个对象（例如，粒子）包括可被检测为序列的一个或多个询问区域的事件; （b）记录多个事件，其中每个单独的事件对应于在预先确定的触发阈值之上可检测的每个个别询问区域; （c）对记录的多个事件进行分组，以及（d）基于分组的事件来表征多个对象。

4. 发明申请

WO2015179848A1 SUBSTRATE-MEDIATED REACTORS FOR BIOASSAYS 审中-公开
标题翻译：生物传感器的基质介质反应器
公开(公告)号：WO2015179848A1
公开(公告)日：2015-11-26
申请号：PCT/US2015/032319
申请日：2015-05-22
申请人： FIREFLY BIOWORKS, INC.
发明人： STONER, Isaac , ERPS, Timothy , PREGIBON, Daniel , TYTELL, Jessica Dawn , WINDEMUTH, Andreas , DORAN, Graeme
IPC分类号： G01N33/538 , G01N33/543
CPC分类号： G01N33/538 , G01N33/5432 , G01N33/5436
摘要： The present invention provides, among other things, methods, compositions and systems for highly efficient, robust, multiplex analysis of biomolecules based on substrate-mediated compartmentalization in conjunction with controlled release of assay reagents for interference-free detection of biomolecules.
摘要翻译：本发明尤其提供了用于基于底物介导的区室化的生物分子的高效，稳健，多重分析以及用于无干扰检测生物分子的测定试剂的受控释放的方法，组合物和系统。

5. 发明申请

WO2013134633A1 METHODS AND APPARATUS FOR CLASSIFICATION AND QUANTIFICATION OF MULTIFUNCTIONAL OBJECTS 审中-公开
标题翻译：多功能对象的分类和量化方法与装置
公开(公告)号：WO2013134633A1
公开(公告)日：2013-09-12
申请号：PCT/US2013/029854
申请日：2013-03-08
申请人： FIREFLY BIOWORKS, INC.
发明人： WINDEMUTH, Andreas , PREGIBON, Daniel , MARINI, Davide
IPC分类号： G01N15/14 , G01N35/00
CPC分类号： G01N33/50 , G01N15/1427 , G01N15/1429 , G01N15/1459 , G01N15/147 , G01N35/00732 , G01N2015/1006 , G01N2015/1402 , G01N2015/1477 , G06M3/08
摘要： A method may include accessing data regarding a number of events, where the events were detected by a particle detection apparatus, and identifying a number of groups in the events. Each of the groups includes two or more events, and each event includes one or more of a time stamp, a time duration, a fluorescence intensity, a scatter measurement, a radio frequency signal, a magnetic signal, a neutron scattering measurement, a light scattering measurement, an electron scattering measurement, an audio signal, an acoustic signal, a mechanical signal, an electrical resistance, a thermal property, and a width of fluorescence signal. The method may include identifying a subset of the groups as a number of objects detected by the particle detection apparatus, where each object is identified based at least in part upon one or more quantities, where each quantity is identified by or derived from the respective two or more events.
摘要翻译：方法可以包括访问关于事件的数量的数据，其中事件由粒子检测装置检测到，并且识别事件中的组的数量。每个组包括两个或更多个事件，并且每个事件包括时间戳，持续时间，荧光强度，散射测量，射频信号，磁信号，中子散射测量，光散射测量，电子散射测量，音频信号，声学信号，机械信号，电阻，热性质和荧光信号的宽度。所述方法可以包括将所述组的子集识别为由所述粒子检测装置检测到的多个对象，其中每个对象至少部分地基于一个或多个数量被识别，其中每个数量由相应的两个或更多的事件。

6. 发明申请

WO2011156434A3 NUCLEIC ACID DETECTION AND QUANTIFICATION BY POST-HYBRIDIZATION LABELING AND UNIVERSAL ENCODING 审中-公开
标题翻译：通过后期杂交标签和通用编码进行核酸检测和定量
公开(公告)号：WO2011156434A3
公开(公告)日：2012-04-12
申请号：PCT/US2011039531
申请日：2011-06-07
申请人： FIREFLY BIOWORKS INC , PREGIBON DANIEL C , STONER ISAAC , WINDEMUTH ANDREAS , ERPS TIMOTHY
发明人： PREGIBON DANIEL C , STONER ISAAC , WINDEMUTH ANDREAS , ERPS TIMOTHY
IPC分类号： C12Q1/68 , C12N15/11 , G01N33/53
CPC分类号： C12Q1/6825 , C12Q1/6809 , C12Q1/6813 , C12Q1/6816 , C12Q1/6834 , C12Q1/6888 , C12Q1/689 , C12Q1/6895 , C12Q1/70 , G01N15/14 , G01N21/47 , G01N21/6428 , G01N33/6803 , C12Q2565/626 , C12Q2525/161 , C12Q2525/191 , C12Q2533/107
摘要： The present invention provides, among other things, methods and compositions for detecting and quantifying target nucleic acids via post-hybridization labeling. In some embodiments, the present invention provides a method for detecting the presence and/or abundance of target nucleic acids in a sample by (a) contacting a plurality of nucleic acid probes with a sample, each nucleic acid probe comprising a capturing sequence for binding a target nucleic acid and an adjacent adapter sequence for binding a universal adapter; (b) incubating the plurality of probes and the sample, in the presence of one or more universal adapters, under conditions that permit binding of both an individual target nucleic acid and an individual universal adapter to a same individual nucleic acid probe; (c) carrying out a reaction that allows coupling of the individual universal adapter to the individual target nucleic acid when hybridized to the same individual nucleic acid probe; (d) detecting the presence of the one or more universal adapters associated with the plurality of nucleic acid probes, thereby detecting the presence of the target nucleic acids in the sample. Typically, universal adapters are labeled with detectable moieties or other labeling groups to facilitate detection. In some embodiments, the plurality of nucleic acid probes suitable for the invention are attached to a substrate or object (e.g., microarray, or particle).
摘要翻译：本发明尤其提供了用于通过后杂交标记检测和定量靶核酸的方法和组合物。在一些实施方案中，本发明提供了通过（a）使多个核酸探针与样品接触来检测样品中靶核酸的存在和/或丰度的方法，每个核酸探针包含用于结合的捕获序列目标核酸和用于结合通用适配器的相邻适配器序列; （b）在一种或多种通用衔接子的存在下，在允许单独的靶核酸和单个通用衔接子与相同的单个核酸探针结合的条件下孵育多个探针和样品; （c）当与相同的单个核酸探针杂交时进行允许单个通用衔接子与单个靶核酸偶联的反应; （d）检测与多个核酸探针相关联的一个或多个通用适配器的存在，从而检测样品中靶核酸的存在。通常，通用衔接子用可检测部分或其他标记基团标记以便于检测。在一些实施方案中，适用于本发明的多个核酸探针连接到底物或物体（例如微阵列或颗粒）上。

7. 发明申请

WO2011156434A2 NUCLEIC ACID DETECTION AND QUANTIFICATION BY POST-HYBRIDIZATION LABELING AND UNIVERSAL ENCODING 审中-公开
标题翻译：通过后期杂交标签和通用编码进行核酸检测和定量
公开(公告)号：WO2011156434A2
公开(公告)日：2011-12-15
申请号：PCT/US2011/039531
申请日：2011-06-07
申请人： FIREFLY BIOWORKS, INC. , PREGIBON, Daniel, C. , STONER, Isaac , WINDEMUTH, Andreas , ERPS, Timothy
发明人： PREGIBON, Daniel, C. , STONER, Isaac , WINDEMUTH, Andreas , ERPS, Timothy
IPC分类号： C12Q1/68 , C12N15/11 , G01N33/53
CPC分类号： C12Q1/6825 , C12Q1/6809 , C12Q1/6813 , C12Q1/6816 , C12Q1/6834 , C12Q1/6888 , C12Q1/689 , C12Q1/6895 , C12Q1/70 , G01N15/14 , G01N21/47 , G01N21/6428 , G01N33/6803 , C12Q2565/626 , C12Q2525/161 , C12Q2525/191 , C12Q2533/107
摘要： The present invention provides, among other things, methods and compositions for detecting and quantifying target nucleic acids via post-hybridization labeling. In some embodiments, the present invention provides a method for detecting the presence and/or abundance of target nucleic acids in a sample by (a) contacting a plurality of nucleic acid probes with a sample, each nucleic acid probe comprising a capturing sequence for binding a target nucleic acid and an adjacent adapter sequence for binding a universal adapter; (b) incubating the plurality of probes and the sample, in the presence of one or more universal adapters, under conditions that permit binding of both an individual target nucleic acid and an individual universal adapter to a same individual nucleic acid probe; (c) carrying out a reaction that allows coupling of the individual universal adapter to the individual target nucleic acid when hybridized to the same individual nucleic acid probe; (d) detecting the presence of the one or more universal adapters associated with the plurality of nucleic acid probes, thereby detecting the presence of the target nucleic acids in the sample. Typically, universal adapters are labeled with detectable moieties or other labeling groups to facilitate detection. In some embodiments, the plurality of nucleic acid probes suitable for the invention are attached to a substrate or object (e.g., microarray, or particle).
摘要翻译：本发明尤其提供了用于通过后杂交标记检测和定量靶核酸的方法和组合物。在一些实施方案中，本发明提供了通过（a）使多个核酸探针与样品接触来检测样品中靶核酸的存在和/或丰度的方法，每个核酸探针包含用于结合的捕获序列目标核酸和用于结合通用适配器的相邻适配器序列; （b）在一种或多种通用衔接子的存在下，在允许单独的靶核酸和单个通用衔接子与相同的单个核酸探针结合的条件下孵育多个探针和样品; （c）当与相同的单个核酸探针杂交时进行允许单个通用衔接子与单个靶核酸偶联的反应; （d）检测与多个核酸探针相关联的一个或多个通用适配器的存在，从而检测样品中靶核酸的存在。通常，通用衔接子用可检测部分或其他标记基团标记以便于检测。在一些实施方案中，适用于本发明的多个核酸探针连接到底物或物体（例如微阵列或颗粒）上。

8. 发明申请

WO2015069713A2 SYSTEMS AND METHODS FOR AUTOMATED MULTIPLEX ASSAY DESIGN 审中-公开
标题翻译：自动多重测量设计的系统与方法
公开(公告)号：WO2015069713A2
公开(公告)日：2015-05-14
申请号：PCT/US2014/064050
申请日：2014-11-05
申请人： FIREFLY BIOWORKS, INC.
发明人： MARINI, Davide , RAFFERTY, Conor , TYTELL, Jessica, Dawn , WINDEMUTH, Andreas
IPC分类号： A61K39/395
CPC分类号： G06F19/28 , C12Q1/6837 , C12Q2537/165
摘要： Described herein, in certain embodiments, are systems and methods for automated multiplex assay design. For example, a statistically significant (and/or biologically meaningful) cluster of probes resulting from an experiment are identified, then analyzed for association with additional probes (different from the experimentally identified probes) by performing a query of one or more databases. In some embodiments, mapping is performed between multiple types of probes, such that an experimentally observed probe is mapped into a database to identify associations with a different kind of probe, thereby designing a multiplex assay.
摘要翻译：在某些实施方案中，本文描述了用于自动多重测定设计的系统和方法。例如，识别由实验产生的统计学上显着的（和/或生物意义上的）探针簇，然后通过执行一个或多个数据库的查询来分析与另外的探针（不同于实验鉴定的探针）的关联。在一些实施例中，在多种类型的探针之间进行映射，使得将实验观察的探针映射到数据库中以识别与不同种类的探针的关联，从而设计多重测定。

9. 发明申请

WO2014176575A1 MULTIPLEXED ANALYSIS OF TARGET NUCLEIC ACIDS 审中-公开
标题翻译：目标核酸的多重分析
公开(公告)号：WO2014176575A1
公开(公告)日：2014-10-30
申请号：PCT/US2014/035578
申请日：2014-04-25
申请人： FIREFLY BIOWORKS, INC.
发明人： PREGIBON, Daniel, C. , STONER, Isaac , FUSCO, Anthony , TACKETT, Michael, R.
IPC分类号： C12Q1/68 , C12Q1/25
CPC分类号： C12Q1/6806 , C12Q1/682 , C12Q2525/155 , C12Q2525/191 , C12Q2525/207 , C12Q2563/149 , C12Q2563/179
摘要： The present invention provides, among other things, methods of detecting target nucleic acid, comprising steps of: a) contacting a sample with one or more capturing probes, each comprising at least one target capturing sequence, under conditions that permit the one or more capturing probes to capture one or more target nucleic acids in the sample; b) amplifying the captured one or more target nucleic acids in a reaction mixture comprising a detectable entity such that the amplified one or more target nucleic acids are labeled with the detectable entity; c) incubating amplification product with a plurality of re-capturing probes such that the amplified one or more target nucleic acids are re-captured by the plurality of the re-capturing probes; and d) detecting signal generated by detectable entity associated with the re-captured amplified one or more target nucleic acids, wherein the presence and/or abundance of the detectable signal indicates the presence and/or abundance of the one or more target nucleic acids in the sample.
摘要翻译：本发明尤其提供了检测靶核酸的方法，包括以下步骤：a）在允许一个或多个捕获的条件下，将样品与一个或多个捕获探针接触，每个捕获探针包含至少一个靶捕获序列探针以捕获样品中的一种或多种靶核酸; b）在包含可检测实体的反应混合物中扩增捕获的一种或多种靶核酸，使得扩增的一个或多个靶核酸用可检测实体标记; c）用多个再捕获探针孵育扩增产物，使得扩增的一个或多个靶核酸被多个重新捕获探针重新捕获; 和d）检测由与被再捕获的扩增的一个或多个靶核酸相关联的可检测实体产生的信号，其中可检测信号的存在和/或丰度表示一个或多个靶核酸的存在和/或丰度例子。

10. 发明申请

WO2014071404A3 AUTOMATED PRODUCT CUSTOMIZATION BASED UPON LITERATURE SEARCH RESULTS 审中-公开
标题翻译：基于文献检索结果的自动产品定制
公开(公告)号：WO2014071404A3
公开(公告)日：2014-06-26
申请号：PCT/US2013068584
申请日：2013-11-05
申请人： FIREFLY BIOWORKS INC
发明人： WINDEMUTH ANDREAS , STONER ISAAC , MARINI DAVIDE , PREGIBON DANIEL
IPC分类号： G06Q30/00
CPC分类号： G06Q30/0621 , G06F17/30867 , G06F19/16 , G06F19/18 , G06F19/324
摘要： In certain embodiments, the invention relates to systems, methods, and apparatus that allow a purchaser to customize a test kit based upon a literature search. A processor receives one or more search terms entered by a user and constructs a query comprising the one or more search terms. The processor obtains from one or more literature repositories a plurality of search results responsive to the query. The processor identifies one or more domain terms (relating to a scientific domain) within the plurality of search results. The processor prioritizes the one or more scientific domain terms based in part upon frequency of occurrence within the plurality of search results, and selects one or more order components relating to a tangible product, each order component relating to a respective scientific domain term of the one or more scientific domain terms. The order information is displayed to a user.
摘要翻译：在某些实施方案中，本发明涉及允许购买者基于文献检索来定制检测试剂盒的系统，方法和设备。处理器接收由用户输入的一个或多个搜索项并构建包括该一个或多个搜索项的查询。处理器从一个或多个文献库获得响应于该查询的多个搜索结果。处理器识别多个搜索结果内的一个或多个领域术语（与科学领域有关）。处理器部分地基于多个搜索结果内的出现频率来优先考虑一个或多个科学领域术语，并且选择与有形产品有关的一个或多个订购部件，每个订购部件涉及一个或多个科学领域术语或更科学的术语。订单信息显示给用户。

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