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1. 发明申请

US20090203086A1 System and method for improved signal detection in nucleic acid sequencing 审中-公开
标题翻译：在核酸测序中改进信号检测的系统和方法
公开(公告)号：US20090203086A1
公开(公告)日：2009-08-13
申请号：US12322284
申请日：2009-01-29
申请人： Yi-Ju Chen , Jong-Bum Kim , Andrew Daniel Kebbel , James Matthew Nealis , Zhoutao Chen
发明人： Yi-Ju Chen , Jong-Bum Kim , Andrew Daniel Kebbel , James Matthew Nealis , Zhoutao Chen
IPC分类号： C12P19/34 , B01J8/00 , C12M1/00 , C07H1/00
CPC分类号： B01L3/5027 , B01J2219/00286 , B01J2219/00391 , B01J2219/00529 , B01J2219/00585 , B01J2219/0059 , B01J2219/00704 , B01J2219/0072 , B01J2219/00722 , B01L3/502715 , B01L3/5085 , B01L7/52 , B01L2200/0647 , B01L2300/0636 , B01L2300/0654 , B01L2300/0877 , B01L2400/0622 , G01N21/03 , G01N2021/0325
摘要： An embodiment of a system for reducing crosstalk in a parallel sequencing platform is described that comprises a substrate with a plurality of individual reaction environments that include a species of nucleic acid template, and a plurality of spatially localized reactants, wherein the localized reactants minimize the transmission of reaction products to a neighboring reaction environment due to a relative position of the localized reactants in the reaction environment.
摘要翻译：描述了用于减少并行测序平台中的串扰的系统的实施例，其包括具有多个单独的反应环境的衬底，所述多个单独的反应环境包括一些核酸模板和多个空间定位的反应物，其中所述局部反应物使传输最小化由于局部反应物在反应环境中的相对位置，反应产物与相邻的反应环境有关。

2. 发明授权

US08748102B2 Bead emulsion nucleic acid amplification 有权
公开(公告)号：US08748102B2
公开(公告)日：2014-06-10
申请号：US13033240
申请日：2011-02-23
申请人： Jan Berka , Yi-Ju Chen , John H. Leamon , Steve Lefkowitz , Kenton L. Lohman , Vinod B. Makhijani , Jonathan M. Rothberg , Gary J. Sarkis , Maithreyan Srinivasan , Michael P. Weiner
发明人： Jan Berka , Yi-Ju Chen , John H. Leamon , Steve Lefkowitz , Kenton L. Lohman , Vinod B. Makhijani , Jonathan M. Rothberg , Gary J. Sarkis , Maithreyan Srinivasan , Michael P. Weiner
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/686 , B01L3/5027 , B01L3/502707 , B01L3/502715 , B01L3/5085 , B01L7/52 , B01L2300/0636 , B01L2300/0819 , B01L2300/0877 , C07H21/00 , C12N15/1075 , C12N15/1093 , C12Q1/6806 , C12Q1/6834 , C12Q1/6844 , C12Q1/6865 , C12Q1/6867 , C12Q1/6869 , C12Q1/6874 , G01N21/253 , G01N21/6428 , G01N21/6452 , G01N21/6458 , G01N2021/6484 , G01R33/1269 , Y02P20/582 , Y10T436/143333 , C12Q2565/119 , C12Q2531/113 , C12Q2565/537 , C12Q2547/107 , C12Q2547/101 , C12Q2537/143 , C12Q2527/125 , C12Q2525/186 , C12Q2565/301 , C12Q2563/149 , C12Q2531/125 , C12Q2537/149 , C12Q2535/119
摘要： Disclosed are methods for nucleic acid amplification wherein nucleic acid templates, beads, and amplification reaction solution are emulsified and the nucleic acid templates are amplified to provide clonal copies of the nucleic acid templates attached to the beads. Also disclosed are kits and apparatuses for performing the methods of the invention.

3. 发明申请

US20110213563A1 SYSTEM AND METHOD TO CORRECT OUT OF PHASE ERRORS IN DNA SEQUENCING DATA BY USE OF A RECURSIVE ALGORITHM 有权
标题翻译：通过使用回归算法来校正DNA序列数据中的相位误差的系统和方法
公开(公告)号：US20110213563A1
公开(公告)日：2011-09-01
申请号：US13043063
申请日：2011-03-08
申请人： Yi-Ju Chen , Chiu Tai Andrew Wong
发明人： Yi-Ju Chen , Chiu Tai Andrew Wong
IPC分类号： G06F19/00
CPC分类号： G06F19/22 , C12Q1/6869 , G06F19/24 , C12Q2565/301 , C12Q2537/165 , C12Q2535/113
摘要： An embodiment of a method for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules is described that comprises the steps of detecting signals generated in response to nucleotide species introduced during a sequencing reaction; generating an observed value for the signal detected from each of the nucleotide species; defining positive incorporation values and negative incorporation values from the observed values using a carry forward value and an incomplete extension value; revising the carry forward value and the incomplete extension value using a noise value that is derived from observed values associated with the negative incorporation values; re-defining the positive incorporation values and the negative incorporation values using the revised carry forward value and the revised incomplete extension value; and repeating the steps of revising and re-defining until convergence of the positive incorporation values and the negative incorporation values
摘要翻译：描述了用于校正与从模板分子群体生成的序列数据的相位同步相关联的错误的方法的实施例，其包括以下步骤：检测响应于在测序反应期间引入的核苷酸种类产生的信号; 产生从每个核苷酸物种检测的信号的观察值; 使用结转值和不完全扩展值从观察值中确定正合并值和负并入值; 使用从与负合并值相关联的观测值导出的噪声值来修正结转值和不完全扩展值; 使用修订的结转值和修订的不完全扩展值重新定义积极的并入价值和负的并入价值; 并重复修正和重新定义的步骤，直到正合并值和负合并值的收敛

4. 发明申请

US20090265614A1 Method for Converting A Computerized Briefing File to A PC-less Briefing File and Briefing System for Presenting the PC-less Briefing File 有权
标题翻译：将计算机简报文件转换为无PC简报文件的方法和用于呈现无PC简报文件的简报系统
公开(公告)号：US20090265614A1
公开(公告)日：2009-10-22
申请号：US12180599
申请日：2008-07-28
申请人： Kuo-Lung CHANG , Yi-Ju Chen , Hsing-Yung Wang , Li-Chin Lin
发明人： Kuo-Lung CHANG , Yi-Ju Chen , Hsing-Yung Wang , Li-Chin Lin
IPC分类号： G06F17/00
CPC分类号： G06F17/217
摘要： A method for converting a computerized briefing file to a PC-less briefing file is disclosed and comprises the steps of: presenting the computerized briefing file via a briefing software, wherein the computerized briefing file has a plurality of pages of briefing data; capturing the plurality of frames of the presented page of briefing data while presenting each page of briefing data, wherein if a difference block is existed between the last frame and the next frame, the difference block being stored in the PC-less file, otherwise, presenting the next frame; judging whether the pagination of the presented frame is changed or not, if not, continuously capturing, comparing and storing the present page of briefing data, otherwise, capturing, comparing and storing the next page of briefing data; and such steps are not stopped until the last page of briefing data has being done.
摘要翻译：公开了一种将计算机简报文件转换为无PC简报文件的方法，包括以下步骤：通过简报软件呈现计算机化简报文件，其中计算机简报文件具有多页简报数据; 在呈现简报数据的每个页面的同时捕获所呈现的简报数据页面的多个帧，其中如果在最后一帧和下一帧之间存在差分块，则差分块被存储在无PC文件中，否则，呈现下一帧; 判断所呈现的帧的分页是否改变，否则，连续地捕获，比较和存储简报数据的当前页面，否则，捕获，比较和存储简报数据的下一页; 并且直到简报数据的最后一页已经完成，这些步骤才停止。

5. 发明授权

US07244567B2 Double ended sequencing 失效
标题翻译：双端测序
公开(公告)号：US07244567B2
公开(公告)日：2007-07-17
申请号：US10768729
申请日：2004-01-28
申请人： Yi-Ju Chen , John H. Leamon , Kenton L. Lohman , Michael T. Ronan , Jonathan M. Rothberg , Maithreyan Srinivasan , Michael P. Weiner
发明人： Yi-Ju Chen , John H. Leamon , Kenton L. Lohman , Michael T. Ronan , Jonathan M. Rothberg , Maithreyan Srinivasan , Michael P. Weiner
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/686 , B01L3/5027 , B01L3/502707 , B01L3/502715 , B01L3/5085 , B01L7/52 , B01L2300/0636 , B01L2300/0819 , B01L2300/0877 , C07H21/00 , C12N15/1075 , C12N15/1093 , C12Q1/6806 , C12Q1/6834 , C12Q1/6844 , C12Q1/6865 , C12Q1/6867 , C12Q1/6869 , C12Q1/6874 , G01N21/253 , G01N21/6428 , G01N21/6452 , G01N21/6458 , G01N2021/6484 , G01R33/1269 , Y02P20/582 , Y10T436/143333 , C12Q2565/119 , C12Q2531/113 , C12Q2565/537 , C12Q2547/107 , C12Q2547/101 , C12Q2537/143 , C12Q2527/125 , C12Q2525/186 , C12Q2565/301 , C12Q2563/149 , C12Q2531/125 , C12Q2537/149 , C12Q2535/119
摘要： This invention relates to methods of sequencing DNA. More specifically, this invention relates to methods of sequencing both the sense and antisense strands of DNA through the use of blocked and unblocked sequencing primers. In brief, these methods include the steps of annealing an unblocked primer to a first strand of nucleic acid; annealing a second blocked primer to a second strand of nucleic acid; elongating the nucleic acid along the first strand with a polymerase; terminating the first sequencing primer; deblocking the second primer; and elongating the nucleic acid along the second strand.
摘要翻译：本发明涉及DNA测序方法。更具体地，本发明涉及通过使用封闭和未封闭的测序引物对DNA的有义链和反义链进行测序的方法。简而言之，这些方法包括将未封闭引物退火至第一条核酸的步骤; 将第二封闭引物退火至核酸的第二链; 用聚合酶沿着第一链延长核酸; 终止第一个测序引物; 解封第二底漆; 并沿着第二链延长核酸。

6. 发明授权

US07035770B2 Fuzzy reasoning model for semiconductor process fault detection using wafer acceptance test data 失效
标题翻译：使用晶圆验收测试数据进行半导体工艺故障检测的模糊推理模型
公开(公告)号：US07035770B2
公开(公告)日：2006-04-25
申请号：US10739857
申请日：2003-12-18
申请人： Shuo-Huei Lin , Ruenn-Sheng Peng , Yi-Ju Chen , Kuo-Rung Hsiao
发明人： Shuo-Huei Lin , Ruenn-Sheng Peng , Yi-Ju Chen , Kuo-Rung Hsiao
IPC分类号： G06F15/00
CPC分类号： H01L21/67253 , G05B23/0281 , G05B2219/1112 , G05B2223/02
摘要： System and method for detecting suspicious process faults. A preferred embodiment comprises determining a strength relationship between wafer acceptance test (WAT) parameters and process steps. The strength relationships indicate the affect of a failed process step on the value of a WAT parameter. Thus, if a WAT parameter is not within the parameters set in the WAT, then the suspicious process steps that caused the failure are the process steps that had a strength relationship with the failed WAT parameter. Furthermore, in a preferred embodiment, negative inferences are determined and utilized to determine a degree of suspiciousness. The degree of suspiciousness is used to determine a total degree of suspiciousness.
摘要翻译：检测可疑过程故障的系统和方法。优选实施例包括确定晶片接受测试（WAT）参数和处理步骤之间的强度关系。强度关系表示失败的过程步骤对WAT参数的值的影响。因此，如果WAT参数不在WAT中设置的参数内，则导致失败的可疑进程步骤是与失败的WAT参数具有强度关系的进程步骤。此外，在优选实施例中，确定并利用负推论来确定可疑程度。怀疑程度用于确定总体怀疑程度。

7. 发明申请

US20050079510A1 Bead emulsion nucleic acid amplification 有权
标题翻译：珠粒乳液核酸扩增
公开(公告)号：US20050079510A1
公开(公告)日：2005-04-14
申请号：US10767899
申请日：2004-01-28
申请人： Jan Berka , Yi-Ju Chen , John Leamon , Steve Lefkowitz , Kenton Lohman , Vinod Makhijani , Jonathan Rothberg , Gary Sarkis , Maithreyan Srinivasan , Michael Weiner
发明人： Jan Berka , Yi-Ju Chen , John Leamon , Steve Lefkowitz , Kenton Lohman , Vinod Makhijani , Jonathan Rothberg , Gary Sarkis , Maithreyan Srinivasan , Michael Weiner
IPC分类号： B01L3/00 , C07H21/00 , C12N15/10 , C12P19/34 , C12Q1/68 , G01N21/25 , G01N21/64
CPC分类号： C12Q1/686 , B01L3/5027 , B01L3/502707 , B01L3/502715 , B01L3/5085 , B01L7/52 , B01L2300/0636 , B01L2300/0819 , B01L2300/0877 , C07H21/00 , C12N15/1075 , C12N15/1093 , C12Q1/6806 , C12Q1/6834 , C12Q1/6844 , C12Q1/6865 , C12Q1/6867 , C12Q1/6869 , C12Q1/6874 , G01N21/253 , G01N21/6428 , G01N21/6452 , G01N21/6458 , G01N2021/6484 , G01R33/1269 , Y02P20/582 , Y10T436/143333 , C12Q2565/119 , C12Q2531/113 , C12Q2565/537 , C12Q2547/107 , C12Q2547/101 , C12Q2537/143 , C12Q2527/125 , C12Q2525/186 , C12Q2565/301 , C12Q2563/149 , C12Q2531/125 , C12Q2537/149 , C12Q2535/119
摘要： Disclosed are methods for nucleic acid amplification wherein nucleic acid templates, beads, and amplification reaction solution are emulsified and the nucleic acid templates are amplified to provide clonal copies of the nucleic acid templates attached to the beads. Also disclosed are kits and apparatuses for performing the methods of the invention.
摘要翻译：公开了用于核酸扩增的方法，其中将核酸模板，珠粒和扩增反应溶液乳化，并扩增核酸模板以提供附着于珠粒上的核酸模板的克隆拷贝。还公开了用于执行本发明的方法的套件和装置。

8. 发明申请

US20130054171A1 System and Method for Correcting Primer Extension Errors in Nucleic Acid Sequence Data 有权
标题翻译：用于校正核酸序列数据中引物延伸错误的系统和方法
公开(公告)号：US20130054171A1
公开(公告)日：2013-02-28
申请号：US13608841
申请日：2012-09-10
申请人： Yi-Ju Chen , Keith McDade , John Simpson
发明人： Yi-Ju Chen , Keith McDade , John Simpson
IPC分类号： G06F19/18
CPC分类号： C12Q1/6848 , C12Q1/6869 , G06F19/22 , G06F19/24 , C12Q2537/165
摘要： An embodiment of method for correcting an error associated with phasic synchrony of sequence data generated from a population of substantially identical copies of a template molecule is described that comprises (a) detecting a signal generated in response to an incorporation of one or more nucleotides in a sequencing reaction; (b) generating a value for the signal; and (c) correcting the value for the phasic synchrony error using a first parameter and a second carry forward parameter.
摘要翻译：描述了用于校正与从模板分子的基本相同拷贝的群体产生的序列数据的相位同步相关联的错误的方法的实施方案，其包括（a）检测响应于在一个或多个核苷酸中的并入产生的信号测序反应; （b）产生该信号的值; 和（c）使用第一参数和第二进位参数来校正所述相位同步误差的值。

9. 发明授权

US08364417B2 System and method to correct out of phase errors in DNA sequencing data by use of a recursive algorithm 有权
标题翻译：通过使用递归算法来纠正DNA测序数据中的相位误差的系统和方法
公开(公告)号：US08364417B2
公开(公告)日：2013-01-29
申请号：US13043063
申请日：2011-03-08
申请人： Yi-Ju Chen , Chiu Tai Andrew Wong
发明人： Yi-Ju Chen , Chiu Tai Andrew Wong
IPC分类号： G06F19/00 , G06F15/00
CPC分类号： G06F19/22 , C12Q1/6869 , G06F19/24 , C12Q2565/301 , C12Q2537/165 , C12Q2535/113
摘要： An embodiment of a method for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules is described that comprises the steps of detecting signals generated in response to nucleotide species introduced during a sequencing reaction; generating an observed value for the signal detected from each of the nucleotide species; defining positive incorporation values and negative incorporation values from the observed values using a carry forward value and an incomplete extension value; and revising the carry forward value and the incomplete extension value using a noise value that is derived from observed values associated with the negative incorporation values.
摘要翻译：描述了用于校正与从模板分子群体生成的序列数据的相位同步相关联的错误的方法的实施例，其包括以下步骤：检测响应于在测序反应期间引入的核苷酸种类产生的信号; 产生从每个核苷酸物种检测的信号的观察值; 使用结转值和不完全扩展值从观察值中确定正合并值和负并入值; 并且使用从与负合并值相关联的观测值导出的噪声值来修正结转值和不完全扩展值。

10. 发明授权

US08301394B2 System and method for correcting primer extension errors in nucleic acid sequence data 有权
标题翻译：用于校正核酸序列数据中引物延伸误差的系统和方法
公开(公告)号：US08301394B2
公开(公告)日：2012-10-30
申请号：US12224065
申请日：2007-02-15
申请人： Yi-Ju Chen , Keith McDade , John Simpson
发明人： Yi-Ju Chen , Keith McDade , John Simpson
IPC分类号： G06F19/00 , G06F15/00
CPC分类号： C12Q1/6848 , C12Q1/6869 , G06F19/22 , G06F19/24 , C12Q2537/165
摘要： An embodiment of method for correcting an error associated with phasic synchrony of sequence data generated from a population of substantially identical copies of a template molecule is described that comprises (a) detecting a signal generated in response to an incorporation of one or more nucleotides in a sequencing reaction; (b) generating a value for the signal; and (c) correcting the value for the phasic synchrony error using a first parameter and a second carry forward parameter.
摘要翻译：描述了用于校正与从模板分子的基本相同拷贝的群体产生的序列数据的相位同步相关联的错误的方法的实施方案，其包括（a）检测响应于在一个或多个核苷酸中的一个或多个核苷酸的引入而产生的信号测序反应; （b）产生该信号的值; 和（c）使用第一参数和第二进位参数来校正所述相位同步误差的值。

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