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11. 发明授权

US5593839A Computer-aided engineering system for design of sequence arrays and lithographic masks 失效
标题翻译：用于设计序列阵列和光刻掩模的计算机辅助工程系统
公开(公告)号：US5593839A
公开(公告)日：1997-01-14
申请号：US460411
申请日：1995-06-02
申请人： Earl A. Hubbell , Robert J. Lipshutz , Macdonald S. Morris , James L. Winkler
发明人： Earl A. Hubbell , Robert J. Lipshutz , Macdonald S. Morris , James L. Winkler
IPC分类号： B01J19/00 , C07B61/00 , C07K1/04 , C40B40/06 , C40B60/14 , G03F1/00 , C12Q1/68 , C07H21/04 , G03F9/00
CPC分类号： B82Y30/00 , B01J19/0046 , C07K1/04 , C07K1/045 , B01J2219/00432 , B01J2219/00529 , B01J2219/00585 , B01J2219/0059 , B01J2219/00596 , B01J2219/00608 , B01J2219/00612 , B01J2219/00626 , B01J2219/00637 , B01J2219/00659 , B01J2219/00689 , B01J2219/00693 , B01J2219/00695 , B01J2219/00711 , B01J2219/00722 , C40B40/06 , C40B60/14
摘要： An improved set of computer tools for forming arrays. According to one aspect of the invention, a computer system is used to select probes and design the layout of an array of DNA or other polymers with certain beneficial characteristics. According to another aspect of the invention, a computer system uses chip design files to design and/or generate lithographic masks.
摘要翻译：一组改进的用于形成阵列的计算机工具。根据本发明的一个方面，计算机系统用于选择探针并设计具有某些有益特征的DNA或其它聚合物阵列的布局。根据本发明的另一方面，计算机系统使用芯片设计文件来设计和/或生成光刻掩模。

12. 发明授权

US5856101A Computer-aided engineering system for design of sequence arrays and lithographic masks 失效
标题翻译：用于设计序列阵列和光刻掩模的计算机辅助工程系统
公开(公告)号：US5856101A
公开(公告)日：1999-01-05
申请号：US721689
申请日：1996-09-27
申请人： Earl A. Hubbell , MacDonald S. Morris , James L. Winkler
发明人： Earl A. Hubbell , MacDonald S. Morris , James L. Winkler
IPC分类号： B01J19/00 , C07B61/00 , C07K1/04 , C40B40/06 , C40B60/14 , G03F1/00 , C12Q1/68 , C12M1/34 , C12M3/04
CPC分类号： B82Y30/00 , B01J19/0046 , C07K1/04 , C07K1/045 , B01J2219/00432 , B01J2219/00529 , B01J2219/00585 , B01J2219/0059 , B01J2219/00596 , B01J2219/00608 , B01J2219/00612 , B01J2219/00626 , B01J2219/00637 , B01J2219/00659 , B01J2219/00689 , B01J2219/00693 , B01J2219/00695 , B01J2219/00711 , B01J2219/00722 , C40B40/06 , C40B60/14
摘要： An improved set of computer tools for forming arrays. According to one aspect of the invention, a computer system (100) is used to select probes and design the layout of an array of DNA or other polymers with certain beneficial characteristics. According to another aspect of the invention, a computer system uses chip design files (104) to design and/or generate lithographic masks (110).
摘要翻译：一组改进的用于形成阵列的计算机工具。根据本发明的一个方面，计算机系统（100）用于选择探针并设计具有某些有益特征的DNA或其它聚合物阵列的布局。根据本发明的另一方面，计算机系统使用芯片设计文件（104）来设计和/或生成光刻掩模（110）。

13. 发明授权

US5571639A Computer-aided engineering system for design of sequence arrays and lithographic masks 失效
公开(公告)号：US5571639A
公开(公告)日：1996-11-05
申请号：US249188
申请日：1994-05-24
申请人： Earl A. Hubbell , MacDonald S. Morris , James L. Winkler
发明人： Earl A. Hubbell , MacDonald S. Morris , James L. Winkler
IPC分类号： B01J19/00 , C07B61/00 , C07K1/04 , C40B40/06 , C40B60/14 , G03F1/00 , G03F7/26 , C12Q1/68 , G03C5/00
CPC分类号： B82Y30/00 , B01J19/0046 , C07K1/04 , C07K1/045 , B01J2219/00432 , B01J2219/00529 , B01J2219/00585 , B01J2219/0059 , B01J2219/00596 , B01J2219/00608 , B01J2219/00612 , B01J2219/00626 , B01J2219/00637 , B01J2219/00659 , B01J2219/00689 , B01J2219/00693 , B01J2219/00695 , B01J2219/00711 , B01J2219/00722 , C40B40/06 , C40B60/14
摘要： An improved set of computer tools for forming arrays. According to one aspect of the invention, a computer system (100) is used to select probes and design the layout of an array of DNA or other polymers with certain beneficial characteristics. According to another aspect of the invention, a computer system uses chip design files (104) to design and/or generate lithographic masks (110).

14. 发明申请

US20110281772A1 Methods, systems and computer software for designing and synthesizing sequence arrays 审中-公开
标题翻译：用于设计和合成序列数组的方法，系统和计算机软件
公开(公告)号：US20110281772A1
公开(公告)日：2011-11-17
申请号：US13180006
申请日：2011-07-11
申请人： Earl A. Hubbell
发明人： Earl A. Hubbell
IPC分类号： C40B50/02
CPC分类号： C40B40/06 , B01J19/0046 , B01J2219/00432 , B01J2219/00529 , B01J2219/00585 , B01J2219/0059 , B01J2219/00596 , B01J2219/00605 , B01J2219/00612 , B01J2219/00626 , B01J2219/00659 , B01J2219/00689 , B01J2219/00695 , B01J2219/00711 , B01J2219/00722 , B82Y30/00 , C40B40/10 , C40B60/14 , G16B25/00 , G16B35/00 , G16B40/00 , G16C20/60
摘要： Embodiments of the invention provides methods, computer software products and systems for arranging polymers during combinatorial polymer synthesis so that the border or edge between synthesis site is minimized. In one embodiment, travelling salesman algorithm is used to minimize the edges. In another embodiment, a locally greedy optimization method is provided. In addition, methods and software products are provided for solving the robust arrangement problem for multi-probe gene expression arrays.
摘要翻译：本发明的实施例提供了在组合聚合物合成期间用于布置聚合物的方法，计算机软件产品和系统，使得合成位点之间的边界或边缘最小化。在一个实施例中，使用旅行推销员算法来使边缘最小化。在另一个实施例中，提供了局部贪心优化方法。此外，提供方法和软件产品，用于解决多探针基因表达阵列的鲁棒排列问题。

15. 发明授权

US08009889B2 Feature intensity reconstruction of biological probe array 有权
标题翻译：生物探针阵列特征强度重建
公开(公告)号：US08009889B2
公开(公告)日：2011-08-30
申请号：US11769600
申请日：2007-06-27
申请人： Earl A. Hubbell
发明人： Earl A. Hubbell
IPC分类号： G06K9/00 , G01N33/50
CPC分类号： G06K9/0014 , G06F19/20 , G06K9/00 , G06K2209/07
摘要： The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data.
摘要翻译：本发明提供了用于从像素级数据重建特征强度的方法和系统。在某些实施例中，本发明使用经验确定的传递函数来构建像素级数据的理论估计，然后基于像素级数据与像素级数据的理论估计之间的最小乘法误差迭代地更新特征强度。

16. 发明授权

US07361468B2 Methods for genotyping polymorphisms in humans 失效
标题翻译：人类基因分型多态性的方法
公开(公告)号：US07361468B2
公开(公告)日：2008-04-22
申请号：US11175859
申请日：2005-07-05
申请人： Guoying Liu , Simon Cawley , Hajime Matsuzaki , Earl A. Hubbell , Geoffrey Yang , Teresa A. Webster , Rui Mei , Xiaojun Di , Richard Chiles
发明人： Guoying Liu , Simon Cawley , Hajime Matsuzaki , Earl A. Hubbell , Geoffrey Yang , Teresa A. Webster , Rui Mei , Xiaojun Di , Richard Chiles
IPC分类号： C12Q1/68 , C07H21/04 , C12M3/00 , C12M1/34
CPC分类号： C12Q1/6883 , C12Q2600/156
摘要： Methods, kits and arrays of nucleic acid probes for genotyping large numbers of human SNPs in parallel are provided. A set of more than 100,000 human SNPs, known to be biallelic in at least two populations is provided. Allele specific perfect match probes and genotyping probe sets are provided for each allele of each biallelic SNP in a set of human SNPs that is useful for genetic analysis within and across populations. Probe sets that include perfect match and mismatch probes are provided. The probe sets are suitable for inclusion in an array. The invention provides the SNP and surrounding sequence and provides the sequences in such a way as to make them available for a variety of analyses including genotyping. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.
摘要翻译：提供了用于并行分析大量人类SNP的核酸探针的方法，试剂盒和阵列。提供了一组超过100,000个人类SNP，已知在至少两个人群中是双向的。为一组人类SNP中的每个双重性SNP的每个等位基因提供等位基因特异性完全匹配探针和基因分型探针组，其可用于群体内和跨群体的遗传分析。提供包括完美匹配和不匹配探针的探针组。探头组适合包含在阵列中。本发明提供了SNP和周围序列，并提供了这样的序列，使得它们可用于各种分析，包括基因分型。因此，本发明涉及受遗传学性质影响的不同领域，包括生物学，医学和医学诊断。

17. 发明授权

US08369596B2 Feature intensity reconstruction of biological probe array 有权
公开(公告)号：US08369596B2
公开(公告)日：2013-02-05
申请号：US13186167
申请日：2011-07-19
申请人： Earl A. Hubbell
发明人： Earl A. Hubbell
IPC分类号： G06K9/00 , G01N33/48
CPC分类号： G06K9/0014 , G06F19/20 , G06K9/00 , G06K2209/07
摘要： The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data.

18. 发明申请

US20110274328A1 Feature Intensity Reconstruction of Biological Probe Array 有权
标题翻译：生物探针阵列特征强度重建
公开(公告)号：US20110274328A1
公开(公告)日：2011-11-10
申请号：US13186167
申请日：2011-07-19
申请人： Earl A. Hubbell
发明人： Earl A. Hubbell
IPC分类号： G06K9/00
CPC分类号： G06K9/0014 , G06F19/20 , G06K9/00 , G06K2209/07
摘要： The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data.
摘要翻译：本发明提供了用于从像素级数据重建特征强度的方法和系统。在某些实施例中，本发明使用经验确定的传递函数来构建像素级数据的理论估计，然后基于像素级数据与像素级数据的理论估计之间的最小乘法误差迭代地更新特征强度。

19. 发明申请

US20080287308A1 SYSTEM, METHOD, AND COMPUTER SOFTWARE PRODUCT FOR GENOTYPE DETERMINATION USING PROBE ARRAY DATA 有权
标题翻译：系统，方法和计算机软件产品使用探针阵列数据进行基因组测定
公开(公告)号：US20080287308A1
公开(公告)日：2008-11-20
申请号：US12123463
申请日：2008-05-19
申请人： Earl A. Hubbell , Simon Cawley
发明人： Earl A. Hubbell , Simon Cawley
IPC分类号： C40B30/02
CPC分类号： G06F19/18 , G06F19/20 , G06F19/24
摘要： An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.
摘要翻译：描述了从生物探针阵列的处理图像分析数据的方法的实施例，其包括：接收包括与生物探针阵列上的探针相关联的多个强度值的多个文件; 对每个数据文件中的强度值进行归一化; 使用来自每个文件的每个分配的一个或多个强度值来确定多个基因型的初始分配; 使用所述多个初始分配估计聚类中心的分布; 将归一化强度值与聚类中心组合以确定每个聚类中心的后验估计; 以及使用来自所述后验估计的所述一个或多个强度值的距离来分配多个基因型呼叫。

20. 发明授权

US06949638B2 Photolithographic method and system for efficient mask usage in manufacturing DNA arrays 有权
公开(公告)号：US06949638B2
公开(公告)日：2005-09-27
申请号：US09824931
申请日：2001-04-03
申请人： Michael P. Mittmann , Earl A. Hubbell
发明人： Michael P. Mittmann , Earl A. Hubbell
IPC分类号： B01J19/00 , C40B40/06 , C40B60/14 , G01N33/543 , G03F1/00 , G06F19/20 , C07H21/00 , C07H17/00 , C12Q1/68 , G01N33/52
CPC分类号： B82Y30/00 , B01J19/0046 , B01J2219/00432 , B01J2219/00527 , B01J2219/00585 , B01J2219/0059 , B01J2219/00596 , B01J2219/00605 , B01J2219/00608 , B01J2219/00659 , B01J2219/00689 , B01J2219/00695 , B01J2219/00711 , B01J2219/00722 , C40B40/06 , C40B60/14 , G01N33/54366 , G06F19/20
摘要： Systems, methods, and products are described for synthesizing probe arrays of polymers. A mask is used that includes reticle areas, each of which includes a number of reticles associated with a same synthesis area on a substrate. A method includes (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate; (b) coupling monomers on the first synthesis area at locations determined by the first reticle; (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and (d) coupling monomers on the first synthesis area at locations determined by the second reticle. The monomers may be, for example, nucleotides, amino acids or saccharides.

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