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1. 发明授权

US07006927B2 Method and system for extracting data from surface array deposited features 有权
公开(公告)号：US07006927B2
公开(公告)日：2006-02-28
申请号：US10086839
申请日：2002-02-28
申请人： Zohar Yakhini , Cynthia Y. Enderwick , Glenda C. Delenstarr , Paul K. Wolber , Nicholas M. Sampas , Herbert F. Cattell , Scott D. Connell
发明人： Zohar Yakhini , Cynthia Y. Enderwick , Glenda C. Delenstarr , Paul K. Wolber , Nicholas M. Sampas , Herbert F. Cattell , Scott D. Connell
IPC分类号： G06F11/32
CPC分类号： G06T7/73 , G06T2207/30072
摘要： A method and system for extracting data signals from a scanned image resulting from optical, radiometric, or other types of analysis of a molecular array. The positions of corner features are first located. Then, an initial feature coordinate grid is determined from the positions of the corner features. A refined feature coordinate grid is then calculated based on the positions of strong features, and is used to identify the positions of weak features and the positions of the local background regions surrounding all features. Finally, signal intensity values are extracted from the features and their respective local background regions in the scanned image, and background-subtracted signal intensity values, background-subtracted and normalized signal intensity ratios, and variability information and confidence intervals are determined based on the extracted values.

2. 发明授权

US06591196B1 Method and system for extracting data from surface array deposited features 有权
公开(公告)号：US06591196B1
公开(公告)日：2003-07-08
申请号：US09589046
申请日：2000-06-06
申请人： Zohar Yakhini , Cynthia Y. Enderwick , Glenda C. Delenstarr , Paul K. Wolber , Nicholas M. Sampas
发明人： Zohar Yakhini , Cynthia Y. Enderwick , Glenda C. Delenstarr , Paul K. Wolber , Nicholas M. Sampas
IPC分类号： G01J102
CPC分类号： G06K9/3275 , G06T7/73 , G06T2207/30072
摘要： A method and system for extracting data signals from a scanned image resulting from optical, radiometric, or other types of analysis of a molecular array. The positions of corner features are first located. Then, an initial feature coordinate grid is determined from the positions of the corner features. A refined feature coordinate grid is then calculated based on the positions of strong features, and is used to identify the positions of weak features and the positions of the local background regions surrounding all features. Finally, signal intensity values are extracted from the features and their respective local background regions in the scanned image, and background-subtracted signal intensity values, background-subtracted and normalized signal intensity ratios, and variability information and confidence intervals are determined based on the extracted values.

3. 发明授权

US09898578B2 Visualizing expression data on chromosomal graphic schemes 有权
公开(公告)号：US09898578B2
公开(公告)日：2018-02-20
申请号：US10817244
申请日：2004-04-03
申请人： Zohar Yakhini , Robert Kincaid , Amir Ben-Dor , Leslie A. Leonard , Nicholas M. Sampas
发明人： Zohar Yakhini , Robert Kincaid , Amir Ben-Dor , Leslie A. Leonard , Nicholas M. Sampas
IPC分类号： G01N33/48 , G01N33/50 , G06F19/26 , G06F19/12 , G06F19/24 , G06F19/18 , G06F19/20
CPC分类号： G06F19/26 , G06F19/12 , G06F19/18 , G06F19/20 , G06F19/24
摘要： Systems and methods for displaying gene- and/or protein-related data with respect to chromosome maps at locations identifying relevant positioning of the genes with which the gene- and/or protein related data are associated. Multiple experiments may be plotted onto the display adjacent one or more chromosome maps. Automatic extraction of genomic location, based on accession numbers or other unique identifiers and cross connection with expression data is provided. Statistical assessments of correlations between expression and genome localization may be performed. Zooming capabilities, thumbnail/fullview toggling, browsability and linked data may be included as features of the visualization systems described.

4. 发明申请

US20070174008A1 Method and system for determining a zero point for array-based comparative genomic hybridization data 审中-公开
标题翻译：用于确定基于阵列的比较基因组杂交数据的零点的方法和系统
公开(公告)号：US20070174008A1
公开(公告)日：2007-07-26
申请号：US11338515
申请日：2006-01-24
申请人： Zohar Yakhini , Doron Lipson , Amir Ben-Dor
发明人： Zohar Yakhini , Doron Lipson , Amir Ben-Dor
IPC分类号： G06F19/00
CPC分类号： G16B25/00 , G16B45/00
摘要： Various embodiments of the present invention determine a zero point, or centralization constant ζ, for an array-based comparative genomic hybridization (“aCGH”) data set by identifying a zero-point value, or centralization constant ζ, that, when used in an aberration-calling analysis of the aCGH data, results in the fewest number of array-probe-complementary genomic sequences identified as having abnormal copy numbers with respect to a control genome, or, in other words, results in the greatest number of array-probe-complementary genomic sequences identified as having normal copy numbers. In one embodiment, interval-based analysis of an aCGH data set may be carried out using a range of putative zero-point values, and the zero-point value for which the maximum number of genomic sequences are determined to have normal copy numbers may then be selected.
摘要翻译：本发明的各种实施方案通过鉴定零点值或中心常数zeta来确定基于阵列的比较基因组杂交（“aCGH”）数据集的零点或中心常数zeta，当在 aCGH数据的像差调查分析导致被认为具有相对于对照基因组具有异常拷贝数的阵列 - 探针互补基因组序列数量最少，换句话说，导致阵列探针数量最多鉴定为具有正常拷贝数的互补基因组序列。在一个实施例中，可以使用推定的零点值的范围来执行aCGH数据集的基于时间的分析，并且可以将确定具有正常拷贝数的最大数目的基因组序列的零点值被选中。

5. 发明授权

US07247426B2 Classifying cancers 失效
标题翻译：分类癌症
公开(公告)号：US07247426B2
公开(公告)日：2007-07-24
申请号：US09921406
申请日：2001-08-02
申请人： Zohar Yakhini , Michael Bittner , Jeff Trent , Amir Ben-Dor , Paul Meltzer , Yidong Chen , Ashani Weeraratna , Yuan Jiang , Nick Sampas , Edward Dougherty
发明人： Zohar Yakhini , Michael Bittner , Jeff Trent , Amir Ben-Dor , Paul Meltzer , Yidong Chen , Ashani Weeraratna , Yuan Jiang , Nick Sampas , Edward Dougherty
IPC分类号： C12Q1/68
CPC分类号： G01N33/5743 , C12Q1/6886 , C12Q2600/106 , C12Q2600/118 , C12Q2600/136
摘要： The overexpression of certain marker genes including Wnt5a has been found useful in the identification of more aggressive forms of malignant melanoma. Therefore, the overexpression of these genes in tumor samples of malignant melanoma may be useful in the diagnosis, profiling, and treatment of patients suffering from this disease. Inhibitors of Wnt5a activity may be useful in the treatment of aggressive forms of malignant melanoma. Inhibition of Wnt5a activity may be effected by any method including anti-sense therapy, gene therapy, and pharmaceutical intervention.
摘要翻译：已经发现某些标记基因（包括Wnt5a）的过表达可用于鉴定更具攻击性的恶性黑素瘤。因此，这些基因在恶性黑素瘤肿瘤样本中的过表达可能用于诊断，分析和治疗患有这种疾病的患者。 Wnt5a活性抑制剂可用于治疗侵袭性恶性黑色素瘤。 Wnt5a活性的抑制可以通过任何方法进行，包括反义治疗，基因治疗和药物干预。

6. 发明申请

US20080125979A1 Method and system for determining ranges for the boundaries of chromosomal aberrations 审中-公开
标题翻译：确定染色体畸变边界范围的方法和系统
公开(公告)号：US20080125979A1
公开(公告)日：2008-05-29
申请号：US11580973
申请日：2006-10-13
申请人： Zohar Yakhini , John F. Corson , Amir Ben-Dor
发明人： Zohar Yakhini , John F. Corson , Amir Ben-Dor
IPC分类号： G06F19/00
CPC分类号： G16B25/00 , G16B40/00 , G16B45/00
摘要： Embodiments of the present invention include methods and systems for analysis of comparative genomic hybridization (“CGH”) data, including CGH data obtained from microarray experiments.
摘要翻译：本发明的实施方案包括用于分析比较基因组杂交（“CGH”）数据的方法和系统，包括从微阵列实验获得的CGH数据。

7. 发明申请

US20080090237A1 Methods and compositions for comparing chromosomal copy number between genomic samples 审中-公开
标题翻译：用于比较基因组样品之间的染色体拷贝数的方法和组合物
公开(公告)号：US20080090237A1
公开(公告)日：2008-04-17
申请号：US11581134
申请日：2006-10-13
申请人： Zohar Yakhini , Bo Curry
发明人： Zohar Yakhini , Bo Curry
IPC分类号： C12Q1/68 , G06F19/00
CPC分类号： C12Q1/6883 , C12Q1/6886 , C12Q2600/16
摘要： Methods and compositions for detecting copy number variations between nucleic acid samples are provided. Also provided are kits for practicing methods in accordance with the invention.
摘要翻译：提供了用于检测核酸样品之间拷贝数变化的方法和组合物。还提供了用于根据本发明的练习方法的试剂盒。

8. 发明申请

US20050207974A1 Endothelial cell markers and related reagents and methods of use thereof 审中-公开
标题翻译：内皮细胞标志物及相关试剂及其使用方法
公开(公告)号：US20050207974A1
公开(公告)日：2005-09-22
申请号：US10802246
申请日：2004-03-17
申请人： David Deng , Anya Tsalenko , Laurakay Bruhn , Zohar Yakhini , Michael Ho , Thomas Quertermous , Eugene Yang
发明人： David Deng , Anya Tsalenko , Laurakay Bruhn , Zohar Yakhini , Michael Ho , Thomas Quertermous , Eugene Yang
IPC分类号： A61K47/48 , A61K51/00 , C07K16/28 , C07K16/46
CPC分类号： C07K16/28 , A61K47/6425
摘要： The present invention provides polynucleotides and polypeptides (VECSM polynucleotides and polypeptides) that are differentially expressed in vascular endothelial cells. The invention further provides a variety of compositions, diagnostic, and therapeutic methods based on identification of these markers. In particular, the invention provides a targeting agent linked to a functional moiety, wherein the functional moiety can comprise any of a number of different agents, including imaging agents, cytotoxic agents, and stimulators or inhibitors of angiogenesis.
摘要翻译：本发明提供在血管内皮细胞中差异表达的多核苷酸和多肽（VECSM多核苷酸和多肽）。本发明还提供了基于鉴定这些标记物的各种组合物，诊断和治疗方法。特别地，本发明提供了与功能部分连接的靶向剂，其中功能性部分可以包含许多不同的试剂，包括成像剂，细胞毒性剂，以及血管发生的刺激剂或抑制剂中的任何一种。

9. 发明申请

US20050170378A1 Methods and systems for joint analysis of array CGH data and gene expression data 审中-公开
标题翻译：数组CGH数据和基因表达数据联合分析的方法和系统
公开(公告)号：US20050170378A1
公开(公告)日：2005-08-04
申请号：US10964207
申请日：2004-10-12
申请人： Zohar Yakhini , Doron Lipson , Amir Ben-Dor
发明人： Zohar Yakhini , Doron Lipson , Amir Ben-Dor
IPC分类号： C12Q1/68 , G01N33/48 , G01N33/50 , G06F19/00
CPC分类号： G16B25/00 , G16B40/00
摘要： Methods, systems and computer readable media for identifying a high-scoring, significantly altered genomic-continuous submatrix, wherein each genomic-continuous submatrix contains a subset of a set of genes measured across a set of samples to generate a DNA copy number data matrix and a gene expression data matrix. The subset of the genes is a genomic-continuous set of genes, and each genomic-continuous submatrix contains a subset of the set of samples measured to generate the DNA copy number data matrix and the gene expression data matrix.
摘要翻译：用于识别高得分，显着改变的基因组连续子矩阵的方法，系统和计算机可读介质，其中每个基因组连续子矩阵包含跨越一组样本测量的一组基因的子集，以产生DNA拷贝数数据矩阵，基因表达数据矩阵。基因的子集是基因组连续的基因组，每个基因组连续子矩阵包含测量的一组样本的子集以产生DNA拷贝数数据矩阵和基因表达数据矩阵。

10. 发明申请

US20100330556A1 GENOME ANALYSIS USING A NICKING ENDONUCLEASE 审中-公开
标题翻译：使用内分泌酶的基因组分析
公开(公告)号：US20100330556A1
公开(公告)日：2010-12-30
申请号：US12495199
申请日：2009-06-30
申请人： Brian Jon Peter , Amir Ben-Dor , Zohar Yakhini , Holly Hogrefe
发明人： Brian Jon Peter , Amir Ben-Dor , Zohar Yakhini , Holly Hogrefe
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6809 , C12Q1/683 , C12Q1/6858 , C12Q2535/101 , C12Q2523/303 , C12Q2521/307
摘要： A method of genome analysis is provided. In certain embodiments, the method of comprises: a) contacting a genomic sample comprising a double-stranded DNA with a site-specific nicking endonuclease to provide a nicked double-stranded DNA comprising a plurality of nick sites, in which the nicking endonuclease nicks a site adjacent to a variable nucleotide; b) contacting the nicked double-stranded DNA with a polymerase in the presence of a nucleotide composition comprising a first labeled nucleotide comprising a first label, thereby producing a labeled double-stranded DNA that is not labeled at every nick site; c) stretching out the labeled double-stranded DNA to provide a stretched, labeled double-stranded DNA; and d) imaging the stretched, labeled double-stranded DNA to identify a labeling pattern on the stretched labeled double-stranded DNA.
摘要翻译：提供了一种基因组分析方法。在某些实施方案中，所述方法包括：a）将包含双链DNA的基因组样品与位点特异性切口内切核酸酶接触以提供包含多个切口位点的切口双链DNA，其中所述切口内切核酸酶切除邻近可变核苷酸的位点; b）在含有包含第一标记的第一标记核苷酸的核苷酸组合物存在的情况下使所述切口双链DNA与聚合酶接触，从而产生未在每个切口位点标记的标记的双链DNA; c）拉伸标记的双链DNA以提供拉伸的标记的双链DNA; 和d）对拉伸的标记的双链DNA进行成像，以鉴定拉伸标记的双链DNA上的标记图谱。

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