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1. 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。

2. 发明申请

US20050152836A1 Diagnostic markers and pharmacological targets in heart failure and related reagents and methods of use thereof 审中-公开
标题翻译：心力衰竭中的诊断标志物和药理学靶标及相关试剂及其使用方法
公开(公告)号：US20050152836A1
公开(公告)日：2005-07-14
申请号：US10850941
申请日：2004-05-21
申请人： Euan Ashley , Mary Chen , Thomas Quertermous , David Xing-Fei Deng , Anya Tsalenko , Amir Ben-dor , Laurakay Bruhn , Zohar Yakhini
发明人： Euan Ashley , Mary Chen , Thomas Quertermous , David Xing-Fei Deng , Anya Tsalenko , Amir Ben-dor , Laurakay Bruhn , Zohar Yakhini
IPC分类号： A61K38/18 , A61K51/00 , C07K16/46 , C12Q1/68 , G01N33/53 , G01N33/566 , G01N33/567 , G01N33/68
CPC分类号： G01N33/6893 , A61K38/1709 , A61K47/6843 , G01N2333/912 , G01N2333/916 , G01N2800/325
摘要： The invention identifies genes whose expression is upregulated or downregulated following mechanical offloading in subjects with heart failure. The invention provides compositions comprising a targeting agent conjugated to a functional moiety, wherein the targeting agent selectively binds to a polypeptide encoded by one of these genes. The functional moiety can be an imaging agent, therapeutic agent, etc. The invention further provides methods for providing diagnostic or prognostic information related to heart failure involving detecting expression or activity of an expression product of one or more of the identified genes. The invention further provides diagnostic and therapeutic methods comprising detecting or administering an apelin peptide to a subject.
摘要翻译：本发明鉴定在具有心力衰竭的受试者中机械卸载后其表达上调或下调的基因。本发明提供了包含与功能部分缀合的靶向剂的组合物，其中所述靶向剂选择性地结合由这些基因之一编码的多肽。功能部分可以是成像剂，治疗剂等。本发明还提供了提供与心力衰竭有关的诊断或预后信息的方法，其涉及检测一种或多种所鉴定的基因的表达产物的表达或活性。本发明进一步提供诊断和治疗方法，其包括向受试者检测或施用apelin肽。

3. 发明申请

US20070253901A1 Atherosclerosis genes and related reagents and methods of use thereof 审中-公开
标题翻译：动脉粥样硬化基因及相关试剂及其使用方法
公开(公告)号：US20070253901A1
公开(公告)日：2007-11-01
申请号：US11412437
申请日：2006-04-27
申请人： David Deng , Anya Tsalenko , Amir Ben-Dor , Zohar Yakhini , Thomas Quertermous , Euan Ashley , Eugene Yang , Raymond Tabibiazar , Philip Tsao
发明人： David Deng , Anya Tsalenko , Amir Ben-Dor , Zohar Yakhini , Thomas Quertermous , Euan Ashley , Eugene Yang , Raymond Tabibiazar , Philip Tsao
IPC分类号： A61K51/00 , A61K49/10 , C07K16/46 , C07K14/54
CPC分类号： G01N33/6893 , G01N2800/323
摘要： The invention provides genes (DEA genes) that are differentially expressed in atherosclerotic lesions and polypeptides encoded by these genes. The invention provides compositions comprising a targeting agent conjugated to a functional moiety, wherein the targeting agent selectively binds to a polypeptide encoded by one a DEA gene. The functional moiety can be an imaging agent, therapeutic agent, etc. The invention further provides methods for providing diagnostic or prognostic information related to atherosclerosis involving detecting expression or activity of an expression product of one or more of the DEA genes. The invention further provides therapeutic methods comprising administering to a subject a composition comprising a targeting agent conjugated to a functional moiety that binds selectively binds to a polypeptide encoded by a DEA gene.
摘要翻译：本发明提供在动脉粥样硬化病变和由这些基因编码的多肽中差异表达的基因（DEA基因）。本发明提供了包含与功能部分缀合的靶向剂的组合物，其中所述靶向剂选择性地结合由DEA基因之一编码的多肽。功能部分可以是显像剂，治疗剂等。本发明还提供了提供涉及检测一种或多种DEA基因的表达产物的表达或活性的动脉粥样硬化相关的诊断或预后信息的方法。本发明进一步提供治疗方法，包括向受试者施用包含与功能性部分缀合的靶向试剂的组合物，其结合选择性结合由DEA基因编码的多肽。

4. 发明申请

US20050048463A1 Systems and methods for determining cell type composition of mixed cell populations using gene expression signatures 审中-公开
标题翻译：使用基因表达特征确定混合细胞群体的细胞类型组成的系统和方法
公开(公告)号：US20050048463A1
公开(公告)日：2005-03-03
申请号：US10841164
申请日：2004-05-07
申请人： David Deng , Anya Tsalenko , Zohar Yakhini , Laurakay Bruhn , Amir Ben-Dor
发明人： David Deng , Anya Tsalenko , Zohar Yakhini , Laurakay Bruhn , Amir Ben-Dor
IPC分类号： C12Q1/68 , C12Q1/70 , G06F19/00
CPC分类号： G16B40/00 , G16B25/00
摘要： The present invention provides systems and methods for determining the cell type composition of a mixed cell population. The invention provides systems and methods for identifying and defining pure cell type specific signatures. These pure cell type specific signatures may be used to determine the cell type composition of a mixed cell population. The systems and methods of the invention may be used for a variety of research and clinical purposes. For example, they may be used to detect the presence or absence of cells of particular types, and to determine whether variations in gene expression, e.g., between different samples, represent true changes in gene expression or differences in cell type composition of the samples.
摘要翻译：本发明提供了用于确定混合细胞群体的细胞类型组成的系统和方法。本发明提供用于识别和定义纯细胞类型特异性特征的系统和方法。这些纯细胞类型特异性标记可用于确定混合细胞群体的细胞类型组成。本发明的系统和方法可用于各种研究和临床目的。例如，它们可以用于检测特定类型的细胞的存在或不存在，并且确定基因表达的变化，例如不同样品之间的变化是否代表基因表达的真实变化或样品的细胞类型组成的差异。

5. 发明申请

US20060190190A1 Method and system for analysis of gene-expression data 审中-公开
标题翻译：用于分析基因表达数据的方法和系统
公开(公告)号：US20060190190A1
公开(公告)日：2006-08-24
申请号：US11048970
申请日：2005-02-02
申请人： Zohar Yakhini , Amir Ben-Dor , Anya Tsalenko , David Deng
发明人： Zohar Yakhini , Amir Ben-Dor , Anya Tsalenko , David Deng
IPC分类号： G06F19/00
CPC分类号： G16B25/00
摘要： In various embodiments of the present invention, initial gene-expression data is initially partitioned into classes by patient, subject, or other identifier of a source of samples, expression-level-differences are computed for each gene with respect to each initial partition, and a rank consistency score or fold-change consistency score is computed for each gene from the expression-level difference metrics computed for each initial partition. In other words, rather than partitioning gene-expression-level data directly into two or more classes relative to an event of interest, the gene-expression-level data is first partitioned according to sample source, and then each sample-source partition is partitioned into two or more classes relative to an event of interest. Levels of significance, or p-values, can be straightforwardly computed for both rank consistency scores and fold-change consistency scores.
摘要翻译：在本发明的各种实施方案中，初始基因表达数据最初按照样品来源的患者，受试者或其他标识符分类，根据每个初始分区计算每个基因的表达水平差异，根据为每个初始分区计算的表达级差异度量，为每个基因计算排序一致性分数或倍数变化一致性分数。换句话说，不是将基因表达级数据直接分为两个或更多相关于感兴趣事件的类别，因此首先根据样本源分割基因表达级数据，然后将每个样本源分区分区相对于感兴趣的事件进入两个或更多个类。对于等级一致性分数和折叠一致性分数，可以直接计算重要程度或p值。

6. 发明申请

US20060173635A1 Analyzing and visualizing enrichment in DNA sequence alterations 审中-公开
标题翻译：分析和可视化DNA序列变异中的富集
公开(公告)号：US20060173635A1
公开(公告)日：2006-08-03
申请号：US11049565
申请日：2005-02-01
申请人： Zohar Yakhini , Amir Ben-Dor , Anya Tsalenko , Doron Lipson
发明人： Zohar Yakhini , Amir Ben-Dor , Anya Tsalenko , Doron Lipson
IPC分类号： G06F19/00
CPC分类号： G16B25/00 , G16B20/00
摘要： Methods, tools, systems and computer readable media for analyzing CGH data, together with data from an independent source. Independent data is compared with the CGH data, wherein the CGH data is characterized by sets of defined regions differentiated by at least one property. Enrichment is assessed for at least one subset of the data from an independent source with regard to at least one of the sets of defined regions in the CGH data. Methods, tools, systems and computer readable media for visualizing CGH data as it is impacted by data from an independent source are also provided. A relationship between at least one defined set of the CGH data and at least one set of sequence elements defined in the data from an independent source may be visualized.
摘要翻译：用于分析CGH数据的方法，工具，系统和计算机可读介质，以及来自独立源的数据。将独立数据与CGH数据进行比较，其中CGH数据由通过至少一个属性区分的限定区域的集合来表征。相对于CGH数据中的至少一个限定区域的集合，来自独立源的至少一个数据子集的浓度被评估。还提供了用于可视化CGH数据的方法，工具，系统和计算机可读介质，因为它受来自独立源的数据的影响。至少一个定义的CGH数据集与来自独立源的数据中定义的至少一组序列元素之间的关系可以被可视化。

7. 发明申请

US20070203653A1 Method and system for computational detection of common aberrations from multi-sample comparative genomic hybridization data sets 审中-公开
标题翻译：用于多样本比较基因组杂交数据集的常见像差的计算检测方法和系统
公开(公告)号：US20070203653A1
公开(公告)日：2007-08-30
申请号：US11363699
申请日：2006-02-28
申请人： Amir Ben-Dor , Anya Tsalenko , Doron Lipson , Zohar Yakhini
发明人： Amir Ben-Dor , Anya Tsalenko , Doron Lipson , Zohar Yakhini
IPC分类号： G06F19/00
CPC分类号： G16B25/00 , G16B30/00 , G16B40/00
摘要： Various embodiments of the present invention are directed to methods and systems for automatic, statistically meaningful detection of aberrations common to multiple samples within a sample set. Many various aberration-calling techniques are used to identify aberrant intervals within each of the samples of the sample set. A set of candidate intervals is constructed to include the aberrant intervals identified by the aberration-calling technique, as well as two-way intersections of the identified aberrant intervals. A score indicating the statistical relevance of each candidate interval with respect to each sample is next assigned to each candidate interval. Then, a total significance score is assigned to each candidate interval based on the individual scores for the candidate interval with respect to each sample. The most statistically significant candidate intervals may be selected based on the total significance scores assigned to the candidate intervals.
摘要翻译：本发明的各种实施例涉及用于对样本集合内的多个样本共同的像差进行自动统计学上有意义的检测的方法和系统。使用许多各种像差调用技术来识别样本集合的每个样本内的异常间隔。一组候选间隔被构造成包括由像差调用技术识别的异常间隔以及所识别的异常间隔的双向交叉。指示每个候选间隔相对于每个样本的统计学相关性的分数接下来分配给每个候选间隔。然后，基于针对每个样本的候选间隔的各个评分，将总重要性得分分配给每个候选间隔。可以基于分配给候选间隔的总重要性得分来选择最具统计意义的候选间隔。

8. 发明申请

US20090068648A1 Method and system for determining a quality metric for comparative genomic hybridization experimental results 审中-公开
标题翻译：用于确定比较基因组杂交实验结果的质量度量的方法和系统
公开(公告)号：US20090068648A1
公开(公告)日：2009-03-12
申请号：US11580345
申请日：2006-10-13
申请人： Zohar Yakhini , Amir Bon-Dor , Anya Tsalenko
发明人： Zohar Yakhini , Amir Bon-Dor , Anya Tsalenko
IPC分类号： C12Q1/68
CPC分类号： G16B25/00
摘要： Various embodiments of the present invention determine various quality metrics that reflect the quality of two or more identically-executed or similar array-based comparative-genomic-hybridization (“aCGH”) experiments. In certain embodiments of the present invention, a pairwise quality metric is generated for each possible pair of aCGH experimental results within a set of aCGH experimental results. The pairwise quality metrics may be summed and optionally normalized to produce an overall quality metric for the set of aCGH experimental results. Various pairwise quality metrics can be used in different embodiments of the present invention, including pairwise quality metrics based on measures of aberration overlap.
摘要翻译：本发明的各种实施方案确定反映两个或多个相同执行或相似的基于阵列的比较 - 基因组杂交（“aCGH”）实验的质量的各种质量度量。在本发明的某些实施方案中，在一组aCGH实验结果中，对于每个可能的aCGH实验结果对，生成成对质量度量。可以将成对质量度量相加并任选地归一化以产生用于aCGH实验结果的集合的总体质量度量。可以在本发明的不同实施例中使用各种成对质量度量，包括基于像差重叠的度量的成对质量度量。

9. 发明申请

US20050273269A1 Method and system for analysis of biological and chemical data 审中-公开
标题翻译：生物和化学数据分析方法和系统
公开(公告)号：US20050273269A1
公开(公告)日：2005-12-08
申请号：US10863045
申请日：2004-06-07
申请人： Zohar Yakhini , Anya Tsalenko , Amir Ben-Dor
发明人： Zohar Yakhini , Anya Tsalenko , Amir Ben-Dor
IPC分类号： G01N33/48 , G01N33/50 , G06F19/00
CPC分类号： G16B40/00 , G16B25/00 , G16B45/00
摘要： In various embodiments of the present invention, initial experimental data is initially partitioned into classes by sample source, concentration or number-of-molecule values are computed with respect to each initial partition, and a rank consistency score or fold-change consistency score is computed for various molecular concentration or number-of-copies determinants with respect to one or more class-specifying events of interest. In other words, rather than partitioning experimental data directly into two or more classes relative to an event of interest, the experimental data is first partitioned according to sample source, and then each sample-source partition is partitioned into two or more classes relative to an event of interest.
摘要翻译：在本发明的各种实施方案中，初始实验数据最初通过样品源分成类别，相对于每个初始分区计算浓度或分子数值，并计算等级一致性分数或折叠变化一致性分数对于关于一个或多个感兴趣的类别指定事件的各种分子浓度或拷贝数决定因素。换句话说，相对于感兴趣的事件，实验数据直接分成两个或更多个类，而不是根据样本源对实验数据进行分区，然后将每个样本源分区分为两个或更多个类感兴趣的事件

10. 发明申请

US20060003338A1 System and methods for the management and treatment of vascular graft disease 审中-公开
标题翻译：血管移植疾病的治疗和治疗的系统和方法
公开(公告)号：US20060003338A1
公开(公告)日：2006-01-05
申请号：US10882014
申请日：2004-06-30
申请人： David Deng , Anya Tsalenko
发明人： David Deng , Anya Tsalenko
IPC分类号： C12Q1/68 , G01N33/53 , C12M1/34
CPC分类号： G01N33/6893 , G01N2800/245
摘要： Various embodiments of the present invention are directed to a system and methods for minimizing risk factors that contribute to the development of vascular graft disease and vascular graft failure. In one embodiment, a microarray-based gene expression analysis may be employed to select pre-implanted vessel candidates suitable as grafts in various vascular transplantation procedures. By using a microarray that includes a set of probe sequences that statistically correlate with vascular graft disease, mRNA expression levels of vascular-graft-disease-related genes within vessel-graft candidates can be determined to produce an expression profile for each vessel tested. Such molecular profile of genes related to various forms of vascular graft disease enables clinicians to select a vessel graft having the lowest probability of developing vascular graft diseases, and having the highest probability of maintaining adequate patency rate. Various types of arteries and veins may be discriminated from one another based on their respective gene expression profiles.
摘要翻译：本发明的各种实施方案涉及用于最小化有助于血管移植物疾病和血管移植物衰竭发展的危险因素的系统和方法。在一个实施方案中，基于微阵列的基因表达分析可用于选择适合于各种血管移植手术中的移植物的预先植入的血管候选物。通过使用包括与血管移植疾病统计学相关的一组探针序列的微阵列，可以确定血管移植物候选物中的血管移植物疾病相关基因的mRNA表达水平以产生每个测试血管的表达谱。与各种形式的血管移植疾病相关的基因的这种分子谱可使临床医生选择血管移植疾病发展概率最低的血管移植物，并具有维持足够通畅率的最高概率。基于各自的基因表达谱，可以区分各种类型的动脉和静脉。

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