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1. 发明申请

WO2018129226A1 SYSTEM, METHOD, COMPUTER-ACCESSIBLE MEDIUM AND APPARATUS FOR DNA MAPPING 审中-公开
公开(公告)号：WO2018129226A1
公开(公告)日：2018-07-12
申请号：PCT/US2018/012449
申请日：2018-01-05
申请人： VIRGINIA COMMONWEALTH UNIVERSITY , NEW YORK UNIVERSITY , UNIVERSITY OF BRISTOL
发明人： REED, Jason , MISHRA, Bhubaneswar , MIKHEYKIN, Andrey , PICCO, Loren , PAYTON, Oliver , RUSSELL-PAVIER, Freddie
IPC分类号： C12N9/22 , C12N15/10 , C12Q1/68 , G01Q60/30
摘要： Exemplary embodiments of the present disclosure can include, for example, an atomic force microscopy (AFM) system, including a cantilever(s), an optical pickup unit(s) (OPU(s)) including a laser positioned over the cantilever(s), and a power source providing noise with a noise level that is below 300 Picometers. The noise level of the power source can be below 200 Picometers. A digitizing arrangement can be included which can be associated with the OPU. The digitizing arrangement(s) can have a bandwidth of about 2 MHZ. The OPU(s) can have a detection bandwidth of at least 80 MHZ. The exemplary apparatus can be combined with a chemical protocol and statistical signal processing and image analysis procedures to map DNA at high speed and accuracy.

2. 发明申请

WO2011103526A2 METHODS, COMPUTER-ACCESSIBLE MEDIUM AND SYSTEMS FOR FACILITATING DATA ANALYSIS AND REASONING ABOUT TOKEN/SINGULAR CAUSALITY 审中-公开
标题翻译：方法，计算机可访问的媒体和系统，用于促进数据分析和关于TOKEN / SINGULAR CAUSALITY
公开(公告)号：WO2011103526A2
公开(公告)日：2011-08-25
申请号：PCT/US2011/025574
申请日：2011-02-20
申请人： NEW YORK UNIVERSITY , KLEINBERG, Samantha , MISHRA, Bhubaneswar
发明人： KLEINBERG, Samantha , MISHRA, Bhubaneswar
IPC分类号： G06F19/00 , G06F17/10
CPC分类号： G06N5/048 , G06N5/045
摘要： Exemplary embodiments of exemplary methods, procedures, computer- accessible medium and systems according to the present disclosure can be provided which can be used for determining token causality. For example, data which comprises token-level time course data and type-level causal relationships can be obtained. In addition, a determination can be made as to whether the type-level causal relationships are instantiated in the token-level time course data, and using a computing arrangement. Further, exemplary significance scores for the causal relationships can be determined based on the determination procedure. It is also possible to determine probabilities associated with the type-level causal relationships using the token-level time course data and a probabilistic temporal model and/or type- level time course data when at least one of the type-level causal relationships have indeterminate truth values. The exemplary determination of the probabilities can be performed using a prior causal information inference procedure.
摘要翻译：可以提供可用于确定令牌因果关系的根据本公开的示例性方法，过程，计算机可访问介质和系统的示例性实施例。例如，可以获得包括令牌级时程数据和类型因果关系的数据。此外，可以确定在令牌级时间过程数据中是否实例化了类型级因果关系，并且使用计算机构。此外，可以基于确定过程来确定因果关系的示例性重要性得分。当类型级别因果关系中的至少一个具有不确定性时，也可以使用令牌级时间过程数据和概率时间模型和/或类型级时间过程数据来确定与类型级因果关系相关联的概率真值。概率的示例性确定可以使用先验因果信息推理过程来执行。

3. 发明申请

WO2008112754A2 METHODS, COMPUTER-ACCESSIBLE MEDIUM, AND SYSTEMS FOR GENERATING A GENOME WIDE HAPLOTYPE SEQUENCE 审中-公开
标题翻译：方法，计算机可用介质和用于生成基因组宽泛的HAPLOTYPE序列的系统
公开(公告)号：WO2008112754A2
公开(公告)日：2008-09-18
申请号：PCT/US2008/056648
申请日：2008-03-12
申请人： NEW YORK UNIVERSITY , MISHRA, Bhubaneswar , ANANTHARAMAN, Thomas , LIM, Sang
发明人： MISHRA, Bhubaneswar , ANANTHARAMAN, Thomas , LIM, Sang
IPC分类号： G06G7/48
CPC分类号： G06F19/18 , G06F19/24
摘要： Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide prob map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the at least one genome wide restriction map and locations of detectable oligonucleotide probes of the at least one genome wide probe map and defining a consensus map indicating restriction sites based on each of the at least one genome wide restriction map and locations of detectable oligonucleotide probes based on each of the at least one genome wide probe map.
摘要翻译：提供了用于产生全基因组探针图和/或全基因组单倍型序列的方法，计算机可用介质和系统。特别地，可以通过获得与用至少一种限制酶切割的至少一个双链核酸分子杂交的多个可检测寡核苷酸探针，并检测可检测寡核苷酸探针的位置来产生全基因组范围概率图。例如，可以通过分析至少一个基因组范围的限制性图谱以及至少一个全基因组范围的探针图来确定全基因组范围的单倍型序列，以确定至少一个全基因组范围的限制性图谱的限制性位点与可检测的寡核苷酸探针的位置之间的距离并且基于所述至少一个全基因组范围的限制性图中的每一个和基于所述至少一个全基因组范围的探针图中的每一个的可检测寡核苷酸探针的位置定义指示限制性位点的共有图。 p>

4. 发明申请

WO2004097577A3 METHODS, SOFTWARE ARRANGEMENTS, STORAGE MEDIA, AND SYSTEMS FOR PROVIDING A SHRINKAGE-BASED SIMILARITY METRIC 审中-公开
公开(公告)号：WO2004097577A3
公开(公告)日：2004-11-11
申请号：PCT/US2004/012921
申请日：2004-04-23
申请人： NEW YORK UNIVERSITY , CHEREPINSKY, Vera , FENG, Jia-Wu , REJALI, Marc , MISHRA, Bhubaneswar
发明人： CHEREPINSKY, Vera , FENG, Jia-Wu , REJALI, Marc , MISHRA, Bhubaneswar
IPC分类号： G01N33/48
摘要： The present invention relates to systems, methods, and software arrangements for determining associations between two or more datasets. The systems, methods, and software arrangements used to determine such associations include a determination of a correlation coefficient that incorporates both prior assumptions regarding such datasets and actual information regarding the datasets. The systems, methods, and software arrangements of the present invention can be useful in an analysis of microarray data, including gene expression arrays, to determine correlations between genotypes and phenotypes. Accordingly, the systems, methods, and software arrangements of the present invention may be utilized to determine a genetic basis of complex genetic disorder ( e.g. those characterized by the involvement of more than one gene).

5. 发明申请

WO2010129301A2 METHOD, COMPUTER-ACCESSIBLE MEDIUM AND SYSTEM FOR BASE-CALLING AND ALIGNMENT 审中-公开
标题翻译：方法，计算机可访问的媒体和基站和对齐的系统
公开(公告)号：WO2010129301A2
公开(公告)日：2010-11-11
申请号：PCT/US2010/032613
申请日：2010-04-27
申请人： NEW YORK UNIVERSITY , MISHRA, Bhubaneswar , NARZISI, Giuseppe
发明人： MISHRA, Bhubaneswar , NARZISI, Giuseppe
IPC分类号： G06F19/00 , C12Q1/68
CPC分类号： G06F19/22
摘要： Exemplary methods, procedures, computer-accessible medium, and systems for base-calling, aligning and polymorphism detection and analysis using raw output from a sequencing platform can be provided. A set of raw outputs can be used to detect polymorphisms in an individual by obtaining a plurality of sequence read data from one or more technologies (e.g., using sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, Sanger sequencing, etc.). For example, provided herein are exemplary methods, procedures, computer-accessible medium and systems, which can include and/or be configured for obtaining raw output from a sequencing platform configured to be used for reading fragment(s) of genomes, obtaining reference sequences for the genomes obtained independently from the raw output, and generating a base-call interpretation and/or alignment using the raw output and the reference sequences. For example, a score function can be determined based on information associated with the sequencing platform that can be used to analyze polymorphisms based on the base-call interpretation and/or alignment.
摘要翻译：可以提供示例性的方法，程序，计算机可访问介质以及使用来自测序平台的原始输出的基本调用，对准和多态性检测和分析的系统。一组原始输出可以用于通过从一种或多种技术获得多个序列读取数据来检测个体中的多态性（例如，使用按合成顺序，通过连接测序，序列化杂交，Sanger 测序等）。例如，本文提供的是示例性方法，程序，计算机可访问介质和系统，其可以包括和/或配置用于从被配置为用于读取基因组片段的测序平台获得原始输出，获得参考序列对于从原始输出独立获得的基因组，以及使用原始输出和参考序列生成基本呼叫解释和/或对齐。例如，可以基于与可以用于基于基本呼叫解释和/或对齐来分析多态性的测序平台相关联的信息来确定分数函数。

6. 发明申请

WO2005013091A3 METHODS, SOFTWARE ARRANGEMENTS, STORAGE MEDIA, AND SYSTEMS FOR GENOTYPING OR HAPLOTYPING POLYMORPHIC GENETIC LOCI OR STRAIN IDENTIFICATION 审中-公开
公开(公告)号：WO2005013091A3
公开(公告)日：2005-02-10
申请号：PCT/US2004/024766
申请日：2004-08-02
申请人： NEW YORK UNIVERSITY , CHEREPINSKY, Vera , MISHRA, Bhubaneswar
发明人： CHEREPINSKY, Vera , MISHRA, Bhubaneswar
IPC分类号： C12Q1/00
摘要： The present invention relates generally to systems, methods, storage media, and software arrangements for genotyping and/or haplotyping a sequence of polymorphic genetic loci in a deoxyribonucleic acid (DNA) sample or identifying a strain variant from the DNA sample. Exemplary embodiments of systems, methods, storage media, and software arrangements may perform the optimization of the design of one or more microarrays, each containing a set of oligonucleotide probes capable of detecting one or more known genotypes and/or haplotypes at given polymorphic genetic loci or identifying the strain variant, by optimizing the set of oligonucleotides to be incorporated into the microarrays and by optimizing the arrangement of a set of oligonucleotides on the microarrays. The optimization may be achieved through the application of one or more optimization procedures. The instant invention may be useful in typing individuals at the HLA loci or other polymorphic genetic loci, or may be employed to quickly identify viral or bacterial pathogens from which genome sequence information is available.

7. 发明申请

WO2002026934A3 SYSTEM AND PROCESS FOR VALIDATING, ALIGNING AND REORDERING GENETIC SEQUENCE MAPS USING ORDERED RESTRICTION MAP 审中-公开
公开(公告)号：WO2002026934A3
公开(公告)日：2002-04-04
申请号：PCT/US2001/030426
申请日：2001-09-28
申请人： NEW YORK UNIVERSITY , ANTONIOTTI, Marco , MISHRA, Bhubaneswar , ANANTHARAMAN, Thomas , PAXIA, Salvatore
发明人： ANTONIOTTI, Marco , MISHRA, Bhubaneswar , ANANTHARAMAN, Thomas , PAXIA, Salvatore
IPC分类号： G01N33/48
摘要： A method and system are provided for comparing ordered segments of a first DNA restriction map to determine a level of accuracy the first DNA map and/or the second DNA map. In particular, the first and second DNA maps can be received (the first DNA map corresponding to a sequence DNA map, and the second DNA map corresponding to a genomic consensus DNA map as provided in an optical DNA map). Then, the accuracy of the first DNA map and/or the second DNA map is validated based on information associated with the first and second DNA maps. In addition, a method and system are provided for aligning a plurality of DNA sequences with a ordered DNA restriction map. The DNA sequences and the DNA map are received (the DNA sequences being fragments of a genome and the DNA map corresponding to a genomic consensus DNA map which relates to an optical ordered DNA map). Then, a level of accuracy of the DNA sequences and the DNA map is obtained based on information associated with the DNA sequences and the DNA map by means of the method and system described above. The locations of the DNA map at which the DNA sequences are capable of being associated with particular segments of the DNA map are located. Furthermore, it is possible to obtain locations of the DNA map(without the validation) by locating an optimal one of the locations for each of the DNA sequences for each of the locations.

8. 发明申请

WO2021211602A1 SYSTEMS AND METHODS FOR TRANSPOSING SPOKEN OR TEXTUAL INPUT TO MUSIC 审中-公开
公开(公告)号：WO2021211602A1
公开(公告)日：2021-10-21
申请号：PCT/US2021/027107
申请日：2021-04-13
申请人： YAO THE BARD, LLC , NEW YORK UNIVERSITY
发明人： VAN DER PLOEG, Leonardus, H. T. , YOUNG, Halley , ARMENTA, Joshua , MISHRA, Bhubaneswar
IPC分类号： G10H7/00
摘要： Described herein are real-time musical translation devices (RETMs) and methods of use thereof. Exemplary uses of RETMs include optimizing the understanding and/or recall of an input message for a user and improving a cognitive process in a user.

9. 发明申请

WO2017048784A1 RANK, CLUSTER, CHARACTERIZE AND CUSTOMIZE USERS, DIGITAL CONTENTS AND ADVERTISEMENT CAMPAIGNS BASED ON IMPLICIT CHARACTERISTIC DETERMINATION 审中-公开
标题翻译：排名，聚类，特征和定制用户，数字内容和基于隐含特征确定的广告投放
公开(公告)号：WO2017048784A1
公开(公告)日：2017-03-23
申请号：PCT/US2016/051641
申请日：2016-09-14
申请人： GENESIS MEDIA LLC , NEW YORK UNIVERSITY
发明人： DATTA, Souptik , FEUER, Joshua , MISHRA, Bhubaneswar
IPC分类号： G06F15/16
CPC分类号： G06Q30/0255 , G06Q30/02 , G06Q30/0251 , G06Q30/0271 , G06Q30/0276 , G06Q30/0277 , G06Q50/01
摘要： A statistical algorithm-driven digital system is provided for automated optimization of a large number of key performance indicators (KPI) involved in social digital interactions among users, contents and advertisement, further augmented by data-driven verification and recommendation. Users include humans from diverse socio-cultural-economic groups, whose identity may be pseudonymous, whose explicit features may remain private, though statistically imputable. Contents include webpages, downloads, videos, music, or content accessed by users. Advertisements include product placement, branding, appeal, surveys, or other third-party contents, not explicitly sought by user. Application executing on server digital device responds to requests received from client devices for delivering requested digital content, customizes selected piece of digital content delivered to client application (in response to request) based on ordinal rankings for users, contents and advertisements, computed by tensor based algorithm. Rankings computed are predictive of user's future social interactions, as determined by past statistical data, summarized in sparse high-dimensional tensors.
摘要翻译：提供统计算法驱动的数字系统，用于自动优化涉及用户，内容和广告之间的社会数字交互的大量关键绩效指标（KPI），并进一步通过数据驱动的验证和推荐来增强。用户包括来自不同社会文化经济群体的人，其身份可能是假名的，其明确的特征可能保持私有化，尽管统计学上无法估量。内容包括用户访问的网页，下载，视频，音乐或内容。广告包括用户未明确寻求的产品展示位置，品牌，呼吁，调查或其他第三方内容。在服务器数字设备上执行的应用响应从客户端设备接收的用于递送所请求的数字内容的请求，根据用户，内容和广告的顺序排列，定制被递送给客户端应用的所选择的数字内容（响应请求），由基于张量的算法。计算的排名是对用户未来社会交往的预测，由过去的统计数据确定，在稀疏高维张量中总结。

10. 发明申请

WO2015066052A1 METHODS, COMPUTER-ACCESSIBLE MEDIUM AND SYSTEMS TO MODEL DISEASE PROGRESSION USING BIOMEDICAL DATA FROM MULTIPLE PATIENTS 审中-公开
标题翻译：方法，计算机可访问的媒介和系统使用生物医学数据从多个患者模型疾病进展
公开(公告)号：WO2015066052A1
公开(公告)日：2015-05-07
申请号：PCT/US2014/062688
申请日：2014-10-28
申请人： NEW YORK UNIVERSITY
发明人： RAMAZZOTTI, Daniele , CARAVAGNA, Giulio , OLDE LOOHUIS, Loes , GRAUDENZI, Alex , KORSUNCKY, Iiya , MAURI, Giancarlo , ANTONIOTTI, Marco , MISHRA, Bhubaneswar
IPC分类号： G06T11/20
CPC分类号： G06F19/3437 , G06F19/00 , G06F19/12 , G16H50/50
摘要： An exemplary embodiment of system, method and computer-accessible medium can be provided to reconstruct models based on the probabilistic notion of causation, which can differ fundamentally from that can be based on correlation. A general reconstruction setting can be complicated by the presence of noise in the data, owing to the intrinsic variability of biological processes as well as experimental or measurement errors. To gain immunity to noise in the reconstruction performance, it is possible to use a shrinkage estimator. On synthetic data, the exemplary procedure can outperform currently known procedures and, for some real cancer datasets, there are biologically significant differences revealed by the exemplary reconstructed progressions. The exemplary system, method and computer accessible medium can be efficient even with a relatively low number of samples and its performance quickly converges to its asymptote as the number of samples increases.
摘要翻译：可以提供系统，方法和计算机可访问介质的示例性实施例，以基于因果关系的概率概念重建模型，这可能与可以基于相关性的概率概念有所不同。由于生物过程的内在变异性以及实验或测量误差，数据中存在噪声可能会使一般的重建设置变得复杂。为了在重建性能中获得对噪声的抵抗能力，可以使用收缩估计器。在合成数据上，示例性程序可以胜过当前已知的程序，并且对于一些真实的癌症数据集，通过示例性重建进程显示出生物学上显着的差异。即使采样数量相对较少，示例性系统，方法和计算机可访问介质也是有效的，并且随着样本数量的增加，其性能迅速收敛到其渐近线。

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