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11.发明授权
公开(公告)号：US5752019A
公开(公告)日：1998-05-12
申请号：US577759
申请日：1995-12-22
申请人： Isidore Rigoutsos , Andrea Califano
发明人： Isidore Rigoutsos , Andrea Califano
CPC分类号： G06F19/709 , G06F19/705 , Y10S707/99933 , Y10S707/99945
摘要： A reference storage process populates a data structure so that the data structure contains all of the molecular structures and/or rigid substructures in the database classified according to attributes of tuples. In a preferred embodiment, the tuples are derived from sites (e.g. atomic sites) of the molecular structures and the attributes can be derived from geometric (and other) information related to the tuples. The attributes are used to define indices in the data structure that are associated with invariant vector information (e.g. information about rotatable bond(s) in skewed local coordinate frames created from tuples). These representations are invariant with respect to the rotation and translation of molecular structures and/or the rotation of substructures about attached rotatable bond(s). Accordingly, the invariant vector information is classified in the data structure with the respective tuple attributes in locations determined by the index derived from the respective tuple. A matching process creates one or more tuples, skewed local reference frames, and indices (called test frame tuple indices) for the structure (substructures) of a test molecule using the same technique that was used to populate the data structure. The test frame tuple index accesses the invariant vector information and tallies the frequency of matching in order to determine the identity of molecules/substructures in the database that are structurally similar to the test molecule. This identification can be achieved even in the presence of conformationally flexible molecules in the database.
摘要翻译： 参考存储过程填充数据结构，使得数据结构包含根据元组的属性分类的数据库中的所有分子结构和/或刚性子结构。 在优选实施例中，元组从分子结构的位点（例如原子位点）导出，并且属性可以从与元组相关的几何（和其他）信息导出。 这些属性用于定义数据结构中与不变向量信息相关联的索引（例如关于从元组创建的偏斜局部坐标系中的可旋转键的信息）。 这些表示关于分子结构的旋转和平移以及/或关于附接的可旋转键的子结构的旋转是不变的。 因此，不变向量信息被分类为数据结构，其中由在从相应元组导出的索引确定的位置中的相应元组属性。 匹配过程使用与填充数据结构相同的技术，为测试分子的结构（子结构）创建一个或多个元组，偏斜的局部参考帧和索引（称为测试帧元组索引）。 测试帧元组索引访问不变矢量信息并提供匹配频率，以确定数据库中与测试分子结构相似的分子/子结构的身份。 即使在数据库中存在构象灵活的分子的情况下也可以实现该鉴定。
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公开(公告)号：US08586726B2
公开(公告)日：2013-11-19
申请号：US12688680
申请日：2010-01-15
CPC分类号： C12N15/113 , C12N2310/141
摘要： The invention provides for isolated nucleic acid sequences of newly discovered micro RNAs that have been identified to exist in normal Human B cells and/or in tumor-related Human B cells, using an integrated bioinformatics method and pipeline described herein.
摘要翻译： 本发明提供了使用本文所述的综合生物信息学方法和流程，已经鉴定存在于正常人B细胞和/或肿瘤相关人B细胞中的新发现的微RNA的分离核酸序列。
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13.发明申请SYSTEM AND METHOD FOR PREDICTION OF PHENOTYPICALLY RELEVANT GENES AND PERTURBATION TARGETS 审中-公开用于预测相关基因和预测目标的系统和方法公开(公告)号：US20110172929A1
公开(公告)日：2011-07-14
申请号：US12863047
申请日：2009-01-16
申请人： Andrea Califano
发明人： Andrea Califano
IPC分类号： G06F19/00
摘要： Disclosed herein is a systems biology approach to prediction of phenotypically relevant genes such as oncogenes and perturbation targets. Interactions from a comprehensive cellular network such as the B Cell Interactome (BCI) can be used to identify those that become affected, or dysregulated, by a phenotype (e.g, disease, tumor and cancer) or perturbation (e.g., drug treatment) based on correlation changes between expression profiles of gene pairs in the interactions upon removal or addition of samples showing the phenotype or perturbation. Genes can be ranked based on the affected interactions involving the genes to predict phenotypically relevant genes and/or perturbation targets.
摘要翻译： 本文公开了一种系统生物学方法来预测表型相关基因，如致癌基因和扰动目标。 来自综合细胞网络（例如B细胞相互作用体（BCI））的相互作用可用于鉴定基于基因的表型（例如疾病，肿瘤和癌症）或扰动（例如，药物治疗）变得受影响或失调的那些 在去除或添加显示表型或扰动的样品之间的相互作用中基因对的表达谱之间的相关性变化。 基因可以基于涉及基因的受影响的相互作用进行排序，以预测表型相关基因和/或扰动目标。
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公开(公告)号：US20100172495A1
公开(公告)日：2010-07-08
申请号：US12727435
申请日：2010-03-19
申请人： Andrea Califano , Stephen Carl Kaufman , Marco Martens , William Robert Pulleyblank , Gustavo Alejandro Stolovitzky , Charles Philippe Tresser , Chai Wah Wu
发明人： Andrea Califano , Stephen Carl Kaufman , Marco Martens , William Robert Pulleyblank , Gustavo Alejandro Stolovitzky , Charles Philippe Tresser , Chai Wah Wu
CPC分类号： H04L9/3231 , H04L9/3236
摘要： A method of processing semiotic data includes receiving semiotic data including at least one data set P, selecting a function h, and for at least one of each data set P to be collected, computing h(P), destroying data set P, and storing h(P) in a database, wherein data set P cannot be extracted from h(P). The method further includes selecting a private key/public key (K, k) once for all cases, one of destroying the private key K and sending the private key K to a trusted party, and choosing function h as the public encryption function corresponding to k.
摘要翻译： 一种处理符号数据的方法包括接收符号数据，包括至少一个数据集P，选择一个函数h，以及对于要收集的每个数据集合P中的至少一个，计算h（P），破坏数据集P和存储 h（P），其中数据集P不能从h（P）中提取。 该方法还包括为所有情况选择一个私钥/公钥（K，k），其中一个破坏私钥K并将私钥K发送给可信方，并且选择功能h作为对应于 k。
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15.发明授权
公开(公告)号：US6041133A
公开(公告)日：2000-03-21
申请号：US764949
申请日：1996-12-13
CPC分类号： G06K9/00067
摘要： The method and apparatus of the present invention provide for automatic recognition of fingerprint images. In an acquisition mode, subsets of the feature points for a given fingerprint image are generated in a deterministic fashion. One or more of the subsets of feature points for the given fingerprint image is selected. For each selected subset, a key is generated that characterizes the fingerprint in the vicinity of the selected subset. A multi-map entry corresponding to the selected subset of feature points is stored and labeled with the corresponding key. In the recognition mode, a query fingerprint image is supplied to the system. The processing of the acquisition mode is repeated in order to generate a plurality of keys associated with a plurality of subsets of feature points of the query fingerprint image. For each key generated in the recognition mode, all entries in the multi-map that are associated with this key are retrieved. For each item retrieved, a hypothesized match between the query fingerprint image and the reference fingerprint image is constructed. Hypothesized matches are accumulated in a vote table. This list of hypotheses and scores stored in the vote table are preferably used to determine whether a match to the query fingerprint image is stored by the system.
摘要翻译： 本发明的方法和装置提供指纹图像的自动识别。 在采集模式中，以确定性方式生成给定指纹图像的特征点的子集。 选择给定指纹图像的特征点的一个或多个子集。 对于每个所选择的子集，生成表征所选子集附近的指纹的密钥。 对应于所选择的特征点子集的多映射条目被存储并用相应的密钥标记。 在识别模式下，向系统提供查询指纹图像。 重复采集模式的处理，以便产生与查询指纹图像的多个特征点子集相关联的多个密钥。 对于在识别模式下生成的每个密钥，检索与该密钥相关联的多映射中的所有条目。 对于检索的每个项目，构建查询指纹图像和参考指纹图像之间的假设匹配。 假设的比赛被累积在投票表中。 存储在投票表中的假设和得分的列表优选地用于确定系统是否存储与查询指纹图像的匹配。
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16.发明授权Method for finding a reference token sequence in an original token string within a database of token strings using appended non-contiguous substrings 失效在使用附加的非连续子字符串的令牌字符串数据库内的原始令牌字符串中查找引用令牌序列的方法
公开(公告)号：US5577249A
公开(公告)日：1996-11-19
申请号：US512794
申请日：1995-08-08
申请人： Andrea Califano
发明人： Andrea Califano
CPC分类号： G06F17/30985 , Y10S707/968
摘要： This method non sequentially compares a reference sequence of tokens to an original sequence of tokens to determine subsequences of tokens which exactly or similarly match. The method has a novel approach for creating a large number of indexes by partitioning strings of tokens into substrings, appending non contiguous substrings together to form tuples, and creating indexes from the tuples. Indexes are created in this manner for both the original and reference strings. Techniques are also provided to approximately or exactly locate the substrings which where used to create the tuples and indexes from the original sequence of tokens. Original and reference indexes are compared and matches are tracked. Higher numbers of matches result in higher scores (votes) in a table and indicate a stronger similarity between the sequences on the the original and reference strings. Using this method, the degree of similarity can also be determined. The Method is useful when comparing a reference sequence of tokens to a large database of original strings of tokens. It has applications in the biological sciences (human genome mapping or analyzing proteins) and in image, speech, and music recognition.
摘要翻译： 该方法不依赖地将令牌的参考序列与原始的令牌序列进行比较，以确定正好或相似匹配的令牌的子序列。 该方法通过将令牌的字符串分割成子字符串来创建大量索引，将非连续子串附加在一起以形成元组，并从元组创建索引。 以原始和参考字符串的方式创建索引。 还提供技术来近似或精确地定位用于从原始的令牌序列创建元组和索引的子串。 比较原始和参考索引，跟踪匹配。 更高数量的匹配导致表中的更高分数（投票），并指示原始和参考字符串之间的序列之间更强的相似性。 使用这种方法，也可以确定相似度。 当将令牌的参考序列与原始字符串的令牌的大型数据库进行比较时，该方法非常有用。 它在生物科学（人类基因组测绘或分析蛋白质）以及图像，语音和音乐识别中都有应用。
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17.发明授权公开(公告)号：US07860660B2
公开(公告)日：2010-12-28
申请号：US12574195
申请日：2009-10-06
摘要： Generally, the present invention applies a transformation to convert a probability distribution of gene expression signals in control samples to a uniform distribution. The uniform distribution allows better comparisons between expression levels for genes. The transformation is derived from gene expression signals of control data, and is applied to gene expression signals of phenotype data. The phenotype data can be represented in a matrix format. A number of gene expression patterns may be determined (in the form of submatrices) that will characterize the phenotype. The uniform distribution helps in this regard, as it allows better comparisons of patterns. The gene expression patterns can then be used to classify samples as belonging to the phenotype set. Preferably, a discriminant function is used to compare a sample with the gene expression patterns that characterize the phenotype. The discriminant function can determine a score that can be used to determine whether the sample belongs to the phenotype.
摘要翻译： 通常，本发明应用将对照样品中的基因表达信号的概率分布转换为均匀分布的转化。 均匀分布可以更好地比较基因的表达水平。 转化源自对照数据的基因表达信号，并应用于表型数据的基因表达信号。 表型数据可以以矩阵格式表示。 可以确定将以表型为特征的许多基因表达模式（以子矩阵的形式）。 统一分配在这方面有所帮助，因为它可以更好地比较模式。 然后可以将基因表达模式用于将样品分类为属于表型集。 优选地，使用判别函数将样品与表征表型的基因表达模式进行比较。 判别函数可以确定可用于确定样本是否属于表型的分数。
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公开(公告)号：US20100299159A1
公开(公告)日：2010-11-25
申请号：US12851258
申请日：2010-08-05
申请人： Andrea Califano , Aristidis Floratos , David Wang , Peter Young , Arthur Holden
发明人： Andrea Califano , Aristidis Floratos , David Wang , Peter Young , Arthur Holden
CPC分类号： G06Q50/24 , G06F19/00 , G06F19/28 , G06Q50/22 , G16H10/20 , G16H10/40 , G16H10/60 , G16H40/20
摘要： The systems and methods provide a dynamic process for obtaining and managing informed consent documentation. In general, the dynamic informed consent process (DICP) makes use of an intermediary organization, e.g., a trusted intermediary, which: (a) provides ICFs which have been dynamically generated for a specified trial or medical procedure and based on particular state or federal requirements, if any; and (b) archives copies of signed ICFs. In certain preferred embodiments, there may also be a procedure to provide training materials, such as audio or video presentations, to be viewed by prospective participants. In certain preferred embodiments, the process also includes contacting subjects who have signed ICFs in the event that there is a change of circumstance which the subject may deem material to whether s/he would continue to consent, or whether the participant needs to provide a different type of consent to participate in particular event or trial.
摘要翻译： 系统和方法为获取和管理知情同意文件提供了一个动态过程。 一般来说，动态知情同意程序（DICP）利用中间组织，例如可信赖的中介机构，其中：（a）提供为指定的试验或医疗程序动态生成的ICF，并基于特定的州或联邦 要求，如果有的话; 和（b）签名的ICF的档案副本。 在某些优选实施例中，还可以存在提供将由潜在参与者观看的训练材料（例如音频或视频呈现）的过程。 在某些优选实施例中，该过程还包括在主体可能认为材料是否被继续同意的情况发生变化的情况下联系已经签署了ICF的受试者，或者参与者是否需要提供不同的 同意参与特定事件或审判的类型。
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公开(公告)号：US07761715B1
公开(公告)日：2010-07-20
申请号：US09457732
申请日：1999-12-10
申请人： Andrea Califano , Stephen Carl Kaufman , Marco Martens , William Robert Pulleyblank , Gustavo Alejandro Stolovitzky , Charles Philippe Tresser , Chai Wah Wu
发明人： Andrea Califano , Stephen Carl Kaufman , Marco Martens , William Robert Pulleyblank , Gustavo Alejandro Stolovitzky , Charles Philippe Tresser , Chai Wah Wu
CPC分类号： H04L9/3231 , H04L9/3236
摘要： A method (as well as system and signal-bearing medium) of processing biometric data, includes receiving biometric data including a data set P, selecting a secure hash function h, and for each data set P to be collected, computing h(P), destroying the data set P, and storing h(P) in a database, wherein data set P cannot be extracted from h(P).
摘要翻译： 处理生物特征数据的方法（以及系统和信号承载介质）包括接收包括数据集P，选择安全散列函数h的生物特征数据，以及对于要收集的每个数据集合P，计算h（P） ，破坏数据集P，并将h（P）存储在数据库中，其中数据集P不能从h（P）中提取。
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20.发明申请公开(公告)号：US20100023273A1
公开(公告)日：2010-01-28
申请号：US12574195
申请日：2009-10-06
IPC分类号： G06F19/00
摘要： Generally, the present invention applies a transformation to convert a probability distribution of gene expression signals in control samples to a uniform distribution. The uniform distribution allows better comparisons between expression levels for genes. The transformation is derived from gene expression signals of control data, and is applied to gene expression signals of phenotype data. The phenotype data can be represented in a matrix format. A number of gene expression patterns may be determined (in the form of submatrices) that will characterize the phenotype. The uniform distribution helps in this regard, as it allows better comparisons of patterns. The gene expression patterns can then be used to classify samples as belonging to the phenotype set. Preferably, a discriminant function is used to compare a sample with the gene expression patterns that characterize the phenotype. The discriminant function can determine a score that can be used to determine whether the sample belongs to the phenotype.
摘要翻译： 通常，本发明应用将对照样品中的基因表达信号的概率分布转换为均匀分布的转化。 均匀分布可以更好地比较基因的表达水平。 转化源自对照数据的基因表达信号，并应用于表型数据的基因表达信号。 表型数据可以以矩阵格式表示。 可以确定将以表型为特征的许多基因表达模式（以子矩阵的形式）。 统一分配在这方面有所帮助，因为它可以更好地比较模式。 然后可以将基因表达模式用于将样品分类为属于表型集。 优选地，使用判别函数将样品与表征表型的基因表达模式进行比较。 判别函数可以确定可用于确定样本是否属于表型的分数。
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