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    • 1. 发明申请
    • ASSOCIATION MARKERS FOR BETA THALASSEMIA TRAIT
    • BETA THALASSEMIA TRAIT的协会标志
    • US20140148344A1
    • 2014-05-29
    • US14007673
    • 2012-03-29
    • Sina Vivekanandan Thrissur KadavilSunil KumarRandeep SinghNevenka Dimitrova
    • Sina Vivekanandan Thrissur KadavilSunil KumarRandeep SinghNevenka Dimitrova
    • C12Q1/68
    • C12Q1/6883C12Q2600/156
    • The present invention relates to isolated nucleic acid molecules of SEQ ID NO: 1 to SEQ ID NO: 14 which show a single polymorphic change at position 501, where the wildtype nucleotide is replaced by an indicator nucleotide, respectively. The present invention further relates to the mentioned nucleic acid molecules wherein a panel of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 of the polymorphic, changed sequences comprising the mentioned indicator nucleotides constitutes a marker for beta thalassemia, in particular of beta thalassemia minor. Further envisaged are specific panels comprising SEQ ID NO: 1; or SEQ ID NO 1 and 2; or SEQ ID NO: 1, 2 and 3, or SEQ ID NO: 1, 2, 3 and 4; or SEQ ID NO: 1 to 5; or SEQ ID NO: 1 to 6; or SEQ ID NO: 1 to 7; or SEQ ID NO: 1 to 14; or SEQ ID NO: 8 and 14; or SEQ ID NO: 8 and 9; or SEQ ID NO: 2, 4 and 13. The present invention further relates to a method of detecting or diagnosing beta thalassemia, preferably of beta thalassemia minor, in a subject, comprising the steps of: (a) isolating a nucleic acid from a subject's sample, (b) determining the nucleotide sequence and/or molecular structure present at one or more of the mentioned polymorphic sites, wherein the presence of an indicator nucleotide indicative of the presence of beta thalassemia. Also envisaged are a corresponding composition for detecting or diagnosing beta thalassemia, the use of the mentioned nucleic acid molecules for detecting or diagnosing beta thalassemia or for screening a population for the presence of beta thalassemia, as well as a corresponding kit. The methods, compositions, uses and kits of the invention also relate to the assessment of the risk of developing beta thalassemia in a subject and/or in a subject's progeny.
    • 本发明涉及SEQ ID NO:1至SEQ ID NO:14的分离的核酸分子,其分别在位置501显示单个多态性变化,其中野生型核苷酸被指示剂核苷酸替代。 本发明还涉及所述核酸分子,其中所述多态性改变的序列的1,2,3,4,5,6,7,8,9,10,11,12,13或14的片段包含 提及的指示剂核苷酸构成β地中海贫血的标志物,特别是β地中海贫血的标记物。 进一步设想的是包含SEQ ID NO:1的特定面板; 或SEQ ID NO 1和2; 或SEQ ID NO:1,2和3,或SEQ ID NO:1,2,3和4; 或SEQ ID NO:1至5; 或SEQ ID NO:1至6; 或SEQ ID NO:1至7; 或SEQ ID NO:1至14; 或SEQ ID NO:8和14; 或SEQ ID NO:8和9; 或SEQ ID NO:2,4和13.本发明还涉及检测或诊断受试者中β地中海贫血,优选地中海贫血地区贫血的方法,包括以下步骤:(a)从核酸 (b)确定存在于一个或多个所述多态性位点处的核苷酸序列和/或分子结构,其中存在指示β-地中海贫血存在的指示剂核苷酸。 还设想了用于检测或诊断β地中海贫血的相应组合物,所述核酸分子用于检测或诊断β地中海贫血或用于筛选群体以获得β地中海贫血以及相应的试剂盒。 本发明的方法,组合物,用途和试剂盒还涉及在受试者和/或受试者的后代中发展β地中海贫血的风险的评估。
    • 2. 发明申请
    • Method for Assembly of Nucleic Acid Sequence Data
    • 核酸序列数据的装配方法
    • US20140249764A1
    • 2014-09-04
    • US14124261
    • 2012-05-24
    • Sunil KumarRandeep SinghNevenka Dimitrova
    • Sunil KumarRandeep SinghNevenka Dimitrova
    • G06F19/22
    • G16B30/00
    • The present invention relates to a method for assembly of nucleic acid sequence data comprising nucleic acid fragment reads into (a) contiguous nucleotide sequence segment(s), comprising the steps of: (a) obtaining a plurality of nucleic acid sequence data from a plurality of nucleic acid fragment reads; (b) aligning said plurality of nucleic acid sequence data to a reference sequence; (c) detecting one or more gaps or regions of non-assembly, or non-matching with the reference sequence in the alignment output of step (b); (d) performing de novo sequence assembly of nucleic acid sequence data mapping to said gaps or regions of non-assembly; and (e) combining the alignment output of step (b) and the assembly output of step (d) in order to obtain (a) contiguous nucleotide sequence segment(s). In addition, a corresponding program element or computer program for assembly of nucleic acid sequence data and a sequence assembly system for transforming nucleic acid sequence data comprising nucleic acid fragment reads into (a) contiguous nucleotide sequence segment(s) is provided.
    • 本发明涉及将包含核酸片段读取的核酸序列数据装配到(a)连续核苷酸序列片段中的方法,包括以下步骤:(a)从多个核酸序列获得多个核酸序列数据 的核酸片段读取; (b)将所述多个核酸序列数据与参考序列对准; (c)检测与步骤(b)的对准输出中的参考序列的非组装或不匹配的一个或多个间隙或区域; (d)执行核酸序列数据的从头序列组装,其映射到所述非组装的间隙或区域; 和(e)组合步骤(b)的比对输出和步骤(d)的组合输出,以获得(a)连续核苷酸序列片段。 此外,提供了用于装配核酸序列数据的相应程序元件或计算机程序和用于将包含核酸片段的核酸序列数据转换成(a)连续核苷酸序列片段的序列组装系统。
    • 3. 发明申请
    • METHOD FOR PROCESSING GENOMIC DATA
    • 处理基因数据的方法
    • US20140229495A1
    • 2014-08-14
    • US13979908
    • 2012-01-19
    • Vishnu Vardhan MakkapatiNevenka DimitrovaRandeep SinghSunil Kumar
    • Vishnu Vardhan MakkapatiNevenka DimitrovaRandeep SinghSunil Kumar
    • G06F19/18
    • G16B20/00G16B30/00
    • The present invention relates to a method for processing a subject's genomic data comprising (a) obtaining a subject's genomic sequence; (b) reducing the complexity and/or amount of the genomic sequence information; and (c) storing the genomic sequence information of step (b) in a rapidly retrievable form. The present invention further relates to a method wherein the step of reducing the complexity and/or amount of the genomic sequence information is carried out by cropping said genomic sequence information except for signature data pertaining to a disease or disorder, or by aligning a subject's genomic sequence with a reference sequence comprising signature data pertaining to a disease or disorder. Furthermore, the invention relates to a method wherein the use of a subject's functional genetic information, in particular gene expression data is included, as well as to a method, wherein the information is encoded in matrices and decoded and represented based on Markov chain processes. The obtained information can also be used for diagnosing, detecting, monitoring or prognosticating a disease and/or for the preparation of a subject's molecular history. In addition, a corresponding clinical decision support and storage system, preferably in the form of an electronic picture/data archiving and communication system, is provided.
    • 本发明涉及一种用于处理受试者的基因组数据的方法,包括(a)获得受试者的基因组序列; (b)降低基因组序列信息的复杂性和/或量; 和(c)以快速可检索的形式存储步骤(b)的基因组序列信息。 本发明还涉及一种方法,其中降低基因组序列信息的复杂性和/或量的步骤是通过除除与疾病或病症有关的签名数据以外的所述基因组序列信息进行的,或者通过使受试者的基因组 序列具有包括与疾病或病症有关的签名数据的参考序列。 此外,本发明涉及一种方法,其中包括使用受试者的功能性遗传信息,特别是基因表达数据,以及一种方法,其中所述信息被编码在矩阵中并且基于马尔科夫链过程进行解码和表示。 获得的信息还可以用于诊断,检测,监测或预测疾病和/或用于制备受试者的分子病史。 此外,提供了优选地以电子图片/数据归档和通信系统的形式的相应的临床决策支持和存储系统。
    • 4. 发明申请
    • IDENTIFICATION OF MULTI-MODAL ASSOCIATIONS BETWEEN BIOMEDICAL MARKERS
    • 鉴定生物医学标记之间的多模式协会
    • US20130196877A1
    • 2013-08-01
    • US13877346
    • 2011-10-04
    • Nilanjana BanerjeeAngel JanevskiSitharthan KamalakaranVinay VaradanNevenka DimitrovaRobert Lucito
    • Nilanjana BanerjeeAngel JanevskiSitharthan KamalakaranVinay VaradanNevenka DimitrovaRobert Lucito
    • G06F19/20
    • G16B25/00G16B5/00G16B20/00
    • The present invention relates to a method for identifying multi-modal associations between biomedical markers which allows for the determination of network nodes and/or high ranking network members or combinations thereof, indicative of having a diagnostic, prognostic or predictive value for a medical condition, in particular ovarian cancer. The present invention further relates to a biomedical marker or group of biomedical markers associated with a high likelihood of responsiveness of a subject to a cancer therapy, preferably a platinum based cancer therapy, wherein said bio-medical marker or group of biomedical markers comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 8, 19, 20 or all markers selected from PKMYT1, SKIL, RAB8A, HIRIP3, CTNNB1, NGFR, ZCCHC11, LSP1, CD200, PAX8, CYBRD1, HOXC11, TCEAL1, FZD10,FZD1, BBS4, IRS2, TLX3, TSPAN2, TXN, and CFLAR. Furthermore, an assay for detecting, diagnosing, graduating, monitoring or prognosticating a medical condition, or for detecting, 1 diagnosing, monitoring or prognosticating the responsiveness of a subject to a therapy against said medical condition, in particular ovarian cancer, is provided, as well as a corresponding method for classifying a subject comprising and a medical decision support system.
    • 本发明涉及一种用于识别生物医学标记之间的多模式关联的方法,其允许确定网络节点和/或高排名网络成员或其组合,指示具有用于医疗状况的诊断,预后或预测值, 特别是卵巢癌。 本发明还涉及与受试者对癌症治疗(优选基于铂的癌症治疗)的高反应性的高可能性相关联的生物医学标记物或生物医学标记物组,其中所述生物医学标记物或生物医学标记物组至少包括 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,8,19,20或选自PKMYT1,SKIL,RAB8A, HIRIP3,CTNNB1,NGFR,ZCCHC11,LSP1,CD200,PAX8,CYBRD1,HOXC11,TCEAL1,FZD10,FZD1,BBS4,IRS2,TLX3,TSPAN2,TXN和CFLAR。 此外,提供了用于检测,诊断,毕业,监测或预测医学状况或用于检测1诊断,监测或预测受试者对于针对所述医学病症,特别是卵巢癌的治疗的反应性的测定法,作为 以及用于分类受试者的相应方法以及医疗决策支持系统。
    • 6. 发明授权
    • Method to automatically decode microarray images
    • 自动解码微阵列图像的方法
    • US08199991B2
    • 2012-06-12
    • US12516931
    • 2007-12-03
    • Lalitha AgnihotriJames David SchafferNevenka Dimitrova
    • Lalitha AgnihotriJames David SchafferNevenka Dimitrova
    • G06K9/36
    • G06K9/00134G06K9/3233G06K9/3275G06T7/70G06T2207/20056G06T2207/30072
    • A method of automatically identifying the microarray chip corners and probes, even if there are no probes at the corners, in a high density and high resolution microarray scanned image having an image space, wherein the method minimizes the error distortions in the image arising in the scanning process by applying to the image a multipass corner finding algorithm comprising: (a) applying a Radon transform to an input microarray image to project the image into an angle and distance space where it is possible to find the orientation of the straight lines; (b) applying a fast Fourier transform to the projected image of (a) to find the optimal tilting angle of the projected image; (c) determining the optimal first and last local maxima for the optimal tilting angle; (d) back projecting the determined first and last local maxima to the image space to find the first approximation of the first and last column lines of the image; (e) rotating the image and repeating steps (a) through (d) to find the first approximation of the top and bottom row lines of the image; (f) determining the first approximation of the four corners of the image from the intersection of the column and row lines; (g) applying a heuristic for determining if the first approximation of step (f) is sufficient; and (h) optionally trimming the scanned image around the first approximation of the four corners and repeating steps (a) through (f).
    • 即使在具有图像空间的高密度和高分辨率的微阵列扫描图像中,即使在角落处没有探针也能够自动识别微阵列芯片角部和探针的方法,其中该方法使图像中产生的图像中的误差失真最小化 扫描过程,通过向图像应用多点角发现算法,包括:(a)将Radon变换应用于输入微阵列图像以将图像投影到可以找到直线的取向的角度和距离空间中; (b)对(a)的投影图像应用快速傅立叶变换以找到投影图像的最佳倾斜角; (c)确定最佳倾斜角的最佳第一和最后局部最大值; (d)将确定的第一和最后局部最大值向前投影到图像空间,以找到图像的第一列和最后一列的第一近似; (e)旋转图像并重复步骤(a)至(d)以找到图像的顶行和下行行的第一近似值; (f)从列和行之间的交点确定图像的四个角的第一近似值; (g)应用启发式来确定步骤(f)的第一近似是否足够; 和(h)可选地修整围绕四个角的第一近似的扫描图像并重复步骤(a)至(f)。
    • 9. 发明申请
    • IN VIVO EXPRESSION ANALYSIS USING ULTRASOUND-INDUCED TRANSFECTION OF REPORTER CONSTRUCTS
    • 使用超声波诱导的报告器结构转移的体检表达分析
    • US20100239502A1
    • 2010-09-23
    • US12668551
    • 2008-06-26
    • Evan Edward SantoNevenka DimitrovaCHIEN Ting Chien
    • Evan Edward SantoNevenka DimitrovaCHIEN Ting Chien
    • A61K49/00C12N15/85C12Q1/68
    • C12N15/1086C12Q1/6897C12Q2565/101
    • The invention features compositions and methods for in vivo expression analysis. The data presented herein demonstrates that ultrasound-enhanced delivery and/or expression of a composition for expression analysis comprising microbubbles vectors as well as a genetic payload, comprising a “always-on” promoter, a “reference” reporter gene, a “query” promoter and an “answer” reporter gene, enables in vivo analysis of gene expression both without requiring prior preparation (especially genetic modification) of the test subject (animal or patient) and without causing long term or systemic effects on the subject. Such an invention can be used, for example, to query the epigenotypic or phenotypic response of the individual subject to a foreign effector substance such as a pyrogen, pharmaceutical compound, pharmaceutical lead compound, an allergen, an autoimmunogene, a toxin, a polyclonal antibody, a monoclonal antibody, an antigen, a lipid, a carbohydrate, a peptide, a protein, a protein-complex, an amino acid, a fatty acid, a nucleotide, DNA, RNA, PNA, siRNA and micro RNA.
    • 本发明的特征在于用于体内表达分析的组合物和方法。 本文提供的数据表明包括微泡载体和遗传有效载荷的用于表达分析的组合物的超声增强递送和/或表达,包括“始终在上”启动子,“参考”报告基因,“查询” 启动子和“答案”报告基因,能够在不需要测试对象(动物或患者)的事先准备(特别是遗传修饰)的情况下进行基因表达的体内分析,并且不会对受试者造成长期或全身影响。 这样的发明可以用于例如查询个体受试者对外源性效应物质如热原,药物化合物,药物引导化合物,变应原,自身免疫原,毒素,多克隆抗体的表型表型或表型反应 ,单克隆抗体,抗原,脂质,碳水化合物,肽,蛋白质,蛋白质复合物,氨基酸,脂肪酸,核苷酸,DNA,RNA,PNA,siRNA和微RNA。
    • 10. 发明申请
    • METHODS AND SYSTEMS FOR IDENTIFICATION OF DNA PATTERNS THROUGH SPECTRAL ANALYSIS
    • 通过光谱分析识别DNA图案的方法和系统
    • US20090129647A1
    • 2009-05-21
    • US12282435
    • 2007-03-07
    • Nevenka DimitrovaYee Him Cheung
    • Nevenka DimitrovaYee Him Cheung
    • G06K9/00
    • G06F19/22G06F19/24G06F19/26
    • Spectrogram extraction from DNA sequence has been known since 2001. A DNA spectrogram is generated by applying Fourier transform to convert a symbolic DNA sequence consisting of letters A, T, C, G into a visual representation that highlights periodicities of co-occurrence of DNA patterns. Given a DNA sequence or whole genomes, with this method it is easy to generate a large number of spectrogram images. However, the difficult part is to elucidate where are the repetitive patterns and to associate a biological and clinical meaning to them. The present disclosure provides systems and methods that facilitate the location and/or identification of repetitive DNA patterns, such as CpG islands, Alu repeats, tandem repeats and various types of satellite repeats. These repetitive elements can be found within a chromosome, within a genome or across genomes of various species. The disclosed systems and methods apply image processing operators to find prominent features in the vertical and horizontal direction of the DNA spectrograms. Systems and methods for fast, full scale analysis of the derived images using supervised machine learning methods are also disclosed. The disclosed systems and methods for detecting and/or classifying repetitive DNA patterns include: (a) comparative histogram method, (b) feature selection and classification using support vector machines and genetic algorithms, and (c) generation of spectrovideo from a plurality of spectral images.
    • 从2001年开始,DNA序列的谱图提取是已知的。通过应用傅立叶变换将由字母A,T,C,G组成的符号DNA序列转换成突出显示DNA图案共同出现周期的视觉表示,生成DNA谱图 。 给定一个DNA序列或整个基因组,用这种方法很容易产生大量的谱图。 然而,困难的部分是阐明重复模式在哪里,并将生物和临床意义与他们联系起来。 本公开提供了促进重复DNA模式(例如CpG岛,Alu重复序列,串联重复序列和各种类型的卫星重复)的定位和/或识别的系统和方法。 这些重复元件可以在染色体内,基因组内或各种物种的基因组中发现。 所公开的系统和方法应用图像处理算子以在DNA谱图的垂直和水平方向上发现显着特征。 还公开了使用监督机器学习方法对衍生图像进行快速,全面分析的系统和方法。 用于检测和/或分类重复DNA模式的所公开的系统和方法包括:(a)比较直方图方法,(b)使用支持向量机和遗传算法的特征选择和分类,以及(c)从多个光谱 图片。