Patents by Inventor Vinay Varadan
Vinay Varadan has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20150310632Abstract: Image texture feature values are computed for a set of image texture features from an image of an anatomical feature of interest in a subject, and the subject is classified respective to a molecular feature of interest based on the computed image texture feature values. The image texture feature values may be computed from one or more gray level co-occurrence matrices (GLCMs), and the image texture features may include Haralick and/or Tamura image texture features. To train the classifier, reference image texture feature values are computed for at least the set of image texture features from images of the anatomical feature of interest in reference subjects. The reference image texture feature values are divided into different population groups representing different values of the molecular feature of interest, and the classifier is trained to distinguish between the different population groups based on the reference image texture feature values.Type: ApplicationFiled: October 25, 2013Publication date: October 29, 2015Inventors: NILANJANA BANERJEE, NEVENKA DIMITROVA, VINAY VARADAN, SITHARTHAN KAMALAKARAN, ANGEL JANEVSKI, SAYAN MAITY
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Publication number: 20150294063Abstract: Relevance of a study genetic variant observed in diagnostic subject genetic data that is associated by a clinical study with a phenotype characteristic is assessed as follows. A set of polymorphisms functionally related to the study genetic variant are identified. A foreground distribution is computed of variants observed in the diagnostic subject genetic data for the set of polymorphisms. A background distribution is computed of variants observed in genetic data of subjects of the clinical study for the set of polymorphisms. A comparison metric is computed comparing the foreground distribution and the background distribution. Relevance of the study variant to the diagnostic subject is quantified based on the comparison metric, with higher similarity of the foreground and background distributions corresponding to higher relevance.Type: ApplicationFiled: November 15, 2013Publication date: October 15, 2015Applicant: KONINKLIJKE PHILIPS N.V.Inventors: Sitharthan Kalalakaran, Vinay Varadan, Nilanjana Banerjee, Angel Janevski, Nevenka Dimitrova
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Patent number: 9074206Abstract: The present invention relates compositions and methods for microRNA (miRNA) expression profiling of colorectal cancer. In particular, the invention relates to a diagnostic kit of molecular markers for identifying one or more mammalian target cells exhibiting or having a predisposition to develop colorectal cancer, the kit comprising a plurality of nucleic acid molecules, each nucleic acid molecule encoding a miRNA sequence, wherein one or more of the plurality of nucleic acid molecules are differentially expressed in the target cells and in one or more control cells, and wherein the one or more differentially expressed nucleic acid molecules together represent a nucleic acid expression signature that is indicative for the presence of or the predisposition to develop colorectal cancer.Type: GrantFiled: November 13, 2009Date of Patent: July 7, 2015Assignee: Fudan UniversityInventors: Ying Wu, Hongguang Zhu, Jian Li, Liang Xu, Wilhelmus F. J. Verhaegh, Yiping Ren, Angel Janevski, Vinay Varadan, Zhaoyong Li, Nevenka Dimitrova
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Publication number: 20150097868Abstract: An imaging visualization workstation (30) includes a graphical display device (32) and an electronic data processor, and is configured to perform a method including: spatially registering a biopsy sample extracted from a medical subject with a medical image (12) of the medical subject; combining the medical image with a graphical representation of information (20, 22) generated from the biopsy sample to generate a combined image in which the graphical representation is spatially delineated based on the spatial registration of the biopsy sample; and displaying the combined image on the graphical display device of the imaging visualization workstation. A method comprises extracting a biopsy sample spatial sample from a medical subject, processing the biopsy sample to generate biopsy information, acquiring a medical image of the subject, spatially registering the biopsy sample with the medical image, and displaying the medical image modified to include an annotation generated from the biopsy information.Type: ApplicationFiled: March 20, 2013Publication date: April 9, 2015Inventors: Nilanjana Banerjee, Sitharthan Kamalakaran, Vinay Varadan, Angel Janevski, Nevenka Dimitrova
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Publication number: 20150058322Abstract: When generating visual representations of gene activity pathways for clinical decision support, a validated pathway database that stores a plurality of validated pathways is accessed, wherein each pathway describes at least one interaction between a plurality of genes. A processor (18) is configured to execute computer-executable instructions stored in a memory (16), the instructions comprising visually representing gene activity level (28) for at least one gene across a plurality of populations, retrieving a pathway (32) from the validated pathway database, wherein the pathway includes the at least one gene, and visually representing gene activity levels for all genes in the pathway.Type: ApplicationFiled: March 27, 2013Publication date: February 26, 2015Applicant: KONINKLIJKE PHILIPS N.V.Inventors: Nevenka Dimitrova, Angel Janevski, Nilanjana Banerjee, Vinay Varadan, Sitharthan Kamalakaran
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Patent number: 8924232Abstract: A method (10) for clinical decision support by comparison of multiple molecular signatures of biological data is provided. The method comprises comparing at least two of said molecular signatures are different kinds of molecular signatures. Furthermore, a device (70), a system (100), and a computer program product (200) and a use for clinical decision support, performing the steps according to the method (10) is provided.Type: GrantFiled: May 5, 2010Date of Patent: December 30, 2014Assignee: Koninklijke Philips N.V.Inventors: Yasser H. Alsafadi, Nilanjana Banerjee, Vinay Varadan, Angel J. Janevski
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Publication number: 20140379379Abstract: In a clinical decision support method, outputs of computer-implemented analytical modules are computed for a patient. Information is displayed for the patient pertaining to a clinical question comprising outputs computed for the patient of analytical modules associated with the clinical question. The analytical modules may include modules configured to perform in silico genetic/genomic tests using genetic/genome sequencing (whole genome, whole exome, whole transcriptome, targeted gene panels, etc) or microarray data. A clinical question-module matrix (CQ-M matrix) may be generated for the patient associating clinical questions with analytical modules, and the method may further include populating the clinical questions with outputs computed for the patient of the analytical modules associated with the clinical questions by the CQ-M matrix.Type: ApplicationFiled: June 24, 2014Publication date: December 25, 2014Inventors: ANGEL JANEVSKI, SITHARTHAN KAMALAKARAN, NILANJANA BANERJEE, VINAY VARADAN, NEVENKA DIMITROVA, MINE DANISMAN TASAR
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Publication number: 20140365243Abstract: A catalog (34) of molecular marker tests specifies molecular marker tests annotated with clinical applicability annotations. An electronic patient medical record (22) stores genetic sequencing data (20) of a patient. A clinical decision support (CDS) system (30) is configured to track the clinical context of the patient wherein the clinical context includes at least a disease diagnosis and a current patient care stage. A catalog search module (32) is configured to search the catalog of molecular marker tests to identify a molecular marker test having clinical applicability to the patient in the clinical context tracked by the CDS system. The search is automatically triggered by occurrence of a trigger event defined by a set of triggering rules. A testing module (44) is configured to perform a molecular marker test identified by the identification module in silico using the genetic sequencing data of the patient stored in the electronic patient medical record.Type: ApplicationFiled: November 29, 2012Publication date: December 11, 2014Inventors: Vinay Varadan, Sitharthan Kamalakaran, Angel Janevski, Nilanjana Banerjee, Nevenka Dimitrova
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Patent number: 8762072Abstract: This invention relates to a method and an apparatus for determining a reliability indicator for at least one set of signatures obtained from clinical data collected from a group of samples. The signatures are obtained by detecting characteristics in the clinical data from the group of sample sand each of the signatures generate a first set of stratification values that stratify the group of samples. At least one additional and parallel stratification source to the signatures obtained from group of sample sis provided, the at least one additional and parallel stratification source to the signatures being independent from the signatures and generates a second set of stratification values. A comparison is done for each respective sample, where the first stratification values are compared with a true reference stratification values, and where the second stratification values are compared with the true reference stratification values.Type: GrantFiled: September 24, 2009Date of Patent: June 24, 2014Assignee: Koninklijke Philips N.V.Inventors: Angel Janevski, Nilanjana Banerjee, Yasser Alsafadi, Vinay Varadan
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Publication number: 20140040264Abstract: The present invention relates to a method for stratifying a patient into a clinically relevant group comprising the identification of the probability of an alteration within one or more sets of molecular data from a patient sample in comparison to a database of molecular data of known phenotypes, the inference of the activity of a biological network on the basis of the probabilities, the identification of a network information flow probability for the patient via the probability of interactions in the network, the creation of multiple instances of network information flow for the patient sample and the calculation of the distance of the patient from other subjects in a patient database using multiple instances of the network information flow.Type: ApplicationFiled: January 30, 2012Publication date: February 6, 2014Applicant: Hgh Tech CampusInventors: Vinay Varadan, Prateek Mittal, Sitharthan Kamalakaran, Nevenka Dimitrova, Angel Janevski, Nilanjana Banerjee
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Publication number: 20130282404Abstract: A state machine (22) stores a current state (30) comprising a clinical context defined by available patient-related information relating to a medical patient, and identifies one or more available analytical tools of a set of analytical tools (24) that are applicable to the current state. A graphical user interface module (16) receives a user selection of an available analytical tool. The state machine loads patient-related information (40) to the user-selected available analytical tool (24sel) and invokes the user-selected available analytical tool to operate on the loaded patient-related information to generate additional patient-related information relating to the medical patient and/or graphical patient-related content relating to the medical patient. The state machine transitions from the current state (30) to a next state (30?) and/or invokes the graphical user interface module to display the graphical patient related content.Type: ApplicationFiled: January 4, 2012Publication date: October 24, 2013Inventors: Angel Janevski, Sitharthan Kamalakaran, Christian Reichelt, Nilanjana Banerjee, Vinay Varadan, Nevenka Dimitrova
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Publication number: 20130196877Abstract: 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.Type: ApplicationFiled: October 4, 2011Publication date: August 1, 2013Applicants: COLD SPRING HARBOR LABORATORY, KONINKLIJKE PHILIPS ELECTRONICS N.V.Inventors: Nilanjana Banerjee, Angel Janevski, Sitharthan Kamalakaran, Vinay Varadan, Nevenka Dimitrova, Robert Lucito
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Publication number: 20120290218Abstract: A method is provided for selecting two or more genes from gene expression data. In the method, gene expression data for a plurality of genes is provided, where the gene expression data include expression levels for each of the plurality of genes. The gene expression data is discretized. Based on the discretized gene expression data, the synergy among the plurality of genes with respect to a phenotype, for example, presence or absence of a disease in a tissue, is evaluated. Two or more genes whose synergy exceeds a predetermined threshold are selected. A system implementing the method is also provided.Type: ApplicationFiled: June 27, 2012Publication date: November 15, 2012Inventors: Dimitris Anastassiou, Vinay Varadan
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Publication number: 20120265446Abstract: A method (10) for forming novel signatures of biological data is provided. The method comprises ranking features based on a trend value, which is created based on multiple signatures identified by a pattern discovery method. Furthermore, a device (30) and a computer program product (40), performing the steps according to the method (10) is provided. Uses of the method, for statistically analyzing clinical data, designing assays based on multiple molecular signatures and interpreting assays based on multiple molecular signatures are also provided.Type: ApplicationFiled: May 18, 2010Publication date: October 18, 2012Applicant: KONINKLIJKE PHILIPS ELECTRONICS N.V.Inventors: Angel Janevski, Vinay Varadan, Nilanjana Banerjee
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Patent number: 8290715Abstract: The disclosed subject matter provides techniques for multiple-factor selection. The factors can be features or elements that are jointly associated with one or more outcomes by their joint presence or absence. There may be a non-causative correlation between the factors, features, or elements and the outcomes. In some embodiments, Entropy Minimization and Boolean Parsimony (EMBP) is used to identify modules of genes jointly associated with disease from gene expression data, and a logic function is provided to connect the combined expression levels in each gene module with the presence of disease. The smallest module of genes whose joint expression levels can predict the presence of disease can be identified.Type: GrantFiled: June 4, 2008Date of Patent: October 16, 2012Assignee: The Trustees of Columbia University in the City of New YorkInventors: Dimitris Anastassiou, Vinay Varadan
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Publication number: 20120253686Abstract: The disclosed subject matter provides techniques for multiple-factor selection. The factors can be features or elements that are jointly associated with one or more outcomes by their joint presence or absence. There may be a non-causative correlation between the factors, features, or elements and the outcomes. In some embodiments, Entropy Minimization and Boolean Parsimony (EMBP) is used to identify modules of genes jointly associated with disease from gene expression data, and a logic function is provided to connect the combined expression levels in each gene module with the presence of disease. The smallest module of genes whose joint expression levels can predict the presence of disease can be identified.Type: ApplicationFiled: June 5, 2012Publication date: October 4, 2012Inventors: Dimitris Anastassiou, Vinay Varadan
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Patent number: 8234077Abstract: A method is provided for selecting two or more genes from gene expression data. In the method, gene expression data for a plurality of genes is provided, where the gene expression data include expression levels for each of the plurality of genes. The gene expression data is discretized. Based on the discretized gene expression data, the synergy among the plurality of genes with respect to a phenotype, for example, presence or absence of a disease in a tissue, is evaluated. Two or more genes whose synergy exceeds a predetermined threshold are selected. A system implementing the method is also provided.Type: GrantFiled: May 10, 2007Date of Patent: July 31, 2012Assignee: The Trustees of Columbia University in the City of New YorkInventors: Dimitris Anastassiou, Vinay Varadan
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Publication number: 20120172238Abstract: The present invention relates to a method for assisting in diagnosing breast cancer and/or monitoring breast cancer progression in a given sample based on the analysis of differential DNA methylation patterns. More particularly, the method is directed to the identification of one or more epigenetic markers that derive from the application of a variety of statistical methods in order to point out the prognostic significance of the difference in methylation states at one or more genomic loci and predict whether the sample analyzed has a good or bad prognosis following treatment.Type: ApplicationFiled: September 15, 2010Publication date: July 5, 2012Applicants: COLD SPRING HARBOR LABORATORIES, KONINKLIJKE PHILIPS ELECTRONICS N.V.Inventors: Vinay Varadan, Sitharthan Kamalakaran, James Bruce Hicks
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Publication number: 20120109678Abstract: A method (10) for clinical decision support by comparison of multiple molecular signatures of biological data is provided. The method comprises comparing at least two of said molecular signatures are different kinds of molecular signatures. Furthermore, a device (70), a system (100), and a computer program product (200) and a use for clinical decision support, performing the steps according to the method (10) is provided.Type: ApplicationFiled: May 5, 2010Publication date: May 3, 2012Applicant: KONINKLIJKE PHILIPS ELECTRONICS N.V.Inventors: Yasser H. Alsafadi, Nilanjana Banerjee, Vinay Varadan, Angel J. Janevski
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Publication number: 20120004855Abstract: A methylation classification list comprising loci DNA, for which loci the methylation status of the DNA is indicative of likelihood of recurrence of cancer, is provided. Furthermore, a method, apparatus and use for predicting probability of relapse free survival of a subject diagnosed with cancer, are provided.Type: ApplicationFiled: December 22, 2009Publication date: January 5, 2012Applicant: KONINKLIJKE PHILIPS ELECTRONICS N.V.Inventors: Sitharthan Kamalakaran, Vinay Varadan, James B. Hicks