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).

  • Patent number: 8924232
    Abstract: 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: Grant
    Filed: May 5, 2010
    Date of Patent: December 30, 2014
    Assignee: Koninklijke Philips N.V.
    Inventors: Yasser H. Alsafadi, Nilanjana Banerjee, Vinay Varadan, Angel J. Janevski
  • Publication number: 20140379379
    Abstract: 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: Application
    Filed: June 24, 2014
    Publication date: December 25, 2014
    Inventors: ANGEL JANEVSKI, SITHARTHAN KAMALAKARAN, NILANJANA BANERJEE, VINAY VARADAN, NEVENKA DIMITROVA, MINE DANISMAN TASAR
  • Publication number: 20140365243
    Abstract: 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: Application
    Filed: November 29, 2012
    Publication date: December 11, 2014
    Inventors: Vinay Varadan, Sitharthan Kamalakaran, Angel Janevski, Nilanjana Banerjee, Nevenka Dimitrova
  • Patent number: 8762072
    Abstract: 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: Grant
    Filed: September 24, 2009
    Date of Patent: June 24, 2014
    Assignee: Koninklijke Philips N.V.
    Inventors: Angel Janevski, Nilanjana Banerjee, Yasser Alsafadi, Vinay Varadan
  • Publication number: 20140040264
    Abstract: 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: Application
    Filed: January 30, 2012
    Publication date: February 6, 2014
    Applicant: Hgh Tech Campus
    Inventors: Vinay Varadan, Prateek Mittal, Sitharthan Kamalakaran, Nevenka Dimitrova, Angel Janevski, Nilanjana Banerjee
  • Publication number: 20130282404
    Abstract: 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: Application
    Filed: January 4, 2012
    Publication date: October 24, 2013
    Inventors: Angel Janevski, Sitharthan Kamalakaran, Christian Reichelt, Nilanjana Banerjee, Vinay Varadan, Nevenka Dimitrova
  • Publication number: 20130196877
    Abstract: 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: Application
    Filed: October 4, 2011
    Publication date: August 1, 2013
    Applicants: COLD SPRING HARBOR LABORATORY, KONINKLIJKE PHILIPS ELECTRONICS N.V.
    Inventors: Nilanjana Banerjee, Angel Janevski, Sitharthan Kamalakaran, Vinay Varadan, Nevenka Dimitrova, Robert Lucito
  • Publication number: 20120290218
    Abstract: 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: Application
    Filed: June 27, 2012
    Publication date: November 15, 2012
    Inventors: Dimitris Anastassiou, Vinay Varadan
  • Publication number: 20120265446
    Abstract: 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: Application
    Filed: May 18, 2010
    Publication date: October 18, 2012
    Applicant: KONINKLIJKE PHILIPS ELECTRONICS N.V.
    Inventors: Angel Janevski, Vinay Varadan, Nilanjana Banerjee
  • Patent number: 8290715
    Abstract: 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: Grant
    Filed: June 4, 2008
    Date of Patent: October 16, 2012
    Assignee: The Trustees of Columbia University in the City of New York
    Inventors: Dimitris Anastassiou, Vinay Varadan
  • Publication number: 20120253686
    Abstract: 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: Application
    Filed: June 5, 2012
    Publication date: October 4, 2012
    Inventors: Dimitris Anastassiou, Vinay Varadan
  • Patent number: 8234077
    Abstract: 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: Grant
    Filed: May 10, 2007
    Date of Patent: July 31, 2012
    Assignee: The Trustees of Columbia University in the City of New York
    Inventors: Dimitris Anastassiou, Vinay Varadan
  • Publication number: 20120172238
    Abstract: 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: Application
    Filed: September 15, 2010
    Publication date: July 5, 2012
    Applicants: COLD SPRING HARBOR LABORATORIES, KONINKLIJKE PHILIPS ELECTRONICS N.V.
    Inventors: Vinay Varadan, Sitharthan Kamalakaran, James Bruce Hicks
  • Publication number: 20120109678
    Abstract: 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: Application
    Filed: May 5, 2010
    Publication date: May 3, 2012
    Applicant: KONINKLIJKE PHILIPS ELECTRONICS N.V.
    Inventors: Yasser H. Alsafadi, Nilanjana Banerjee, Vinay Varadan, Angel J. Janevski
  • Publication number: 20120004855
    Abstract: 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: Application
    Filed: December 22, 2009
    Publication date: January 5, 2012
    Applicant: KONINKLIJKE PHILIPS ELECTRONICS N.V.
    Inventors: Sitharthan Kamalakaran, Vinay Varadan, James B. Hicks
  • Publication number: 20110281756
    Abstract: 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: Application
    Filed: November 13, 2009
    Publication date: November 17, 2011
    Inventors: Ying Wu, Hongguang Zhu, Jian Li, Liang Xu, Wilhelmus F.J. Verhaegh, Yiping Ren, Angel Janevski, Vinay Varadan, Zhaoyong Li, Nevenka Dimitrova
  • Publication number: 20110173201
    Abstract: 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: Application
    Filed: September 24, 2009
    Publication date: July 14, 2011
    Applicant: KONINKLIJKE PHILIPS ELECTRONICS N.V.
    Inventors: Angel Janevski, Nilanjana Banerjee, Yasser Alsafadi, Vinay Varadan
  • Publication number: 20110077964
    Abstract: The present invention relates to effective diagnosis of patients and assisting clinicians in treatment planning. In particular, invention provides a medical analysis system that enables refinement of molecular classification. The system provides a molecular profiling solution that will allow improved diagnosis, prognosis, response prediction to provide the right chemotherapy, and follow-up to monitor for cancer recurrence.
    Type: Application
    Filed: May 6, 2009
    Publication date: March 31, 2011
    Applicant: KONINKLIJKE PHILIPS ELECTRONICS N.V.
    Inventors: Angel J. Janevski, Nevenka Dimitrova, Sitharthan Kamalakaran, Yasser Alsafadi, Nilanjana Banerjee, Anca Ioana Daniela Bacur, Jasper Van Leeuwen, Vinay Varadan
  • Publication number: 20090299643
    Abstract: Systems and methods for selecting factors from a data set of measurements are provided. The measurements include values of factors and/or outcomes. Two or more factors that are jointly associated with one or more outcomes from the data set are identified. Each of the two or more factors are analyzed to determine at least one cooperative interaction among the factors with respect to an outcome. The two or more factors can be a module of factors.
    Type: Application
    Filed: May 10, 2007
    Publication date: December 3, 2009
    Inventors: Dimitris Anastassiou, Vinay Varadan
  • Publication number: 20080300799
    Abstract: 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: Application
    Filed: June 4, 2008
    Publication date: December 4, 2008
    Inventors: Dimitris Anastassiou, Vinay Varadan