Patents by Inventor Nevenka Dimitrova

Nevenka Dimitrova 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).

  • Publication number: 20210020269
    Abstract: Methods, systems and apparatus for detecting patterns in constituents of at least one biological organism are disclosed. In accordance with one method, clusters of the constituents are determined by selecting different subsets of at least one of genes or proteins and identifying the clusters from biological data corresponding to the selected subsets. Here, membership values for the constituents, indicating membership within the clusters, are calculated for use as a basis of an additional cluster determination process to obtain final clusters of constituents. By underpinning the preliminary clustering on different subsets of biological data and formulating the higher-level clustering on the basis of the membership values, the embodiments can enable an evaluation of a large variety of biological data in a practical, accurate and highly efficient manner.
    Type: Application
    Filed: October 2, 2020
    Publication date: January 21, 2021
    Inventors: Konstantin Volyanskyy, Nevenka Dimitrova
  • Publication number: 20200394491
    Abstract: A system and method for providing sequencing of biomolecules, which can be used for differential analysis of a test sample from a normal sample.
    Type: Application
    Filed: August 13, 2018
    Publication date: December 17, 2020
    Inventors: Yee Him Cheung, Nevenka Dimitrova, Balaji Srinivasan Santhanam
  • Publication number: 20200395128
    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: June 2, 2020
    Publication date: December 17, 2020
    Inventors: Angel Janevski, Nevenka Dimitrova, Sitharthan Kamalakaran, Yasser Alsafadi, Nilanjana Banerjee, Anca Ioana Daniela Bucur, Jasper Johannes Adrianus van Leeuwen, Vinay Varadan
  • Publication number: 20200357484
    Abstract: A genomic/proteomic test synthesis method includes receiving a genomic/proteomic data set (12) comprising samples corresponding to persons with each sample including values of features of a set of features derived from genomic/proteomic data for the corresponding person. For each feature, univariate analysis (30) is performed to generate a sample density versus feature value data set for the feature, for example represented as a kernel density estimate (KDE) (52). Multivariate analysis (32, 34) is performed on the features using the KDEs to generate a set of discriminative features (36, 38). In one example, the multivariate analysis (32) uses energy spectral density (ESD) characteristics of the KDEs. In another example, the multivariate analysis (34) uses peak location characteristics of the KDEs.
    Type: Application
    Filed: October 23, 2018
    Publication date: November 12, 2020
    Inventors: Kostyantyn Volyanskyy, Nevenka Dimitrova
  • Patent number: 10832799
    Abstract: Methods, systems and apparatus for detecting patterns in constituents of at least one biological organism are disclosed. In accordance with one method, clusters of the constituents are determined (208) by selecting (210) different subsets of at least one of genes or proteins and identifying (212) the clusters from biological data corresponding to the selected subsets. Here, membership values for the constituents, indicating membership within the clusters, are calculated for use as a basis of an additional cluster determination process (208) to obtain final clusters of constituents. By underpinning the preliminary clustering on different subsets of biological data and formulating the higher-level clustering on the basis of the membership values, the embodiments can enable an evaluation of a large variety of biological data in a practical, accurate and highly efficient manner.
    Type: Grant
    Filed: August 12, 2016
    Date of Patent: November 10, 2020
    Assignee: Koninklijke Philips N.V.
    Inventors: Konstantin Volyanskyy, Nevenka Dimitrova
  • Patent number: 10734095
    Abstract: The present disclosure describes systems and methods for generating a priority score for a variant of a gene based on its potential significance to a disease. Priority scores may be calculated for multiple variants, and the variants may be ranked based on the generated priority scores.
    Type: Grant
    Filed: July 28, 2016
    Date of Patent: August 4, 2020
    Assignee: Koninklijke Philips N.V.
    Inventors: Vartika Agrawal, Nevenka Dimitrova
  • Publication number: 20200234801
    Abstract: A method (100) for recruiting a patient for a clinical trial, comprising: receiving (110) a dataset comprising information about one or more clinical trials each including patient eligibility criteria; extracting (120) the patient eligibility criteria from each of the clinical trials; converting (130) the patient eligibility criteria to a standardized patient eligibility criterion using a structured clinical trial mark-up language; storing (140) the patient eligibility criterion in a database (862), each of the criterion associated with one or more clinical trials; receiving (150) patient-specific data values about a patient; querying (160) the clinical trial eligibility criteria database using the patient-specific data values to identify eligibility criterion satisfied by the patient-specific data value; identifying (170) a clinical trial associated with the one or more standardized patient eligibility criterion satisfied by a received patient-specific data value; and providing (180) a report of the identifi
    Type: Application
    Filed: October 5, 2018
    Publication date: July 23, 2020
    Inventors: Yong Mao, Woei-Jye Yee, Alexander Ryan Mankovich, Qingxin Wu, Kostyantyn Volyanskyy, Nevenka Dimitrova
  • Patent number: 10679726
    Abstract: 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: Grant
    Filed: November 15, 2013
    Date of Patent: June 9, 2020
    Assignee: Koninklijke Philips N.V.
    Inventors: Sitharthan Kalalakaran, Vinay Varadan, Nilanjana Banerjee, Angel Janevski, Nevenka Dimitrova
  • Publication number: 20200152292
    Abstract: A system to identify genes that confer antibiotic resistance, comprising: a processor configured to: (i) identify a set of genes present in a sample of genome sequences sequenced from potentially pathogenic isolates; (ii) generate a genome sequence without the identified set of genes; (iii) generate a gene presence-absence matrix listing the genes present in each of the genome sequences, comprising an identification of each of the plurality of genes and an identification of each of the plurality of genome sequences, and comprising an identification of whether each of the genome sequences is obtained from an organism resistant to at least one antibiotic, and further comprising an identification of either presence or absence of the respective gene within the respective genome sequence; and (iv) identify at least one gene or mutation in the plurality of genome sequences associated with antibiotic resistance; and a user interface configured to provide a report.
    Type: Application
    Filed: January 17, 2020
    Publication date: May 14, 2020
    Inventors: KARTHIKEYAN MURUGESAN, NEVENKA DIMITROVA, HENRY LIN, PRAMOD MAYIGOWDA
  • Patent number: 10629291
    Abstract: Methods and systems for identifying causal genetic mechanisms of antibiotic resistance in pathogens. In accordance with at least one embodiment, the system includes a gene resistance module to identify genes present in an antibiotic resistant pathogen, a single nucleotide polymorphism module to identify mutations present in an antibiotic resistant pathogen, and an antibiotic resistance module configured to output the causation of antibiotic resistance based on the identified genes and mutations.
    Type: Grant
    Filed: March 9, 2017
    Date of Patent: April 21, 2020
    Assignee: Koninklijke Philips N.V.
    Inventors: Karthikeyan Murugesan, Nevenka Dimitrova, Henry Lin, Pramod Mayigowda
  • Publication number: 20200024658
    Abstract: A method and a system for interpreting data between two quantitative genomic datasets are described, wherein datasets are associated with the same disease or condition, for example, samples from the same patient obtained on different genomic platforms with varying data acquisition parameters. The data samples in each of the first and second datasets are rank ordered and the relative distances among the data samples are determined. The value ranks and relative distances are then used to correlate to data samples in the first and second quantitative genomic datasets, with the output provided to a user, such as a clinician or a patient.
    Type: Application
    Filed: March 28, 2018
    Publication date: January 23, 2020
    Inventors: Kostyantyn Volyanskyy, Nevenka Dimitrova, Yong Mao
  • Patent number: 10541052
    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: Grant
    Filed: November 29, 2012
    Date of Patent: January 21, 2020
    Assignee: Koninklijke Philip N.V.
    Inventors: Vinay Varadan, Sitharthan Kamalakaran, Angel Janevski, Nilanjana Banerjee, Nevenka Dimitrova
  • Publication number: 20200020421
    Abstract: A clinical genomic data processing device includes at least one microprocessor (10) and a non-transitory storage medium (12) storing instructions to implement functions of the device. A user interface (26, 28) receives requests for execution of genomic workflows and to display output generated by the execution of the genomic workflows. A genomic workflow manager manages an asynchronous messaging queue (24) and manages the execution of the genomic workflows. Service providers (20) performs jobs associated with the genomic workflows. The genomic workflow manager communicates with the service providers by messages exchanged via the asynchronous messaging queue to manage the execution of the genomic workflows via jobs performed by the service providers.
    Type: Application
    Filed: September 29, 2017
    Publication date: January 16, 2020
    Inventors: Nevenka Dimitrova, Ronen Solomon, Keswarpu Payal, Mine Danisman-Tasar, Moran Bentzur, Nadav Sharabi, Sergey Yussim, Alexander Ryan Mankovich, Vartika Agrawal, Julie Gu, Iliya Fridman, Kostyantyn Volyanskyy
  • Publication number: 20200020423
    Abstract: A system and method for providing a prioritized list of clinical trials that are relevant to a patient suffering from an illness or disease, such as cancer, are disclosed. Specifically, a method for conducting an automated, real time clinical trial search and a prioritization analysis is described. The method comprises the steps of conducting an automated full-text clinical trial search based on structuralization of clinical trial eligibility data and knowledge-based inference, initiating a query from the patient's side, and providing a prioritized list of all accessible clinical trials fulfilling a particular query. The system provides better sensitivity, precision and negative predictive value than the current most known clinical trial matching tool: clinicaltrials.gov.
    Type: Application
    Filed: September 26, 2017
    Publication date: January 16, 2020
    Inventors: Qingxin Wu, Alexander Ryan Mankovich, Abhishek Talluli, Kostyantyn Volyanskyy, Nevenka Dimitrova, Yong Mao, Charles Yee
  • Patent number: 10528758
    Abstract: Methods and apparatus for a secure framework for storing and analyzing genomic data. Embodiments of the present invention apply persistent governance to sensitive information and to the analytics that operate upon it, managing the interaction between the two.
    Type: Grant
    Filed: April 24, 2015
    Date of Patent: January 7, 2020
    Assignees: Koninklijke Philips N.V., Intertrust Technologies Corporation
    Inventors: Nevenka Dimitrova, William Knox Carey, Raymond J. Krasinski, Jarl Nilsson, Bart Grantham, Alexander Ryan Mankovich, Vartika Agrawal
  • Patent number: 10460831
    Abstract: In a predictive outcome assessment test for predicting whether a patient undergoing a breast cancer treatment regimen will achieve pathological complete response (pCR), differential gene expression level information are generated for an input set of genes belonging to the TGF-? signaling pathway. The differential gene expression level information compares baseline gene expression level information from a baseline sample (70) of a breast tumor of a patient acquired before initiating (71) a breast cancer therapy regimen to the patient and response gene expression level information from a response sample (72) of the breast tumor acquired after initiating the breast cancer therapy regimen by administering a first dose of bevacizumab to the patient. A pCR prediction for the patient is computed based on the differential gene expression level information for the input set of genes belonging to the TGF-? signaling pathway. Related predictive outcome assessment test development methods are also disclosed.
    Type: Grant
    Filed: November 22, 2013
    Date of Patent: October 29, 2019
    Assignee: Koninklijke Philips N.V.
    Inventors: Vinay Varadan, Sitharthan Kamalakaran, Angel Janevski, Nilanjana Banerjee, Nevenka Dimitrova, Lyndsay Harris
  • Patent number: 10340027
    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 biomedical 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: Grant
    Filed: October 4, 2011
    Date of Patent: July 2, 2019
    Assignee: Koninklijke Philips N.V.
    Inventors: Nilanjana Banerjee, Angel Janevski, Sitharthan Kamalakaran, Vinay Varadan, Nevenka Dimitrova, Robert Lucito
  • Publication number: 20190189248
    Abstract: Methods, systems and apparatus for detecting subpopulations of constituents of at least one biological organism are disclosed. In accordance with exemplary embodiments, cluster partitions of biological data samples compiled from constituents of at least one biological organism are evaluated (114) by computing inconsistency scores for the partitions based on an inconsistency measure. In addition, for at least one of the plurality of partitions, a non-zero value is allocated to the inconsistency measure of at least one cluster that has only one biological data sample. Further, the subpopulations are identified by selecting the partition of having the minimum inconsistency score as the subpopulations.
    Type: Application
    Filed: May 11, 2017
    Publication date: June 20, 2019
    Applicant: Koninklijke Philips N.V.
    Inventors: Konstantin VOLYANSKYY, Nevenka DIMITROVA, Yong MAO
  • Publication number: 20190079938
    Abstract: In patient cohort identification, clustering (30) of patients is performed using a patient comparison metric dependent on a set of features (24). Information is displayed on sample patients who are similar or dissimilar to a query patient according to the clustering. User inputted comparison values are received comparing the sample patients with the query patient. The set of features and/or feature weights are adjusted to generate an adjusted patient comparison metric having improved agreement with the user inputted comparison values. The clustering is repeated using the adjusted patient comparison metric. A patient cohort is identified from a cluster (34) containing the query patient produced by the last clustering repetition. The information on the sample patients may be shown by simultaneously displaying two or more graphical modality representations (70, 72, 74) each plotting the sample patients and the query patient against two or more features of the modality.
    Type: Application
    Filed: March 8, 2017
    Publication date: March 14, 2019
    Inventors: Vartika Agrawal, Alexander Ryan Mankovich, Nevenka Dimitrova, Nilanjana Banerjee, Yee Him Cheung, Johanna Maria De Bont, Jozef Hieronymus Maria Raijmakers
  • Publication number: 20190071718
    Abstract: A system for characterizing intercellular communication and heterogeneity in cancer tumors, and more particularly a method for detecting sub-populations and receptor-ligand states for providing predictive information in relation to cancer and cancer treatment is disclosed. The system comprises the steps of obtaining from a NGS sequencer, single-cell RNA-seq for a plurality of cells within a tumor, correlation with a plurality of data sets from a curated gene list of receptor-ligand pairs, normalizing their transcript abundance data, assigning states (e.g. 0,1,2,3) to each curated receptor-ligand pair in each cell (e.g.
    Type: Application
    Filed: April 7, 2017
    Publication date: March 7, 2019
    Inventors: Balaji Srinivasan Santhanam, Yee Him Cheung, Vartika Agrawal, Johanna Maria De Bont, Nevenka Dimitrova