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).

  • 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
  • Publication number: 20180341746
    Abstract: The present disclosure pertains to a system, a method of using such a system, and a non-transitory computer-readable medium containing instructions to such a system for generating annotated gene fusion data from processing both a patient's DNA and RNA sequence information thereby filtering out weak candidate gene fusions. Thus the annotated gene fusion data contains clinically relevant information and accurate gene fusion detections (low false-positives) for use in clinical and/or R&D settings. The system, method and computer-readable medium allows a user to generate gene fusion data by detecting breakpoints from a patient's DNA-SEQ and RNA-SEQ, creating candidate breakpoint data by combining matching breakpoints from the DNA-SEQ and RNA-SEQ breakpoint data, determining confidence levels of the candidate breakpoint, identifying corresponding gene fusions, and annotating clinically relevant information about the gene fusions.
    Type: Application
    Filed: May 22, 2018
    Publication date: November 29, 2018
    Inventors: Yong Mao, Nevenka Dimitrova, Kostyantyn Volyanskyy
  • Publication number: 20180330805
    Abstract: A data-driven integrative visualization system and a method for visualization and exploration of the multi-modal features of a cohort of samples, is disclosed Specifically, a method for providing an interactive computation and visualization front-end of a genomics platform for presenting the complex multiparametric and high dimensional, multi-omic data of a patient with respect to a cohort of samples, that assists the user in understanding the similarities and differences across individual or groups of samples, identify correlation among different features and improve treatment planning and long term patient care, is described. The method may include obtaining and inputting multi-omic data of a patient and/or cohorts, identifying multi-modal feature variations and their relationships, and displaying this information in an interactive circular format on a GUI, from which the user can access further information.
    Type: Application
    Filed: May 8, 2018
    Publication date: November 15, 2018
    Inventors: Yee Him Cheung, Yong Mao, Nevenka Dimitrova, Nilanjana Banerjee, Johanna Maria de Bont, Jozef Hieronymus Maria Raijmakers, Kostyantyn Volyanskyy
  • Publication number: 20180314795
    Abstract: A data-driven integrative visualization system and method for summarizing and presenting genomic aberrations, their drug responses and multi-omic data of a patient, is disclosed. Specifically, a method for displaying genomic aberrations and multi-omic data of a patient in an interactive tool which allows the medical practitioner to access underlying supporting biologic and scientific evidence from relevant knowledge bases through a set of graphical interactions, is described. The method comprises the steps of obtaining and inputting multi-omic data of a patient or cohorts, identifying genomic aberrations and their drug responses, and displaying this information in a first level interactive classical/circular ideogram in one or multiple layers on a GUI, from which the user can access and view further information on the gene and molecular levels. The system provides an improved process of integrative analysis on a patient's multi-omic data for effective treatment planning.
    Type: Application
    Filed: April 27, 2018
    Publication date: November 1, 2018
    Inventors: Yee Him Cheung, Nevenka Dimitrova, Johanna Maria de Bont
  • Publication number: 20180247010
    Abstract: A system and method for determining the functional impact of somatic mutations and genomic aberrations on downstream cellular processes by integrating multi-omics measurements in cancer samples with community-curated biological pathways are disclosed.
    Type: Application
    Filed: August 26, 2016
    Publication date: August 30, 2018
    Inventors: Abolfazl Razi, Vinay Varadan, Nevenka Dimitrova, Nilanjana Banerjee
  • Publication number: 20180225414
    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: Application
    Filed: August 12, 2016
    Publication date: August 9, 2018
    Inventors: Konstantin Volyanskyy, Nevenka Dimitrova
  • Publication number: 20180218116
    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: Application
    Filed: July 26, 2016
    Publication date: August 2, 2018
    Inventors: Vartika Agrawal, Nevenka Dimitrova
  • Publication number: 20180089368
    Abstract: Methods, systems and apparatus for detecting subpopulations of constituents of at least one biological organism are disclosed. In accordance with exemplary embodiments, biological data compiled from a cohort of the constituents of at least one biological organism is formulated (112) as a set of discrete-time real valued vector signals. Further, frequency domain analysis is performed (114) on the vector signals of the biological data to compile spectral properties of the vector signals. The spectral properties can be employed to efficiently detect subpopulations of the cohort while maintaining a high degree of accuracy.
    Type: Application
    Filed: May 24, 2016
    Publication date: March 29, 2018
    Inventors: Konstantin Wolanski, Nevenka Dimitrova
  • Publication number: 20180089392
    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: November 29, 2017
    Publication date: March 29, 2018
    Inventors: Angel Janevski, Nevenka Dimitrova, Sitharthan Kamalakaran, Yasser Alsafadi, Nilanjana Banerjee, Anca Ioana Daniela Bacur, Jasper Johannes Adrianus van Leeuwen, Vinay Varadan
  • Patent number: 9858392
    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: Grant
    Filed: May 6, 2009
    Date of Patent: January 2, 2018
    Assignee: Koninklijke Philips 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: 20170364633
    Abstract: A method of identifying co-expressed coding and noncoding genes is disclosed. The method may include receiving genetic sequences, mapping the genetic sequences to known coding and noncoding genes, correlating the mapped genes, and generating a co-expression network. A system for generating a co-expression network and providing the co-expression network to a user on a display is disclosed. The system may include a memory, one or more processors, one or more databases, and a display.
    Type: Application
    Filed: December 7, 2015
    Publication date: December 21, 2017
    Inventors: NILANJANA BANERJEE, NEVENKA DIMITROVA, SONIA CHOTHANI, WILHELMUS FRANCISCUS JOHANNES VERHAEGH, YEE HIM CHEUNG
  • Patent number: 9798856
    Abstract: 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: Grant
    Filed: March 20, 2013
    Date of Patent: October 24, 2017
    Assignee: Koninklijke Philips N.V.
    Inventors: Nilanjana Banerjee, Sitharthan Kamalakaran, Vinay Varadan, Angel Janevski, Nevenka Dimitrova
  • Publication number: 20170286597
    Abstract: Methods and systems for visualizing gene expression data in a way that permits the comparison of different patient groups to facilitate medical applications, including cancer diagnostics and treatment planning, particularly breast cancer. The method organises gene expression data for at least one patient into a plurality of windows of a specified size, calculates an average RSEM score for all of the genes in each window and presents the average RSEM scores in a two-dimensional array, wherein one axis organises the windows by patient and the other axis organises the windows by sequence.
    Type: Application
    Filed: August 17, 2015
    Publication date: October 5, 2017
    Inventors: ALEXANDER RYAN MANKOVICH, NEVENKA DIMITROVA, VARTIKA AGRAWAL, NILANJANA BANERJEE
  • Publication number: 20170270244
    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: Application
    Filed: March 9, 2017
    Publication date: September 21, 2017
    Inventors: Karthikeyan Murugesan, Nevenka Dimitrova, Henry Lin, Pramod Mayigowda
  • Publication number: 20170262579
    Abstract: The amount of genomic data as well the sensitivity of the information carried necessitates the need to develop smart and efficient ways to transmit genomic data in a secure way. While encryption schemes exist, there is also the need to first reduce the amount of massive information and then apply an encoding and encryption method that will be effective both in the economic sense as well as for security of genomic data. In this invention, we discuss novel techniques to encode processed variant information and send it across to a remote site ensuring covert transmission. The protocols not only encode and encrypts the information; it condenses the information that needs to be transferred.
    Type: Application
    Filed: November 18, 2015
    Publication date: September 14, 2017
    Inventors: VARTIKA AGRAWAL, NEVENKA DIMITROVA, RAYMOND J. KRASINSKI
  • Publication number: 20170249422
    Abstract: Data-driven generalized regression-based frameworks that support the transformation of measurements, applicable but not limited to gene expressions, from one platform to another over a wide dynamic range, with selected summary statistics/feature values as predictors for the model parameters. The framework consists of primary model training and transformation, and additional levels of categorical regression and transformation processes.
    Type: Application
    Filed: October 16, 2015
    Publication date: August 31, 2017
    Inventors: YEE HIM CHEUNG, WILHELMUS FRANCISCUS JOHANNES VERHAEGH, NEVENKA DIMITROVA
  • Publication number: 20170068826
    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: Application
    Filed: April 24, 2015
    Publication date: March 9, 2017
    Inventors: NEVENKA DIMITROVA, WILLIAM KNOX CAREY, RAYMOND J. KRASINSKI, JARL NILSSON, BART GRANTHAM, ALEXANDER RYAN MANKOVICH, VARTIKA AGRAWAL