Patents by Inventor Sitharthan Kamalakaran
Sitharthan Kamalakaran 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: 20180004892Abstract: Systems, methods, and apparatuses are disclosed for reducing the computational time of assigning a species to an infection isolate. A method for dividing a search index into one or more sub-indices based on a phylogenetic tree of reference sequences is disclosed. A method for dividing reads into test sets and aligning to sub-indices for assigning a species to an infection isolate is disclosed. A system for aligning sequence reads to a database of reference sequences using sub-indices is disclosed.Type: ApplicationFiled: December 21, 2015Publication date: January 4, 2018Applicant: KONINKLIJKE PHILIPS N.V.Inventor: Sitharthan Kamalakaran
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Patent number: 9858392Abstract: 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: GrantFiled: May 6, 2009Date of Patent: January 2, 2018Assignee: 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
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Patent number: 9798856Abstract: 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: GrantFiled: March 20, 2013Date of Patent: October 24, 2017Assignee: Koninklijke Philips N.V.Inventors: Nilanjana Banerjee, Sitharthan Kamalakaran, Vinay Varadan, Angel Janevski, Nevenka Dimitrova
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Publication number: 20170235873Abstract: The present disclosure describes systems and methods for determining sources of infection transmission. Phylogenetic methods are used for determining the evolutionary history and replication rates of infection isolates. The evolutionary distance and/or replication rate of an infection isolate maybe compared to other isolates. Based on a comparison of the evolutionary distance and/or replication rate, a determination of the source of infection transmission is made.Type: ApplicationFiled: August 11, 2015Publication date: August 17, 2017Applicant: KONINKLIJKE PHILIPS N.V.Inventors: Sitharthan Kamalakaran, Joseph N. Paulson
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Publication number: 20170228497Abstract: The present disclosure describes systems and methods for determining and flagging sequences that deviate from one or more reference sequences. Phylogenetic methods are used for determining the evolutionary history and evolutionary distances of sample isolates. The evolutionary distances of sample isolates may be compared to each other and/or reference isolates. Based on a comparison of the evolutionary distances, a determination of deviance is made for a sample sequence. The sample sequence is flagged for further analysis to determine the cause of deviation.Type: ApplicationFiled: September 8, 2015Publication date: August 10, 2017Inventors: Sitharthan Kamalakaran, Joseph N. Paulson
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Patent number: 9552649Abstract: 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: GrantFiled: October 25, 2013Date of Patent: January 24, 2017Assignee: Koninklijke Philips N.V.Inventors: Nilanjana Banerjee, Nevenka Dimitrova, Vinay Varadan, Sitharthan Kamalakaran, Angel Janevski, Sayan Maity
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Publication number: 20160031091Abstract: A force feedback gripping device employs a mechanical gripper (23), an electromagnetic actuator (22) and a force feedback controller (21). The mechanical gripper (23) is operable to be actuated to one of a plurality of gripping poses for gripping an object. The electromagnetic actuator (22) includes a magnetorheological elastomer (“MRE”), wherein the MRE is operable to be transitioned between a plurality of shapes dependent upon a variable strength of a magnetic field applied to the MRE, and wherein each shape of the MRE actuates the mechanical gripper (23) to one of the gripping poses. The force feedback controller (21) is operable to control the variable strength of the magnetic field applied to the MRE based on an estimation of a gripping force of the mechanical gripper (23) and on a sensing of a load force of the object responsive to the gripping force of the mechanical gripper (23).Type: ApplicationFiled: October 22, 2014Publication date: February 4, 2016Inventors: ALEKSANDRA POPOVIC, SITHARTHAN KAMALAKARAN, DOUGLAS ALLEN STANTON
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Publication number: 20150347679Abstract: 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: ApplicationFiled: November 22, 2013Publication date: December 3, 2015Inventors: VINAY VARADAN, SITHARTHAN KAMALAKARAN, ANGEL JANEVSKI, NILANJANA BANERJEE, NEVENKA DIMITROVA, LYNDSAY HARRIS
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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: 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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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: 8652777Abstract: The invention relates to a method for the analysis of ovarian cancer disorders, comprising determining the genomic methylation status of one or more CpG dinucleotides in a sequence selected from the group of sequences according to SEQ ID NO. 1 to 10 and/or SEQ ID NO. 50 to SEQ ID NO. 60. Optionally, additionally following steps are performed, the one or more results from the methylation status test is input into a classifier that is obtained from a Diagnostic Multi Variate Model, calculating a likelihood as to whether the sample is from a normal tissue or an ovarian cancer tissue and/or, calculating an associated p-value for the confidence in the prediction.Type: GrantFiled: September 16, 2008Date of Patent: February 18, 2014Assignees: Koninklijke Philips N.V., Cold Spring Harbor LaboratoriesInventors: Sitharthan Kamalakaran, Robert Lucito, James Bruce Hicks
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Publication number: 20140046178Abstract: A medical device and methods for locating the device include a structure having a length dimension and a surface (102). A volume (106) is associated with the surface and extends along a portion of the length dimension. Nanomaterials (108) are incorporated in the volume and configured to be responsive to an excitation signal such that the excitation signal generates a response from the nanomaterials to enable location of the structure within a subject.Type: ApplicationFiled: April 16, 2012Publication date: February 13, 2014Applicant: KONINKLIJKE PHILIPS N.V.Inventors: Sitharthan Kamalakaran, Balasundar Raju
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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: 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: 20120053071Abstract: The present invention relates to a method for the detection of a DNA methylation signature associated with the presence of or the predisposition to develop a disorder, the method comprising the identification of one or more candidate genes exhibiting differential DNA methylation in target and reference samples as well as the respective determination of the nucleic acid sites in said candidate genes that are differentially methylated and the recognition sites for DNA binding factors, said DNA binding factors each recognizing such a differentially methylated nucleic acid site, wherein the patterns of differentially methylated nucleic acid sites and of DNA binding factor recognition sites obtained together represent a DNA methylation signature that is indicative for the presence of or the predisposition to develop a disorder in a target sample.Type: ApplicationFiled: December 14, 2009Publication date: March 1, 2012Applicant: KONINKLIJKE PHILIPS ELECTRONICS N.V.Inventors: Nevenka Dimitrova, Chetan Mittal, Sitharthan Kamalakaran