Patents by Inventor Nikita Kotlov
Nikita Kotlov 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: 20220005551Abstract: Aspects of the disclosure relate to methods for determining whether or a subject is likely to respond to certain adoptive cell therapies (e.g., chimeric antigen receptor (CAR) T-cell therapy, etc.). In some embodiments, the methods comprise the steps of identifying a subject as having a tumor microenvironment (TME) type based upon a molecular-functional (MF) expression signature of the subject, and determining whether or not the subject is likely to respond to a chimeric antigen receptor (CAR) T-cell therapy based upon the TME type. In some embodiments, the methods comprise determining the lymphoma microenvironment (LME) type of a lymphoma (e.g., Diffuse Large B cell lymphoma (DLBCL)) subject and identifying the subject's prognosis based upon the LME type determination.Type: ApplicationFiled: July 6, 2021Publication date: January 6, 2022Applicant: BostonGene CorporationInventors: Nikita Kotlov, Georgy Sagaradze, Alexander Bagaev, Grigorii Nos, Lev Bedniagin, Dmitry Kravchenko, Anna Gribkova
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Publication number: 20210249107Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for a biological sample; determining a molecular-functional (MF) profile for a subject using the data; determining visual characteristics GUI elements using the data; generating a GUI personalized to the subject using the determined visual characteristics; and presenting the generated personalized GUI to a user.Type: ApplicationFiled: May 11, 2020Publication date: August 12, 2021Applicant: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Publication number: 20210174899Abstract: Techniques for determining one or more characteristics of a biological sample using rankings of gene expression levels in expression data obtained using one or more sequencing platforms is described. The techniques may include obtaining expression data for a biological sample of a subject. The techniques further include ranking genes in a set of genes based on their expression levels in the expression data to obtain a gene ranking and determining using the gene ranking and a statistical model, one or more characteristics of the biological sample.Type: ApplicationFiled: December 5, 2020Publication date: June 10, 2021Inventors: Zoia Antysheva, Viktor Svekolkin, Nikita Kotlov, Anton Karelin, Ekaterina Postovalova
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Publication number: 20200335180Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for a biological sample from a subject; determining a molecular-functional (MF) profile for the subject; identifying an MF profile cluster with which to associate the MF profile for the subject; and clustering the plurality of MF profiles to obtain the MF profile clusters.Type: ApplicationFiled: July 2, 2020Publication date: October 22, 2020Applicant: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Publication number: 20200273543Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for a biological sample; determining a molecular-functional (MF) profile for a subject using the data; determining visual characteristics GUI elements using the data; generating a GUI personalized to the subject using the determined visual characteristics; and presenting the generated personalized GUI to a user.Type: ApplicationFiled: May 11, 2020Publication date: August 27, 2020Applicant: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Patent number: 10720230Abstract: Techniques for determining whether a subject is likely to respond to an immune checkpoint blockade therapy.Type: GrantFiled: June 12, 2018Date of Patent: July 21, 2020Assignee: BostonGene CorporationInventors: Feliks Frenkel, Nikita Kotlov, Alexander Bagaev, Maksym Artomov, Ravshan Ataullakhanov
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Patent number: 10706954Abstract: Techniques for determining whether a subject is likely to respond to an immune checkpoint blockade therapy.Type: GrantFiled: November 26, 2019Date of Patent: July 7, 2020Assignee: BostonGene CorporationInventors: Feliks Frenkel, Nikita Kotlov, Alexander Bagaev, Maksym Artomov, Ravshan Ataullakhanov
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Publication number: 20200175135Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for a biological sample; determining a molecular-functional (MF) profile for the subject at least in part by determining first and second visual characteristics for first and second GUI elements using the data; generating a personalized GUI personalized to the subject using the first and second visual characteristics; and presenting the generated personalized GUI to a user.Type: ApplicationFiled: June 12, 2018Publication date: June 4, 2020Applicant: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Publication number: 20200175134Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for a biological sample from a plurality of subjects, determining a respective plurality of molecular-functional (MF) profiles for the plurality of subjects, and storing the plurality of MF profiles in association with information identifying the particular cancer type.Type: ApplicationFiled: June 12, 2018Publication date: June 4, 2020Applicant: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Publication number: 20200175133Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for a biological sample from a subject; determining a molecular-functional (MF) profile for the subject; identifying an MF profile cluster with which to associate the MF profile for the subject; and clustering the plurality of MF profiles to obtain the MF profile clusters.Type: ApplicationFiled: June 12, 2018Publication date: June 4, 2020Applicant: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Patent number: 10650911Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for a biological sample; determining a molecular-functional (MF) profile for a subject using the data; determining visual characteristics GUI elements using the data; generating a GUI personalized to the subject using the determined visual characteristics; and presenting the generated personalized GUI to a user.Type: GrantFiled: June 12, 2018Date of Patent: May 12, 2020Assignee: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Publication number: 20200098443Abstract: Techniques for determining whether a subject is likely to respond to an immune checkpoint blockade therapy.Type: ApplicationFiled: November 26, 2019Publication date: March 26, 2020Applicant: BostonGene CorporationInventors: Feliks Frenkel, Nikita Kotlov, Alexander Bagaev, Maksym Artomov, Ravshan Ataullakhanov
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Patent number: 10580517Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for biological samples; determining a respective plurality of molecular-functional (MF) profiles for a plurality of subjects; clustering the plurality of MF profiles to obtain MF profile clusters; determining a molecular-functional (MF) profile for an additional subject; and identifying, from among the MF profile clusters, a particular MF profile cluster with which to associate the MF profile for the subject.Type: GrantFiled: July 26, 2019Date of Patent: March 3, 2020Assignee: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Publication number: 20200005903Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for biological samples; determining a respective plurality of molecular-functional (MF) profiles for a plurality of subjects; clustering the plurality of MF profiles to obtain MF profile clusters; determining a molecular-functional (MF) profile for an additional subject; and identifying, from among the MF profile clusters, a particular MF profile cluster with which to associate the MF profile for the subject.Type: ApplicationFiled: July 26, 2019Publication date: January 2, 2020Applicant: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Publication number: 20190332744Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for a biological sample; determining a molecular-functional (MF) profile for a subject using the data; determining visual characteristics GUI elements using the data; generating a GUI personalized to the subject using the determined visual characteristics; and presenting the generated personalized GUI to a user.Type: ApplicationFiled: June 12, 2018Publication date: October 31, 2019Applicant: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Patent number: 10395761Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for biological samples; determining a respective plurality of molecular-functional (MF) profiles for a plurality of subjects; clustering the plurality of MF profiles to obtain MF profile clusters; determining a molecular-functional (MF) profile for an additional subject; and identifying, from among the MF profile clusters, a particular MF profile cluster with which to associate the MF profile for the subject.Type: GrantFiled: April 22, 2019Date of Patent: August 27, 2019Assignee: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Publication number: 20190252046Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for biological samples; determining a respective plurality of molecular-functional (MF) profiles for a plurality of subjects; clustering the plurality of MF profiles to obtain MF profile clusters; determining a molecular-functional (MF) profile for an additional subject; and identifying, from among the MF profile clusters, a particular MF profile cluster with which to associate the MF profile for the subject.Type: ApplicationFiled: April 22, 2019Publication date: August 15, 2019Applicant: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Publication number: 20190243943Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for a biological sample; determining a molecular-functional (MF) profile using the data; determining sets of visual characteristics for GUI elements using the data; generating a personalized GUI using the determined visual characteristics; and presenting the generated personalized GUI to a user.Type: ApplicationFiled: June 12, 2018Publication date: August 8, 2019Applicant: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov
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Publication number: 20190179998Abstract: Techniques for determining whether a subject is likely to respond to an immune checkpoint blockade therapy.Type: ApplicationFiled: June 12, 2018Publication date: June 13, 2019Applicant: BostonGene CorporationInventors: Feliks Frenkel, Nikita Kotlov, Alexander Bagaev, Maksym Artomov, Ravshan Ataullakhanov
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Patent number: 10311967Abstract: Various methods, systems, computer readable media, and graphical user interfaces (GUIs) are presented and described that enable a subject, doctor, or user to characterize or classify various types of cancer precisely. Additionally, described herein are methods, systems, computer readable media, and GUIs that enable more effective specification of treatment and improved outcomes for patients with identified types of cancer. Some embodiments of the methods, systems, computer readable media, and GUIs described herein comprise obtaining RNA expression data and/or whole exome sequencing (WES) data for biological samples; determining a respective plurality of molecular-functional (MF) profiles for a plurality of subjects; clustering the plurality of MF profiles to obtain MF profile clusters; determining a molecular-functional (MF) profile for an additional subject; and identifying, from among the MF profile clusters, a particular MF profile cluster with which to associate the MF profile for the subject.Type: GrantFiled: June 12, 2018Date of Patent: June 4, 2019Assignee: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov