Patents by Inventor Alexander Bagaev
Alexander Bagaev 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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Patent number: 11373733Abstract: 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: GrantFiled: July 2, 2020Date of Patent: June 28, 2022Assignee: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov, Olga Isaeva
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Patent number: 11367509Abstract: 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: GrantFiled: June 12, 2018Date of Patent: June 21, 2022Assignee: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov, Olga Isaeva
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Publication number: 20220186318Abstract: Aspects of the disclosure relate to methods, systems, computer-readable storage media, and graphical user interfaces (GUIs) that are useful for characterizing subjects having certain cancers, for example lymphomas. The disclosure is based, in part, on methods for determining the tumor microenvironment (TME) type of a lymphoma (e.g., follicular lymphoma) subject and identifying the subject's prognosis based upon the TME type determination.Type: ApplicationFiled: December 10, 2021Publication date: June 16, 2022Applicant: BostonGene CorporationInventors: Mark Meerson, Nikita Kotlov, Olga Kudryashova, Alexander Bagaev
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Patent number: 11335439Abstract: 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: GrantFiled: June 12, 2018Date of Patent: May 17, 2022Assignee: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov, Olga Isaeva
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Patent number: 11322226Abstract: 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: GrantFiled: June 12, 2018Date of Patent: May 3, 2022Assignee: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov, Olga Isaeva
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Patent number: 11315658Abstract: Techniques for determining one or more cell composition percentages from expression data. The techniques include obtaining expression data for a biological sample, the biological sample previously obtained from a subject, the expression data including first expression data associated with a first set of genes associated with a first cell type; determining a first cell composition percentage for the first cell type using the expression data and one or more non-linear regression models including a first non-linear regression model, wherein the first cell composition percentage indicates an estimated percentage of cells of the first cell type in the biological sample, wherein determining the first cell composition percentage for the first cell type comprises: processing the first expression data with the first non-linear regression model to determine the first cell composition percentage for the first cell type; and outputting the first cell composition percentage.Type: GrantFiled: March 12, 2021Date of Patent: April 26, 2022Assignee: BostonGene CorporationInventors: Aleksandr Zaitsev, Maksim Chelushkin, Ilya Cheremushkin, Ekaterina Nuzhdina, Vladimir Zyrin, Daniiar Dyikanov, Alexander Bagaev, Ravshan Ataullakhanov, Boris Shpak
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Publication number: 20220119881Abstract: Described herein are various methods of collecting and processing of tumor and/or healthy tissue samples to extract nucleic acid and perform nucleic acid sequencing. Also described herein are various methods of processing nucleic acid sequencing data to remove bias from the nucleic acid sequencing data. Also described herein are various methods of evaluating the quality of nucleic acid sequence information. The identity and/or integrity of nucleic acid sequence data is evaluated prior to using the sequence information for subsequent analysis (for example for diagnostic, prognostic, or clinical purposes). The methods enable a subject, doctor, or user to characterize or classify various types of cancer precisely, and thereby determine a therapy or combination of therapies that may be effective to treat a cancer in a subject based on the precise characterization.Type: ApplicationFiled: December 30, 2021Publication date: April 21, 2022Applicant: BostonGene CorporationInventors: Ekaterina Nuzhdina, Alexander Bagaev, Maksim Chelushkin, Yaroslav Lozinsky, Natalia Miheecheva, Aleksandr Zaitsev
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Publication number: 20220122252Abstract: Techniques for processing multiplexed immunofluorescence (MxIF) images. The techniques include obtaining at least one MxIF image of a same tissue sample, obtaining information indicative of locations of cells in the at least one MxIF image, identifying multiple groups of cells in the at least one MxIF image at least in part by determining feature values for at least some of the cells using the at least one MxIF image and the information indicative of locations of the at least some cells in the at least one MxIF image and grouping the at least some of the cells into the multiple groups using the determined feature values, and determining at least one characteristic of the tissue sample using the multiple cell groups.Type: ApplicationFiled: December 27, 2021Publication date: April 21, 2022Applicant: BostonGene CorporationInventors: Viktor Svekolkin, Ilia Galkin, Ekaterina Postovalova, Ravshan Ataullakhanov, Alexander Bagaev, Arina Varlamova, Pavel Ovcharov
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Patent number: 11302420Abstract: 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: May 11, 2020Date of Patent: April 12, 2022Assignee: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Nikita Kotlov, Ravshan Ataullakhanov, Olga Isaeva
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Patent number: 11250568Abstract: Techniques for processing multiplexed immunofluorescence (MxIF) images. The techniques include obtaining at least one MxIF image of a same tissue sample, obtaining information indicative of locations of cells in the at least one MxIF image, identifying multiple groups of cells in the at least one MxIF image at least in part by determining feature values for at least some of the cells using the at least one MxIF image and the information indicative of locations of the at least some cells in the at least one MxIF image and grouping the at least some of the cells into the multiple groups using the determined feature values, and determining at least one characteristic of the tissue sample using the multiple cell groups.Type: GrantFiled: March 6, 2021Date of Patent: February 15, 2022Assignee: BostonGene CorporationInventors: Viktor Svekolkin, Ilia Galkin, Ekaterina Postovalova, Ravshan Ataullakhanov, Alexander Bagaev, Arina Varlamova, Pavel Ovcharov
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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: 20210287759Abstract: Techniques for determining one or more cell composition percentages from expression data. The techniques include obtaining expression data for a biological sample, the biological sample previously obtained from a subject, the expression data including first expression data associated with a first set of genes associated with a first cell type; determining a first cell composition percentage for the first cell type using the expression data and one or more non-linear regression models including a first non-linear regression model, wherein the first cell composition percentage indicates an estimated percentage of cells of the first cell type in the biological sample, wherein determining the first cell composition percentage for the first cell type comprises: processing the first expression data with the first non-linear regression model to determine the first cell composition percentage for the first cell type; and outputting the first cell composition percentage.Type: ApplicationFiled: March 12, 2021Publication date: September 16, 2021Inventors: Alexander Zaitsev, Maksim Chelushkin, Ilya Cheremushkin, Ekaterina Nuzhdina, Vladimir Zyrin, Daniyar Dyykanov, Alexander Bagaev, Ravshan Ataullakhanov, Boris Shpak
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Publication number: 20210279866Abstract: Techniques for processing multiplexed immunofluorescence (MxIF) images. The techniques include: obtaining at least one MxIF image of a same tissue sample; obtaining information indicative of locations of cells in the at least one MxIF image; identifying multiple groups of cells in the at least one MxIF image at least in part by: determining feature values for at least some of the cells using the at least one MxIF image and the information indicative of locations of the at least some cells in the at least one MxIF image; and grouping the at least some of the cells into the multiple groups using the determined feature values; and determining at least one characteristic of the tissue sample using the multiple cell groups.Type: ApplicationFiled: March 6, 2021Publication date: September 9, 2021Inventors: Viktor Svekolkin, Ilia Galkin, Ekaterina Postovalova, Ravshan Ataullakhanov, Alexander Bagaev, Arina Varlamova, Pavel Ovcharov
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Publication number: 20210257058Abstract: Techniques for generating therapy biomarker scores and visualizing same. The techniques include determining, using a patient's sequence data and distributions of biomarker values across one or more reference populations, a first set of normalized scores for a first set of biomarkers associated with a first therapy, and a second set of normalized scores for a second set of biomarkers associated with a second therapy, generating a graphical user interface (GUI) including a first portion associated with the first therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the first set of normalized scores; and a second portion associated with a second therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the second set of normalized scores; and displaying the generated GUI.Type: ApplicationFiled: April 22, 2021Publication date: August 19, 2021Applicant: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Ravshan Ataullakhanov
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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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Patent number: 11004542Abstract: Techniques for generating therapy biomarker scores and visualizing same. The techniques include determining, using a patient's sequence data and distributions of biomarker values across one or more reference populations, a first set of normalized scores for a first set of biomarkers associated with a first therapy, and a second set of normalized scores for a second set of biomarkers associated with a second therapy, generating a graphical user interface (GUI) including a first portion associated with the first therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the first set of normalized scores; and a second portion associated with a second therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the second set of normalized scores; and displaying the generated GUI.Type: GrantFiled: April 23, 2020Date of Patent: May 11, 2021Assignee: BostonGene CorporationInventors: Alexander Bagaev, Feliks Frenkel, Ravshan Ataullakhanov
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Publication number: 20210005284Abstract: Described herein are various methods of collecting and processing of tumor and/or healthy tissue samples to extract nucleic acid and perform nucleic acid sequencing. Also described herein are various methods of processing nucleic acid sequencing data to remove bias from the nucleic acid sequencing data. Also described herein are various methods of evaluating the quality of nucleic acid sequence information. The identity and/or integrity of nucleic acid sequence data is evaluated prior to using the sequence information for subsequent analysis (for example for diagnostic, prognostic, or clinical purposes). The methods enable a subject, doctor, or user to characterize or classify various types of cancer precisely, and thereby determine a therapy or combination of therapies that may be effective to treat a cancer in a subject based on the precise characterization.Type: ApplicationFiled: July 3, 2020Publication date: January 7, 2021Inventors: Ekaterina Nuzhdina, Alexander Bagaev, Maksim Chelushkin, Yaroslav Lozinsky, Natalia Miheecheva, Alexander Zaitsev
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Publication number: 20210005283Abstract: Described herein are various methods of collecting and processing of tumor and/or healthy tissue samples to extract nucleic acid and perform nucleic acid sequencing. Also described herein are various methods of processing nucleic acid sequencing data to remove bias from the nucleic acid sequencing data. Also described herein are various methods of evaluating the quality of nucleic acid sequence information. The identity and/or integrity of nucleic acid sequence data is evaluated prior to using the sequence information for subsequent analysis (for example for diagnostic, prognostic, or clinical purposes). The methods enable a subject, doctor, or user to characterize or classify various types of cancer precisely, and thereby determine a therapy or combination of therapies that may be effective to treat a cancer in a subject based on the precise characterization.Type: ApplicationFiled: July 3, 2020Publication date: January 7, 2021Inventors: Ekaterina Nuzhdina, Alexander Bagaev, Maksim Chelushkin, Yaroslav Lozinsky, Natalia Miheecheva, Alexander Zaitsev
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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