Patents by Inventor Hanyoup Kim

Hanyoup Kim 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: 20250197847
    Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.
    Type: Application
    Filed: February 26, 2025
    Publication date: June 19, 2025
    Inventors: Hanyoup Kim, David Sukovich, Layla Katiraee, Augusto Manuel Tentori
  • Publication number: 20250189483
    Abstract: The present disclosure provides electrophoretic systems, methods and compositions for spatial analysis, which can serve to magnify or demagnify spatial resolution of analytes of interest that are captured using electrophoresis. Some implementations can use a diverging or converging electric field in an electrophoretic capture system. Such a divergent or convergent electric field, as opposed to a parallel electric field, can be generated by, for example, utilizing different sizes of electrodes associated with or imbedded in substrates. Also provided herein are electrophoretic systems, methods and compositions for spatial analysis, which can serve to selectively migrate one or more analytes from a region of interest in the biological sample for capture using electrophoresis.
    Type: Application
    Filed: February 14, 2025
    Publication date: June 12, 2025
    Inventors: Hanyoup Kim, Augusto Manuel Tentori, Rajiv Bharadwaj
  • Publication number: 20250179565
    Abstract: Compositions and methods for enhanced detection of variant nucleotides (e.g., SNPs, intron retention variants) in nucleic acids within biological samples have been developed for spatial gene profiling of biological samples. Nucleic acid probes configured to hybridize in proximity to a target variant nucleic acid are extended to include the target sequence and amplified by rolling circle amplification (RCA). DNA probes are hybridized with RCA products and are extended using the nucleic acid probe as template and the extended DNA probe captured on a spatial array. The methods are broadly applicable and can be implemented into existing methodologies to enhance the resolution and accuracy of systems for spatial profiling of analytes within biological samples.
    Type: Application
    Filed: November 26, 2024
    Publication date: June 5, 2025
    Inventors: Hanyoup Kim, Hardeep Pal Singh, David Sukovich
  • Publication number: 20250182305
    Abstract: A method for aligning a sample to an array is provided. An image of sample image of a sample can be received by a data processor. The sample image having a first resolution. An array image including an overlay of an array with the sample and an array fiducial can be received by the data processor. The array image having a second resolution lower than the first resolution of the sample image. The sample image can be regisered to the array image by aligning the sample image and the array image. An aligned image can be generated based on the registering. The aligned image can can include an overlay of the sample image with the array. The aligned image can be provided by the data processor. A method for detecing fiducials associated with an array is provided. Systems and non-transitory computer readable mediums performing the method are also provided.
    Type: Application
    Filed: January 30, 2025
    Publication date: June 5, 2025
    Inventors: Augusto Manuel Tentori, Hanyoup Kim, Siyuan Xing, Felice Alessio Bava, Rajiv Bharadwaj, Cedric Uytingco, Erica Graziosa
  • Publication number: 20250163501
    Abstract: Provided herein are methods of analyzing an analyte in a fixed biological sample on a first substrate that has been stored for a long period of time, the method comprising: (a) hybridizing a first probe and a second probe to the analyte of the fixed biological sample; (b) coupling the first probe and the second probe, thereby generating a connected probe; (c) aligning the first substrate with a second substrate comprising an array, wherein the array comprises a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises: (i) a spatial barcode and (ii) a capture domain; (d) when the biological sample is aligned with at least a portion of the array, (i) releasing the connected probe from the analyte and (ii) migrating the connected probe from the biological sample to the array; and (e) hybridizing the connected probe to the capture domain.
    Type: Application
    Filed: January 31, 2023
    Publication date: May 22, 2025
    Inventors: Hardeep Pal Singh, David Sukovich, Augusto Manuel Tentori, Hanyoup Kim
  • Patent number: 12281357
    Abstract: Provided herein are materials and methods for in situ labeling of a biological sample for use in spatial analysis of one or more analytes in the biological sample. In some aspects, in situ labeling of a biological sample includes labeling the biological sample with one or more spatial barcodes.
    Type: Grant
    Filed: February 12, 2021
    Date of Patent: April 22, 2025
    Assignee: 10x Genomics, Inc.
    Inventors: Augusto Manuel Tentori, Rajiv Bharadwaj, Bill Kengli Lin, Hanyoup Kim, Denis Pristinski
  • Patent number: 12249085
    Abstract: A method for aligning a sample to an array is provided. An image of sample image of a sample can be received by a data processor. The sample image having a first resolution. An array image including an overlay of an array with the sample and an array fiducial can be received by the data processor. The array image having a second resolution lower than the first resolution of the sample image. The sample image can be registered to the array image by aligning the sample image and the array image. An aligned image can be generated based on the registering. The aligned image can include an overlay of the sample image with the array. The aligned image can be provided by the data processor. A method for detecting fiducials associated with an array is provided. Systems and non-transitory computer readable mediums performing the method are also provided.
    Type: Grant
    Filed: March 17, 2023
    Date of Patent: March 11, 2025
    Assignee: 10x Genomics, Inc.
    Inventors: Augusto Manuel Tentori, Hanyoup Kim, Siyuan Xing, Felice Alessio Bava, Rajiv Bharadwaj, Cedric Uytingco, Erica Graziosa
  • Patent number: 12241060
    Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.
    Type: Grant
    Filed: March 3, 2023
    Date of Patent: March 4, 2025
    Assignee: 10x Genomics, Inc.
    Inventors: Hanyoup Kim, David Sukovich, Layla Katiraee, Augusto Manuel Tentori
  • Publication number: 20250066762
    Abstract: A method of capturing analytes from a sample is provided. A first substrate including a sample is mounted on a first member of a sample handling device and mounting a second substrate including an array of capture probes on a second member of the sample handling device. A first reagent medium is applied to the first and/or second substrate and moving the first member and/or the second member to fluidically couple the sample and the array of capture probes via the first reagent medium. The sample and the array of capture probes are fluidically decoupled by moving the first member and/or the second member and a second reagent medium is applied to the first and/or second substrate and moving the first member and/or the second member to fluidically couple the sample and the array of capture probes via the second reagent medium. Related systems and apparatuses are also provided.
    Type: Application
    Filed: September 10, 2024
    Publication date: February 27, 2025
    Inventors: Liza S. Man, Augusto Manuel Tentori, Hanyoup Kim, Rajiv Bharadwaj, Ace George Santiago
  • Patent number: 12228544
    Abstract: The present disclosure provides electrophoretic systems, methods and compositions for spatial analysis, which can serve to magnify or demagnify spatial resolution of analytes of interest that are captured using electrophoresis. Some implementations can use a diverging or converging electric field in an electrophoretic capture system. Such a divergent or convergent electric field, as opposed to a parallel electric field, can be generated by, for example, utilizing different sizes of electrodes associated with or imbedded in substrates. Also provided herein are electrophoretic systems, methods and compositions for spatial analysis, which can serve to selectively migrate one or more analytes from a region of interest in the biological sample for capture using electrophoresis.
    Type: Grant
    Filed: February 23, 2023
    Date of Patent: February 18, 2025
    Assignee: 10x Genomics, Inc.
    Inventors: Hanyoup Kim, Augusto Manuel Tentori, Rajiv Bharadwaj
  • Patent number: 12195790
    Abstract: Provided herein are methods, compositions, and systems for improved in situ detection of analytes and spatial analysis using, e.g., a sequencing readout.
    Type: Grant
    Filed: September 7, 2023
    Date of Patent: January 14, 2025
    Assignee: 10x Genomics, Inc.
    Inventors: David Sukovich, Felice Alessio Bava, Augusto Manuel Tentori, Hanyoup Kim, Amanda Janesick
  • Publication number: 20250002980
    Abstract: Quantitative methods for optimizing the permeabilization of cellular tissues for spatial transcriptomics are provided. Also provided is an instrument for quantitatively optimiz-ing the permeabilization of cellular tissues used for spatial transcriptomics.
    Type: Application
    Filed: September 13, 2024
    Publication date: January 2, 2025
    Inventors: Augusto Manuel Tentori, Rajiv Bharadwaj, Hanyoup Kim, Siyuan Xing
  • Publication number: 20240417784
    Abstract: Provided herein are methods of enhancing spatial resolution of an analyte using sandwich maker system. The methods and systems used herein include a first substrate that includes a plurality of probes that include a capture domain and a spatial domain and a second substrate that includes a plurality of probes comprising a capture domain and a spatial domain.
    Type: Application
    Filed: August 26, 2024
    Publication date: December 19, 2024
    Inventors: David Sukovich, Hanyoup Kim, Jerald Sapida, Spontaneous Rose McKnight Russell, Layla Katiraee, Augusto Manuel Tentori
  • Publication number: 20240408593
    Abstract: Provided herein is a fluid delivery method for permeabilizing a biological sample. The method includes delivering the fluid to a first substrate and/or a second substrate. At least one of the first substrate and the second substrate includes a spacer. The method further includes assembling, subsequent to the delivering, a chamber comprising the first substrate, the second substrate, the biological sample, and the spacer. The spacer may be disposed between the first substrate and second substrate. The spacer may be configured to maintain the fluid within the chamber and maintain a separation distance between the first substrate and the second substrate. The spacer may be positioned to at least partially surround an area on the first substrate on which the biological sample is disposed and/or at least partially surround the array disposed on the second substrate.
    Type: Application
    Filed: May 14, 2024
    Publication date: December 12, 2024
    Inventors: Hanyoup Kim, Augusto Manuel Tentori, Siyuan Xing, Rajiv Bharadwaj, Bill Kengli Lin, Felice Alessio Bava, Pratomo Putra Alimsijah, Nabil Mikhaiel
  • Publication number: 20240401109
    Abstract: The present disclosure features methods, compositions, and kits for multiple barcoding, high-density barcoding, and/or selective release of barcoded capture probes to capture analytes, or proxies thereof, from a biological sample.
    Type: Application
    Filed: June 17, 2024
    Publication date: December 5, 2024
    Inventors: Hanyoup Kim, Nabil Mikhaiel, Augusto Manuel Tentori, David Michael Patterson, Yifeng Yin, Sultan Doganay Tuncer, Meghan L. F. Frey, Shea Thompson Lance
  • Publication number: 20240401118
    Abstract: Provided herein are methods of enhancing spatial resolution of an analyte using sandwich maker system. The methods and systems used herein include a first substrate that includes a plurality of probes that include poly-thymine sequence and a second substrate that includes a plurality of probes comprising a capture domain and a spatial domain.
    Type: Application
    Filed: July 8, 2024
    Publication date: December 5, 2024
    Inventors: Augusto Manuel Tentori, Hanyoup Kim, Felice Alessio Bava, Rajiv Bharadwaj
  • Publication number: 20240385088
    Abstract: A system for capturing analytes from a sample is provided. The system includes an upper housing including a linear actuator, a linear motion member coupled to the linear actuator, a tilt member rotatably coupled to the linear motion member, and at least one sample support member coupled to the tilt member. The system includes a lower housing including a base support member. The system also includes an alignment mechanism coupling the upper housing to the lower housing. The upper housing and the lower housing have an open configuration and a closed configuration. The alignment mechanism is configured to move the upper housing and the lower housing between the open configuration and the closed configuration. In the closed configuration, the linear actuator is configured to, upon energizing, translate the at least one sample support member towards the base support member. Related apparatuses and methods of use are also provided.
    Type: Application
    Filed: May 16, 2024
    Publication date: November 21, 2024
    Inventors: Hanyoup Kim, Liza S. Man, Nabil Mikhaiel, Pratomo Putra Alimsijah, Hendricus Marindra
  • Patent number: 12128403
    Abstract: Provided herein is a fluid delivery method for permeabilizing a biological sample. The method includes delivering the fluid to a first substrate and/or a second substrate. At least one of the first substrate and the second substrate includes a spacer. The method further includes assembling, subsequent to the delivering, a chamber comprising the first substrate, the second substrate, the biological sample, and the spacer. The spacer may be disposed between the first substrate and second substrate. The spacer may be configured to maintain the fluid within the chamber and maintain a separation distance between the first substrate and the second substrate. The spacer may be positioned to at least partially surround an area on the first substrate on which the biological sample is disposed and/or at least partially surround the array disposed on the second substrate.
    Type: Grant
    Filed: July 26, 2022
    Date of Patent: October 29, 2024
    Assignee: 10x Genomics, Inc.
    Inventors: Hanyoup Kim, Augusto Manuel Tentori, Siyuan Xing, Rajiv Bharadwaj, Bill Kengli Lin, Felice Alessio Bava, Pratomo Putra Alimsijah, Nabil Mikhaiel
  • Patent number: 12129516
    Abstract: Quantitative methods for optimizing the permeabilization of cellular tissues for spatial transcriptomics are provided. Also provided is an instrument for quantitatively optimizing the permeabilization of cellular tissues used for spatial transcriptomics.
    Type: Grant
    Filed: February 5, 2021
    Date of Patent: October 29, 2024
    Assignee: 10x Genomics, Inc.
    Inventors: Augusto Manuel Tentori, Rajiv Bharadwaj, Hanyoup Kim, Siyuan Xing
  • Patent number: D1064308
    Type: Grant
    Filed: September 17, 2021
    Date of Patent: February 25, 2025
    Assignee: 10x Genomics, Inc.
    Inventors: Pratomo Putra Alimsijah, Hendricus Marindra, Augusto Manuel Tentori, Spontaneous Rose McKnight Russell, Hanyoup Kim, Colin Bruce Kennedy