Patents by Inventor Siyuan Xing

Siyuan Xing 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: 20240060127
    Abstract: Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate using a minimal mask scheme. Systems and kits employing the methods are also disclosed. In some embodiments, a method disclosed herein comprises using photomasks and photoresist for photocontrollable hybridization and/or ligation of nucleic acid molecules, wherein photoresist removal allows hybridization and/or ligation of nucleic acid molecules at the exposed area. A large diversity of barcodes can be created in molecules on the substrate via sequential rounds of light exposure, hybridization, and ligation.
    Type: Application
    Filed: June 28, 2023
    Publication date: February 22, 2024
    Inventors: Denis PRISTINSKI, Preyas SHAH, Siyuan XING
  • Publication number: 20240033743
    Abstract: A sample holder is provided. The sample holder includes a first member including a first retaining mechanism configured to retain a first substrate comprising a sample. The first retaining mechanism configured to retain the first substrate disposed in a first plane. The sample holder further includes a second member including a second retaining mechanism configured to retain a second substrate including a reagent medium disposed in a second plane. The sample holder further includes an alignment mechanism connected to one or both of the first member and the second member. The alignment mechanism configured to align the first and second members along the first plane and/or the second plane such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned and within a threshold distance along an axis orthogonal to the second plane.
    Type: Application
    Filed: September 17, 2021
    Publication date: February 1, 2024
    Inventors: Augusto Manuel Tentori, Hanyoup Kim, Siyuan Xing, Rajiv Bharadwaj, Bill Kengli Lin, Felice Alessio Bava, Pratomo Putra Alimsijah, Hendricus Marindra, Spontaneous Rose Mcknight Russell, Nabil Mikhaiel
  • Publication number: 20230351619
    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: Application
    Filed: September 17, 2021
    Publication date: November 2, 2023
    Inventors: Augusto Manuel Tentori, Hanyoup Kim, Siyuan Xing, Felice Alessio Bava, Rajiv Bharadwaj, Cedric Uytingco, Erica Graziosa
  • Publication number: 20230347312
    Abstract: Systems and methods for dispensing a liquid on a substrate are disclosed. The system may be used to coat a substrate and/or a sample (e.g., a biological sample) with a liquid. The system includes a rotating device configured to rotate about an axis and a substrate disposed on the rotating device. The substrate comprises a well configured to hold a liquid and the substrate is positioned on a surface of the rotating device perpendicular to and concentric with the axis. The system further includes a liquid handler configured to dispense the liquid into the well. The rotating device is configured to rotate at a speed sufficient to disperse the liquid within the well.
    Type: Application
    Filed: April 5, 2023
    Publication date: November 2, 2023
    Inventors: Yiran ZHANG, Siyuan XING, Denis PRISTINSKI
  • Publication number: 20230312209
    Abstract: Systems that include blister packs and methods of use thereof are disclosed. In various embodiments, a system includes a blister pack having at least one blister comprising a base and a top layer. The blister contains a liquid reagent. The system further includes an actuator configured to release the liquid reagent from the blister. The system further includes a substrate configured to hold a tissue sample and receive the liquid reagent from the blister upon release.
    Type: Application
    Filed: April 5, 2023
    Publication date: October 5, 2023
    Inventors: David MORGAN, Evan DEJARNETTE, Eric EVJE, Yiran ZHANG, Siyuan XING
  • Publication number: 20230278028
    Abstract: Flowcell devices configured for reversible assembly, and methods of assembly, disassembly, and use thereof are provided. The methods and devices allow the interior of the flowcell device to be accessed without damaging, or otherwise disturbing sensitive samples and surfaces.
    Type: Application
    Filed: February 16, 2023
    Publication date: September 7, 2023
    Inventors: Siyuan XING, Pratomo Putra Alimsijah, Denis Pristinski, David Morgan, Rajiv Bharadwaj, Augusto Manuel Tentori, Francis Marcogliese, Yiran Zhang
  • Publication number: 20230271190
    Abstract: Devices (e.g., flow cell holders) and methods for flow cell assembly and disassembly are provided. The flow cell holders and methods can be used to join or separate the bottom and top layers of a flow cell.
    Type: Application
    Filed: February 28, 2023
    Publication date: August 31, 2023
    Inventors: Hendricus MARINDRA, Denis Pristinski, David Morgan, Siyuan Xing
  • Publication number: 20230267625
    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 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: Application
    Filed: March 17, 2023
    Publication date: August 24, 2023
    Inventors: Augusto Manuel Tentori, Hanyoup Kim, Siyuan Xing, Felice Alessio Bava, Rajiv Bharadwaj, Cedric Uytingco, Erica Graziosa
  • Publication number: 20230264186
    Abstract: Disclosed herein are devices and methods for contacting a tissue sample with liquids to perform a variety of processes and analyses. In various embodiments, the device includes a hydrophilic flow path defined at least in part by a surface pattern (e.g., bounded by hydrophobic regions). The flow path includes a sample area sized to receive a biological sample. The flow path includes at least one valve configured to control flow in the flow path in response to an external stimulus.
    Type: Application
    Filed: January 6, 2023
    Publication date: August 24, 2023
    Inventors: Bill Kengli LIN, Siyuan Xing, Hanyoup Kim
  • Publication number: 20230184663
    Abstract: Devices, systems, and methods for reducing the introduction of bubbles to flow cells and removing existing bubbles from flow cells are provided. The devices, systems, and methods detect and redirect bubbles away from the flow cell before the bubble reaches the inlet or wash away bubbles from within the flow cell.
    Type: Application
    Filed: December 14, 2022
    Publication date: June 15, 2023
    Inventors: Siyuan XING, William STANISLAUS, Yiran ZHANG
  • Publication number: 20230167489
    Abstract: The present invention features devices and methods for supplying a biological sample with a fluid. In various embodiments, a device includes a first layer and a second layer. The first layer includes a window having a thickness of about 1 ?m to about 1000 ?m. The first and second layers reversibly seal to form a flow path having an inlet and an outlet and bounded in part by the window.
    Type: Application
    Filed: November 29, 2022
    Publication date: June 1, 2023
    Inventors: Yiran ZHANG, Siyuan XING, Rajiv BHARADWAJ
  • Publication number: 20230047782
    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: Application
    Filed: February 5, 2021
    Publication date: February 16, 2023
    Applicant: 10x Genomics, Inc.
    Inventors: Augusto Manuel Tentori, Rajiv Bharadwaj, Hanyoup Kim, Siyuan Xing
  • Patent number: 11578365
    Abstract: Provided in the present invention is a chicken whole-genome SNP chip and application thereof. There are a total of 50,000 SNP loci on the chip: including 19,600 SNP loci for white-feather broilers, yellow-feather and partridge chickens having a MAF value greater than 0.05 and uniformly distributed across the genome which were derived from the data of the whole-genome resequencing of main indigenous chicken breeds in China and introduced chicken breeds; 14,000 SNP loci associated with economic traits, and 16,400 SNP loci for making up for the genomic regions that are not covered by the first two types of probes. The 50,000 SNP loci on the chicken whole-genome SNP chip of the present invention have DNA sequences represented by SEQ ID NOs. 1 to 50,000.
    Type: Grant
    Filed: October 10, 2017
    Date of Patent: February 14, 2023
    Assignee: INST. OF ANIMAL SCI., CHINESE ACAD. OF AG. SCIENCE
    Inventors: Jie Wen, Ranran Liu, Guiping Zhao, Maiqing Zheng, Qinghe Li, Huanxian Cui, Siyuan Xing
  • Publication number: 20230017773
    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: July 26, 2022
    Publication date: January 19, 2023
    Inventors: Hanyoup Kim, Augusto Manuel Tentori, Siyuan Xing, Rajiv Bharadwaj, Bill Kengli Lin, Felice Alessio Bava, Pratomo Putra Alimsijah, Nabil Mikhaiel
  • Publication number: 20220358106
    Abstract: Proxy-based scaling may be performed for databases. A proxy may be implemented for a database that can establish a connection between the proxy and a database engine to perform a database queries received from a client at the proxy. A scaling event may be detected for the database responsive to which the proxy may establish a connection with a new database engine which may, in some embodiments, have different capabilities or resources that address the features or criteria that triggered the scaling event. Session state may be copied from the database engine to the new database engine so that the new database engine may be able to provide access to the database on behalf of requests received from the client through the proxy.
    Type: Application
    Filed: July 22, 2022
    Publication date: November 10, 2022
    Applicant: Amazon Technologies, Inc.
    Inventors: Saileshwar Krishnamurthy, Alexey Kuznetsov, Mushahid Alam, Anurag Windlass Gupta, Kamal Kant Gupta, Tengiz Kharatishvili, Bohan Liu, Sandor Loren Maurice, Alok Nandan Nikhil, Nicholas Piers O'Shea, Debanjan Saha, Yoni Shalom, Jagdeep Singh Sidhu, Hongbo Song, Alexandre Olegovich Verbitski, Lawrence Douglas Webley, Siyuan Xing, Yuhui Yuan, Yibo Zhu
  • Patent number: 11397711
    Abstract: Proxy-based scaling may be performed for databases. A proxy may be implemented for a database that can establish a connection between the proxy and a database engine to perform a database queries received from a client at the proxy. A scaling event may be detected for the database responsive to which the proxy may establish a connection with a new database engine which may, in some embodiments, have different capabilities or resources that address the features or criteria that triggered the scaling event. Session state may be copied from the database engine to the new database engine so that the new database engine may be able to provide access to the database on behalf of requests received from the client through the proxy.
    Type: Grant
    Filed: May 4, 2018
    Date of Patent: July 26, 2022
    Assignee: Amazon Technologies, Inc.
    Inventors: Saileshwar Krishnamurthy, Alexey Kuznetsov, Mushahid Alam, Anurag Windlass Gupta, Kamal Kant Gupta, Tengiz Kharatishvili, Bohan Liu, Sandor Loren Maurice, Alok Nandan Nikhil, Nicholas Piers O'Shea, Debanjan Saha, Yoni Shalom, Jagdeep Singh Sidhu, Hongbo Song, Alexandre Olegovich Verbitski, Lawrence Douglas Webley, Siyuan Xing, Yuhui Yuan, Yibo Zhu
  • Publication number: 20220228210
    Abstract: Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate. Compositions such as nucleic acid arrays produced by the methods are also disclosed. In some embodiments, a method disclosed herein comprises using photoresist for photocontrollable hybridization and/or ligation of nucleic acid molecules, wherein photoresist removal allows hybridization and/or ligation of nucleic acid molecules at the exposed area. A large diversity of barcodes can be created in molecules on the substrate via sequential rounds of light exposure, hybridization, and ligation.
    Type: Application
    Filed: December 29, 2021
    Publication date: July 21, 2022
    Inventors: David Michael PATTERSON, Denis PRISTINSKI, Preyas SHAH, Steven William SHORT, Dieter WILK, Siyuan XING
  • Patent number: 11384478
    Abstract: The present disclosure provides articles of manufacture with improved moisture control as well as methods of making such articles. In some embodiments, provided herein the article has a fabric with an outer hydrophobic surface and an inner surface with hydrophobic and hydrophilic regions where the hydrophilic regions can form a pattern, allowing moisture to collect and move through the pattern, and the hydrophobic regions prevent the whole inner surface from becoming moist and the outer hydrophobic regions does not show moisture. The fabric may be used to make garments. The entire inner surface of the garment may be patterned with hydrophilic patterns for partial absorption, and the entire outer surface of the garment is hydrophobic, thereby preventing perspiration from being seen from outside of the garment. Further provided herein are methods of making fabrics with improved moisture control including by printing or knitting.
    Type: Grant
    Filed: April 17, 2020
    Date of Patent: July 12, 2022
    Assignee: DRYCO, INC.
    Inventors: Siyuan Xing, Rachel Foote
  • Publication number: 20210139962
    Abstract: Provided in the present invention is a chicken whole-genome SNP chip and application thereof. There are a total of 50,000 SNP loci on the chip: including 19,600 SNP loci for white-feather broilers, yellow-feather and partridge chickens having a MAF value greater than 0.05 and uniformly distributed across the genome which were derived from the data of the whole-genome resequencing of main indigenous chicken breeds in China and introduced chicken breeds; 14,000 SNP loci associated with economic traits, and 16,400 SNP loci for making up for the genomic regions that are not covered by the first two types of probes. The 50,000 SNP loci on the chicken whole-genome SNP chip of the present invention have DNA sequences represented by SEQ ID NOs. 1 to 50,000.
    Type: Application
    Filed: October 10, 2017
    Publication date: May 13, 2021
    Inventors: Jie Wen, Ranran Liu, Guiping Zhao, Maiqing Zheng, Qinghe Li, Huanxian Cui, Siyuan Xing
  • Patent number: 10900818
    Abstract: A fabric based digital droplet flowmetry (DDF) method and platform are provided utilizing a fluid collection network, a microfluidic junction for droplet formation and removal, and digital counting and measurement circuitry. The fluidic junction has a droplet emitter, such as a nozzle, and droplet receiver separated by a gap. The measurement circuitry detects the transient formation of a liquid bridge (the closed-circuit state) and the breakup of the bridge (the open-circuit state) as an electrical switching event. The duration of the bridge formation only lasts for a few milliseconds. The platform produces consistent droplet volume over varying flow rates and droplet size is controlled by the selection of structural parameters such as nozzle dimensions, channel geometries, surface wettability, and inlet/outlet pressures.
    Type: Grant
    Filed: August 12, 2019
    Date of Patent: January 26, 2021
    Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Tingrui Pan, Yahui Yang, Zecong Fang, Siyuan Xing, Ruya Li, Hong Liu