Patents by Inventor Ali Agah

Ali Agah 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).

  • Patent number: 11378544
    Abstract: A biosensor for base calling is provided. The biosensor comprises a sampling device, which includes a sample surface that has an array of pixel areas and a solid-state imager that has an array of sensors. Each sensor generates pixel signals in each base calling cycle. Each pixel signal represents light gathered in one base calling cycle from one or more clusters in a corresponding pixel area of the sample surface. The biosensor further comprises a signal processor configured for connection to the sampling device. The signal processor receives and processes the pixel signals from the sensors for base calling in a base calling cycle, and uses the pixel signals from fewer sensors than a number of clusters base called in the base calling cycle. The pixel signals from the fewer sensors include at least one pixel signal representing light gathered from at least two clusters in the corresponding pixel area.
    Type: Grant
    Filed: January 7, 2019
    Date of Patent: July 5, 2022
    Assignee: Illumina, Inc.
    Inventors: Dietrich Dehlinger, Ali Agah, Tracy Helen Fung, Emrah Kostem
  • Publication number: 20220120684
    Abstract: Provided herein include various examples of an apparatus, flow cells that include these examples of the apparatus, and methods of making these examples of the apparatus. The apparatus can include a molding layer over a substrate and covering sides of a light detection device. The molding layer comprises a first region and a second region, which, with the active surface of the light detection device, form a contiguous surface. A waveguide integration layer is between the contiguous surface and a waveguide. The waveguide integration layer comprises optical coupling structures over the first and second regions, to optically couple light waves from a light source to the waveguide. The waveguide utilizes the light waves to excite light sensitive materials in nanowells. A nanostructure layer over the waveguide comprises the nanowells. Each nanowell shares a vertical axis with a location on the active surface of the light detection device.
    Type: Application
    Filed: June 25, 2020
    Publication date: April 21, 2022
    Applicant: ILLUMINA, INC.
    Inventors: Arvin EMADI, Arnaud RIVAL, Fabien ABEILLE, Ali AGAH, Craig CIESLA, Aathavan KARUNAKARAN
  • Publication number: 20220097060
    Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an integrated circuit, and an imaging assembly. The flow cell body defines one or more flow channels and a plurality of wells. Each flow channel is configured to receive a flow of fluid. Each well is fluidically coupled with the corresponding flow channel. Each well is configured to contain at least one polynucleotide. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are operable to effect writing of polynucleotides in the corresponding wells. The integrated circuit is operable to drive selective deposition or activation of selected nucleotides to attach to polynucleotides in the wells to thereby generate polynucleotides representing machine-written data in the wells. The imaging assembly is operable to capture images indicative of one or more nucleotides in a polynucleotide.
    Type: Application
    Filed: December 14, 2021
    Publication date: March 31, 2022
    Inventors: Ali Agah, Aathavan Karunakaran, Tarun Khurana, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Patent number: 11282588
    Abstract: A system writes input data to a storage device as machine-written polynucleotides; and reads machine written polynucleotides from the storage device as output data. The storage device includes a flow cell including a plurality of storage wells in which machine written polynucleotides may be stored. The storage device may include a set of electrodes corresponding to the storage wells that allow for selective interactions with wells across the surface of a flow cell. Operation of the storage device may include receiving a read request associated with a particular location in the storage device, creating a copy of a nucleotide sequence located at the particular location in the storage device, transferring the copy of the nucleotide sequence to a read location, and reading the copy of the nucleotide sequence at the read location.
    Type: Grant
    Filed: May 26, 2020
    Date of Patent: March 22, 2022
    Assignee: ILLUMINA, INC.
    Inventors: Craig Ciesla, Ali Agah, Stanley Hong, Tarun Khurana, Aathavan Karunakaran, Arvin Emadi, Merek Siu
  • Patent number: 11229909
    Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an integrated circuit, and an imaging assembly. The flow cell body defines one or more flow channels and a plurality of wells. Each flow channel is configured to receive a flow of fluid. Each well is fluidically coupled with the corresponding flow channel. Each well is configured to contain at least one polynucleotide. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are operable to effect writing of polynucleotides in the corresponding wells. The integrated circuit is operable to drive selective deposition or activation of selected nucleotides to attach to polynucleotides in the wells to thereby generate polynucleotides representing machine-written data in the wells. The imaging assembly is operable to capture images indicative of one or more nucleotides in a polynucleotide.
    Type: Grant
    Filed: May 26, 2020
    Date of Patent: January 25, 2022
    Assignee: ILLUMINA, INC.
    Inventors: Ali Agah, Aathavan Karunakaran, Tarun Khurana, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Publication number: 20220003728
    Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.
    Type: Application
    Filed: September 20, 2021
    Publication date: January 6, 2022
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Publication number: 20210405019
    Abstract: Methods are used for obtaining, cataloguing, and/or storing data derived from a biological source using a flow cell body, electrodes, and an imaging assembly. The data may include DNA and/or RNA obtained from a biological source, such as from the cells of an organism. The methods may be used to obtain, catalog, and/or store data such as DNA or RNA sequence from a pathogen such as a virus and/or a bacteria, human health data over time, and immune system information from an individual. The data obtained using the disclosed methods may be used for a variety of different purposes, including the manufacture of vaccine compositions, and for restoring the immune system of an individual who has undergone an immune system depleting event. The methods may be used for storage of biological cells, which may be used for the screening of compounds, such as small molecules with potential for therapeutic indications.
    Type: Application
    Filed: September 9, 2021
    Publication date: December 30, 2021
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Xi-Jun Chen
  • Publication number: 20210362151
    Abstract: A method for reducing sequencing by synthesis cycle time using a microfluidic device is provided. The microfluidic device comprises a flow cell having an inlet port, an outlet port, and a flow channel extending between the inlet port and the outlet port, wherein the flow channel receives an analyte of interest and one or more reagents for analyzing and detecting molecules. To aid in the acceleration of the reactions, the microfluidic device comprises a mixing device to increase the rates of diffusion of the reagents from the fluid bulk to an active surface of the flow cell. The mixing device comprises at least one of an electrothermal mixing device, an active mechanical mixing device, and a vibrational mixing device.
    Type: Application
    Filed: February 7, 2020
    Publication date: November 25, 2021
    Inventors: Aathavan Karunakaran, Arnaud Rival, Ali Agah, Fabien Abeille, Steven Barnard, Craig Ciesla, Murali Venkatesan, Pargol Gheissari, Jennifer Wang, Dietrich Dehlinger
  • Patent number: 11143638
    Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.
    Type: Grant
    Filed: May 26, 2020
    Date of Patent: October 12, 2021
    Assignee: ILLUMINA, INC.
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Patent number: 11137385
    Abstract: Methods are used for obtaining, cataloguing, and/or storing data derived from a biological source using a flow cell body, electrodes, and an imaging assembly. The data may include DNA and/or RNA obtained from a biological source, such as from the cells of an organism. The methods may be used to obtain, catalog, and/or store data such as DNA or RNA sequence from a pathogen such as a virus and/or a bacteria, human health data over time, and immune system information from an individual. The data obtained using the disclosed methods may be used for a variety of different purposes, including the manufacture of vaccine compositions, and for restoring the immune system of an individual who has undergone an immune system depleting event. The methods may be used for storage of biological cells, which may be used for the screening of compounds, such as small molecules with potential for therapeutic indications.
    Type: Grant
    Filed: May 26, 2020
    Date of Patent: October 5, 2021
    Assignee: ILLUMINA, INC.
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Xi-Jun Chen
  • Publication number: 20210272863
    Abstract: Provided herein include various examples of an apparatus, a sensor system and examples of a method for manufacturing aspects of an apparatus, a sensor system. The apparatus may include a die. The apparatus may also include a substrate comprising a cavity. The die may be oriented in a portion of the cavity in the substrate, where the orientation defines a first space in the cavity adjacent to a first edge of the upper surface of the die and a second space in the cavity adjacent to the second edge of the upper surface of the die. The apparatus may further include fluidics fan-out regions comprising a first cured material deposited in the first space and the second space, a surface of the fluidics fan-out regions being contiguous with the upper surface of the die.
    Type: Application
    Filed: February 19, 2021
    Publication date: September 2, 2021
    Inventors: Arvin Emadi, Arnaud Rival, Ali Agah, Tara Bozorg-Grayeli
  • Publication number: 20210151129
    Abstract: A system writes input data to a storage device as machine-written polynucleotides; and reads machine written polynucleotides from the storage device as output data. The storage device includes a flow cell including a plurality of storage wells in which machine written polynucleotides may be stored. The storage device may include a set of electrodes corresponding to the storage wells that allow for selective interactions with wells across the surface of a flow cell. Operation of the storage device may include receiving a read request associated with a particular location in the storage device, creating a copy of a nucleotide sequence located at the particular location in the storage device, transferring the copy of the nucleotide sequence to a read location, and reading the copy of the nucleotide sequence at the read location.
    Type: Application
    Filed: May 26, 2020
    Publication date: May 20, 2021
    Inventors: Craig Ciesla, Ali Agah, Stanley Hong, Tarun Khurana, Aathavan Karunakaran, Arvin Emadi, Merek Siu
  • Publication number: 20210147833
    Abstract: A method includes grafting oligonucleotides to a flow cell and preparing a library of polynucleotides. Each polynucleotide has been written to contain retrievable information and includes a region complementary to one of the sequencing initiation primers grafted to the flow cell. Each polynucleotide is indexed to permit discrete identification of that polynucleotide and the information it contains over other polynucleotides in the library. Another method includes writing two polynucleotides including two sequences with reverse complementary joining sequences onto a flow cell. One of the polynucleotides is extended to generate a third polynucleotide comprising a sequence that is the combination of the first and second sequences. A fourth polynucleotide is written with a third joining sequence of a fourth sequence.
    Type: Application
    Filed: May 26, 2020
    Publication date: May 20, 2021
    Inventors: Yir-Shyuan Wu, Amirali Kia, Tarun Khurana, Ali Agah, Aathavan Karunakaran, Xi-Jun Chen
  • Publication number: 20210148872
    Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.
    Type: Application
    Filed: May 26, 2020
    Publication date: May 20, 2021
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Publication number: 20210146354
    Abstract: Devices, systems, and methods for non-volatile storage include a well activation device operable to modify one or more wells from a plurality of wells of a flow cell to provide a set of readable wells. Readable wells are configured to allow exposure of a well to substances from nucleotide sequencing fluids, and prevent exposure to other substances and fluids, such as nucleotide synthesizing fluids. The well activation device may also modify wells to provide a set of writeable wells. This set of wells is configured to allow exposure to the nucleotide synthesizing fluids and substances; and prevent exposure to the nucleotide sequencing fluids and substances. There may also be provisions made for risk mitigation for data errors such as generating commands to write specified data to a nucleotide sequence associated with a particular location in a storage device, reading the nucleotide sequence and performing a comparison.
    Type: Application
    Filed: May 26, 2020
    Publication date: May 20, 2021
    Inventors: Merek Siu, Ali Agah, Stanley Hong, Tarun Khurana, Aathavan Karunakaran, Craig Ciesla
  • Publication number: 20210146356
    Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an integrated circuit, and an imaging assembly. The flow cell body defines one or more flow channels and a plurality of wells. Each flow channel is configured to receive a flow of fluid. Each well is fluidically coupled with the corresponding flow channel. Each well is configured to contain at least one polynucleotide. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are operable to effect writing of polynucleotides in the corresponding wells. The integrated circuit is operable to drive selective deposition or activation of selected nucleotides to attach to polynucleotides in the wells to thereby generate polynucleotides representing machine-written data in the wells. The imaging assembly is operable to capture images indicative of one or more nucleotides in a polynucleotide.
    Type: Application
    Filed: May 26, 2020
    Publication date: May 20, 2021
    Inventors: Ali Agah, Aathavan Karunakaran, Tarun Khurana, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Publication number: 20210131940
    Abstract: Flow cells and corresponding methods are provided. The flow cells may include a support frame with top and back sides, and at least one cavity extending from the top side. The flow cells may include at least one light detection device with an active area disposed within the at least one cavity. The flow cells may include a support material disposed within the at least one cavity between the support frame and the periphery of the at least one light detection device coupling them together. The flow cells may include a lid extending over the at least one light detection device and coupled to the support frame about the periphery of the at least one light detection device. The lid and at least a top surface of the at least one light detection device form a flow channel therebetween.
    Type: Application
    Filed: January 13, 2021
    Publication date: May 6, 2021
    Applicant: Illumina, Inc.
    Inventors: Arnaud RIVAL, Ali AGAH, Tracy H. FUNG, Dietrich DEHLINGER, Poorya SABOUNCHI, Tarun KHURANA, Craig M. CIESLA, M. Shane BOWEN
  • Publication number: 20210116436
    Abstract: Methods are used for obtaining, cataloguing, and/or storing data derived from a biological source using a flow cell body, electrodes, and an imaging assembly. The data may include DNA and/or RNA obtained from a biological source, such as from the cells of an organism. The methods may be used to obtain, catalog, and/or store data such as DNA or RNA sequence from a pathogen such as a virus and/or a bacteria, human health data over time, and immune system information from an individual. The data obtained using the disclosed methods may be used for a variety of different purposes, including the manufacture of vaccine compositions, and for restoring the immune system of an individual who has undergone an immune system depleting event. The methods may be used for storage of biological cells, which may be used for the screening of compounds, such as small molecules with potential for therapeutic indications.
    Type: Application
    Filed: May 26, 2020
    Publication date: April 22, 2021
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Xi-Jun Chen
  • Publication number: 20210098521
    Abstract: An example image sensor structure includes an image layer. The image layer includes an array of light detectors disposed therein. A device stack is disposed over the image layer. An array of light guides is disposed in the device stack. Each light guide is associated with at least one light detector of the array of light detectors. A passivation stack is disposed over the device stack. The passivation stack includes a bottom surface in direct contact with a top surface of the light guides. An array of nanowells is disposed in a top layer of the passivation stack. Each nanowell is associated with a light guide of the array of light guides. A crosstalk blocking metal structure is disposed in the passivation stack. The crosstalk blocking metal structure reduces crosstalk within the passivation stack.
    Type: Application
    Filed: December 11, 2020
    Publication date: April 1, 2021
    Inventors: Xiuyu CAI, Ali AGAH, Tracy H. FUNG, Dietrich DEHLINGER
  • Patent number: 10921233
    Abstract: Flow cells and corresponding methods are provided. The flow cells may include a support frame with top and back sides, and at least one cavity extending from the top side. The flow cells may include at least one light detection device with an active area disposed within the at least one cavity. The flow cells may include a support material disposed within the at least one cavity between the support frame and the periphery of the at least one light detection device coupling them together. The flow cells may include a lid extending over the at least one light detection device and coupled to the support frame about the periphery of the at least one light detection device. The lid and at least a top surface of the at least one light detection device form a flow channel therebetween.
    Type: Grant
    Filed: September 11, 2019
    Date of Patent: February 16, 2021
    Assignee: Illumina, Inc.
    Inventors: Arnaud Rival, Ali Agah, Tracy H. Fung, Dietrich Dehlinger, Poorya Sabounchi, Tarun Khurana, Craig M. Ciesla, M. Shane Bowen