Patents by Inventor Aathavan Karunakaran

Aathavan Karunakaran 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: 20240060954
    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: October 31, 2023
    Publication date: February 22, 2024
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Xi-Jun Chen
  • Patent number: 11867672
    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: February 9, 2023
    Date of Patent: January 9, 2024
    Assignee: ILLUMINA, INC.
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Publication number: 20230407386
    Abstract: Defocus is introduced during sequencing by synthesis by tilt of a flow cell and by variations in flatness of the flow cell. Effects of the defocus are reduced, and base calling quality is improved using techniques relating to dependence of base calling on flow cell tilt. For example, the flow cell surface height is measured throughout the flow cell. A focal height of an imager having a sensor for the sequencing is set, optionally adaptively, one or more times during the sequencing. Each image captured by the sensor is partitioned, e.g., based on differences between focal height and the measured flow cell surface height across areas of the sensor. Filters, e.g., related to defocus correction, are selected based at least in part on the difference between the focal height and the measured flow cell surface height at a particular area of the image being corrected for defocus.
    Type: Application
    Filed: June 9, 2023
    Publication date: December 21, 2023
    Applicants: Illumina, Inc., Illumina Software, Inc.
    Inventors: Stanley Hong, Michael Gallaspy, Merek Siu, Jeffrey Gau, Anindita Dutta, Aathavan Karunakaran, Simon Prince
  • Patent number: 11835510
    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: September 9, 2021
    Date of Patent: December 5, 2023
    Assignee: ILLUMINA, INC.
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Xi-Jun Chen
  • Publication number: 20230383342
    Abstract: Embodiments of the present disclosure relate to kits, compositions, and methods for nucleic acid sequencing, for example, two-channel nucleic acid sequencing by synthesis using blue and green light excitation. In particular, unlabeled nucleotides for incorporation may be used in conjunction with affinity reagents containing detectable labels excitable by blue and/or green lights, for specific binding to each type of nucleotides incorporated.
    Type: Application
    Filed: May 30, 2023
    Publication date: November 30, 2023
    Inventors: Xiaolin Wu, Patrick McCauley, Madushani Dharmarwardana, Saurabh Nirantar, Misha Golynskiy, Xiangyuan Yang, Ramesh Neelakandan, Benedict Mackworth, Carole Anastasi, Aathavan Karunakaran, Gery M. Vessere, David Bracher
  • Publication number: 20230321651
    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, 2023
    Publication date: October 12, 2023
    Inventors: Ali Agah, Aathavan Karunakaran, Tarun Khurana, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Publication number: 20230296516
    Abstract: Artificial intelligence driven signal enhancement of sequencing images enables enhanced sequencing by synthesis that determines a sequence of bases in genetic material with any one or more of: improved performance, improved accuracy, and/or reduced cost. A training set of images taken at unreduced and reduced power levels used to excite fluorescence during sequencing by synthesis is used to train a neural network to enable the neural network to recover enhanced images, as if taken at the unreduced power level, from unenhanced images taken at the reduced power level.
    Type: Application
    Filed: February 17, 2023
    Publication date: September 21, 2023
    Applicants: Illumina, Inc., Illumina Software, Inc.
    Inventors: Anindita Dutta, Michael Gallaspy, Jeffrey Gau, Stanley Hong, Aathavan Karunakaran, Simon Prince, Merek Siu, Yina Wang, Rishi Verma
  • Publication number: 20230295719
    Abstract: Systems and methods of identifying nucleobases in a template polynucleotide are disclosed. In one embodiment, such a method may include providing a substrate comprising a plurality of double stranded template polynucleotides in a cluster. Each double stranded template polynucleotide may comprise a first strand and a second strand. The method may further include contacting the plurality of double stranded template polynucleotides with first primers which bind to the first strand and second primers which bind to the second strand. The method may further include extending the first primers and the second primers by contacting the cluster with labeled nucleobases to form first labeled primers and second labeled primers. The method may further include stimulating light emissions from the first and second labeled primers, wherein an amplitude of the signal generated by the first labeled primers is greater than an amplitude of the signal generated by the second labeled primers.
    Type: Application
    Filed: March 15, 2023
    Publication date: September 21, 2023
    Inventors: Aathavan Karunakaran, Nileshi Saraf, Samantha Antonio Leong, Ramir Villa Vega, Gery Vessere
  • Publication number: 20230285974
    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: January 31, 2023
    Publication date: September 14, 2023
    Inventors: Merek Siu, Ali Agah, Stanley Hong, Tarun Khurana, Aathavan Karunakaran, Craig Ciesla, Amirali Kia
  • Publication number: 20230260096
    Abstract: Artificial intelligence driven enhancement of motion blurred sequencing images enables enhanced sequencing that determines a sequence of bases in genetic material with any one or more of: improved performance, improved accuracy, and/or reduced cost. A training set of images taken after unreduced and reduced movement settling times during sequencing is used to train a neural network to enable the neural network to recover enhanced images, as if taken after the unreduced movement settling time, from unenhanced images taken after the reduced movement settling time.
    Type: Application
    Filed: February 17, 2023
    Publication date: August 17, 2023
    Applicants: Illumina, Inc., Illumina Software, Inc.
    Inventors: Simon Prince, Stanley Hong, Michael Gallaspy, Merek Siu, Jeffrey Gau, Anindita Dutta, Aathavan Karunakaran, Yina Wang, Rishi Verma
  • Patent number: 11691146
    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: August 30, 2022
    Date of Patent: July 4, 2023
    Assignee: ILLUMINA, INC.
    Inventors: Ali Agah, Aathavan Karunakaran, Tarun Khurana, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Publication number: 20230184725
    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: February 9, 2023
    Publication date: June 15, 2023
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Publication number: 20230183799
    Abstract: Systems and methods of identifying nucleobases in a template polynucleotide are disclosed. In one embodiment, such a method may include providing a substrate comprising a plurality of the template polynucleotides in a cluster. The method may further include generating light to stimulate fluorescent emissions from the cluster. The method may further include receiving a first signal emitted at a first intensity from a first plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a first site. The method may further include receiving a second signal emitted at a second intensity from a second plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a second site. The method may further include identifying the nucleobases hybridized at the first and second sites of the template polynucleotide based on a combination of the first and second signals.
    Type: Application
    Filed: December 8, 2022
    Publication date: June 15, 2023
    Inventors: Shaun E. Hunter, Paul Sangiorgio, Aathavan Karunakaran, David Bracher
  • Patent number: 11604175
    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: June 22, 2022
    Date of Patent: March 14, 2023
    Assignee: ILLUMINA, INC.
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Patent number: 11590505
    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: Grant
    Filed: May 26, 2020
    Date of Patent: February 28, 2023
    Assignee: ILLUMINA, INC.
    Inventors: Merek Siu, Ali Agah, Stanley Hong, Tarun Khurana, Aathavan Karunakaran, Craig Ciesla, Amirali Kia
  • Publication number: 20230023831
    Abstract: In situ-generated microfluidic capture structures incorporating a solidified polymer network, methods of preparation and use, compositions and kits therefor are described. Microfluidic capture structures may be advantageously used for assays performed within the microfluidic environment, providing flexibility in assaying micro-objects such as biological cells. Assay reagents and analytes may be incorporated within the microfluidic capture structures.
    Type: Application
    Filed: September 8, 2022
    Publication date: January 26, 2023
    Applicant: BERKLEY LIGHTS, INC.
    Inventors: Kristin G. BEAUMONT, Peter J. BEEMILLER, Volker L.S. KURZ, Gregory G. LAVIEU, Xiaohua WANG, Aathavan KARUNAKARAN
  • Publication number: 20220410154
    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: August 30, 2022
    Publication date: December 29, 2022
    Inventors: Ali Agah, Aathavan Karunakaran, Tarun Khurana, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Publication number: 20220356429
    Abstract: Systems, methods and kits are described for culturing one or more biological cells in a microfluidic device, including provision of nutrients and gaseous components configured to enhance cell growth, viability, portability, or any combination thereof. In some embodiments, culturing a single cell may produce a clonal population in the microfluidic device.
    Type: Application
    Filed: May 12, 2022
    Publication date: November 10, 2022
    Inventors: Randall D. LOWE, JR., Kristin G. BEAUMONT, Aathavan KARUNAKARAN, Natalie C. MARKS, Jason M. MCEWEN, Mark P. WHITE, J. Tanner NEVILL, Gang F. WANG, Andrew W. MCFARLAND, Daniele Malleo, Keith J. BREINLINGER, Xiao GUAN, Kevin T. CHAPMAN
  • Publication number: 20220317100
    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: June 22, 2022
    Publication date: October 6, 2022
    Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
  • Patent number: 11454629
    Abstract: In situ-generated microfluidic capture structures incorporating a solidified polymer network, methods of preparation and use, compositions and kits therefor are described. Microfluidic capture structures may be advantageously used for assays performed within the microfluidic environment, providing flexibility in assaying micro-objects such as biological cells. Assay reagents and analytes may be incorporated within the microfluidic capture structures.
    Type: Grant
    Filed: June 22, 2020
    Date of Patent: September 27, 2022
    Assignee: Berkeley Lights, Inc.
    Inventors: Kristin G. Beaumont, Peter J. Beemiller, Volker L. S. Kurz, Gregory G. Lavieu, Xiaohua Wang, Aathavan Karunakaran