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: 20250108375
    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: December 12, 2024
    Publication date: April 3, 2025
    Inventors: Aathavan Karunakaran, Arnaud Rival, Ali Agah, Fabien Abeille, Steven Barnard, Craig Ciesla, Murali Venkatesan, Pargol Gheissari, Jennifer Wang, Dietrich Dehlinger
  • Publication number: 20250101493
    Abstract: The disclosure provides compositions, methods, and kits that facilitate the characterization of omic variation in tissues while preserving spatial information related to the origin of target analytes in the tissue.
    Type: Application
    Filed: December 29, 2022
    Publication date: March 27, 2025
    Inventors: Andrea MANZO, Aathavan KARUNAKARAN, Jeffrey S. FISHER, Jeffrey G. MANDELL, Eric Hans VERMAAS, Fiona KAPER, Adam WHITE, Andrew J. PRICE, Andrew Zachary OSTROW, Jeffrey BRODIN, Sarah Munchel SHULTZABERGER
  • Publication number: 20250084357
    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: September 23, 2024
    Publication date: March 13, 2025
    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: 20250084402
    Abstract: The invention relates to methods and kits for use in nucleic acid sequencing, in particular methods for use in concurrent sequencing, including concurrent sequencing of tandem insert libraries. Further, the invention relates to methods of detecting mismatched base pairs in nucleic acid sequences. In another embodiment, the disclosed technology relates to using next generation sequencing to determine the nucleotide sequences of two or more polynucleotide sequence portions in a single sequencing run.
    Type: Application
    Filed: September 13, 2024
    Publication date: March 13, 2025
    Inventors: Eli CARRAMI, Jonathan BOUTELL, Oliver MILLER, Aathavan KARUNAKARAN, Stephen BRUINSMA, Niall GORMLEY, Gery VESSERE, Roberto ANDRES, Michael BUREK, Shagesh SRIDHARAN, Nileshi SARAF, Come RACZY, Jeff GAU
  • Publication number: 20250043275
    Abstract: The invention relates to methods and kits for use in nucleic acid sequencing, in particular methods for use in concurrent sequencing, and in particular concurrent sequencing of tandem insert libraries.
    Type: Application
    Filed: September 13, 2024
    Publication date: February 6, 2025
    Inventors: Eli M. Carrami, Jonathan Mark Boutell, Oliver Jon Miller, Aathavan Karunakaran, Stephen Paul Bruinsma, Niall Anthony Gormley
  • Patent number: 12201985
    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: January 31, 2023
    Date of Patent: January 21, 2025
    Assignee: Illumina, Inc.
    Inventors: Merek Siu, Ali Agah, Stanley Hong, Tarun Khurana, Aathavan Karunakaran, Craig Ciesla, Amirali Kia
  • Patent number: 12186746
    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: Grant
    Filed: February 7, 2020
    Date of Patent: January 7, 2025
    Assignee: ILLUMINA, INC.
    Inventors: Aathavan Karunakaran, Arnaud Rival, Ali Agah, Fabien Abeille, Steven Barnard, Craig Ciesla, Murali Venkatesan, Pargol Gheissari, Jennifer Wang, Dietrich Dehlinger
  • Patent number: 12134758
    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: Grant
    Filed: May 12, 2022
    Date of Patent: November 5, 2024
    Assignee: BRUKER CELLULAR ANALYSIS, INC.
    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: 20240360503
    Abstract: The invention relates to methods for use in nucleic acid sequencing, in particular methods for use in concurrent sequencing.
    Type: Application
    Filed: March 15, 2023
    Publication date: October 31, 2024
    Inventors: Gery VESSERE, Aathavan KARUNAKARAN, Come RACZY, Jeff GAU, Jonathan BOUTELL, Roberto ANDRES, Michael BUREK, Eli CARRAMI
  • Publication number: 20240352515
    Abstract: A method of base calling nucleobases of two or more polynucleotide sequence portions, wherein said polynucleotide sequence portions have been selectively processed such that an intensity of the signals obtained based upon the respective first nucleobase is greater than an intensity of the signals obtained based upon the respective second nucleobase.
    Type: Application
    Filed: March 15, 2023
    Publication date: October 24, 2024
    Inventors: Gery VESSERE, Aathavan KARUNAKARAN, Come RACZY, Jeff GAU, Jonathan BOUTELL, Roberto ANDRES, Michael BUREK, Eli CARRAMI
  • Patent number: 12111262
    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: Grant
    Filed: June 25, 2020
    Date of Patent: October 8, 2024
    Assignee: Illumina Inc.
    Inventors: Arvin Emadi, Arnaud Rival, Fabien Abeille, Ali Agah, Craig Ciesla, Aathavan Karunakaran
  • Publication number: 20240301464
    Abstract: The invention relates to methods of detecting modified cytosines in nucleic acid sequences.
    Type: Application
    Filed: January 16, 2024
    Publication date: September 12, 2024
    Inventors: Aathavan Karunakaran, Shagesh Sridharan, Jonathan Mark Boutell, Gery M. Vessere
  • Publication number: 20240287578
    Abstract: The invention relates to methods of detecting modified cytosines in nucleic acid sequences.
    Type: Application
    Filed: January 16, 2024
    Publication date: August 29, 2024
    Inventors: Niall Anthony Gormley, Jonathan Mark Boutell, Aathavan Karunakaran
  • Patent number: 12062419
    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: March 1, 2022
    Date of Patent: August 13, 2024
    Assignee: ILLUMINA, INC.
    Inventors: Craig Ciesla, Ali Agah, Stanley Hong, Tarun Khurana, Aathavan Karunakaran, Arvin Emadi, Merek Siu
  • Publication number: 20240212791
    Abstract: The technology disclosed is directed to context-dependent base calling. The technology disclosed describes a system including memory storing k-mer-specific centroids for k-mers. The k-mer-specific centroids are learned by training a base calling pipeline to represent base calls of an already base called sequence in k-mer-specific time series, transform the k-mer-specific time series into predicted k-mer-specific centroids, merge the predicted k-mer-specific centroids on a sequencing cycle-by-sequencing cycle basis to generate predicted per-sequencing cycle intensity values, determine a training loss (e.g., a transformation loss) based on comparing the predicted per-sequencing cycle intensity values against known intensity values of the base calls, update the predicted k-mer-specific centroids based on the determined training loss, and store the updated centroids as the k-mer-specific centroids.
    Type: Application
    Filed: December 20, 2023
    Publication date: June 27, 2024
    Inventors: Gery Vessere, David Olmstead Bracher, Aathavan Karunakaran
  • Publication number: 20240209429
    Abstract: This application relates to methods of monoclonal clustering. In some examples, the monoclonal clustering utilizes double-stranded DNA.
    Type: Application
    Filed: December 6, 2023
    Publication date: June 27, 2024
    Applicant: Illumina, Inc.
    Inventors: Aathavan Karunakaran, David Bracher
  • Publication number: 20240177807
    Abstract: The technology disclosed is directed to cluster segmentation and base calling. The technology disclosed describes a computer-implemented method including segmenting a population of clusters into a plurality of subpopulations of clusters based on one or more prior bases called at one or more prior sequencing cycles of a sequencing run. At a current sequencing cycle of the sequencing run, the method includes applying a mixture of four distributions to current sequenced data of each subpopulation of clusters in the plurality of subpopulations of clusters, the four distributions corresponding to four bases adenine (A), cytosine (C), guanine (G), and thymine (T), and the current sequenced data being generated at the current sequencing cycle. The method further includes base calling clusters in a particular subpopulation of clusters using a corresponding mixture of four distributions.
    Type: Application
    Filed: September 15, 2023
    Publication date: May 30, 2024
    Inventors: John S. Vieceli, Eric Jon Ojard, Aathavan Karunakaran, David Olmstead Bracher, Gery Vessere
  • 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