Patents by Inventor Jonathan M. Rothberg

Jonathan M. Rothberg 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: 11828729
    Abstract: Micromachined ultrasonic transducers integrated with complementary metal oxide semiconductor (CMOS) substrates are described, as well as methods of fabricating such devices. Fabrication may involve two separate wafer bonding steps. Wafer bonding may be used to fabricate sealed cavities in a substrate. Wafer bonding may also be used to bond the substrate to another substrate, such as a CMOS wafer. At least the second wafer bonding may be performed at a low temperature.
    Type: Grant
    Filed: August 5, 2020
    Date of Patent: November 28, 2023
    Assignee: BFLY OPERATIONS, INC.
    Inventors: Jonathan M. Rothberg, Susan A. Alie, Keith G. Fife, Nevada J. Sanchez, Tyler S. Ralston
  • Publication number: 20230375475
    Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device may include multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes a surface having a trench region recessed from a portion of the surface and an array of sample wells, disposed in the trench region. The integrated device also includes a waveguide configured to couple excitation energy to at least one sample well in the array and positioned at a first distance from a surface of the trench region and at a second distance from the surface in a region separate from the trench region. The first distance is smaller than the second distance. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.
    Type: Application
    Filed: July 20, 2023
    Publication date: November 23, 2023
    Applicant: Quantum-Si Incorporated
    Inventors: Jonathan M. Rothberg, Ali Kabiri, Gerard Schmid, Keith G. Fife, James Beach, Jason W. Sickler, Lawrence C. West, Paul E. Glenn, Kyle Preston, Farshid Ghasemi, Benjamin Cipriany, Jeremy Lackey
  • Publication number: 20230374586
    Abstract: The disclosure relates, in part, to a method for detecting an analyte in a sample, comprising: contacting a substrate construct with a sample that may comprise the analyte, and using evanescent wave imaging to detect the analyte.
    Type: Application
    Filed: April 28, 2023
    Publication date: November 23, 2023
    Applicant: 454 Corporation
    Inventors: Jonathan M. Rothberg, Isaac Bean, William A. Hansen, Jose Camara, Lawrence C. West, Henry Kemble, Lindsay Schneider, David Honeybun, Jaime Scott Zahorian
  • Publication number: 20230366019
    Abstract: The disclosure is directed to a method for nucleic acid sequencing, comprising: using evanescent wave imaging to identify a 3?-unblocked protected nucleotide incorporated into a sequencing primer.
    Type: Application
    Filed: April 28, 2023
    Publication date: November 16, 2023
    Applicant: 454 Corporation
    Inventors: Jonathan M. Rothberg, Isaac Bean, William A. Hansen, Jose Camara, Lawrence C. West, Henry Kemble, Lindsay Schneider, David Honeybun, Jaime Scott Zahorian
  • Publication number: 20230366026
    Abstract: The disclosure is directed to (i) controlling a first light source to emit a first light into a substrate on which substrate polynucleotides are immobilized, wherein a plurality of substrate polynucleotides are each annealed to a sequencing primer and bound with a polymerase, wherein the substrate polynucleotides are in a presence of a pool of protected nucleotides, and wherein each protected nucleotide comprises a detectable moiety and a photocleavable terminating moiety; (ii) processing a fluorescence signal to identify protected nucleotides incorporated in the sequencing primers; (iii) controlling a second light source to emit a second light into the substrate to cleave the detectable moieties from the incorporated protected nucleotides; (iv) determining one of both of: a percentage of the sequencing primers that incorporated a protected nucleotide and a percentage of the detectable moieties cleaved from the incorporated protected nucleotides; and (v) modifying one or more parameters of a sequencing primer
    Type: Application
    Filed: April 28, 2023
    Publication date: November 16, 2023
    Applicant: 454 Corporation
    Inventors: Jonathan M. Rothberg, Isaac Bean, William A. Hansen, Jose Camara, Lawrence C. West, Henry Kemble, Lindsay Schneider, David Honeybun, Jaime Scott Zahorian
  • Publication number: 20230364618
    Abstract: The disclosure is directed to an imaging device comprising: a reservoir having an interior lower surface; a substrate arranged below the reservoir, wherein at least a portion of an upper surface of the substrate forms the interior lower surface of the reservoir; a first light source arranged proximate to the substrate and configured to direct light into the substrate; an image sensor arranged below the substrate and configured to receive emission light produced within the reservoir.
    Type: Application
    Filed: April 28, 2023
    Publication date: November 16, 2023
    Applicant: 454 Corporation
    Inventors: Jonathan M. Rothberg, Isaac Bean, William A. Hansen, Jose Camara, Lawrence C. West, Henry Kemble, Lindsay Schneider, David Honeybun, Jaime Scott Zahorian
  • Publication number: 20230366025
    Abstract: The disclosure is directed to a method for nucleic acid sequencing, comprising: contacting a substrate polynucleotide immobilized to a substrate with a protected nucleotide and a sequencing primer in a presence of a polymerase such that the polymerase incorporates the protected nucleotide into the sequencing primer, wherein the protected nucleotide comprises a detectable moiety and a photocleavable terminating moiety; using evanescent wave imaging to identify the protected nucleotide incorporated into the sequencing primer; and using evanescent wave imaging to cleave the photocleavable terminating moiety of the protected nucleotide.
    Type: Application
    Filed: April 28, 2023
    Publication date: November 16, 2023
    Applicant: 454 Corporation
    Inventors: Jonathan M. Rothberg, Isaac Bean, William A. Hansen, Jose Camara, Lawrence C. West, Henry Kemble, Lindsay Schneider, David Honeybun, Jaime Scott Zahorian
  • Publication number: 20230366822
    Abstract: The disclosure is directed to a method for preparing a sample for evanescent wave imaging, comprising: isothermally amplifying a target nucleic acid present in the sample in a reservoir to produce one or more amplicons, wherein the one or more amplicons are immobilized to a bottom surface of the reservoir; and contacting the one or more amplicons with an aqueous solution comprising sequencing reagents comprising a pool of 3?-unblocked protected nucleotides.
    Type: Application
    Filed: April 28, 2023
    Publication date: November 16, 2023
    Applicant: 454 Corporation
    Inventors: Jonathan M. Rothberg, Isaac Bean, William A. Hansen, Jose Camara, Lawrence C. West, Henry Kemble, Lindsay Schneider, David Honeybun, Jaime Scott Zahorian
  • Publication number: 20230365612
    Abstract: The disclosure is directed to a compound of formula III: wherein: X is a heteroatom; Base is a nucleobase; R1 and R2 are each independently selected from the group consisting of H, CF3, CN, a C1-C12 straight chain or branched alkyl, a C2-C12 straight chain or branched alkenyl or polyenyl, a C2-C12 straight chain or branched alkynyl or polyalkynyl, a C1-C12 ether, and an aromatic group (e.g., a phenyl, a naphthyl, a pyridine), with the proviso that at least one of R1 and R2 is CF3, CN, a C1-C12 straight chain or branched alkyl, a C2-C12 straight chain or branched alkenyl or polyenyl, a C2-C12 straight chain or branched alkynyl or polyalkynyl, a C1-C12 ether, or an aromatic group (e.g., a phenyl, a naphthyl, a pyridine); R3 is NO2; R4 is H; R5 comprises a C1-C12 alkyne, an amide, and/or an amine; R6 is OMe or S—C6H6; and R7 is H or NO2.
    Type: Application
    Filed: April 28, 2023
    Publication date: November 16, 2023
    Applicant: 454 Corporation
    Inventors: Jonathan M. Rothberg, Isaac Bean, William A. Hansen, Jose Camara, Lawrence C. West, Henry Kemble, Lindsay Schneider, David Honeybun, Jaime Scott Zahorian
  • Publication number: 20230355516
    Abstract: The present invention relates to methods and compositions for treating lymphangioleiomyomatosis in a human subject in need of such treatment. The methods comprise administering to the subject via inhalation an aerosol composition comprising rapamycin or a prodrug or derivative (including analog) thereof.
    Type: Application
    Filed: July 20, 2023
    Publication date: November 9, 2023
    Inventors: Henri Lichenstein, Jonathan M. Rothberg, Thomas Armer, Lawrence S. Melvin, JR.
  • Patent number: 11808700
    Abstract: Instrument control and data acquisition in advanced analytic systems that utilize optical pulses for sample analysis are described. Clocking signals for data acquisition, data processing, communication, and/or other data handling functionalities can be derived from an on-board pulsed optical source, such as a passively mode-locked laser. The derived clocking signals can operate in combination with one or more clocking signals from a stable oscillator, so that instrument operation and data handling can tolerate interruptions in operation of the pulsed optical source.
    Type: Grant
    Filed: June 14, 2019
    Date of Patent: November 7, 2023
    Assignee: Quantum-Si Incorporated
    Inventors: Jonathan M. Rothberg, Benjamin Cipriany, Faisal R. Ahmad, Joseph D. Clark, Daniel B. Frier, Michael Ferrigno, Mel Davey, Tom Thurston, Brett J. Gyarfas, Todd Rearick, Jeremy Christopher Jordan
  • Publication number: 20230333188
    Abstract: According to some aspects, a method of suppressing noise in an environment of a magnetic resonance imaging system is provided. The method comprising estimating a transfer function based on multiple calibration measurements obtained from the environment by at least one primary coil and at least one auxiliary sensor, respectively, estimating noise present in a magnetic resonance signal received by the at least one primary coil based at least in part on the transfer function, and suppressing noise in the magnetic resonance signal using the noise estimate.
    Type: Application
    Filed: April 24, 2023
    Publication date: October 19, 2023
    Applicant: Hyperfine Operations, Inc.
    Inventors: Todd Rearick, Gregory L. Charvat, Matthew Scot Rosen, Jonathan M. Rothberg
  • Patent number: 11789104
    Abstract: Techniques for removing artefacts, such as RF interference and/or noise, from magnetic resonance data. The techniques include: obtaining input magnetic resonance (MR) data using at least one radio-frequency (RF) coil of a magnetic resonance imaging (MRI) system; and generating an MR image from input MR data at least in part by using a neural network model to suppress at least one artefact in the input MR data.
    Type: Grant
    Filed: August 15, 2019
    Date of Patent: October 17, 2023
    Assignee: Hyperfine Operations, Inc.
    Inventors: Carole Lazarus, Prantik Kundu, Sunli Tang, Seyed Sadegh Mohseni Salehi, Michal Sofka, Jo Schlemper, Hadrien A. Dyvorne, Rafael O'Halloran, Laura Sacolick, Michael Stephen Poole, Jonathan M. Rothberg
  • Publication number: 20230320668
    Abstract: Aspects relate to providing radio frequency components responsive to magnetic resonance signals. According to some aspects, a radio frequency component comprises at least one coil having a conductor arranged in a plurality of turns oriented about a region of interest to respond to corresponding magnetic resonant signal components. According to some aspects, the radio frequency component comprises a plurality of coils oriented to respond to corresponding magnetic resonant signal components. According to some aspects, an optimization is used to determine a configuration for at least one radio frequency coil.
    Type: Application
    Filed: June 14, 2023
    Publication date: October 12, 2023
    Applicant: Hyperfine Operations, Inc.
    Inventors: Michael Stephen Poole, Gregory L. Charvat, Todd Rearick, Jonathan M. Rothberg
  • Publication number: 20230324481
    Abstract: According to some aspects, a portable magnetic resonance imaging system is provided, comprising a Bo magnet configured to produce a Bo magnetic field for an imaging region of the magnetic resonance imaging system, a noise reduction system configured to detect and suppress at least some electromagnetic noise in an operating environment of the portable magnetic resonance imaging system, and electromagnetic shielding provided to attenuate at least some of the electromagnetic noise in the operating environment of the portable magnetic resonance imaging system, the electromagnetic shielding arranged to shield a fraction of the imaging region of the portable magnetic resonance imaging system. According to some aspects, the electromagnetic shield comprises at least one electromagnetic shield structure adjustably coupled to the housing to provide electromagnetic shielding for the imaging region in an amount that can be varied. According to some aspects, substantially no shielding of the imaging region is provided.
    Type: Application
    Filed: June 15, 2023
    Publication date: October 12, 2023
    Applicant: Hyperfine Operations, Inc.
    Inventors: Michael Stephen Poole, Cedric Hugon, Hadrien A. Dyvorne, Laura Sacolick, William J. Mileski, Jeremy Christopher Jordan, Alan B. Katze, JR., Jonathan M. Rothberg, Todd Rearick, Christopher Thomas McNulty
  • Patent number: 11774401
    Abstract: In one embodiment, a device is described. The device includes a material defining a reaction region. The device also includes a plurality of chemically-sensitive field effect transistors have a common floating gate in communication with the reaction region. The device also includes a circuit to obtain respective output signals from the chemically-sensitive field effect transistors indicating an analyte within the reaction region.
    Type: Grant
    Filed: October 7, 2022
    Date of Patent: October 3, 2023
    Assignee: Life Technologies Corporation
    Inventors: Jonathan M. Rothberg, Keith G Fife, Jordan Owens, James Bustillo
  • Patent number: 11766696
    Abstract: A method of forming an ultrasonic transducer device includes forming a patterned metal electrode layer over a substrate, the patterned metal electrode layer comprising a lower layer and an upper layer formed on the lower layer; forming an insulation layer over the patterned metal electrode layer; and planarizing the insulation layer to the upper layer of the patterned metal electrode layer, wherein the upper layer comprises a electrically conductive material that serves as a chemical mechanical polishing (CMP) stop layer that has CMP selectivity with respect to the insulation layer and the lower layer, and wherein the upper layer has a CMP removal rate slower than that of the insulation layer.
    Type: Grant
    Filed: February 6, 2020
    Date of Patent: September 26, 2023
    Assignee: BFLY OPERATIONS, INC.
    Inventors: Lingyun Miao, Jianwei Liu, Jonathan M. Rothberg
  • Publication number: 20230295706
    Abstract: Aspects of the disclosure relate to compositions and methods for amplifying and/or detecting one or more target nucleic acid sequences (e.g., a nucleic acid sequence of one or more pathogens) in a biological sample obtained from a subject. In some embodiments, the pathogens are viral, bacterial, fungal, parasitic, or protozoan pathogens, such as SARS-CoV-2 or an influenza virus. In some embodiments, the methods comprise isothermal amplification of a target nucleic acid and subsequent detection of the amplification products.
    Type: Application
    Filed: January 12, 2023
    Publication date: September 21, 2023
    Applicants: Detect, Inc., Board of Regents, The University of Texas System
    Inventors: Spencer Glantz, Jonathan M. Rothberg, Xinghua Shi, Benjamin Rosenbluth, Jaymin Patel, William A. Hansen, Jonathan Naccache, Hope Kronman, Henry Kemble, Caixia Lv, Andrew Ellington, Sanchita Bhadra
  • Patent number: 11744797
    Abstract: The present invention relates to methods and compositions for treating lymphangioleiomyomatosis in a human subject in need of such treatment. The methods comprise administering to the subject via inhalation an aerosol composition comprising rapamycin or a prodrug or derivative (including analog) thereof.
    Type: Grant
    Filed: August 27, 2021
    Date of Patent: September 5, 2023
    Assignee: AI Therapeutics, Inc.
    Inventors: Henri Lichenstein, Jonathan M. Rothberg, Thomas Armer, Lawrence S. Melvin, Jr.
  • Patent number: 11737665
    Abstract: Aspects of the present disclosure provide improved techniques for imaging a subject's retina fundus. Some aspects relate to an imaging apparatus that may be substantially binocular shaped and/or may house multiple imaging devices configured to provide multiple corresponding modes of imaging the subject's retina fundus. Some aspects relate to techniques for imaging a subject's eye using white light, fluorescence, infrared (IR), optical coherence tomography (OCT), and/or other imaging modalities that may be employed by a single imaging apparatus. Some aspects relate to improvements in white light, fluorescence, IR, OCT, and/or other imaging technologies that may be employed alone or in combination with other techniques. Some aspects relate to multi-modal imaging techniques that enable determination of a subject's health status.
    Type: Grant
    Filed: June 19, 2020
    Date of Patent: August 29, 2023
    Assignee: Tesseract Health, Inc.
    Inventors: Tyler S. Ralston, Maurizio Arienzo, Owen Kaye-Kauderer, Benjamin Rosenbluth, Jonathan M. Rothberg, Lawrence C. West, Paul E. Glenn