Patents by Inventor Robert Osborne

Robert Osborne 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: 20240132965
    Abstract: Described herein is a method for detecting cancer DNA in a test sample of DNA from a patient. In some embodiments, the method may comprise: (a) sequencing multiple aliquots of the test sample to produce, for each aliquot, sequence reads corresponding to two or more target regions that each have one or more sequence variations present within the patient's cancer; (b) for each aliquot, for each target region: i. determining the number of sequence reads that have the sequence variation; ii. determining the total number of sequence reads; and iii. comparing i. and ii. to one or more error probability distribution models for the sequence variation, wherein the one or more models are obtained from DNA that does not contain the sequence variation; and (c) integrating the collective results of step (b) to determine if there is cancer DNA in the test sample.
    Type: Application
    Filed: February 2, 2023
    Publication date: April 25, 2024
    Inventors: Malcolm PERRY, Giovanni MARSICO, Robert OSBORNE, Nitzan ROSENFELD, Tim FORSHEW
  • Publication number: 20240084384
    Abstract: Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.
    Type: Application
    Filed: November 16, 2023
    Publication date: March 14, 2024
    Inventors: Sydney Brenner, Gi Mikawa, Robert Osborne, Andrew Slatter
  • Publication number: 20240077294
    Abstract: A blade for a measuring tape device may include a first end at which an end hook is configurable, a second end configured to be operably coupled to a reel assembly of the measuring tape device, a metallic strip of material extending between the first end and second end, and a reinforcement strip applied to a longitudinal centerline of a selected portion of the metallic strip proximate to the first end. The reinforcement strip may be applied to a top or bottom of the metallic strip. A width of the reinforcement strip may be between about 10% to about 100% of a width of the metallic strip and a thickness of the reinforcement strip may be between about 50% to about 300% a thickness of the metallic strip.
    Type: Application
    Filed: January 21, 2022
    Publication date: March 7, 2024
    Inventor: Robert Osborne Struble, III
  • Publication number: 20240026313
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.
    Type: Application
    Filed: September 28, 2023
    Publication date: January 25, 2024
    Inventors: Robert Osborne, Vesna Mitchell, Khin Yu Naing Htwe, Xiyun Zhang, Erika M. Milczek, Jeffrey C. Moore
  • Publication number: 20240002940
    Abstract: The invention relates to a method of generating a nucleic acid library for sequencing with error rates <1 error per 100 million base pairs and uses thereof. Provided are methods for detecting mutations (including driver mutations) present in single DNA molecules, such as a single DNA molecule from a polyclonal population of cells, and use of the methods in measuring somatic mutation rates, mutational signatures and driver mutations in vivo or in vitro. Also provided are methods of discovering somatic mutations involved in disease and detecting mutations from cells in culture, diagnosing disease and for detecting the presence and/or identity of a suspected mutation in a cell cultured in vitro and/or subjected to a mutagenic process in vitro. Further provided is a method of computational analysis of duplex sequencing data.
    Type: Application
    Filed: November 24, 2021
    Publication date: January 4, 2024
    Inventors: Federico ABASCAL, Stefanie LENSING, Inigo MARTINCORENA, Robert OSBORNE
  • Publication number: 20240002912
    Abstract: Disclosed is a hybridisation capture method based on the pyrophosphorolysis reaction. According to the present invention, there is provided a method for increasing the ratio of a first nucleic acid sequence to second nucleic acid sequence in a sample.
    Type: Application
    Filed: March 10, 2023
    Publication date: January 4, 2024
    Inventors: Robert Osborne, Magdalena Stolarek-Januszkiewicz, Barnaby Balmforth
  • Patent number: 11807874
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.
    Type: Grant
    Filed: February 15, 2022
    Date of Patent: November 7, 2023
    Assignee: Codexis, Inc.
    Inventors: Robert Osborne, Vesna Mitchell, Khin Yu Naing Htwe, Xiyun Zhang, Erika M. Milczek, Jeffrey C. Moore
  • Publication number: 20230272354
    Abstract: The present invention provides engineered proline hydroxylase polypeptides for the production of hydroxylated compounds, polynucleotides encoding the engineered proline hydroxylases, host cells capable of expressing the engineered proline hydroxylases, and methods of using the engineered proline hydroxylases to prepare compounds useful in the production of active pharmaceutical agents.
    Type: Application
    Filed: March 8, 2023
    Publication date: August 31, 2023
    Inventors: Jovana Nazor, Robert Osborne, Jack Liang, Jonathan Vroom, Xiyun Zhang, David Entwistle, Rama Voladri, Ravi David Garcia, Jeffrey C. Moore, Shane Grosser, Birgit Kosjek, Matthew Truppo
  • Publication number: 20230250403
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.
    Type: Application
    Filed: January 12, 2023
    Publication date: August 10, 2023
    Inventors: Robert Osborne, Vesna Mitchell, Khin Yu Naing Htwe, Xiyun Zhang, Erika M. Milczek, Jeffrey C. Moore
  • Publication number: 20230242981
    Abstract: Described herein is a method of sequencing a template that comprises a direct repeat, comprising: (a) in the same reaction, hybridizing a primer to a first site that is upstream of the first repeat sequence and hybridizing a primer to a second site that is upstream of the second repeat sequence, wherein the first and second sites are: (i) upstream of the first and second repeat sequences, respectively, and (ii) equidistant from the first and second repeat sequences; and (b) subjecting the hybridization product of (a) to a sequencing-by-synthesis sequencing reaction to produce a sequence read that comprises a combination of the first and second repeat sequences.
    Type: Application
    Filed: November 18, 2022
    Publication date: August 3, 2023
    Inventor: Robert Osborne
  • Patent number: 11634754
    Abstract: Disclosed is a hybridisation capture method based on the pyrophosphorolysis reaction. According to the present invention, there is provided a method for increasing the ratio of a first nucleic add sequence to second nucleic add sequence in a sample.
    Type: Grant
    Filed: April 15, 2022
    Date of Patent: April 25, 2023
    Inventors: Robert Osborne, Magdalena Stolarek-Januszkiewicz, Barnaby Balmforth
  • Patent number: 11634695
    Abstract: The present invention provides engineered proline hydroxylase polypeptides for the production of hydroxylated compounds, polynucleotides encoding the engineered proline hydroxylases, host cells capable of expressing the engineered proline hydroxylases, and methods of using the engineered proline hydroxylases to prepare compounds useful in the production of active pharmaceutical agents.
    Type: Grant
    Filed: October 16, 2020
    Date of Patent: April 25, 2023
    Assignee: Codexis, Inc.
    Inventors: Jovana Nazor, Robert Osborne, Jack Liang, Jonathan Vroom, Xiyun Zhang, David Entwistle, Rama Voladri, Ravi David Garcia, Jeffrey C. Moore, Shane Grosser, Birgit Kosjek, Matthew Truppo
  • Publication number: 20230065345
    Abstract: Described herein is a method of sequencing, comprising: splitting an asymmetrically tagged library into a plurality of subsamples, tagging the adaptor-ligated DNA in the sub-samples with sequence tags that identify the subsamples, optionally pooling the sub-samples, sequencing polynucleotides from each of the tagged sub-samples, or copies of the same, to produce sequence reads each comprising: i. a sub-sample identifier sequence and ii. the sequence of at least part of a fragment in the sample, wherein some of the sequence reads are derived from the top strand of a fragment in the sample and some of the sequence reads of are derived from the bottom strand of the same fragment.
    Type: Application
    Filed: September 19, 2022
    Publication date: March 2, 2023
    Inventor: Robert OSBORNE
  • Patent number: 11591578
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.
    Type: Grant
    Filed: March 16, 2021
    Date of Patent: February 28, 2023
    Assignee: Codexis, Inc.
    Inventors: Robert Osborne, Vesna Mitchell, Khin Yu Naing Htwe, Xiyun Zhang, Erika M. Milczek, Jeffrey C. Moore
  • Patent number: 11512346
    Abstract: Described herein is a method of sequencing a template that comprises a direct repeat, comprising: (a) in the same reaction, hybridizing a primer to a first site that is upstream of the first repeat sequence and hybridizing a primer to a second site that is upstream of the second repeat sequence, wherein the first and second sites are: (i) upstream of the first and second repeat sequences, respectively, and (ii) equidistant from the first and second repeat sequences; and (b) subjecting the hybridization product of (a) to a sequencing-by-synthesis sequencing reaction to produce a sequence read that comprises a combination of the first and second repeat sequences.
    Type: Grant
    Filed: February 27, 2020
    Date of Patent: November 29, 2022
    Assignee: GENOME RESEARCH LIMITED
    Inventor: Robert Osborne
  • Publication number: 20220340957
    Abstract: Disclosed is a hybridisation capture method based on the pyrophosphorolysis reaction. According to the present invention, there is provided a method for increasing the ratio of a first nucleic acid sequence to second nucleic acid sequence in a sample.
    Type: Application
    Filed: April 15, 2022
    Publication date: October 27, 2022
    Inventors: Robert Osborne, Magdalena Stolarek-Januszkiewicz, Barnaby Balmforth
  • Patent number: 11479815
    Abstract: Described herein is a method of sequencing, comprising: splitting an asymmetrically tagged library into a plurality of subsamples, tagging the adaptor-ligated DNA in the sub-samples with sequence tags that identify the subsamples, optionally pooling the sub-samples, sequencing polynucleotides from each of the tagged sub-samples, or copies of the same, to produce sequence reads each comprising: i. a sub-sample identifier sequence and ii. the sequence of at least part of a fragment in the sample, wherein some of the sequence reads are derived from the top strand of a fragment in the sample and some of the sequence reads of are derived from the bottom strand of the same fragment.
    Type: Grant
    Filed: September 1, 2016
    Date of Patent: October 25, 2022
    Assignee: OXFORD NANOPORE TECHNOLOGIES PLC
    Inventor: Robert Osborne
  • Publication number: 20220169994
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.
    Type: Application
    Filed: February 15, 2022
    Publication date: June 2, 2022
    Inventors: Robert Osborne, Vesna Mitchell, Khin Yu Naing Htwe, Xiyun Zhang, Erika M. Milczek, Jeffrey C. Moore
  • Patent number: 11332775
    Abstract: Among other things, a method for normalizing a sample is provided. In some embodiments, the method comprises: (a) reacting a sample with a limiting amount of a single-turnover sequence-specific endonuclease that recognizes a target sequence, thereby cleaving a portion of the nucleic acid molecules that comprise the target sequence and producing a normalized amount of a first cleavage product; and (b) isolating, transcribing or selectively amplifying the normalized amount of the first cleavage product. In this method, because a limiting amount of the endonuclease is used, the normalized amount of the first cleavage product is determined by the limiting amount of the first single-turnover sequence-specific endonuclease used in step (a).
    Type: Grant
    Filed: January 10, 2018
    Date of Patent: May 17, 2022
    Assignee: AGENCY FOR SCIENCE, TECHNOLOGY AND RESEARCH (“A*STAR”)
    Inventor: Robert Osborne
  • Patent number: 11279917
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.
    Type: Grant
    Filed: May 13, 2020
    Date of Patent: March 22, 2022
    Assignee: Codexis, Inc.
    Inventors: Robert Osborne, Vesna Mitchell, Khin Yu Naing Htwe, Xiyun Zhang, Erika M. Milczek, Jeffrey C. Moore