Patents by Inventor Robert C. James

Robert C. James 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: 12292446
    Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.
    Type: Grant
    Filed: July 29, 2024
    Date of Patent: May 6, 2025
    Assignee: ENCODIA, INC.
    Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
  • Publication number: 20250102513
    Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.
    Type: Application
    Filed: December 2, 2024
    Publication date: March 27, 2025
    Applicant: Encodia, Inc.
    Inventors: Mark S. CHEE, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
  • Publication number: 20240377409
    Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.
    Type: Application
    Filed: July 29, 2024
    Publication date: November 14, 2024
    Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
  • Patent number: 12130291
    Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.
    Type: Grant
    Filed: August 11, 2022
    Date of Patent: October 29, 2024
    Assignee: Encodia, Inc.
    Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
  • Patent number: 11788080
    Abstract: Provided herein are modified cleavases for removing amino acids from peptides, polypeptides, and proteins. Also provided are methods of using the modified cleavases for treating polypeptides, and kits comprising the modified cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.
    Type: Grant
    Filed: June 27, 2022
    Date of Patent: October 17, 2023
    Assignee: Encodia, Inc.
    Inventors: Kevin Desai, Kevin L. Gunderson, Robert C. James, Lei Shi, Stephen Verespy, III
  • Patent number: 11782062
    Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.
    Type: Grant
    Filed: February 8, 2023
    Date of Patent: October 10, 2023
    Assignee: Encodia, Inc.
    Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
  • Patent number: 11639366
    Abstract: The present invention relates to methods to use cyclohexan-1,2-dione (CHD) groups to attach labels, linkers, and other molecules to a target compound comprising a CHD-reactive group such as a guanidine, amidine, urea, thiourea and the like. Methods of the invention include milder conditions than those previously known for promoting reaction of CHD with CHD-reactive groups, which makes the methods suitable for use with base-sensitive compounds and complex biomolecules. Methods of the invention are especially useful for attaching linking and labeling groups to a peptide that comprises at least one arginine residue, and can also be used to link such peptides to other target molecules such as nucleic acids. The invention also provides CHD-containing conjugation reagents and compositions comprising CHD-containing intermediates, and precursors useful for making CHD-containing compounds that can be used in the methods of the invention.
    Type: Grant
    Filed: November 24, 2021
    Date of Patent: May 2, 2023
    Assignee: Encodia, Inc.
    Inventors: Robert C. James, Stephen Verespy, III, Eric Cunyu Zhou, Eric Okerberg, Kelsey Rose Schramma, Fei Huang
  • Publication number: 20230021091
    Abstract: Provided herein are modified cleavases for removing amino acids from peptides, polypeptides, and proteins. Also provided are methods of using the modified cleavases for treating polypeptides, and kits comprising the modified cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.
    Type: Application
    Filed: June 27, 2022
    Publication date: January 19, 2023
    Applicant: Encodia, Inc.
    Inventors: Kevin DESAI, Kevin L. Gunderson, Robert C. James, Lei Shi, Stephen Verespy, III
  • Patent number: 11513126
    Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.
    Type: Grant
    Filed: October 31, 2018
    Date of Patent: November 29, 2022
    Assignee: Encodia, Inc.
    Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
  • Patent number: 11427814
    Abstract: Provided herein are modified cleavases for removing amino acids from peptides, polypeptides, and proteins. Also provided are methods of using the modified cleavases for treating polypeptides, and kits comprising the modified cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.
    Type: Grant
    Filed: March 25, 2021
    Date of Patent: August 30, 2022
    Assignee: ENCODIA, INC.
    Inventors: Kevin Desai, Kevin L. Gunderson, Robert C. James, Lei Shi, Stephen Verespy, III
  • Publication number: 20220144885
    Abstract: The present invention relates to methods to use cyclohexan-1,2-dione (CHD) groups to attach labels, linkers, and other molecules to a target compound comprising a CHD-reactive group such as a guanidine, amidine, urea, thiourea and the like. Methods of the invention include milder conditions than those previously known for promoting reaction of CHD with CHD-reactive groups, which makes the methods suitable for use with base-sensitive compounds and complex biomolecules. Methods of the invention are especially useful for attaching linking and labeling groups to a peptide that comprises at least one arginine residue, and can also be used to link such peptides to other target molecules such as nucleic acids. The invention also provides CHD-containing conjugation reagents and compositions comprising CHD-containing intermediates, and precursors useful for making CHD-containing compounds that can be used in the methods of the invention.
    Type: Application
    Filed: November 24, 2021
    Publication date: May 12, 2022
    Applicant: Encodia, Inc.
    Inventors: Robert C. James, Stephen Verespy, III, Eric Cunyu Zhou, Eric Okerberg, Kelsey Rose Schramma, Fei HUANG
  • Patent number: 6051263
    Abstract: A package is capable of enclosing a food product in two different gaseous atmospheres at different times. Initially, the food product may be packaged in a low oxygen atmosphere in order to prolong the shelf life of the product. When it is time to sell the product for example, it may be desirable to supply oxygen to the food product. In the case of red meats, the oxygenation process causes the meat to turn a bright red color. The package includes a tray covered by a film with a plurality of apertures formed in the tray. The package may be maintained at a pressure below atmospheric pressure. The apertures are covered by a bacterial barrier layer covered by resealable tape which can be removed to allow air ingress and then resealed to protect the integrity of the tray contents.
    Type: Grant
    Filed: March 31, 1999
    Date of Patent: April 18, 2000
    Assignee: World Class Packaging Systems, Inc.
    Inventors: Michael P. Gorlich, Robert F. McPherson, Jr., Robert C. James
  • Patent number: 5866184
    Abstract: A package is capable of enclosing a food product in two different gaseous atmospheres at different times. Initially the food product may be packaged in a low oxygen atmosphere in order to prolong the shelf life of the product. When it is time to sell the product for example, it may be desirable to supply oxygen to the food product. In the case of red meats, the oxygenation process causes the meat to turn a bright red color. The package includes a tray covered by a film with a plurality of apertures formed in the tray. The apertures are covered by a resealable gas impermiable tape which can be removed to allow air ingress and then resealed to protect the integrity of the tray contents.
    Type: Grant
    Filed: March 12, 1997
    Date of Patent: February 2, 1999
    Assignee: World Class Packaging Systems, Inc.
    Inventors: Michael P. Gorlich, Robert F. McPherson, Jr., Robert C. James
  • Patent number: 5333703
    Abstract: A system for monitoring carbon monoxide (CO) levels produced by the operation of a vehicle's engine. The system includes a detector in the vehicle's passenger compartment for detecting the concentration of CO inside the compartment and circuitry for generating a HIGH CO signal when the detected concentration of CO inside the compartment is greater than a predetermined level. The system disables the operation of the engine in response to the HIGH CO signal. The system also senses a status condition of the vehicle and inhibits the disabling of the engine when the status condition is sensed.
    Type: Grant
    Filed: January 7, 1993
    Date of Patent: August 2, 1994
    Assignee: The Thames Group Ltd.
    Inventors: Robert C. James, Dale M. Cherney
  • Patent number: 5310262
    Abstract: A flexible pouch package for fluid products including a composite bag having inner and outer package walls formed of flexible film folded over and sealed together about the outer edges thereof to define a chamber therein. The package may include an easy open feature.
    Type: Grant
    Filed: June 2, 1992
    Date of Patent: May 10, 1994
    Assignee: Bemis Company, Inc.
    Inventors: Lyle D. Robison, Robert C. James
  • Patent number: 5184997
    Abstract: A case sealed by a strip of pressure-sensitive tape having an integral end portion of the tape at an end thereof folded back on the adhesive face of the tape and adhered thereto to form a tab which is unadhered to the case for being grasped and pulled to peel the tape away from the case, and a method of and apparatus for taping cases with this easy-open feature.
    Type: Grant
    Filed: January 13, 1988
    Date of Patent: February 9, 1993
    Assignee: Curwood, Inc.
    Inventors: Robert C. James, Richard J. Pederson
  • Patent number: 5092831
    Abstract: A method of opening a folded web of flexible heat-sealable packaging material prior to formation of the material into sealed reclosable packages. The web has a pair of interlockable reclosable closure strips extending longitudinally of the web on an inside face of the web, and one section of the web is folded over on another section of the web so that the closure strips are interlocked. The method comprises advancing the folded web in a first plane to a web-opening station, and opening the folded web while maintaining the closure strips interlocked as the web advances through the web-opening station. The web is opened by diverting both sections of the web relative to one another so that they assume a co-planar position in a second plane different from the first plane.
    Type: Grant
    Filed: October 16, 1990
    Date of Patent: March 3, 1992
    Assignee: Hayssen Manufacturing Co.
    Inventors: Robert C. James, Lloyd Kovacs
  • Patent number: 5092102
    Abstract: An escapement system in which units are movable by and with an endless conveyor in an endless path, and an escapement system is provided for retarding the units as they move through a part of their path, then releasing them; the system being incorporated in packaging apparatus in which the endless conveyor is a wheel and the units are sealing dies on the wheel.
    Type: Grant
    Filed: February 7, 1991
    Date of Patent: March 3, 1992
    Assignee: Hayssen Manufacturing Company
    Inventors: Robert C. James, Lloyd Kovacs, Matthew R. Lind
  • Patent number: 4999974
    Abstract: Method of and apparatus for forming filling and sealing packages in which flexible packaging material is formed into tubing, the tubing is fed downwardly and transversely heat sealed at package length intervals by closing a pair of sealing members, the seal area is cut to form a top seal of the package being completed and a bottom seal for the next package to be formed, a quantity of product with which the packages are to be filled is delivered into the lower end of the tubing to provide a fill for each package, the tubing is pinched closed, after the delivery of each fill, above and below the level of the next seal to be made, the pinches are maintained as the sealing members are opened, following the formation of the aforementioned top and bottom seals, to keep product for the next fill from dropping down on the bottom seal, and to hold the package being completed from dropping away, and air is blown on the top and bottom seals to cool them while the pinches are maintained.
    Type: Grant
    Filed: March 26, 1990
    Date of Patent: March 19, 1991
    Assignee: Hayssen Manufacturing Company
    Inventors: Lloyd Kovacs, Robert C. James, Gianfranco Ceriani
  • Patent number: 4891928
    Abstract: A carton loading machine comprising an endless conveyor carrying a series of holders each adapted to hold an erected carton in upright position and movable to move each holder from a carton receiving station for entry of an erected carton in the holder from the outside of the conveyor to a loading station for loading the carton and thence to a discharage station for discharge of the loaded carton, each holder having a fixed side and a movable side and latch members associated with said sides, the latch member associated with the fixed side and the movable side and latch member associated therewith being movable between open and closed positions.
    Type: Grant
    Filed: September 14, 1988
    Date of Patent: January 9, 1990
    Assignee: Hayssen Manufacturing Company
    Inventors: Robert C. James, Lloyd Kovacs, Matthew R. Lind