Patents by Inventor John Mannion
John Mannion 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).
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Patent number: 11892444Abstract: Improved multi-cell nanopore-based sequencing chips and methods can employ formation, characterization, calibration, and/or normalization techniques. For example, various methods may include one or more steps of performing physical checks of cell circuitry, forming and characterizing a lipid layer on the cells, performing a zero point calibration of the cells, forming and characterizing nanopores on the lipid layers of each cell, performing a sequencing operation to accumulate sequencing signals from the cells, normalizing those sequencing signals, and determining bases based on the normalized sequencing signals.Type: GrantFiled: October 21, 2020Date of Patent: February 6, 2024Assignee: Roche Sequencing Solutions, Inc.Inventors: Morgan Mager, John Mannion
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Patent number: 11788132Abstract: Techniques for measuring sequences of nucleic acids are provided. Time-based measurements (e.g., forming a histogram) particular to a given sequencing cell can be used to generate a tailored model. The model can include probability functions, each corresponding to different states (e.g., different states of a nanopore). Such probability functions can be fit to a histogram of measurements obtained for that cell. The probability functions can be updated over a sequencing run of the nucleic acid so that drifts in physical properties of the sequencing cell can be compensated. A hidden Markov model can use such probability functions as emission probabilities for determining the most likely nucleotide states over time. For sequencing cells involving a polymerase, a 2-state classification between bound and unbound states of the polymerase can be performed. The bound regions can be further analyzed by a second classifier to distinguish between states corresponding to different bound nucleotides.Type: GrantFiled: March 1, 2022Date of Patent: October 17, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: John Mannion, Morgan Mager
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Publication number: 20230230459Abstract: A Self-Service Terminal (SST) that provides valuable media deposit features is enhanced with an apparatus fastened to an outside surface of the SST. The apparatus is adapted to receive an externally provided valuable media cassette and connect/interface a port of the cassette to an unload infeed port. A transaction interface is enhanced to identify the cassette as a source device for obtaining valuable media during a deposit transaction. The SST feeds the valuable media from the externally connected cassette through media validation and transport modules of the SST into cassettes of a safe and the SST returns rejected media for the deposit transaction back through the modules to return rejected media to the externally interfaced cassette.Type: ApplicationFiled: March 23, 2023Publication date: July 20, 2023Inventors: Grant Buchanan Fraser, John Mannion
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Patent number: 11699332Abstract: A Self-Service Terminal (SST) that provides valuable media deposit features is enhanced with an apparatus fastened to an outside surface of the SST. The apparatus is adapted to receive an externally provided valuable media cassette and connect/interface a port of the cassette to an unload infeed port. A transaction interface is enhanced to identify the cassette as a source device for obtaining valuable media during a deposit transaction. The SST feeds the valuable media from the externally connected cassette through media validation and transport modules of the SST into cassettes of a safe and the SST returns rejected media for the deposit transaction back through the modules to return rejected media to the externally interfaced cassette.Type: GrantFiled: March 9, 2022Date of Patent: July 11, 2023Assignee: NCR CorporationInventors: Grant Buchanan Fraser, John Mannion
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Publication number: 20220343738Abstract: A Self-Service Terminal (SST) that provides valuable media deposit features is enhanced with an apparatus fastened to an outside surface of the SST. The apparatus is adapted to receive an externally provided valuable media cassette and connect/interface a port of the cassette to an unload infeed port. A transaction interface is enhanced to identify the cassette as a source device for obtaining valuable media during a deposit transaction. The SST feeds the valuable media from the externally connected cassette through media validation and transport modules of the SST into cassettes of a safe and the SST returns rejected media for the deposit transaction back through the modules to return rejected media to the externally interfaced cassette.Type: ApplicationFiled: March 9, 2022Publication date: October 27, 2022Inventors: Grant Buchanan Fraser, John Mannion
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Publication number: 20220267840Abstract: Techniques for measuring sequences of nucleic acids are provided. Time-based measurements (e.g., forming a histogram) particular to a given sequencing cell can be used to generate a tailored model. The model can include probability functions, each corresponding to different states (e.g., different states of a nanopore). Such probability functions can be fit to a histogram of measurements obtained for that cell. The probability functions can be updated over a sequencing run of the nucleic acid so that drifts in physical properties of the sequencing cell can be compensated. A hidden Markov model can use such probability functions as emission probabilities for determining the most likely nucleotide states over time. For sequencing cells involving a polymerase, a 2-state classification between bound and unbound states of the polymerase can be performed. The bound regions can be further analyzed by a second classifier to distinguish between states corresponding to different bound nucleotides.Type: ApplicationFiled: March 1, 2022Publication date: August 25, 2022Inventors: John MANNION, Morgan MAGER
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Patent number: 11328563Abstract: A Self-Service Terminal (SST) that provides valuable media deposit features is enhanced with an apparatus fastened to an outside surface of the SST. The apparatus is adapted to receive an externally provided valuable media cassette and connect/interface a port of the cassette to an unload infeed port. A transaction interface is enhanced to identify the cassette as a source device for obtaining valuable media during a deposit transaction. The SST feeds the valuable media from the externally connected cassette through media validation and transport modules of the SST into cassettes of a safe and the SST returns rejected media for the deposit transaction back through the modules to return rejected media to the externally interfaced cassette.Type: GrantFiled: April 23, 2021Date of Patent: May 10, 2022Assignee: NCR CorporatonInventors: Grant Buchanan Fraser, John Mannion
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Patent number: 11293062Abstract: Techniques for measuring sequences of nucleic acids are provided. Time-based measurements (e.g., forming a histogram) particular to a given sequencing cell can be used to generate a tailored model. The model can include probability functions, each corresponding to different states (e.g., different states of a nanopore). Such probability functions can be fit to a histogram of measurements obtained for that cell. The probability functions can be updated over a sequencing run of the nucleic acid so that drifts in physical properties of the sequencing cell can be compensated. A hidden Markov model can use such probability functions as emission probabilities for determining the most likely nucleotide states over time. For sequencing cells involving a polymerase, a 2-state classification between bound and unbound states of the polymerase can be performed. The bound regions can be further analyzed by a second classifier to distinguish between states corresponding to different bound nucleotides.Type: GrantFiled: April 8, 2020Date of Patent: April 5, 2022Assignee: Roche Sequencing Solutions, Inc.Inventors: John Mannion, Morgan Mager
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Publication number: 20210109082Abstract: Improved multi-cell nanopore-based sequencing chips and methods can employ formation, characterization, calibration, and/or normalization techniques. For example, various methods may include one or more steps of performing physical checks of cell circuitry, forming and characterizing a lipid layer on the cells, performing a zero point calibration of the cells, forming and characterizing nanopores on the lipid layers of each cell, performing a sequencing operation to accumulate sequencing signals from the cells, normalizing those sequencing signals, and determining bases based on the normalized sequencing signals.Type: ApplicationFiled: October 21, 2020Publication date: April 15, 2021Inventors: Morgan MAGER, John MANNION
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Patent number: 10816537Abstract: Improved multi-cell nanopore-based sequencing chips and methods can employ formation, characterization, calibration, and/or normalization techniques. For example, various methods may include one or more steps of performing physical checks of cell circuitry, forming and characterizing a lipid layer on the cells, performing a zero point calibration of the cells, forming and characterizing nanopores on the lipid layers of each cell, performing a sequencing operation to accumulate sequencing signals from the cells, normalizing those sequencing signals, and determining bases based on the normalized sequencing signals.Type: GrantFiled: April 15, 2019Date of Patent: October 27, 2020Assignee: Roche Sequencing Solutions, Inc.Inventors: Morgan Mager, John Mannion
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Publication number: 20200232026Abstract: Techniques for measuring sequences of nucleic acids are provided. Time-based measurements (e.g., forming a histogram) particular to a given sequencing cell can be used to generate a tailored model. The model can include probability functions, each corresponding to different states (e.g., different states of a nanopore). Such probability functions can be fit to a histogram of measurements obtained for that cell. The probability functions can be updated over a sequencing run of the nucleic acid so that drifts in physical properties of the sequencing cell can be compensated. A hidden Markov model can use such probability functions as emission probabilities for determining the most likely nucleotide states over time. For sequencing cells involving a polymerase, a 2-state classification between bound and unbound states of the polymerase can be performed. The bound regions can be further analyzed by a second classifier to distinguish between states corresponding to different bound nucleotides.Type: ApplicationFiled: April 8, 2020Publication date: July 23, 2020Inventors: John MANNION, Morgan MAGER
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Patent number: 10648027Abstract: Techniques for measuring sequences of nucleic acids are provided. Time-based measurements (e.g., forming a histogram) particular to a given sequencing cell can be used to generate a tailored model. The model can include probability functions, each corresponding to different states (e.g., different states of a nanopore). Such probability functions can be fit to a histogram of measurements obtained for that cell. The probability functions can be updated over a sequencing run of the nucleic acid so that drifts in physical properties of the sequencing cell can be compensated. A hidden Markov model can use such probability functions as emission probabilities for determining the most likely nucleotide states over time. For sequencing cells involving a polymerase, a 2-state classification between bound and unbound states of the polymerase can be performed. The bound regions can be further analyzed by a second classifier to distinguish between states corresponding to different bound nucleotides.Type: GrantFiled: August 4, 2017Date of Patent: May 12, 2020Assignee: Roche Sequencing Solutions, Inc.Inventors: John Mannion, Morgan Mager
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Publication number: 20190242869Abstract: Improved multi-cell nanopore-based sequencing chips and methods can employ formation, characterization, calibration, and/or normalization techniques. For example, various methods may include one or more steps of performing physical checks of cell circuitry, forming and characterizing a lipid layer on the cells, performing a zero point calibration of the cells, forming and characterizing nanopores on the lipid layers of each cell, performing a sequencing operation to accumulate sequencing signals from the cells, normalizing those sequencing signals, and determining bases based on the normalized sequencing signals.Type: ApplicationFiled: April 15, 2019Publication date: August 8, 2019Inventors: Morgan MAGER, John MANNION
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Patent number: 10317392Abstract: Improved multi-cell nanopore-based sequencing chips and methods can employ formation, characterization, calibration, and/or normalization techniques. For example, various methods may include one or more steps of performing physical checks of cell circuitry, forming and characterizing a lipid layer on the cells, performing a zero point calibration of the cells, forming and characterizing nanopores on the lipid layers of each cell, performing a sequencing operation to accumulate sequencing signals from the cells, normalizing those sequencing signals, and determining bases based on the normalized sequencing signals.Type: GrantFiled: June 23, 2017Date of Patent: June 11, 2019Assignee: Roche Sequencing Solutions, Inc.Inventors: Morgan Mager, John Mannion
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Publication number: 20180037948Abstract: Techniques for measuring sequences of nucleic acids are provided. Time-based measurements (e.g., forming a histogram) particular to a given sequencing cell can be used to generate a tailored model. The model can include probability functions, each corresponding to different states (e.g., different states of a nanopore). Such probability functions can be fit to a histogram of measurements obtained for that cell. The probability functions can be updated over a sequencing run of the nucleic acid so that drifts in physical properties of the sequencing cell can be compensated. A hidden Markov model can use such probability functions as emission probabilities for determining the most likely nucleotide states over time. For sequencing cells involving a polymerase, a 2-state classification between bound and unbound states of the polymerase can be performed. The bound regions can be further analyzed by a second classifier to distinguish between states corresponding to different bound nucleotides.Type: ApplicationFiled: August 4, 2017Publication date: February 8, 2018Inventors: John MANNION, Morgan MAGER
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Publication number: 20170370903Abstract: Improved multi-cell nanopore-based sequencing chips and methods can employ formation, characterization, calibration, and/or normalization techniques. For example, various methods may include one or more steps of performing physical checks of cell circuitry, forming and characterizing a lipid layer on the cells, performing a zero point calibration of the cells, forming and characterizing nanopores on the lipid layers of each cell, performing a sequencing operation to accumulate sequencing signals from the cells, normalizing those sequencing signals, and determining bases based on the normalized sequencing signals.Type: ApplicationFiled: June 23, 2017Publication date: December 28, 2017Inventors: Morgan MAGER, John MANNION
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Patent number: 9752978Abstract: A micromachined flow cell includes a substrate and a freestanding tube, delimiting a fluidic conduit therein and being integrally formed from material of the substrate.Type: GrantFiled: February 3, 2012Date of Patent: September 5, 2017Assignee: Agilent Technologies, Inc.Inventors: Karsten Kraiczek, John Mannion, Kevin P. Killeen
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Patent number: 9683958Abstract: This disclosure provides, among other things, a nanofluidic device sensing device is provided. In certain embodiments, the device contains: a) a channel comprising a floor and a ceiling, b) an array of charge sensors in the floor and/or ceiling of the channel, arranged along the longitudinal axis of the channel; c) a capture area in the floor and/or ceiling of the channel at the entrance end of the channel; and d) a first electrode and a second electrode, wherein the first and second electrodes are positioned to provide an electrophoretic force along the longitudinal axis of the channel. Other embodiments, e.g., methods, are also described.Type: GrantFiled: September 10, 2014Date of Patent: June 20, 2017Assignee: Agilent Technologies, Inc.Inventors: John Mannion, Bo Curry, Brian Jon Peter
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Patent number: 9546398Abstract: A method for sequencing a nucleic acid is provided. In certain embodiments the method comprises obtaining a duplex comprising a nucleic acid and a primer, wherein the primer has a nuclease resistant 3? end, combining the duplex with a chain terminator nucleotide and a proof-reading polymerase to produce a reaction in which the polymerase idles on the added chain terminator nucleotide, identifying the chain terminator nucleotide added to the end of the primer; and adding a nuclease-resistant nucleotide to the end of the primer after the polymerase has idled on and removed the added chain terminator nucleotide, thereby producing a duplex comprising the template and an extended primer that has a nuclease resistant 3? end.Type: GrantFiled: November 11, 2014Date of Patent: January 17, 2017Assignee: Agilent Technologies, Inc.Inventors: Brian Jon Peter, John Mannion, Joel Myerson
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Publication number: 20150132756Abstract: A method for sequencing a nucleic acid is provided. In certain embodiments the method comprises obtaining a duplex comprising a nucleic acid and a primer, wherein the primer has a nuclease resistant 3? end, combining the duplex with a chain terminator nucleotide and a proof-reading polymerase to produce a reaction in which the polymerase idles on the added chain terminator nucleotide, identifying the chain terminator nucleotide added to the end of the primer; and adding a nuclease-resistant nucleotide to the end of the primer after the polymerase has idled on and removed the added chain terminator nucleotide, thereby producing a duplex comprising the template and an extended primer that has a nuclease resistant 3? end.Type: ApplicationFiled: November 11, 2014Publication date: May 14, 2015Inventors: Brian Jon Peter, John Mannion, Joel Myerson