Patents by Inventor Jonathan Rothberg
Jonathan 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).
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Patent number: 9618475Abstract: Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.Type: GrantFiled: September 15, 2010Date of Patent: April 11, 2017Assignee: Life Technologies CorporationInventors: Jonathan Rothberg, Todd Rearick
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Publication number: 20160272954Abstract: In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.Type: ApplicationFiled: April 6, 2016Publication date: September 22, 2016Inventors: Chieh-Yuan LI, David RUFF, Shiaw-Min CHEN, Jennifer O'NEIL, Rachel KASINSKAS, Jonathan ROTHBERG, Bin LI, Kai Qin LAO, Wolfgang HINZ
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Patent number: 9404920Abstract: Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes.Type: GrantFiled: January 9, 2014Date of Patent: August 2, 2016Assignee: Life Technologies CorporationInventors: Jonathan Rothberg, Wolfgang Hinz
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Patent number: 9371557Abstract: In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.Type: GrantFiled: June 20, 2013Date of Patent: June 21, 2016Assignee: Life Technologies CorporationInventors: Chieh-Yuan Li, David Ruff, Jennifer O'Neil, Rachel Kasinskas, Shiaw-Min Chen, Jonathan Rothberg, Bin Li, Kai Qin Lao
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Patent number: 9334531Abstract: In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.Type: GrantFiled: September 10, 2013Date of Patent: May 10, 2016Assignee: Life Technologies CorporationInventors: Chieh-Yuan Li, David Ruff, Shiaw-Min Chen, Jennifer O'Neil, Rachel Kasinskas, Jonathan Rothberg, Bin Li, Kai Qin Lao
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Patent number: 9309557Abstract: In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.Type: GrantFiled: March 15, 2013Date of Patent: April 12, 2016Assignee: Life Technologies CorporationInventors: Chieh-Yuan Li, David Ruff, Shiaw-Min Chen, Jennifer O'Neil, Rachel Kasinskas, Jonathan Rothberg, Bin Li, Kai Qin Lao
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Patent number: 9309558Abstract: In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.Type: GrantFiled: November 20, 2013Date of Patent: April 12, 2016Assignee: Life Technologies CorporationInventors: Chieh-Yuan Li, David Ruff, Jennifer O'Neil, Rachel Kasinskas, Shiaw-Min Chen, Jonathan Rothberg, Bin Li, Kai Qin Lao
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Publication number: 20160032375Abstract: In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.Type: ApplicationFiled: July 1, 2015Publication date: February 4, 2016Inventors: Chieh-Yuan LI, David RUFF, Jennifer O'NEIL, Rachel KASINSKAS, Shiaw-Min CHEN, Jonathan ROTHBERG
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Publication number: 20150260680Abstract: Methods, compositions, systems, apparatuses and kits comprising modified proteins, particularly modified nucleic acid-binding proteins with altered buffering properties are provided. For example, in some embodiments, methods of forming modified proteins including one or more amino acid modifications to achieve desired pKa values are described. Furthermore, the invention provides methods for using such modified proteins in ion-producing reactions, such as ion-based nucleic acid sequencing reactions.Type: ApplicationFiled: May 28, 2015Publication date: September 17, 2015Inventors: John DAVIDSON, Wolfgang HINZ, Jonathan ROTHBERG, Richard WHITAKER
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Patent number: 9134269Abstract: Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis.Type: GrantFiled: March 11, 2013Date of Patent: September 15, 2015Assignee: Life Technologies CorporationInventors: Jonathan Rothberg, Wolfgang Hinz, Kim Johnson, James Bustillo
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Patent number: 9039888Abstract: Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes.Type: GrantFiled: September 23, 2013Date of Patent: May 26, 2015Assignee: Life Technologies CorporationInventors: Jonathan Rothberg, Wolfgang Hinz
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Patent number: 9005427Abstract: Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes.Type: GrantFiled: January 9, 2014Date of Patent: April 14, 2015Assignee: Life Technologies CorporationInventors: Jonathan Rothberg, Wolfgang Hinz
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Patent number: 8936763Abstract: The invention is directed to apparatus and chips comprising a large scale chemical field effect transistor arrays that include an array of sample-retaining regions capable of retaining a chemical or biological sample from a sample fluid for analysis. In one aspect such transistor arrays have a pitch of 10 ?m or less and each sample-retaining region is positioned on at least one chemical field effect transistor which is configured to generate at least one output signal related to a characteristic of a chemical or biological sample in such sample-retaining region.Type: GrantFiled: October 22, 2009Date of Patent: January 20, 2015Assignee: Life Technologies CorporationInventors: Jonathan Rothberg, James Bustillo, Mark Milgrew, Jonathan Schultz, David Marran, Todd Rearick, Kim Johnson
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Publication number: 20140235452Abstract: Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.Type: ApplicationFiled: September 15, 2010Publication date: August 21, 2014Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Jonathan Rothberg, Todd Rearick
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Publication number: 20140235463Abstract: Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.Type: ApplicationFiled: January 21, 2014Publication date: August 21, 2014Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Jonathan ROTHBERG, Todd REARICK
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Publication number: 20140202883Abstract: The invention is directed to apparatus and methods for delivering multiple reagents to, and monitoring, a plurality of analytical reactions carried out on a large-scale array of electronic sensors under minimal noise conditions. In one aspect, the invention provides method of improving signal-to-noise ratios of output signals from the electronic sensors sensing analytes or reaction byproducts by subtracting an average of output signals measured from neighboring sensors where analyte or reaction byproducts are absent. In other aspects, the invention provides an array of electronic sensors integrated with a microwell array for confining analytes and/or particles for analytical reactions and a method for identifying microwells containing analytes and/or particles by passing a sensor-active reagent over the array and correlating sensor response times to the presence or absence of analytes or particles.Type: ApplicationFiled: January 23, 2014Publication date: July 24, 2014Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: John NOBILE, George T. ROTH, Todd REARICK, Jonathan M. SCHULTZ, Jonathan ROTHBERG, David MARRAN
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Publication number: 20140194298Abstract: Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes.Type: ApplicationFiled: January 9, 2014Publication date: July 10, 2014Applicant: Life Technologies CorporationInventors: Jonathan Rothberg, Wolfgang Hinz
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Publication number: 20140194297Abstract: Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes.Type: ApplicationFiled: January 9, 2014Publication date: July 10, 2014Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Jonathan Rothberg, Wolfgang Hinz
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Patent number: 8764969Abstract: Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis.Type: GrantFiled: July 20, 2012Date of Patent: July 1, 2014Assignee: Life Technologies CorporationInventors: Jonathan Rothberg, Wolfgang Hinz, Kim Johnson, James Bustillo
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Publication number: 20140147852Abstract: In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.Type: ApplicationFiled: November 20, 2013Publication date: May 29, 2014Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Chieh-Yuan LI, David RUFF, Jennifer O'NEIL, Rachel KASINSKAS, Shiaw-Min CHEN, Jonathan ROTHBERG