Patents by Inventor David Ruff
David Ruff 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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Publication number: 20200392589Abstract: Provided herein are methods and systems for identifying and characterizing proteins, in particular cell surface proteins, of different cell types at the single-cell level. Also provided are methods and systems for distinguishing cells by their protein expression profiles. Further, methods and systems to quantitate and characterize proteins in single cells at ultrahigh throughput are provided. The methods and systems provided herein are able to sensitively profile all epitopes in a proteome of a single cell.Type: ApplicationFiled: April 2, 2020Publication date: December 17, 2020Inventors: Dalia Dhingra, David Ruff, Pedro Mendez, Aik Ooi
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Patent number: 10858695Abstract: In some embodiments, provided are 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. In some embodiments, methods for nucleic acid amplification comprise a amplifying at least one polynucleotide onto a surface under isothermal amplification conditions, optionally in the presence of a polymer.Type: GrantFiled: October 23, 2018Date of Patent: December 8, 2020Assignee: Life Technologies CorporationInventors: Chieh-Yuan Li, David Ruff, Jennifer O'Neil, Rachel Kasinskas, Shiaw-Min Chen, Jonathan M. Rothberg, Bin Li, Kai Qin Lao
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Publication number: 20200340039Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.Type: ApplicationFiled: May 11, 2020Publication date: October 29, 2020Inventors: Mark ANDERSEN, David RUFF
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Publication number: 20200325522Abstract: Provided herein are methods for detection and characterization of a target nucleic acid from a single cell. Some embodiments highlight the capability of identifying the biologically relevant variants at the moment of the diagnosis, but also how the treatment positively select resistant cellular clones based on the mutation signature. This positions the Tapestri™ platform described herein as the only tool available to study how genetic variants co-exist and which combinations are sensitive and resistant to certain treatments.Type: ApplicationFiled: April 2, 2020Publication date: October 15, 2020Applicant: Mission Bio, Inc.Inventors: Pedro Mendez, Dalia Dhingra, David Ruff, Aik Ooi
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Publication number: 20200232011Abstract: Provided herein are methods for detection of a target nucleic acid from a single cell. Preferred embodiments of the method include selecting one or more target nucleic acid sequence of interest in an individual cell, where the target nucleic acid sequence is typically complementary to cellular DNA, including a genomic DNA, and an RNA in a cell. A cell sample is provided, and in preferred embodiments the sample is from a single cell. The cell is lysed and in a single reaction both DNA and RNA can be detected without sub-dividing the sample. This can be accomplished by providing nucleic acid amplification primer sets complementary to one or more target nucleic acid, and in particular primer sets that selectively amplify particular target nucleic acids or amplicons in an amplification reaction. Also provided are methods of primer design for these methods and apparatus and system used to perform the methods.Type: ApplicationFiled: January 22, 2020Publication date: July 23, 2020Applicant: Mission BioInventors: David Ruff, Dalia Dhingra
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Patent number: 10689695Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.Type: GrantFiled: October 17, 2017Date of Patent: June 23, 2020Assignee: Applied Biosystems, LLCInventors: Mark Andersen, David Ruff
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Publication number: 20200102592Abstract: Methods of detecting at least one analyte and at least one nucleic acid in a sample are provided. Reagents for carrying out the methods are also provided.Type: ApplicationFiled: September 18, 2019Publication date: April 2, 2020Inventors: Mark SHANNON, David RUFF
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Publication number: 20200048695Abstract: This application relates to methods for ligating oligonucleotides having complementarity to a target nucleic acid, and amplifying the ligated oligonucleotides, where ligation and amplification occur in the same reaction mixture.Type: ApplicationFiled: October 18, 2019Publication date: February 13, 2020Inventors: Shiaw-Min CHEN, Elana SWARTZMAN, David RUFF, Mark SHANNON, Julia LU, Stephen HENDRICKS
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Patent number: 10526601Abstract: In certain embodiments, the present invention provides a way of “digitally” marking different the alleles of different chromosomes by using a transposase to insert differently barcoded transposons into genomic DNA before further analysis. According to this method, each allele becomes marked with a unique pattern of transposon barcodes. Because each unique pattern of transposon barcodes identifies a particular allele, the method facilitates determinations of ploidy and copy number variation, improves the ability to discriminate among homozygotes, heterozygotes, and patterns arising from sequencing errors, and allows loci separated by uninformative stretches of DNA to be identified as linked loci, thereby facilitating haplotype determinations. Also provided is a novel artificial transposon end that includes a barcode sequence in two or more positions that are not essential for transposition.Type: GrantFiled: May 21, 2015Date of Patent: January 7, 2020Assignee: Digenomix CorporationInventors: Lei Xi, Xiaohui Wang, Marc Unger, David Ruff
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Patent number: 10472671Abstract: This application relates to methods for ligating oligonucleotides having complementarity to a target nucleic acid, and amplifying the ligated oligonucleotides, where ligation and amplification occur in the same reaction mixture.Type: GrantFiled: December 1, 2015Date of Patent: November 12, 2019Assignee: Life Technologies CorporationInventors: Shiaw-Min Chen, Elana Swartzman, David Ruff, Mark Shannon, Julia Lu, Stephen Hendricks
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Publication number: 20190338258Abstract: The present disclosure provides methods, compositions, kits and systems for nucleic acid amplification. In some embodiments, nucleic acid amplification methods include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, nucleic acid amplification methods include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the nucleic acid amplification method employs 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 and/or 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: June 14, 2019Publication date: November 7, 2019Inventors: Chieh-Yuan LI, David RUFF, Shiaw-Min CHEN, Jennifer O'NEIL, Rachel KASINSKAS, Jonathan ROTHBERG, Bin LI, Kai Qin LAO
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Publication number: 20190292581Abstract: Methods and reagents for detection and analysis of nucleic acids and proteins using proximity extension assays.Type: ApplicationFiled: April 2, 2019Publication date: September 26, 2019Inventors: Camila Egidio, Ramesh Ramakrishnan, David Ruff
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Patent number: 10329544Abstract: 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: April 6, 2016Date of Patent: June 25, 2019Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: 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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Publication number: 20190119738Abstract: In some embodiments, provided are 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. In some embodiments, methods for nucleic acid amplification comprise a amplifying at least one polynucleotide onto a surface under isothermal amplification conditions, optionally in the presence of a polymer.Type: ApplicationFiled: October 23, 2018Publication date: April 25, 2019Inventors: Chieh-Yuan LI, David RUFF, Jennifer O'NEIL, Rachel KASINSKAS, Shiaw-Min CHEN, Jonathan M. ROTHBERG, Bin LI, Kai Qin LAO
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Patent number: 10113195Abstract: 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: July 1, 2015Date of Patent: October 30, 2018Assignee: 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: 20180135104Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.Type: ApplicationFiled: October 17, 2017Publication date: May 17, 2018Inventors: Mark Andersen, David Ruff
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Patent number: 9822405Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.Type: GrantFiled: June 26, 2015Date of Patent: November 21, 2017Assignee: APPLIED BIOSYSTEMS, LLCInventors: Mark Andersen, David Ruff
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Patent number: 9518296Abstract: The present teachings provide methods, compositions, and kits for detecting the presence of protein aggregates. In some embodiments, the protein aggregate is treated with a labeled precursor, and the labeled precursor is incorporated into the protein aggregate to form a labeled protein aggregate. The labeled protein aggregate is then measured, thus detecting the presence of the protein aggregate. In some embodiments, the labeled protein aggregate is detected by interaction of labeled precursors, for example by a proximity ligation assay.Type: GrantFiled: August 23, 2013Date of Patent: December 13, 2016Assignee: APPLIED BIOSYSTEMS LLCInventors: David Ruff, Mark Shannon, Kenneth Livak, Karl Guegler, Kevin Hennessy
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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: 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