Patents by Inventor Frank Steemers
Frank Steemers 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: 20230383284Abstract: Provided is a method, including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments. Also provided is a method including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments.Type: ApplicationFiled: August 10, 2023Publication date: November 30, 2023Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Maria Candelaria Rogert BACIGALUPO, Frank STEEMERS, Jeffrey FISHER, Andrew SLATTER, Lewis KRAFT, Niall GORMLEY, M. Shane BOWEN
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Patent number: 11760994Abstract: Provided is a method, including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments. Also provided is a method including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments.Type: GrantFiled: June 25, 2021Date of Patent: September 19, 2023Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Maria Candelaria Rogert Bacigalupo, Frank Steemers, Jeffrey Fisher, Andrew Slatter, Lewis Kraft, Niall Gormley, M. Shane Bowen
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Publication number: 20230235385Abstract: Provided herein, among other things, is a method for synthesizing spatially addressed nucleic acid barcodes in or on a cellular sample in situ. In some embodiments, the method may comprise: obtaining a cellular sample comprising nucleic acid molecules that are protected by a reversible terminator, deprotecting the nucleic acid molecules in a set of areas of the sample by selectively applying an external stimulus to the set of areas to produce deprotected nucleic acid molecules in the areas, applying a reversible terminator nucleotide to the cellular sample, resulting in addition of a reversible terminator onto the deprotected nucleic acid molecules, optionally removing any unreacted reversible terminator nucleotide from the sample, and repeating the steps one or more times.Type: ApplicationFiled: March 9, 2023Publication date: July 27, 2023Inventors: Frank STEEMERS, Garry P. NOLAN
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Publication number: 20220356461Abstract: Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the sequencing library includes nucleic acids that represent the chromatin accessibility from the plurality of single cells. In one embodiment, the nucleic acids include three index sequences. In another embodiment, the present disclosure provides methods for characterizing rare events in isolated cells and nuclei.Type: ApplicationFiled: December 18, 2020Publication date: November 10, 2022Applicants: Illumina, Inc., University of WashingtonInventors: Jay Shendure, Darren Cusanovich, Riza Daza, Frank Steemers, Andrew Kennedy
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Publication number: 20220002711Abstract: Provided is a method, including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments. Also provided is a method including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments.Type: ApplicationFiled: June 25, 2021Publication date: January 6, 2022Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Maria Candelaria Rogert BACIGALUPO, Frank STEEMERS, Jeffrey FISHER, Andrew SLATTER, Lewis KRAFT, Niall GORMLEY, M. Shane BOWEN
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Publication number: 20210380972Abstract: The present disclosure is concerned with compositions, methods, and kits for preparing a sequencing library. In one embodiment, methods include producing a library of target nucleic acids having the same adapter at each end and then switching the identity of one adapter to result in target nucleic acids flanked by distinct adapters.Type: ApplicationFiled: June 10, 2021Publication date: December 9, 2021Applicants: Illumina, Inc., Illumina Cambridge Limited, Oregon Health & Science UniversityInventors: Andrew C. Adey, Ryan Mulqueen, Frank Steemers, Dmitry K Pokholok, Fan Zhang, Esther Musgrave-Brown
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Publication number: 20210332349Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating biomolecules for performing sequential reactions on the biomolecules. Some embodiments include preparation of nucleic acid reactions within the bead, wherein the bead includes pores that allow diffusion of molecules into or out of the beads while retaining other molecules of interest.Type: ApplicationFiled: July 1, 2021Publication date: October 28, 2021Inventors: Steven Norberg, Dmitry Pokholok, Ramesh Ramji, Frank Steemers, Fan Zhang
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Patent number: 10738350Abstract: This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.Type: GrantFiled: November 17, 2017Date of Patent: August 11, 2020Assignee: Illumina, Inc.Inventors: Kevin Gunderson, Frank Steemers
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Publication number: 20180320225Abstract: This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.Type: ApplicationFiled: November 17, 2017Publication date: November 8, 2018Inventors: Kevin Gunderson, Frank Steemers
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Publication number: 20150284784Abstract: This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.Type: ApplicationFiled: May 18, 2015Publication date: October 8, 2015Inventors: Kevin GUNDERSON, Frank STEEMERS
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Patent number: 9045796Abstract: This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.Type: GrantFiled: June 17, 2004Date of Patent: June 2, 2015Assignee: Illumina, Inc.Inventors: Kevin Gunderson, Frank Steemers
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Patent number: 8609341Abstract: The invention provides a method for preparing and analysing a population of fragmented polynucleotide sequences having a substantially uniform size. The method can include steps of (a) binding at least one protection molecule to at least one polynucleotide sequence; (b) cleaving the at least one polynucleotide sequence to generate a plurality of polynucleotide fragment sequences of substantially uniform size; (c) amplifying the polynucleotide fragments; and (d) determining a sequence characteristic of a plurality of the polynucleotide fragments.Type: GrantFiled: May 16, 2012Date of Patent: December 17, 2013Assignee: Illumina, Inc.Inventors: Frank Steemers, Jonathan Mark Boutell
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Publication number: 20120225787Abstract: The invention provides a method for preparing and analysing a population of fragmented polynucleotide sequences having a substantially uniform size. The method can include steps of (a) binding at least one protection molecule to at least one polynucleotide sequence; (b) cleaving the at least one polynucleotide sequence to generate a plurality of polynucleotide fragment sequences of substantially uniform size; (c) amplifying the polynucleotide fragments; and (d) determining a sequence characteristic of a plurality of the polynucleotide fragments.Type: ApplicationFiled: May 16, 2012Publication date: September 6, 2012Applicant: ILLUMINA, INC.Inventors: Frank Steemers, Jonathan Mark Boutell
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Patent number: 8202691Abstract: The invention provides a method for preparing and analysing a population of fragmented polynucleotide sequences having a substantially uniform size. The method can include steps of (a) binding at least one protection molecule to at least one polynucleotide sequence; (b) cleaving the at least one polynucleotide sequence to generate a plurality of polynucleotide fragment sequences of substantially uniform size; (c) amplifying the polynucleotide fragments; and (d) determining a sequence characteristic of a plurality of the polynucleotide fragments.Type: GrantFiled: January 22, 2009Date of Patent: June 19, 2012Assignee: Illumina, Inc.Inventors: Frank Steemers, Jonathan Mark Boutell
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Patent number: 7670810Abstract: This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.Type: GrantFiled: June 17, 2004Date of Patent: March 2, 2010Assignee: Illumina, Inc.Inventors: Kevin Gunderson, Frank Steemers
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Publication number: 20090191563Abstract: The invention provides a method for preparing and analysing a population of fragmented polynucleotide sequences having a substantially uniform size. The method can include steps of (a) binding at least some protection molecule to at least one polynucleotide sequence; (b) cleaving the at least one polynucleotide sequence to generate a plurality of polynucleotide fragment sequences of substantially uniform size; (c) amplifying the polynucleotide fragments; and (d) determining a sequence characteristic of a plurality of the polynucleotide fragments.Type: ApplicationFiled: January 22, 2009Publication date: July 30, 2009Applicant: Illumina, Inc.Inventors: Frank Steemers, Jonathan Mark Boutell
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Publication number: 20080242560Abstract: The present invention relates to methods for generating an array of amplified nucleic acid sequences. The methods can utilize amplicons that form nucleic acid balls that can be arrayed on a solid support. The invention additionally provides methods for obtaining targeted nucleic acid sequences.Type: ApplicationFiled: November 20, 2007Publication date: October 2, 2008Inventors: Kevin L. GUNDERSON, Frank Steemers
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Publication number: 20070122861Abstract: The present invention provides a novel cross-reactive sensor system utilizing cross-reactive recognition elements. In the inventive system, each of said one or more cross-reactive recognition elements is capable of interacting with more than one species of liquid analyte of interest, whereby each of said one or more cross-reactive recognition elements reacts in a different manner with each of said one or more species of liquid analytes of interest to produce a detectable agent of each analyte of interest, whereby said detectable agent is analyzed and the information is processed for data acquisition and interpretation.Type: ApplicationFiled: March 14, 2001Publication date: May 31, 2007Inventors: David Walt, Caroline Schauer, Frank Steemers
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Publication number: 20050181394Abstract: This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.Type: ApplicationFiled: December 7, 2004Publication date: August 18, 2005Applicant: Illumina, Inc.Inventors: Frank Steemers, Weihua Chang, Min-Jui Shen, Kevin Gunderson
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Publication number: 20050059048Abstract: This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.Type: ApplicationFiled: June 17, 2004Publication date: March 17, 2005Applicant: Illumina, Inc.Inventors: Kevin Gunderson, Frank Steemers