Patents by Inventor Mark Chee

Mark Chee 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).

  • Entangled mate sequencing
    Patent number: 10385391
    Abstract: Methods and compositions are provided for performing a set of N DNA sequencing reaction cycles whereby sequence information is obtained for approximately 2*N nucleotide bases.
    Type: Grant
    Filed: September 22, 2010
    Date of Patent: August 20, 2019
    Assignee: President and Fellows of Harvard College
    Inventors: Frederick P. Roth, Joseph C. Mellor, Yong Lu, Mark Chee
  • MACROMOLECULE ANALYSIS EMPLOYING NUCLEIC ACID ENCODING
    Publication number: 20190145982
    Abstract: A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.
    Type: Application
    Filed: May 2, 2017
    Publication date: May 16, 2019
    Applicant: Encodia, Inc.
    Inventors: Mark CHEE, Kevin GUNDERSON, Michael Phillip WEINER
  • Compositions and methods for preparing oligonucleotide solutions
    Patent number: 9745573
    Abstract: The present invention is directed to methods and compositions for generating a pool of oligonucleotides. The invention finds use in preparing a population or subpopulations of oligonucleotides in solution. The pool of oligonucleotides finds use in a variety of nucleic acid detection and/or amplification assays.
    Type: Grant
    Filed: August 15, 2016
    Date of Patent: August 29, 2017
    Assignee: Illumina, Inc.
    Inventors: John R. Stuelpnagel, Mark Chee
  • COMPOSITIONS AND METHODS FOR PREPARING OLIGONUCLEOTIDE SOLUTIONS
    Publication number: 20160348098
    Abstract: The present invention is directed to methods and compositions for generating a pool of oligonucleotides. The invention finds use in preparing a population or subpopulations of oligonucleotides in solution. The pool of oligonucleotides finds use in a variety of nucleic acid detection and/or amplification assays.
    Type: Application
    Filed: August 15, 2016
    Publication date: December 1, 2016
    Applicant: ILLUMINA, INC.
    Inventors: John R. Stuelpnagel, Mark Chee
  • Compositions and methods for preparing oligonucleotide solutions
    Patent number: 9416411
    Abstract: The present invention is directed to methods and compositions for generating a pool of oligonucleotides. The invention finds use in preparing a population or subpopulations of oligonucleotides in solution. The pool of oligonucleotides finds use in a variety of nucleic acid detection and/or amplification assays.
    Type: Grant
    Filed: January 16, 2014
    Date of Patent: August 16, 2016
    Assignee: Illumina, Inc.
    Inventors: John R. Stuelpnagel, Mark Chee
  • COMPOSITIONS AND METHODS FOR PREPARING OLIGONUCLEOTIDE SOLUTIONS
    Publication number: 20140135233
    Abstract: The present invention is directed to methods and compositions for generating a pool of oligonucleotides. The invention finds use in preparing a population or subpopulations of oligonucleotides in solution. The pool of oligonucleotides finds use in a variety of nucleic acid detection and/or amplification assays.
    Type: Application
    Filed: January 16, 2014
    Publication date: May 15, 2014
    Applicant: ILLUMINA, INC.
    Inventors: John R. Stuelpnagel, Mark Chee
  • Methods of using an array of pooled probes in genetic analysis
    Patent number: 8586312
    Abstract: The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger normalized binding to the first region than to the aggregate of binding to the second and third regions due to cooperative binding of pooled probes in the first region. The invention provides methods of using such arrays for e.g., linkage analysis, sequence analysis, and expression monitoring.
    Type: Grant
    Filed: August 17, 2010
    Date of Patent: November 19, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Erik Gentalen, Mark Chee
  • Arrays of Nucleic Acid Probes for Analyzing Biotransformation Genes
    Publication number: 20130150248
    Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set.
    Type: Application
    Filed: December 2, 2010
    Publication date: June 13, 2013
    Applicant: AFFYMETRIX, INC.
    Inventors: Maureen T. Cronin, Charles G. Miyada, Earl A. Hubbell, Mark Chee, Stephen P.A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris, Edward L. Sheldon
  • ARRAYS OF NUCLEIC ACID PROBES FOR DETECTING CYSTIC FIBROSIS
    Publication number: 20120329677
    Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the CFTR gene.
    Type: Application
    Filed: August 18, 2006
    Publication date: December 27, 2012
    Inventors: Maureen T. Cronin, Charles Garrett Miyada, Earl A. Hubbell, Mark Chee, Stephen P.A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris, Edward L. Sheldon
  • COMBINATORIAL DECODING OF RANDOM NUCLEIC ACID ARRAYS
    Publication number: 20120264622
    Abstract: Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence.
    Type: Application
    Filed: June 25, 2012
    Publication date: October 18, 2012
    Inventors: Mark Chee, David R. Walt
  • Entangled Mate Sequencing
    Publication number: 20120245039
    Abstract: Methods and compositions are provided for performing a set of N DNA sequencing reaction cycles whereby sequence information is obtained for approximately 2*N nucleotide bases.
    Type: Application
    Filed: September 22, 2010
    Publication date: September 27, 2012
    Applicant: President and Fellows of Harvard College
    Inventors: Frederick P. Roth, Joseph C. Mellor, Yong Lu, Mark Chee
  • COMBINATORIAL DECODING OF RANDOM NUCLEIC ACID ARRAYS
    Publication number: 20110251101
    Abstract: Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence.
    Type: Application
    Filed: June 13, 2011
    Publication date: October 13, 2011
    Inventors: Mark Chee, David R. Walt
  • METHODS OF USING AN ARRAY OF POOLED PROBES IN GENETIC ANALYSIS
    Publication number: 20110009289
    Abstract: The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger normalized binding to the first region than to the aggregate of binding to the second and third regions due to cooperative binding of pooled probes in the first region. The invention provides methods of using such arrays for e.g., linkage analysis, sequence analysis, and expression monitoring.
    Type: Application
    Filed: August 17, 2010
    Publication date: January 13, 2011
    Applicant: AFFYMETRIX, INC.
    Inventors: ERIK GENTALEN, MARK CHEE
  • Arrays of nucleic acid probes for analyzing biotransformation genes
    Patent number: 7846659
    Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set.
    Type: Grant
    Filed: April 11, 2006
    Date of Patent: December 7, 2010
    Assignee: Affymetrix, Inc.
    Inventors: Maureen T. Cronin, Charles G Miyada, Earl A. Hubbell, Mark Chee, Stephen P. A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris, Edward L. Sheldon
  • METHODS OF USING AN ARRAY OF POOLED PROBES IN GENETIC ANALYSIS
    Publication number: 20100041569
    Abstract: The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger normalized binding to the first region than to the aggregate of binding to the second and third regions due to cooperative binding of pooled probes in the first region. The invention provide methods of using such arrays for e.g., linkage analysis, sequence analysis, and expression monitoring.
    Type: Application
    Filed: October 23, 2007
    Publication date: February 18, 2010
    Applicant: Affymetrix, INC.
    Inventors: Erik Gentalen, Mark Chee
  • COMBINATORIAL DECODING OF RANDOM NUCLEIC ACID ARRAYS
    Publication number: 20090286688
    Abstract: Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence.
    Type: Application
    Filed: July 20, 2009
    Publication date: November 19, 2009
    Inventors: Mark Chee, David R. Walt
  • Composite arrays utilizing microspheres with a hybridization chamber
    Patent number: 7612020
    Abstract: The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.
    Type: Grant
    Filed: January 28, 2004
    Date of Patent: November 3, 2009
    Assignee: Illumina, Inc.
    Inventors: John Stuelpnagel, Mark Chee, Steven Auger
  • Methods of making and using composite arrays for the detection of a plurality of target analytes
    Patent number: 7510841
    Abstract: The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.
    Type: Grant
    Filed: January 28, 2004
    Date of Patent: March 31, 2009
    Assignee: Illumina, Inc.
    Inventors: John Stuelpnagel, Mark Chee, Steven Auger
  • Arrays of nucleic acid probes for detecting cystic fibrosis
    Publication number: 20080261832
    Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the CFTR gene.
    Type: Application
    Filed: August 18, 2006
    Publication date: October 23, 2008
    Inventors: Maureen T. Cronin, Charles Garrett Miyada, Earl A. Hubbell, Mark Chee, Stephen P.A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris, Edward L. Sheldon
  • Method of comparing a target nucleic acid and a reference nucleic acid
    Patent number: 7399584
    Abstract: The invention provides methods of comparing a target nucleic acid with a reference nucleic acid using nucleic acid arrays.
    Type: Grant
    Filed: February 22, 2000
    Date of Patent: July 15, 2008
    Assignee: Affymetrix, Inc.
    Inventors: Maureen T. Cronin, Charles Garrett Miyada, Earl A. Hubbell, Mark Chee, Stephen P. A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris, Edward L. Sheldon