Patents by Inventor Earl Hubbell

Earl Hubbell 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).

  • Publication number: 20050181431
    Abstract: The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.
    Type: Application
    Filed: March 25, 2005
    Publication date: August 18, 2005
    Applicant: Affymetrix, INC.
    Inventors: Martin Goldberg, Martin Diggelman, Earl Hubbell, Glenn McGall, Nam Ngo, MacDonald Morris, Mel Yamamoto, Jennifer Tan, Richard Rava
  • Publication number: 20050181396
    Abstract: The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.
    Type: Application
    Filed: December 17, 2004
    Publication date: August 18, 2005
    Applicant: Affymetrix, Inc.
    Inventors: Martin Goldberg, Martin Diggelman, Earl Hubbell, Glenn McGall, Nam Ngo, MacDonald Morris, Mel Yamamoto, Jennifer Tan, Richard Rava
  • Publication number: 20050118627
    Abstract: Methods and computer software products are provided for analyzing gene expression data. In one embodiment, linear programming is used to estimate relative transcripts. Bootstrapping methods are used to obtain confidence interval for estimators.
    Type: Application
    Filed: October 20, 2004
    Publication date: June 2, 2005
    Applicant: Affymetrix, INC.
    Inventor: Earl Hubbell
  • Publication number: 20050026203
    Abstract: Systems and method for organizing information relating to the design of polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of chips having complex designs.
    Type: Application
    Filed: August 24, 2004
    Publication date: February 3, 2005
    Applicant: Affymetrix, Inc.
    Inventors: David Balaban, Earl Hubbell, Michael Mittmann, Gloria Cheung, Josie Dai
  • Publication number: 20050019797
    Abstract: Experimental and analytical methods enable reconstruction of signal transduction networks from gene expression profiles. Signal transduction pathways can be reverse-engineered by 1) experimentally manipulating individual genes, 2) generating cellular expression profiles, and 3) analyzing for common patterns among these profiles. Analysis of patterns among profiles permits reconstruction of pathways and networks of interrelationships among genes and their products.
    Type: Application
    Filed: May 28, 2004
    Publication date: January 27, 2005
    Applicant: Affymetrix, Inc.
    Inventors: Jonathan Oliner, Earl Hubbell
  • Patent number: 6826296
    Abstract: Systems and method for organizing information relating to the design of polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of chips having complex designs.
    Type: Grant
    Filed: December 14, 2000
    Date of Patent: November 30, 2004
    Assignee: Affymetrix, Inc.
    Inventors: David J. Balaban, Earl Hubbell, Michael P. Mittmann, Gloria Cheung, Josie Dai
  • Publication number: 20040132099
    Abstract: Embodiments of the invention provides methods, computer software products and systems for arranging polymers during combinatorial polymer synthesis so that the border or edge between synthesis site is minimized. In one embodiment, travelling salesman algorithm is used to minimize the edges. In another embodiment, a locally greedy optimization method is provided. In addition, methods and software products are provided for solving the robust arrangement problem for multi-probe gene expression arrays.
    Type: Application
    Filed: July 25, 2003
    Publication date: July 8, 2004
    Applicant: Affymetrix, INC.
    Inventor: Earl A. Hubbell
  • Patent number: 6746844
    Abstract: Experimental and analytical methods enable reconstruction of signal transduction networks from gene expression profiles. Signal transduction pathways can be reverse-engineered by 1) experimentally manipulating individual genes, 2) generating cellular expression profiles, and 3) analyzing for common patterns among these profiles. Analysis of patterns among profiles permits reconstruction of pathways and networks of interrelationships among genes and their products.
    Type: Grant
    Filed: January 22, 2002
    Date of Patent: June 8, 2004
    Assignee: Affymetrix, Inc.
    Inventors: Jonathan D. Oliner, Earl Hubbell
  • Publication number: 20040105932
    Abstract: The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.
    Type: Application
    Filed: November 25, 2003
    Publication date: June 3, 2004
    Applicant: Affymetrix, Inc.
    Inventors: Martin Goldberg, Martin Diggelman, Earl Hubbell, Glenn McGall, Nam Quoc Ngo, MacDonald Morris, Mel Yamamoto, Jennifer Tan, Richard P. Rava
  • Patent number: 6706875
    Abstract: The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.
    Type: Grant
    Filed: November 20, 2000
    Date of Patent: March 16, 2004
    Assignee: Affyemtrix, Inc.
    Inventors: Martin Goldberg, Martin Diggelman, Earl Hubbell, Glenn McGall, Nam Quoc Ngo, MacDonald Morris, Mel Yamamoto, Jennifer Tan, Richard P. Rava
  • Publication number: 20030165830
    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: March 1, 2001
    Publication date: September 4, 2003
    Inventors: Maureen Cronin, Charles Miyada, Earl Hubbell, Mark Chee, Stephen Fodor, Xiaohua Huang, Robert Lipshutz, Peter Lobban, MacDonald Morris, Edward Shelton
  • Publication number: 20030165823
    Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the CFTR gene.
    Type: Application
    Filed: February 22, 2000
    Publication date: September 4, 2003
    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
  • Publication number: 20030134291
    Abstract: The present invention generally provides a rapid efficient method for analyzing polymorphic or biallelic markers, and arrays for carrying out these analyses. In general, the methods of the present invention employ arrays of oligonucleotide probes that are complementary to target nucleic acids which correspond to the marker sequences of an individual. The probes are typically arranged in detection blocks, each block being capable of discriminating the three genotypes for a given marker, e.g., the heterozygote or either of the two homozygotes. The method allows for rapid, automatable analysis of genetic linkage to even complex polygenic traits.
    Type: Application
    Filed: March 28, 2002
    Publication date: July 17, 2003
    Applicant: Affymetrix, Inc.
    Inventors: Robert J. Lipshutz, Mark S. Chee, Maureen T. Cronin, Stephen P.A. Fodor, Earl A. Hubbell, MacDonald S. Morris, Charles Garrett Miyada
  • Publication number: 20030073125
    Abstract: Methods, computer software and systems are provided for biological data analysis. In one embodiment, a probe logarithmic intensity error resolver is provided to analyze gene expression data obtained using multiprobes.
    Type: Application
    Filed: October 16, 2002
    Publication date: April 17, 2003
    Applicant: Affymetrix, INC.
    Inventor: Earl A. Hubbell
  • Publication number: 20030003450
    Abstract: Methods and computer software products are provided for analyzing gene expression data. In one embodiment, linear programming is used to estimate relative transcripts. Bootstrapping methods are used to obtain confidence interval for estimators.
    Type: Application
    Filed: December 21, 2000
    Publication date: January 2, 2003
    Applicant: Affymetrix, Inc.
    Inventor: Earl Hubbell
  • Patent number: 6468744
    Abstract: The invention provides methods for detecting variations in polymorphic sites and/or variations in gene copy number. The methods are particularly useful for analysis of biotransformation genes, such as cytochromes P450.
    Type: Grant
    Filed: November 17, 1999
    Date of Patent: October 22, 2002
    Assignee: Affymetrix, Inc.
    Inventors: Maureen T. Cronin, Edward L. Sheldon, Charles G. Miyada, Earl A. Hubbell, Mark Chee, Stephen P. A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris
  • Publication number: 20020133301
    Abstract: Methods and computer software products are provided for selecting nucleic acid probes. In one embodiment, dynamic programming is employed to select a set of k probes from n probes so that the selected probes have a maximum aggregate adjusted quality score.
    Type: Application
    Filed: December 21, 2000
    Publication date: September 19, 2002
    Inventor: Earl Hubbell
  • Publication number: 20020102564
    Abstract: Systems, methods, and products are described for synthesizing probe arrays of polymers. A mask is used that includes reticle areas, each of which includes a number of reticles associated with a same synthesis area on a substrate. A method includes (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate; (b) coupling monomers on the first synthesis area at locations determined by the first reticle; (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and (d) coupling monomers on the first synthesis area at locations determined by the second reticle. The monomers may be, for example, nucleotides, amino acids or saccharides.
    Type: Application
    Filed: April 3, 2001
    Publication date: August 1, 2002
    Inventors: Michael P. Mittmann, Earl A. Hubbell
  • Publication number: 20020094518
    Abstract: Experimental and analytical methods enable reconstruction of signal transduction networks from gene expression profiles. Signal transduction pathways can be reverse-engineered by 1) experimentally manipulating individual genes, 2) generating cellular expression profiles, and 3) analyzing for common patterns among these profiles. Analysis of patterns among profiles permits reconstruction of pathways and networks of interrelationships among genes and their products.
    Type: Application
    Filed: January 22, 2002
    Publication date: July 18, 2002
    Applicant: Affymetrix, Inc.
    Inventors: Jonathan D. Oliner, Earl Hubbell
  • Patent number: 6340565
    Abstract: Experimental and analytical methods enable reconstruction of signal transduction networks from gene expression profiles. Signal transduction pathways can be reverse-engineered by 1) experimentally manipulating individual genes, 2) generating cellular expression profiles, and 3) analyzing for common patterns among these profiles. Analysis of patterns among profiles permits reconstruction of pathways and networks of interrelationships among genes and their products.
    Type: Grant
    Filed: November 1, 1999
    Date of Patent: January 22, 2002
    Assignee: Affymetrix, Inc.
    Inventors: Jonathan D. Oliner, Earl Hubbell