Patents by Inventor Timothy D. Harris

Timothy D. Harris 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).

  • Patent number: 9657344
    Abstract: The invention provides methods for sequencing a polynucleotide comprising stopping an extension cycle in a sequence by synthesis reaction before the reaction has run to near or full completion.
    Type: Grant
    Filed: March 19, 2015
    Date of Patent: May 23, 2017
    Assignee: Fluidigm Corporation
    Inventors: Stanley N. Lapidus, Philip R. Buzby, Timothy D. Harris
  • Publication number: 20150292008
    Abstract: The invention provides methods for sequencing a polynucleotide comprising stopping an extension cycle in a sequence by synthesis reaction before the reaction has run to near or full completion.
    Type: Application
    Filed: March 19, 2015
    Publication date: October 15, 2015
    Inventors: Stanley N. Lapidus, PHILIP R. BUZBY, TIMOTHY D. HARRIS
  • Publication number: 20150159210
    Abstract: The invention provides methods for improving the fidelity of a sequencing-by-synthesis reaction by resequencing at least a portion of a nucleic acid template.
    Type: Application
    Filed: July 9, 2014
    Publication date: June 11, 2015
    Inventors: Timothy D. Harris, Eric S. Lander
  • Publication number: 20110255756
    Abstract: Methods and apparatus for screening large numbers of chemical compounds and performing a wide variety of fluorescent assays, including live cell assays. The methods utilize a laser linescan confocal microscope with high speed, high resolution and multi-wavelength capabilities and real time data-processing. Imaging may be done at video-rates and with use of ultraviolet illumination.
    Type: Application
    Filed: June 1, 2011
    Publication date: October 20, 2011
    Applicant: GE HEALTHCARE BIO-SCIENCES CORP.
    Inventors: TIMOTHY D. HARRIS, RICHARD L. HANSEN, WILLIAM KARSH, NEAL A. NICKLAUS, JAY K. TRAUTMAN
  • Patent number: 7957911
    Abstract: Methods and apparatus for screening large numbers of chemical compounds and performing a wide variety of fluorescent assays, including live cell assays. The methods utilize a laser linescan confocal microscope with high speed, high resolution and multi-wavelength capabilities and real time data-processing. Imaging may be done at video-rates and with use of ultraviolet illumination.
    Type: Grant
    Filed: February 8, 2008
    Date of Patent: June 7, 2011
    Assignee: GE Healthcare Bio-Sciences Corp.
    Inventors: Timothy D. Harris, Richard L. Hansen, William Karsh, Neal A. Nicklaus, Jay K. Trautman
  • Publication number: 20110027790
    Abstract: The disclosure provides methods of reducing the range of representation levels of nucleic acid targets. The methods are particularly useful for multi-target analyses benefiting from a low variance of target representations, such as, e.g., single molecule sequencing and/or heterozygous genotyping, and pathogen diagnosis. Two general methods are provided. In Method 1, starting concentrations of probes are adjusted. In Method 2, target-specific probes are “binned,” i.e., several subsets of probes are selected based on similar representation levels. Thereafter, each subset of corresponding targets is extracted, with or without amplification, using a separate portion of the sample (i.e., separate vessels).
    Type: Application
    Filed: August 31, 2010
    Publication date: February 3, 2011
    Applicant: Helicos Biosciences Corporation
    Inventors: Timothy D. Harris, John J. Boyce, IV
  • Publication number: 20100304447
    Abstract: The disclosure provides methods of generating paired reads in sequencing-by-synthesis process, particularly, in systems with relatively short read lengths (e.g., 15-35 bases), such as for example, in single molecule sequencing by synthesis. Several implementations of the methods are provided. Of particular advantage are the methods that permit re-sequencing of the template, which yields lower error rates. The invention further provides methods of using paired reads, for example, for positioning them over repeats or for assembly into large sequences, including whole genome assembly.
    Type: Application
    Filed: July 20, 2010
    Publication date: December 2, 2010
    Applicant: Helicos Biosciences Corporation
    Inventor: Timothy D. Harris
  • Patent number: 7790391
    Abstract: The disclosure provides methods of reducing the range of representation levels of nucleic acid targets. The methods are particularly useful for multi-target analyses benefiting from a low variance of target representations, such as, e.g., single molecule sequencing and/or heterozygous genotyping, and pathogen diagnosis. Two general methods are provided. In Method 1, starting concentrations of probes are adjusted. In Method 2, target-specific probes are “binned,” i.e., several subsets of probes are selected based on similar representation levels. Thereafter, each subset of corresponding targets is extracted, with or without amplification, using a separate portion of the sample (i.e., separate vessels).
    Type: Grant
    Filed: March 28, 2008
    Date of Patent: September 7, 2010
    Assignee: Helicos Biosciences Corporation
    Inventors: Timothy D. Harris, John J. Boyce, IV
  • Patent number: 7767400
    Abstract: The disclosure provides methods of generating paired reads in sequencing-by-synthesis process, particularly, in systems with relatively short read lengths (e.g., 15-35bases), such as for example, in single molecule sequencing by synthesis. Several implementations of the methods are provided. Of particular advantage are the methods that permit re-sequencing of the template, which yields lower error rates. The invention further provides methods of using paired reads, for example, for positioning them over repeats or for assembly into large sequences, including whole genome assembly.
    Type: Grant
    Filed: February 3, 2008
    Date of Patent: August 3, 2010
    Assignee: Helicos Biosciences Corporation
    Inventor: Timothy D. Harris
  • Publication number: 20090246760
    Abstract: The disclosure provides methods of reducing the range of representation levels of nucleic acid targets. The methods are particularly useful for multi-target analyses benefiting from a low variance of target representations, such as, e.g., single molecule sequencing and/or heterozygous genotyping, and pathogen diagnosis. Two general methods are provided. In Method 1, starting concentrations of probes are adjusted. In Method 2, target-specific probes are “binned,” i.e., several subsets of probes are selected based on similar representation levels. Thereafter, each subset of corresponding targets is extracted, with or without amplification, using a separate portion of the sample (i.e., separate vessels).
    Type: Application
    Filed: March 28, 2008
    Publication date: October 1, 2009
    Applicant: HELICOS BIOSCIENCES CORPORATION
    Inventors: Timothy D. Harris, John J. Boyce, IV
  • Publication number: 20090226906
    Abstract: The disclosure provides methods and compositions for reducing nucleotide impurities in reagents and reaction mixtures. Generally, the methods of the invention involve the inclusion of so-called “scrubbing oligonucleotides” (or “scrubbers”) that preferentially incorporate nucleotide impurities, thereby reducing available free impurities. The disclosure further provides methods of sequencing a target nucleic acid by synthesis that utilize “live” scrubbing. Scrubbing oligonucleotides of various structures are disclosed, including hairpin scrubbers and homopolymeric scrubbers.
    Type: Application
    Filed: May 1, 2008
    Publication date: September 10, 2009
    Applicant: HELICOS BIOSCIENCES CORPORATION
    Inventors: David Z. Xie, Philip R. Buzby, Timothy D. Harris
  • Publication number: 20090197257
    Abstract: The disclosure provides methods of generating paired reads in sequencing-by-synthesis process, particularly, in systems with relatively short read lengths (e.g., 15-35 bases), such as for example, in single molecule sequencing by synthesis. Several implementations of the methods are provided. Of particular advantage are the methods that permit re-sequencing of the template, which yields lower error rates. The invention further provides methods of using paired reads, for example, for positioning them over repeats or for assembly into large sequences, including whole genome assembly.
    Type: Application
    Filed: February 3, 2008
    Publication date: August 6, 2009
    Applicant: Helicos BioSciences Corporation
    Inventor: Timothy D. Harris
  • Publication number: 20090156412
    Abstract: The disclosure provides methods of capturing target nucleic acids (e.g., gene or gene fragments) onto a solid support for further analysis. The disclosed methods utilize a capture probe that selectively circularizes only the target nucleic acid. Following the circularization of the target, the linear, non-target, nucleic acids are removed from the sample. Next, the circularized target is linearized and bound to a solid support. To allow for linearization, the capture probe may include a cleavage site that can be a noncanonical nucleotide(s) (e.g., uracil in DNA) and/or a rare-cutter site (e.g., the Not I restriction site). In some embodiments, the target nucleic acid is captured onto a support without an intermediate amplification step.
    Type: Application
    Filed: December 17, 2007
    Publication date: June 18, 2009
    Applicant: HELICOS BIOSCIENCES CORPORATION
    Inventors: John J. Boyce, IV, Timothy D. Harris
  • Publication number: 20090075252
    Abstract: The invention provides methods for improving the fidelity of a sequencing-by-synthesis reaction by resequencing at least a portion of a nucleic acid template.
    Type: Application
    Filed: December 15, 2006
    Publication date: March 19, 2009
    Applicant: Helicos BioSciences Corporation
    Inventors: Timothy D. Harris, Eric S. Lander
  • Publication number: 20090053705
    Abstract: The invention provides methods for improving the accuracy of a sequencing-by-synthesis reaction by sequencing at least a portion of a template and at least a portion of template complementary sequence.
    Type: Application
    Filed: October 15, 2007
    Publication date: February 26, 2009
    Applicant: HELICOS BIOSCIENCES CORPORATION
    Inventor: Timothy D. Harris
  • Publication number: 20080262741
    Abstract: Methods and apparatus for screening large numbers of chemical compounds and performing a wide variety of fluorescent assays, including live cell assays. The methods utilize a laser linescan confocal microscope with high speed, high resolution and multi-wavelength capabilities and real time data-processing. Imaging may be done at video-rates and with use of ultraviolet illumination.
    Type: Application
    Filed: February 8, 2008
    Publication date: October 23, 2008
    Applicant: GE HEALTHCARE BIO-SCIENCES CORP.
    Inventors: TIMOTHY D. HARRIS, RICHARD L. HANSEN, WILLIAM KARSH, NEAL A. NICKLAUS, JAY K. TRAUTMAN
  • Publication number: 20080246949
    Abstract: In one aspect the invention relates to an apparatus for analyzing the presence of a single molecule using total internal reflection. In one embodiment an apparatus for single molecule analysis includes a support having a sample located thereon; two sources of light at distinct wavelengths, a collimator for directing the light onto the sample through a total internal reflection objective; a receiver for receiving a fluorescent emission produced by a single molecule in the sample in response to the light; and a detector for detecting each of the wavelengths in the fluorescent emission. In another embodiment the apparatus further comprises a focusing laser for maintaining focus of the objective on the sample.
    Type: Application
    Filed: October 30, 2007
    Publication date: October 9, 2008
    Applicant: Helicos BioSciences Corporation
    Inventors: Timothy D. Harris, Philip R. Buzby, Mirna Jarosz, Jaime Gill, Howard Weiss, Stanley N. Lapidus
  • Publication number: 20080233575
    Abstract: The invention provides methods for improving the fidelity of a sequencing-by-synthesis reaction by resequencing at least a portion of a nucleic acid template.
    Type: Application
    Filed: October 30, 2007
    Publication date: September 25, 2008
    Applicant: HELICOS BIOSCIENCES CORPORATION
    Inventors: Timothy D. Harris, Eric S. Lander
  • Patent number: 7282337
    Abstract: The invention provides methods for improving the accuracy of a sequencing-by-synthesis reaction by sequencing at least a portion of a template and at least a portion of template complementary sequence.
    Type: Grant
    Filed: April 14, 2006
    Date of Patent: October 16, 2007
    Assignee: Helicos BioSciences Corporation
    Inventor: Timothy D. Harris
  • Publication number: 20030036855
    Abstract: Methods and apparatus for screening large numbers of chemical compounds and performing a wide variety of fluorescent assays, including live cell assays. The methods utilize a laser linescan confocal microscope with high speed, high resolution and multi-wavelength capabilities and real time data-processing. Imaging may be done at video-rates and with use of ultraviolet illumination.
    Type: Application
    Filed: August 16, 2002
    Publication date: February 20, 2003
    Applicant: Praelux Incorporated, a corporation of New Jersey
    Inventors: Timothy D. Harris, Richard L. Hansen, William Karsh, Neal A. Nicklaus, Jay K. Trautman