Patents by Inventor Mark F. Oldham

Mark F. Oldham 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).

  • Methods for improving the performance of a detector
    Patent number: 7764378
    Abstract: A system and method for allowing adjustments of various parameters associated with the operation of charge-coupled devices adapted for use in biological analysis devices. Gate voltage signal applied to the CCDs can be adjusted to advantageously affect the manner in which charge is transferred from pixels. The manner in which transferred charges from the pixels are processed in a readout process can also be adjusted to advantageously change the speed of the CCD based detector. Various methods of performing such adjustments are disclosed.
    Type: Grant
    Filed: June 12, 2008
    Date of Patent: July 27, 2010
    Assignee: Applied Biosystems, LLC
    Inventor: Mark F. Oldham
  • PARTICLES FOR USE IN SUPPORTED NUCLEIC ACID LIGATION AND DETECTION SEQUENCING
    Publication number: 20100179075
    Abstract: Compositions and methods to modify the surface of particles to which biomolecules are attached are disclosed. The particles can include beads and nanoparticles which are composed of metallics, metal alloys, glass, polymers and derivatives and composites thereof. The surface of the particles are modified to be hydrophilic for ease in the attachment of biomolecules to the particle surface and immobilization of the particles to a substrate to facilitate process such as nucleic acid sequencing, PCR and sequencing by ligation.
    Type: Application
    Filed: July 30, 2009
    Publication date: July 15, 2010
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Aldrich N.K. LAU, Mark F. OLDHAM
  • Systems, Methods, and Apparatus for Single Molecule Sequencing
    Publication number: 20100178691
    Abstract: An embodiment generally relates to a system for analysis of an analyte. The system can include a transparent substrate. The system also includes an excitation light source configured to induce an evanescent wave excitation of a fluorescently labeled molecule near the access to the transparent substrate and a detector for detecting the fluorescently labeled molecule.
    Type: Application
    Filed: March 23, 2010
    Publication date: July 15, 2010
    Applicant: APPLIED BIOSYSTEMS, LLC
    Inventors: Richard T. Reel, Mark F. Oldham, Eric S. Nordman, Steven J. Boege, Steven M. Menchen
  • COMBINATION READER
    Publication number: 20100163710
    Abstract: An imaging system for collecting images of signals associated with a sample tile comprising a stage supporting the sample tile, a ring illuminator system emitting a uniform excitation energy upon an entirety of the sample tile causing at least a first signal to be generated from the sample tile, and an image collecting device collecting a first image of the first signal. The image collecting device further collecting a second image of a second signal emitted from the sample tile, wherein the second signal being different than the first signal.
    Type: Application
    Filed: October 2, 2009
    Publication date: July 1, 2010
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Mark F. OLDHAM, Howard King, Douwe Haga, Tracy Ferea
  • Luminescence reference standards
    Patent number: 7742164
    Abstract: The present teachings provide for systems, and components thereof, for detecting and/or analyzing light. These systems can include, among others, optical reference standards utilizing luminophores, such as nanocrystals, for calibrating, validating, and/or monitoring light-detection systems, before, during, and/or after sample analysis.
    Type: Grant
    Filed: December 18, 2008
    Date of Patent: June 22, 2010
    Assignee: Applied Biosystems, LLC
    Inventors: J. Michael Phillips, Aldrich N. K. Lau, Mark F. Oldham, Kevin S. Bodner, Steven J. Boege, Donald R. Sandell, David H. Tracy
  • Signal noise reduction for imaging in biological analysis
    Patent number: 7715004
    Abstract: A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.
    Type: Grant
    Filed: July 28, 2008
    Date of Patent: May 11, 2010
    Assignee: Applied Biosystems, LLC
    Inventors: Austin B. Tomaney, Mark F. Oldham
  • Normalization of Data Using Controls
    Publication number: 20100113285
    Abstract: A method of using a standard to correct for variability in sample handling, can comprise (a) adding a template of known concentration to an assay comprising a sample; (b) preamplifying the assay; (c) amplifying the assay; (d) collecting data during the amplifying; and (e) correcting the data using a comparison of data collected from the template to data collected from the sample.
    Type: Application
    Filed: April 28, 2009
    Publication date: May 6, 2010
    Applicant: Life Technologies Corporation
    Inventors: H. Pin Kao, Ian A. Harding, Kathleen C. Hayashibara, Achim Karger, Fiona C. Laird Hyland, Mark F. Oldham, Omead Ostadan, Mark R. Pratt, Junko F. Stevens, Austin B. Tomaney, Greg Young
  • Systems, methods and apparatus for single molecule sequencing
    Patent number: 7709808
    Abstract: An embodiment generally relates to a system for analysis of an analyte. The system can include a transparent substrate. The system also includes an excitation light source configured to induce an evanescent wave excitation of a fluorescently labeled molecule near the access to the transparent substrate and a detector for detecting the fluorescently labeled molecule.
    Type: Grant
    Filed: May 16, 2007
    Date of Patent: May 4, 2010
    Assignee: Applied Biosystems, LLC
    Inventors: Richard T. Reel, Mark F. Oldham, Eric S. Nordman, Steven J. Boege, Steven M. Menchen
  • DNA Sequencing System
    Publication number: 20100103416
    Abstract: An apparatus for detecting labeled beads is provided. The apparatus can include: one or more irradiation sources disposed for irradiating the one or more detection zones with radiation; at least one detector disposed for collecting charges corresponding to light signals emitted from labeled beads in the one or more detection zones, which have been excited by the radiation; and a system coupled to the at least one detector for effecting time delay integration of the charges by accumulating the charges before reading the charges at the output of the at least one detector.
    Type: Application
    Filed: December 3, 2009
    Publication date: April 29, 2010
    Applicant: Applied Biosystems, LLC
    Inventors: Mark F. OLDHAM, Eric S. Nordman, Richard T. Reel, Janice S. Shigeura
  • Normalization of Gene Expression Data
    Publication number: 20100036616
    Abstract: A method for determining bias across two domains comprising gene expression data. The method can comprise (a) providing a first domain and a second domain; (b) obtaining information indicative of a bias within the first domain; (c) obtaining information indicative of a bias within the second domain; and (d) using the information indicative of the bias within the first domain and the information indicative of the bias within the second domain to produce an indication of bias across the two domains.
    Type: Application
    Filed: September 11, 2009
    Publication date: February 11, 2010
    Applicant: Life Technologies Corporation
    Inventors: Mark E. Shannon, Mark F. Oldham, David W. Ruff
  • Time-delay integration in detection of labeled beads
    Patent number: 7636159
    Abstract: An apparatus for detecting labeled beads is provided. The apparatus can include: one or more irradiation sources disposed for irradiating the one or more detection zones with radiation; at least one detector disposed for collecting charges corresponding to light signals emitted from labeled beads in the one or more detection zones, which have been excited by the radiation; and a system coupled to the at least one detector for effecting time delay integration of the charges by accumulating the charges before reading the charges at the output of the at least one detector.
    Type: Grant
    Filed: September 17, 2008
    Date of Patent: December 22, 2009
    Assignee: Applied Biosystems, LLC
    Inventors: Mark F. Oldham, Eric S. Nordman, Richard T. Reel, John S. Shigeura, Janice G. Shigeura, legal representative
  • Apparatus and method for differentiating multiple fluorescence signals by excitation wavelength
    Patent number: 7635588
    Abstract: An apparatus and method are provided for differentiating multiple detectable signals by excitation wavelength. The apparatus can include a light source that can emit respective excitation light wavelengths or wavelength ranges towards a sample in a sample retaining region, for example, in a well. The sample can contain two or more detectable markers, for example, fluorescent dyes, each of which can be capable of generating increased detectable emissions when excited in the presence of a target component. The detectable markers can have excitation wavelength ranges and/or emission wavelength ranges that overlap with the ranges of the other detectable markers. A detector can be arranged for detecting an emission wavelength or wavelength range emitted from a first marker within the overlapping wavelength range of at least one of the other markers.
    Type: Grant
    Filed: May 19, 2003
    Date of Patent: December 22, 2009
    Assignee: Applied Biosystems, LLC
    Inventors: Howard G. King, Steven J. Boege, Eugene F. Young, Mark F. Oldham
  • System for detecting markers
    Patent number: 7636160
    Abstract: An apparatus for detecting labeled beads is provided. The apparatus can include: one or more irradiation sources disposed for irradiating the one or more detection zones with radiation; at least one detector disposed for collecting charges corresponding to light signals emitted from labeled beads in the one or more detection zones, which have been excited by the radiation; and a system coupled to the at least one detector for effecting time delay integration of the charges by accumulating the charges before reading the charges at the output of the at least one detector.
    Type: Grant
    Filed: January 26, 2009
    Date of Patent: December 22, 2009
    Assignee: Applied Biosystems, LLC
    Inventors: Mark F. Oldham, Eric S. Nordman, Richard T. Reel, John S. Shigeura, Janice G. Shigeura, legal representative
  • Method and System for Multiplex Genetic Analysis
    Publication number: 20090305909
    Abstract: A method for selectively immobilizing a molecule of interest on a substrate is disclosed. A substrate having a first surface component and a second surface component is provided. The first and second surface components have different surface characteristics. The molecule of interest is selectively coupled to the first surface component based upon a difference between the surface characteristics of the first surface component and the surface characteristics of the second surface component.
    Type: Application
    Filed: June 11, 2009
    Publication date: December 10, 2009
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Eric S. Nordman, Mark F. Oldham, Timothy Woudenberg
  • Method and System for Multiplex Genetic Analysis
    Publication number: 20090305287
    Abstract: A method for identifying nucleotides in a nucleic acid sequence is disclosed. A plurality of polymerization complexes are provided within a plurality of confined reaction environments. Each complex comprises a polymerase enzyme and a template nucleic acid. The plurality of complexes are contacted with a plurality of types of nucleotide analogs labeled with distinguishable fluorescent labels under conditions suitable for polymerization. Fluorescent signals associated with incorporation of a nucleotide analog are transmitted to a detector, wherein the location of the fluorescent signal on the detector is indicative of the individual confined reaction environment and the type of nucleotide incorporated. The nucleotide in a nucleic acid sequence is identified based upon the type of nucleotide incorporated and the confined reaction environment.
    Type: Application
    Filed: June 11, 2009
    Publication date: December 10, 2009
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Eric S. Nordman, Mark F. Oldham, Timothy Woudenberg
  • Method and System for Multiplex Genetic Analysis
    Publication number: 20090305908
    Abstract: A method for preferentially localizing desired molecules within an optical confinement disposed upon a substrate is disclosed. The desired molecules are deposited over the surface of the substrate. The desired molecules that are not within the optical confinement are selectively removed from the surface of the substrate.
    Type: Application
    Filed: June 11, 2009
    Publication date: December 10, 2009
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Eric S. Nordman, Mark F. Oldham, Timothy Woudenberg
  • Scanning system and method for imaging and sequencing
    Publication number: 20090250615
    Abstract: A scanning detection system is provided wherein emissions from locations in a flow cell are detected. In some embodiments, the system can comprise an excitation source, a photocleavage source, and modulating optics configured to cause an excitation beam generated by the excitation source to irradiate a first group of the fixed locations and to cause a photocleavage beam generated by the photocleavage source to irradiate a second group of the fixed locations, which is separate and apart from the first group of fixed locations. Methods of detecting sequencing reactions using such a system are also provided.
    Type: Application
    Filed: April 6, 2009
    Publication date: October 8, 2009
    Applicant: Life Technologies Corporation
    Inventors: Mark F. Oldham, Eric S. Nordman, Hongye Sun, Steven J. Boege
  • Optical scanning configurations, systems, and methods involving at least one actuator for scanning a scan head
    Patent number: 7599060
    Abstract: An optical system includes a sample substrate having a surface, the surface defining a 2-dimensional sample plane. The system includes an excitation source configured to provide excitation light to the sample substrate. The system further includes an optical detector configured to receive emission light from the sample substrate and generate detection data. The system also includes a scan head configured at least (i) to direct the excitation light towards the sample substrate, (ii) to receive emission light from the sample substrate and direct the emission light towards the optical detector, and (iii) for scanning relative to the sample substrate.
    Type: Grant
    Filed: August 18, 2008
    Date of Patent: October 6, 2009
    Assignee: Applied Biosystems, LLC
    Inventors: Jon A. Hoshizaki, Howard G. King, Johannes P. Sluis, Steven J. Boege, Mark F. Oldham
  • Normalization of data
    Patent number: 7586600
    Abstract: Methods for normalizing output from an instrument employing a reference standard or non-fluorescing substance disposed within at least one of a plurality of reaction chambers. The method comprises collecting and analyzing a signal associated with the reference standard or non-fluorescing substance to determine a normalizing bias. The normalizing bias is then applied to the data signal collected from a remainder of the plurality of reaction chambers.
    Type: Grant
    Filed: July 21, 2008
    Date of Patent: September 8, 2009
    Assignee: Applied Biosystem, LLC
    Inventors: H. Pin Kao, Ian A. Harding, Achim Karger, Mark F. Oldham, Omead Ostadan, Greg Young
  • Optical camera alignment
    Patent number: 7570443
    Abstract: A camera alignment system that can enable alignment in at least one of three planes and about an axis of at least one of the planes. An alignment mount can mate to a camera and lens. The alignment mount can comprise a mechanism to adjust the camera relative to the lens to that an image plane of the camera aligns with an image plane of the lens in a predetermined orientation. One predetermined orientation can be that the image plane of the camera being parallel to the image plane of the lens.
    Type: Grant
    Filed: March 22, 2005
    Date of Patent: August 4, 2009
    Assignee: Applied Biosystems, LLC
    Inventors: Barry J. Blasenheim, H. Pin Kao, Mark F. Oldham