Patents Assigned to IBIS Biosciences, Inc.
  • Patent number: 10697009
    Abstract: Provided herein is technology relating to sequencing nucleic acids, but not exclusively, to compositions, methods, systems, and kits related to nucleotides comprising an electrochemically detectable moiety and one or more photolabile synthesis-inhibiting moieties.
    Type: Grant
    Filed: August 12, 2019
    Date of Patent: June 30, 2020
    Assignee: IBIS BIOSCIENCES INC.
    Inventors: Mark A. Hayden, Jeffrey Huff, Mark W. Eshoo, John Picuri
  • Patent number: 10662485
    Abstract: The present invention compositions, methods and systems to identify, detect, and/or quantify bacterial DNA in the presence of contaminating non-bacterial DNA. In particular, the present invention provides oligonucleotides configured to detect a relatively small amount of bacterial DNA in the presence of an overwhelmingly large amount of contaminating human DNA.
    Type: Grant
    Filed: April 13, 2018
    Date of Patent: May 26, 2020
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: David J. Ecker, Steven A. Hofstadler, Rangarajan Sampath, Lawrence B. Blyn, Thomas A. Hall, Mark W. Eshoo
  • Patent number: 10584377
    Abstract: Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, and systems for sequencing a nucleic acid using one or more labels and signal amplitude to distinguish bases.
    Type: Grant
    Filed: May 2, 2013
    Date of Patent: March 10, 2020
    Assignee: IBIS BIOSCIENCES, INC.
    Inventor: Mark W. Eshoo
  • Patent number: 10550428
    Abstract: Provided herein are systems and methods for nucleic acid sequencing by synthesis in a plurality of wells using detectably labeled chain terminating nucleotides with photolabile blocking groups and pulses of photocleaving light. In certain embodiments, the systems and methods provides a plurality of deblock-scan cycles comprising an initial deblock time period followed by a scanning light period, wherein at least one of the following occurs in each deblock-scan cycle: 1) the deblock time period is shorter than the scan time period; 2) the deblock time period is only long enough to deblock the photolabile groups that are part of a primer in less than all of the plurality of wells; or 3) the deblock time period is between 25 and 150 mSec and the scan time is at least 200 mSec. Such shorter deblock time periods help prevent the addition of more than one nucleotide to the primer prior to scanning (e.g., accuracy is enhanced).
    Type: Grant
    Filed: September 16, 2015
    Date of Patent: February 4, 2020
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: Mark W. Eshoo, John M. Clemens, Mark A. Hayden
  • Patent number: 10550423
    Abstract: Provided herein is technology relating to depositing and/or placing a macromolecule at a desired site for an assay and particularly, but not exclusively, to methods and systems for transporting a macromolecule such as a protein, a nucleic acid, or a protein:nucleic acid complex to an assay site, such as the bottom of a nanopore, a nanowell, or a zero mode waveguide.
    Type: Grant
    Filed: October 30, 2017
    Date of Patent: February 4, 2020
    Assignee: IBIS BIOSCIENCES, INC.
    Inventor: Phillip N. Gray
  • Patent number: 10544454
    Abstract: Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, and systems for sequencing a nucleic acid using two or more labels and signal ratios to distinguish bases.
    Type: Grant
    Filed: May 2, 2013
    Date of Patent: January 28, 2020
    Assignee: IBIS BIOSCIENCES, INC.
    Inventor: Mark W. Eshoo
  • Patent number: 10428379
    Abstract: Provided herein is technology relating to sequencing nucleic acids, but not exclusively, to compositions, methods, systems, and kits related to nucleotides comprising an electrochemically detectable moiety and one or more photolabile synthesis-inhibiting moieties.
    Type: Grant
    Filed: March 12, 2014
    Date of Patent: October 1, 2019
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: Mark A. Hayden, Jeffrey Huff, Mark W. Eshoo, John Picuri
  • Patent number: 10227582
    Abstract: The present disclosure relates to systems and methods for nucleic acid isolation from cellular samples. In particular, the present disclosure provides systems and methods for lysing cells and recovering nucleic acids.
    Type: Grant
    Filed: May 9, 2016
    Date of Patent: March 12, 2019
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: Thomas N. Chiesl, Michelle Toro, Steven Gerald Haupt
  • Patent number: 10202642
    Abstract: Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, systems, and kits for sequencing a nucleic acid using a degenerate two-base code. Particular embodiments provide: 1) that the two-base degenerate code relates a first element to a base comprising adenine (A) or guanine (G) and a second element to a base comprising cytosine (C) or thymine (T); 2) that the two-base degenerate code relates a first element to a base comprising A or C and a second element to a base comprising G or T; and 3) that the two-base degenerate code relates a first element to a base comprising G or C and a second element to a base comprising A or T.
    Type: Grant
    Filed: May 2, 2013
    Date of Patent: February 12, 2019
    Assignee: IBIS BIOSCIENCES, INC.
    Inventor: Mark W. Eshoo
  • Patent number: 10150993
    Abstract: Provided herein is technology relating to depositing and/or placing a macromolecule at a desired site for an assay and particularly, but not exclusively, to methods and systems for placing or guiding a macromolecule such as a protein, a nucleic acid, or a protein: nucleic acid complex to an assay site, such as near a nanopore, a nanowell, or a zero mode waveguide.
    Type: Grant
    Filed: December 21, 2012
    Date of Patent: December 11, 2018
    Assignee: IBIS BIOSCIENCES, INC.
    Inventor: Mark A. Hayden
  • Patent number: 10119164
    Abstract: The present invention provides systems, methods, and compositions for performing molecular tests. In particular, the present invention provides methods, compositions and systems for generating target sequence-linked solid supports (e.g., beads) using a solid support linked to a plurality of capture sequences and capture primers composed of a 3? target-specific portion and a 5? capture sequence portion. In certain embodiments, the target sequence linked solid support is used in sequencing methods (e.g., pyrosequencing, zero-mode waveguide type sequencing, nanopore sequencing, etc.) to determine the sequence of the target sequence (e.g., in order to detect the identity of a target nucleic acid in sample).
    Type: Grant
    Filed: August 15, 2016
    Date of Patent: November 6, 2018
    Assignee: IBIS BIOSCIENCES, INC.
    Inventor: Mark A. Hayden
  • Patent number: 10041061
    Abstract: The invention provides methods for extraction of fungal (e.g., yeast spp., filamentous fungal spp.) nucleic acid (e.g., DNA, RNA) from a sample (e.g., be human or veterinary clinical or research samples, agricultural samples, agricultural commodity samples, food products, or environmental samples). In some embodiments, the present invention provides enhanced nucleic acid extraction from samples comprising fungal cell(s) wherein enzymatic (e.g., lysostaphin treatment, lyticase treatment) sample treatment is performed in combination with mechanical (e.g., bead beating) sample treatment.
    Type: Grant
    Filed: September 23, 2011
    Date of Patent: August 7, 2018
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: Gerard Gundling, Thomas Laffler, Cristina A. Ivy, Lendell Cummins
  • Patent number: 10011866
    Abstract: The present disclosure relates to systems and methods for nucleic acid ligation. In particular, the present disclosure provides oligonucleotide adaptors for use in nucleic acid ligation reactions.
    Type: Grant
    Filed: November 28, 2016
    Date of Patent: July 3, 2018
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: Mark W. Eshoo, John Picuri, Stanley T. Motley, Curtis Phillipson
  • Patent number: 9970061
    Abstract: The present invention compositions, methods and systems to identify, detect, and/or quantify bacterial DNA in the presence of contaminating non-bacterial DNA. In particular, the present invention provides oligonucleotides configured to detect a relatively small amount of bacterial DNA in the presence of an overwhelmingly large amount of contaminating human DNA.
    Type: Grant
    Filed: December 27, 2012
    Date of Patent: May 15, 2018
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: David J. Ecker, Steven A. Hofstadler, Rangarajan Sampath, Lawrence B. Blyn, Thomas A. Hall, Mark W. Eshoo
  • Patent number: 9914965
    Abstract: The present invention provides compositions and methods for rapidly amplifying target nucleic acid (e.g., using whole genome amplification) that allows small amounts of starting nucleic acid to be employed. In certain embodiments, the methods employ compositions that comprise: phi29 polymerase, exo? Klenow polymerase and/or Klenow polymerase, dNTPs, primers, and a buffering agent. In some embodiments, the target nucleic acid is amplified at a rate that would result in at least 1000-fold amplification in thirty minutes.
    Type: Grant
    Filed: August 29, 2016
    Date of Patent: March 13, 2018
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: Mark Eshoo, Stanley Motley, John Picuri
  • Patent number: 9890408
    Abstract: The present invention provides methods kits and systems for performing multiple displacement amplification reactions. In one method a sample of nucleic acid is provided. The nucleic acid is contacted with a reaction mixture which includes a set of oligonucleotide primers, a one or more polymerase enzymes and a detergent. The reaction mixture is then subjected to conditions under which the nucleic acid sequence is amplified to produce an amplified product in a multiple displacement reaction. The method may also be carried out by contacting the nucleic acid with the reaction mixture in the form of an emulsion. A kit is also provided for carrying out either the methods described above. The kit includes one or more polymerases, a plurality of primers and a detergent. The kit may also include a hydrophobic polymer and may include instructions for performing a multiple displacement amplification reaction on a nucleic acid sample.
    Type: Grant
    Filed: October 15, 2010
    Date of Patent: February 13, 2018
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: Mark W. Eshoo, John Picuri, Curtis Phillipson
  • Patent number: 9873119
    Abstract: Provided herein are systems and methods for performing complex chemical, physical and biological assays. In particular, provided herein are systems and methods for performing microfluidic assays.
    Type: Grant
    Filed: December 28, 2012
    Date of Patent: January 23, 2018
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: Mark W. Eshoo, John Picuri
  • Patent number: 9873906
    Abstract: The present invention provides methods and kits for repair of degraded DNA which may then be used as a template for efficient amplification by a number of different amplification reactions. The method relies upon a series of enzymatic activities provided by DNA repair enzymes.
    Type: Grant
    Filed: October 7, 2010
    Date of Patent: January 23, 2018
    Assignee: IBIS BIOSCIENCES, INC.
    Inventor: Mark W. Eshoo
  • Patent number: 9835620
    Abstract: Provided herein is technology relating to testing biological samples and particularly, but not exclusively, to devices, systems, and kits for performing multiple, simultaneous real-time assays on a sample in a single-use disposable format. For example, the technology relates to an apparatus that finds use, for example, for point-of-care diagnostics, including use at accident sites, emergency rooms, in surgery, in intensive care units, as well as for non-medical applications.
    Type: Grant
    Filed: August 4, 2015
    Date of Patent: December 5, 2017
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: Jared J. Drader, Gordon Bruce Collier, Steven A. Hofstadler
  • Patent number: 9803188
    Abstract: The present disclosure relates to systems and methods for nucleic acid isolation. In particular, the present disclosure provides systems and methods for isolating nucleic acids from aqueous samples (e.g., blood or urine).
    Type: Grant
    Filed: December 21, 2012
    Date of Patent: October 31, 2017
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: Mark W. Eshoo, Christopher Crowder