Patents by Inventor Tyson A. Clark

Tyson A. Clark 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: 20210331091
    Abstract: In a wastewater treatment system, a clarifier has a submerged effluent launder, with a sloped, submerged plate that allows clarified liquid to exit through submerged openings. The sloped surface tends to accumulate solids, which can lead to algae growth. Typical internal scum collection system equipment prevents any efficient way to clear the accumulated sludge off the launder surface because of interferences. As disclosed here, a scum discharge area or box is placed external to the clarifier in one embodiment. Scum is wiped from a vertical surface of the launder assembly, above the sloped launder surface, and swept over a scum beach at one position in the clarifier, to drop into a lower trough and the flow out through the clarifier wall to a drop out box or scum discharge area. This allows for a rake-attached, sweeping launder wiper to be moved with the clarifier's rake to remove the accumulation of sludge from the launder's submerged surface, without elaborate moving parts.
    Type: Application
    Filed: July 19, 2019
    Publication date: October 28, 2021
    Inventors: Tyson Beaman, Garret Beaman, Ryan Clark, John Vorwaller, Robert E. Hanford
  • Publication number: 20210269876
    Abstract: Compositions, methods and systems are provided for isolating nucleic acids. A polymerase-nucleic acid complex can be formed by mixing a polymerase enzyme comprising strand displacement activity and a mixture of double stranded nucleic acids. Nucleic acid synthesis can then be initiated by the polymerase enzyme to produce a nascent strand complementary to the first strand, thereby displacing a portion of the second strand. After halting or reducing the rate of nucleic acid synthesis, a hybridizing a hook oligonucleotide can be used hybridize to the nucleic acid through a capture region on the hook oligonucleotide that is complementary to the displaced portion of the second strand. The nucleic acid can then be isolated from the mixture of nucleic acids using the hook oligonucleotide.
    Type: Application
    Filed: February 26, 2021
    Publication date: September 2, 2021
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Patent number: 10934585
    Abstract: Compositions, methods and systems are provided for the loading of extended polymerase-nucleic acid complexes onto substrates. Primed polymerase-template complex comprising a polymerase enzyme and a circular nucleic acid template comprising a double stranded region connected at each end by a single-stranded hairpin region are provides in which the circular nucleic acid template comprises at least one reversible pause point. Nucleic acid synthesis is carried out such that a nascent strand is synthesized up to the reversible stop point producing an extended polymerase-template complex. The extended polymerase-template complex is then attached to a substrate. Such attached complexes can be used for single molecule sequencing in which the nucleic acid synthesis is re-initiated such that nucleic acid synthesis continues past the reversible stop point.
    Type: Grant
    Filed: June 13, 2018
    Date of Patent: March 2, 2021
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Publication number: 20200399690
    Abstract: Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.
    Type: Application
    Filed: March 24, 2020
    Publication date: December 24, 2020
    Inventors: Thang Tat Pham, Yu-Chih Tsai, Jonas Korlach, Tyson A. Clark, Stephen Turner
  • Patent number: 10640818
    Abstract: Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.
    Type: Grant
    Filed: November 16, 2016
    Date of Patent: May 5, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Thang Tat Pham, Yu-Chih Tsai, Jonas Korlach, Tyson A. Clark, Stephen Turner
  • Patent number: 10590484
    Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
    Type: Grant
    Filed: January 19, 2018
    Date of Patent: March 17, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jonas Korlach, Stephen Turner, Tyson A. Clark
  • Publication number: 20190311780
    Abstract: Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.
    Type: Application
    Filed: March 12, 2019
    Publication date: October 10, 2019
    Applicant: AFFYMETRIX, INC.
    Inventors: Alan Williams, Simon Cawley, John E. Blume, Hui Wang, Tyson Clark
  • Patent number: 10294523
    Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
    Type: Grant
    Filed: September 23, 2015
    Date of Patent: May 21, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Benjamin Flusberg, Jonas Korlach, Jeffrey Wegener, Tyson A. Clark, Igor Drasko Vilfan, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Jessica Lee, Lei Jia, Dale Webster, John Lyle, Jeremiah Hanes
  • Publication number: 20190136313
    Abstract: Compositions, methods and systems are provided for the loading of extended polymerase-nucleic acid complexes onto substrates. Primed polymerase-template complex comprising a polymerase enzyme and a circular nucleic acid template comprising a double stranded region connected at each end by a single-stranded hairpin region are provides in which the circular nucleic acid template comprises at least one reversible pause point. Nucleic acid synthesis is carried out such that a nascent strand is synthesized up to the reversible stop point producing an extended polymerase-template complex. The extended polymerase-template complex is then attached to a substrate. Such attached complexes can be used for single molecule sequencing in which the nucleic acid synthesis is re-initiated such that nucleic acid synthesis continues past the reversible stop point.
    Type: Application
    Filed: June 13, 2018
    Publication date: May 9, 2019
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Patent number: 10275568
    Abstract: Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.
    Type: Grant
    Filed: March 27, 2012
    Date of Patent: April 30, 2019
    Assignee: Affymetrix, Inc.
    Inventors: Alan Williams, Simon Cawley, John E. Blume, Hui Wang, Tyson Clark
  • Publication number: 20190062833
    Abstract: Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.
    Type: Application
    Filed: August 21, 2018
    Publication date: February 28, 2019
    Inventors: Tyson A. Clark, Jonas Korlach, Cheryl Heiner, Kevin Travers, Erik Miller
  • Publication number: 20190024162
    Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
    Type: Application
    Filed: January 19, 2018
    Publication date: January 24, 2019
    Inventors: Jonas Korlach, Stephen Turner, Tyson A. Clark
  • Patent number: 10081836
    Abstract: Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.
    Type: Grant
    Filed: July 15, 2016
    Date of Patent: September 25, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Tyson A. Clark, Jonas Korlach, Cheryl Heiner, Kevin Travers, Erik Miller
  • Patent number: 10000805
    Abstract: Compositions, methods and systems are provided for isolating DNA having a modified or unnatural base. Circular DNA fragments, each comprising a double stranded DNA central region and single stranded regions on the ends of the double stranded regions, are obtained. Some of the fragments have one or more modified or unnatural base. The DNA fragments are treated with a primer and a polymerase such that the polymerase extends the primer to copy at least one of the strand of the double stranded region. This results in rendering the other strand single stranded. A binding protein or antibody that is specific to the modified or unnatural base is then used to isolate strands containing the modified or unnatural bases. Methods for loading such complexes onto substrates and for single molecule sequencing of such complexes are also provided.
    Type: Grant
    Filed: September 20, 2016
    Date of Patent: June 19, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Publication number: 20170145492
    Abstract: Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.
    Type: Application
    Filed: November 16, 2016
    Publication date: May 25, 2017
    Inventors: Thang Tat Pham, Yu-Chih Tsai, Jonas Korlach, Tyson A. Clark, Stephen Turner
  • Publication number: 20170107570
    Abstract: Compositions, methods and systems are provided for isolating DNA having a modified or unnatural base. Circular DNA fragments, each comprising a double stranded DNA central region and single stranded regions on the ends of the double stranded regions, are obtained. Some of the fragments have one or more modified or unnatural base. The DNA fragments are treated with a primer and a polymerase such that the polymerase extends the primer to copy at least one of the strand of the double stranded region. This results in rendering the other strand single stranded. A binding protein or antibody that is specific to the modified or unnatural base is then used to isolate strands containing the modified or unnatural bases. Methods for loading such complexes onto substrates and for single molecule sequencing of such complexes are also provided.
    Type: Application
    Filed: September 20, 2016
    Publication date: April 20, 2017
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Publication number: 20170009289
    Abstract: Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.
    Type: Application
    Filed: July 15, 2016
    Publication date: January 12, 2017
    Inventors: Tyson A. Clark, Jonas Korlach, Cheryl Heiner, Kevin Travers, Erik Miller
  • Patent number: 9528107
    Abstract: Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.
    Type: Grant
    Filed: October 31, 2013
    Date of Patent: December 27, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Thang Tat Pham, Yu-Chih Tsai, Jonas Korlach, Tyson A. Clark, Stephen Turner
  • Patent number: 9475054
    Abstract: Compositions, methods and systems are provided for the isolation of polymerase-nucleic acid complexes. Complexes can be separated from free enzyme by using hook molecules to target single stranded regions on the nucleic acid. Hook oligonucleotides are used to capture polymerase nucleic acid complexes where the nucleic acids comprise circular nucleic acids having a double stranded central region with hairpin regions on each end. Methods for loading such complexes onto substrates and for single molecule sequencing of such complexes are also provided.
    Type: Grant
    Filed: January 9, 2014
    Date of Patent: October 25, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Patent number: 9416414
    Abstract: Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.
    Type: Grant
    Filed: October 22, 2014
    Date of Patent: August 16, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Tyson A. Clark, Jonas Korlach, Cheryl Heiner, Kevin Travers, Erik Miller