Patents by Inventor Stephen R. Quake

Stephen R. Quake 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: 10016132
    Abstract: Glaucoma is the second most common cause of blindness in the global world. It is a multifactorial disease with several risk factors, of which intraocular pressure (IOP) is the most important. IOP measurements are used for glaucoma diagnosis and patient monitoring. IOP has wide diurnal fluctuation, and is dependent on body posture, so the occasional measurements done by the eye care expert in clinic can be misleading. We provide an implantable sensor, based on microfluidic principles, which in one example has 1 mmHg limit of detection, high sensitivity and excellent reproducibility. This sensor has an optical interface, which enables IOP to be read with, for example, a cell phone camera. The design, fabrication, along with the option of self-monitoring are promising steps toward better patient care and treatment for this devastating disease.
    Type: Grant
    Filed: February 28, 2014
    Date of Patent: July 10, 2018
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Yosef Mandel, Ismail E Araci, Stephen R Quake
  • Publication number: 20180171401
    Abstract: The invention generally relates to methods for obtaining a sequence, such as a consensus sequence or a haplotype sequence. In certain embodiments, methods of the invention involve determining an amount of amplifiable nucleic acid present in a sample, partitioning the nucleic acid based upon results of the determining step such that each partitioned portion includes, on average, a subset of unique sequences, sequencing the nucleic acid to obtain sequence reads, and assembling a consensus sequence from the reads.
    Type: Application
    Filed: July 31, 2017
    Publication date: June 21, 2018
    Inventors: Dmitry Pushkarev, Stephen R. Quake, Ayelet Voskoboynik, Michael Kertesz
  • Publication number: 20180127827
    Abstract: High-throughput long read sequencing is used to perform immunogenomic characterization of expressed antibody repertoires in the context of vaccination. Informatic analysis allows global characterizations of isotype distributions, determination of the lineage structure of the repertoire and measure age and antigen related mutational activity. Global analysis of the immune system's clonal structure provides direct insight into the effects of vaccination and provides a detailed molecular portrait of age-related effects.
    Type: Application
    Filed: December 20, 2017
    Publication date: May 10, 2018
    Inventors: Stephen R. Quake, Joshua Weinstein, Ning Jiang, Daniel S. Fisher
  • Patent number: 9944982
    Abstract: Surface chemistries for the visualization of labeled single molecules (analytes) with improved signal-to-noise properties are provided. To be observed, analyte molecules are bound to surface attachment features that are spaced apart on the surface such that when the analytes are labeled adjacent analytes are optically resolvable from each other. One way to express this concept is that binding elements should be spaced apart such that the Guassian point spread functions of adjacent labels do not overlap. Another way of expressing this concept is that the surface binding elements should be spaced apart by a distance equal to at least the diffraction limit for an optical label attached to the bound analytes.
    Type: Grant
    Filed: November 27, 2013
    Date of Patent: April 17, 2018
    Assignees: STANFORD UNIVERSITY, UNIVERSITY OF CHICAGO, CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Jerrod Schwartz, Stephen R. Quake, Milan Mrksich
  • Publication number: 20180094294
    Abstract: This invention provides microfabricated devices and methods for detecting, analyzing and sorting biological materials and particles. Droplets containing the particles are provided in an extrusion fluid, passed through a detection region, and then directed into a branch channel according to predetermined characteristics. For example, cells or viral particles contained in droplets of aqueous solvent are flowed past a detector in the nonpolar extrusion fluid decane, and routed into a selected branch channel for subsequent analysis or use.
    Type: Application
    Filed: July 14, 2017
    Publication date: April 5, 2018
    Inventors: Stephen R. Quake, Todd Thorsen
  • Patent number: 9932687
    Abstract: High throughput screening of crystallization of a target material is accomplished by simultaneously introducing a solution of the target material into a plurality of chambers of a microfabricated fluidic device. The microfabricated fluidic device is then manipulated to vary the solution condition in the chambers, thereby simultaneously providing a large number of crystallization environments. Control over changed solution conditions may result from a variety of techniques, including but not limited to metering volumes of crystallizing agent into the chamber by volume exclusion, by entrapment of volumes of crystallizing agent determined by the dimensions of the microfabricated structure, or by cross-channel injection of sample and crystallizing agent into an array of junctions defined by intersecting orthogonal flow channels.
    Type: Grant
    Filed: October 9, 2015
    Date of Patent: April 3, 2018
    Assignee: California Institute of Technology
    Inventors: Carl L. Hansen, Stephen R. Quake
  • Patent number: 9909180
    Abstract: High-throughput long read sequencing is used to perform immunogenomic characterization of expressed antibody repertoires in the context of vaccination. Informatic analysis allows global characterizations of isotype distributions, determination of the lineage structure of the repertoire and measure age and antigen related mutational activity. Global analysis of the immune system's clonal structure provides direct insight into the effects of vaccination and provides a detailed molecular portrait of age-related effects.
    Type: Grant
    Filed: February 4, 2014
    Date of Patent: March 6, 2018
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen R. Quake, Joshua Weinstein, Ning Jiang, Daniel S. Fisher
  • Publication number: 20180030514
    Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.
    Type: Application
    Filed: October 19, 2017
    Publication date: February 1, 2018
    Inventors: Stephen R. Quake, Thomas M. Snyder, Hannah Valantine
  • Patent number: 9850483
    Abstract: Methods are provided for diagnosis and prognosis of disease by analyzing expression of a set of genes obtained from single cell analysis. Classification allows optimization of treatment, and determination of whether on whether to proceed with a specific therapy, and how to optimize dose, choice of treatment, and the like. Single cell analysis also provides for the identification and development of therapies which target mutations and/or pathways in disease-state cells.
    Type: Grant
    Filed: July 19, 2011
    Date of Patent: December 26, 2017
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Michael F. Clarke, Stephen R. Quake, Piero D. Dalerba, Huiping Liu, Anne A. Leyrat, Tomer Kalisky, Maximilian Diehn, Michael Rothenberg, Jianbin Wang, Neethan Lobo
  • Patent number: 9845497
    Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.
    Type: Grant
    Filed: February 24, 2014
    Date of Patent: December 19, 2017
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen R. Quake, Thomas M. Snyder, Hannah Valantine
  • Publication number: 20170321821
    Abstract: A fluid valve is provided that includes a first planar substrate having a smooth surface or a surface with features, an elastomer disposed on the first substrate, a second planar substrate disposed on another side of the elastomer, where the second substrate has a smooth surface or features, where the first and second substrate are more rigid than the elastomer, where the first substrate, the second substrate or the elastomer has a fluid channel, where the channel is open when the first or second substrate are in a first thermal state or a first compression state, where the channel is closed or partially closed when the first or second substrate are in a second thermal state or a second compression state, where the second thermal state is a different temperature than the first thermal state, where the second compression state is a different pressure than the first compression state.
    Type: Application
    Filed: May 8, 2017
    Publication date: November 9, 2017
    Inventors: Nate Cira, Stephen R. Quake, Michael Robles, Jason Khoo
  • Publication number: 20170298422
    Abstract: Provided herein is a method for analyzing genomic DNA. In some embodiments, the method may comprise labeling a genomic sample by adding a capture tag to the ends of the DNA molecules in the sample and labeling molecules that comprise hydroxymethylcytosine with a first fluorophore, immobilizing the labeled DNA molecules on a support, and imaging individual molecules of hydroxymethylated genomic DNA on the support.
    Type: Application
    Filed: March 27, 2017
    Publication date: October 19, 2017
    Inventors: Chunxiao Song, Stephen R. Quake, Axel Brunger, Jiajie Diao
  • Publication number: 20170247690
    Abstract: Compositions and methods for treating infection-associated cancer include the use of a nuclease that cuts nucleic acid of an oncovirus in combination with an adjunct chemotherapeutic that treats cancerous cells. For example, a Cas9 endonuclease and a guide RNA that matches a target in a viral genome without having any corresponding match in the human genome can be delivered along with an anti-apoptotic inhibitor.
    Type: Application
    Filed: February 24, 2017
    Publication date: August 31, 2017
    Inventors: Stephen R. Quake, Derek D. Sloan
  • Publication number: 20170247703
    Abstract: Methods and compositions treat a viral infection use a nuclease and an inhibitor that prevents DNA repair, such as a CRISPR-associated nuclease and a small molecule that inhibits an enzyme of a repair pathway. Under guidance of a targeting sequence, the nuclease cuts viral nucleic acid without cutting the patient's genome. The cut ends of the viral nucleic acid are not repaired because the inhibitor prevents a repair mechanism.
    Type: Application
    Filed: February 24, 2017
    Publication date: August 31, 2017
    Inventors: Derek D. Sloan, Xin Cindy Xiong, Stephen R. Quake
  • Publication number: 20170246261
    Abstract: Compositions and methods are disclosed for reducing toxicity and immunogenicity of nucleases, especially when in use for cutting viral nucleic acids in host cells. Different nucleases that cut the same target are delivered at different times to avoid an immune response that interferes with a therapeutic effect of the nucleases.
    Type: Application
    Filed: February 24, 2017
    Publication date: August 31, 2017
    Inventors: Ed Mocarski, Stephen R. Quake, Xin Cindy Xiong
  • Publication number: 20170246260
    Abstract: A modified programmable nuclease provided as an antiviral therapeutic includes a programmable nuclease such as an RNA-guided nuclease, a DNA-guided nuclease, or a protein-guided nuclease linked to a secondary moiety to improve uptake, half-life, efficacy, or other properties. The nuclease is programmed to cleave viral genetic material in an infected patient.
    Type: Application
    Filed: July 7, 2016
    Publication date: August 31, 2017
    Inventors: Derek Sloan, Stephen R. Quake
  • Patent number: 9725765
    Abstract: The invention generally relates to methods for obtaining a sequence, such as a consensus sequence or a haplotype sequence. In certain embodiments, methods of the invention involve determining an amount of amplifiable nucleic acid present in a sample, partitioning the nucleic acid based upon results of the determining step such that each partitioned portion includes, on average, a subset of unique sequences, sequencing the nucleic acid to obtain sequence reads, and assembling a consensus sequence from the reads.
    Type: Grant
    Filed: September 10, 2012
    Date of Patent: August 8, 2017
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Dmitry Pushkarev, Stephen R. Quake, Ayelet Voskoboynik, Michael Kertesz
  • Patent number: 9719140
    Abstract: Methods and materials for detection of aneuploidy and other chromosomal abnormalities using fetal tissue are disclosed. Results can be obtained rapidly, without cell culture. The method uses digital PCR for amplification and detection of single target sequences, allowing an accurate count of a specific chromosome or chromosomal region. Specific polynucleic acid primers and probes are disclosed for chromosomes 1, 13, 18, 21, X and Y. These polynucleic acid sequences are chosen to be essentially invariant between individuals, so the test is not dependent on sequence differences between fetus and mother.
    Type: Grant
    Filed: November 4, 2013
    Date of Patent: August 1, 2017
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Hei-Mun Christina Fan, Stephen R. Quake
  • Patent number: 9714443
    Abstract: High-density microfluidic chips contain plumbing networks with thousands of micromechanical valves and hundreds of individually addressable chambers. These fluidic devices are analogous to electronic integrated circuits fabricated using large scale integration (LSI). A component of these networks is the fluidic multiplexor, which is a combinatorial array of binary valve patterns that exponentially increases the processing power of a network by allowing complex fluid manipulations with a minimal number of inputs. These integrated microfluidic networks can be used to construct a variety of highly complex microfluidic devices, for example the microfluidic analog of a comparator array, and a microfluidic memory storage device resembling electronic random access memories.
    Type: Grant
    Filed: November 16, 2012
    Date of Patent: July 25, 2017
    Assignee: California Institute of Technology
    Inventors: Sebastian J. Maerkl, Todd A. Thorsen, Xiaoyan Bao, Stephen R. Quake, Vincent Studer
  • Publication number: 20170182190
    Abstract: Viral infection is a persistent cause of human disease. Guided nuclease systems of the invention target the genomes of viral infections, rendering the viruses incapacitated. The invention further provides delivery methods and compositions for antiviral therapeutics. Methods and compositions are provided for targeted delivery of antiviral therapeutics into cells of interest using, for example, viral vectors such as adenovirus, AAV, and replication incompetent HSV. These and other delivery systems can be used as vehicles to deliver DNA vectors encoding a nuclease or a cell-killing gene. These delivery methods can also be used to deliver naked DNA or RNA, protein products, plasmids containing a promoter that is active only in a latent viral state which drives a cell-killing gene, or other therapeutic agents.
    Type: Application
    Filed: November 28, 2016
    Publication date: June 29, 2017
    Applicant: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen R. Quake, Jianbin Wang