Patents Examined by G. Steven Vanni
  • Patent number: 11053493
    Abstract: Systems and methods for isolating DNA molecules that can include the steps of: providing a transposon mutant collection, the transposon mutant collection being stored in a plurality of wells; dispatching aliquots from each well in the transposon mutant collection to a set of pools in a combinatorial pooling array that uses pool address coordinates, the aliquots being dispatched to the set of pools based on a location of the aliquots within the transposon mutant collection; constructing an amplicon library, the amplicon library including a sequencing dataset; parsing the sequencing dataset to a set of putative transposon insertion locations and pool address coordinates; calculating a likelihood for each location and pool address coordinates within the set of putative transposon insertion locations and pool address coordinates using a Bayesian inference algorithm informed by internal self-consistency; and generating a progenitor collection catalog based on location and pool address coordinates verified in the c
    Type: Grant
    Filed: May 5, 2017
    Date of Patent: July 6, 2021
    Inventors: Buz Barstow, Michael Baym, Lev Shaket, Isao Anzai, Oluwakemi Adesina
  • Patent number: 11053550
    Abstract: Methods for generating a prognostic and/or subtype signature for a subject with pancreatic ductal adenocarcinoma (PDAC) are provided. In some embodiments, the methods include determining expression levels for one or more genes listed in Tables 2-5, 9, 10, or 11, and/or the DE-S and/or DE-T subset of genes in PDAC cells obtained from the subject, wherein the determining provides a prognostic and/or subtype signature for the subject. Also provided are methods for classifying a subject diagnosed with pancreatic ductal adenocarcinoma (PDAC) as having an activated stroma subtype or a normal stroma subtype of PDAC and/or a basal subtype or a classical subtype of PDAC; and methods for identifying a differential treatment strategy for a subject diagnosed with pancreatic ductal adenocarcinoma (PDAC).
    Type: Grant
    Filed: October 14, 2015
    Date of Patent: July 6, 2021
    Assignee: The University of North Carolina at Chapel Hill
    Inventors: Richard Moffitt, Jen Jen Yeh, Naim Ur Rashid
  • Patent number: 11056213
    Abstract: A method of identifying regions of malicious organic sequences includes identifying a plurality of benign snippets derived from a first sequence obtained from at least one benign organism; extracting a plurality of candidate signature snippets from a second sequence obtained from a malicious organism; determining, for each of the plurality of candidate signature snippets, whether the candidate signature snippet matches at least one of the plurality of benign snippets; and responsive to the candidate signature snippet not matching the at least one of the plurality of benign snippets, identifying the candidate signature snippet as a malicious signature snippet.
    Type: Grant
    Filed: December 7, 2016
    Date of Patent: July 6, 2021
    Assignee: Raytheon BBN Technologies Corp.
    Inventors: Jacob Stuart Michael Beal, Daniel Wyschogrod, Steven Wayne Jilcott, Jr.
  • Patent number: 11056214
    Abstract: The present invention relates to methods and systems for the analysis of nucleic acids present in biological samples, and more specifically, relates to clustering melt curves derived from high resolution thermal melt analysis performed on a sample of nucleic acids, the resulting clusters being usable, in one embodiment, for analyzing the sequences of nucleic acids and to classify their genotypes that are useful for determining the identity of the genotype of a nucleic acid that is present in a biological sample.
    Type: Grant
    Filed: June 23, 2017
    Date of Patent: July 6, 2021
    Assignee: Canon U.S.A., Inc.
    Inventors: Yang Yang, Bradley Scott Denney, Attaullah Seikh
  • Patent number: 11041158
    Abstract: Methods for making a synthetic gene are provided. The methods find use in optimizing a candidate gene nucleic acid sequence for expression in a selected target expression system. The method identifies stable or retained sequences in the candidate gene nucleic acid sequence, identifies disallowed sequences, develops a statistical model based on a whole genome, a partial genome, or transcriptome sequences of the target expression system, generates an optimized candidate gene nucleic acid sequence for use in the target expression system, and makes a synthetic gene comprising the optimized candidate gene nucleic acid sequence. The method allows for optimization of the candidate gene nucleic acid sequence without removing certain stable or retained sequences. Rather, the activity of these sites is positionally modulated or inactivated through upstream and downstream modifications of codons and/or sequence patterns.
    Type: Grant
    Filed: December 21, 2015
    Date of Patent: June 22, 2021
    Assignee: AgBiome, Inc.
    Inventor: James R. Henriksen
  • Patent number: 11031100
    Abstract: A classification of a level of cancer in an organism is determined by analyzing a biological sample of the organism. The biological sample comprises clinically-relevant DNA and other DNA. At least some of the DNA is cell-free in the biological sample. An amount of a first set of DNA fragments from the biological sample corresponding to each of a plurality of sizes is measured. A first value of a first parameter is calculated based on the amounts of DNA fragments at the plurality of sizes. The first value is compared to a reference value. A classification of a level of cancer in the organism is determined based on the comparison.
    Type: Grant
    Filed: June 26, 2020
    Date of Patent: June 8, 2021
    Assignee: The Chinese University of Hong Kong
    Inventors: Yuk Ming Dennis Lo, Wai Kwun Rossa Chiu, Kwan Chee Chan, Wenli Zheng, Peiyong Jiang, Jiawei Liao
  • Patent number: 11017880
    Abstract: Disclosed in some examples are methods including selecting a first plurality of single gene mutants from a pool of possible single gene mutants of an organism. The first plurality of single gene mutants is less than a number of possible single mutants. A computer processor is used to iteratively select a second plurality of single gene mutants by selecting single gene mutants from the pool of possible single gene mutants that increases a sum of products of similarities between the first plurality of single gene mutants and corresponding functional relationships. The second plurality of single gene mutants is larger in number than the first plurality of single gene mutants, and wherein the second plurality of single gene mutants is less than the number of possible single gene mutants of the organism. A set of genes is outputted comprising the first and second pluralities of single gene mutants.
    Type: Grant
    Filed: March 31, 2017
    Date of Patent: May 25, 2021
    Assignee: Regents of the University of Minnesota
    Inventors: Raamesh Deshpande, Justin Nelson, Chad L. Myers, Scott William Simpkins
  • Patent number: 11006878
    Abstract: Brain activity of a user is detected, and a mental state of the user is determined. In one technique, life/work context is automatically presented to the user in a manner that modulates the mental state of the user. In another technique, an entertainment selection is presented to the user, and an entertainment selection list is automatically modified in response to the determined mental state of the user. In still another technique, the mental state that is determined is a negative emotional state, and life/work context is automatically presented to the user in a manner that promotes a cognitive state of the user in response to the determined emotional state of the user. In yet another technique, the wellness of the user is automatically tracked over a time period based on the determined mental state.
    Type: Grant
    Filed: March 31, 2020
    Date of Patent: May 18, 2021
    Assignee: HI LLC
    Inventors: Bryan Johnson, Husam Katnani, Antonio H. Lara
  • Patent number: 11006873
    Abstract: To reduce errors in determining a degree of arousal due to variations in blinking among an individual or between individuals. To execute the steps of: acquiring first biological information related to an ocular potential of a user from a processing device worn by the user; and calculating a degree of arousal of the user based on a distance between a projection axis parallel to an equal degree of arousal line and a point where the first biological information is plotted in a coordinate space where a height and width are the axes for an ocular potential peak.
    Type: Grant
    Filed: January 30, 2018
    Date of Patent: May 18, 2021
    Assignee: JINS HOLDINGS Inc.
    Inventor: Taiki Komoda
  • Patent number: 11008623
    Abstract: The invention provides a method for determining the level of risk for development or progression of a hematologic neoplasia in a subject by analyzing the level of a phosphatidylinositol glycan anchor biosynthesis protein, and providing an appropriate treatment or preventive measure, on the basis of this risk.
    Type: Grant
    Filed: February 16, 2017
    Date of Patent: May 18, 2021
    Assignee: THE PENN STATE RESEARCH FOUNDATION
    Inventor: Jeffrey Pu
  • Patent number: 11001900
    Abstract: Embodiments of a method and/or system for characterizing one or more female reproductive system-related conditions can include determining a microorganism dataset associated with a set of subjects; and/or performing a characterization process associated with the one or more female reproductive system-related conditions, based on the microorganism dataset, where performing the characterization process can additionally or alternatively include performing a female reproductive system-related characterization process for the one or more female reproductive system-related conditions, and/or determining one or more therapies.
    Type: Grant
    Filed: August 28, 2018
    Date of Patent: May 11, 2021
    Assignee: PSOMAGEN, INC.
    Inventors: Zachary Apte, Elisabeth Bik, Sara W. Bird, Luis E. Leon, Pamela A. Nieto, Victor Alegria-Mera, Cristian Bravo, Juan P. Cardenas, Paulo Covarrubias, Sarah L. Gupta, Kira Harman, Juan Jimenez, Felipe Melis-Arcos, Camila F. Navas, Harold Nunez, Eduardo Olivares, Nicolas Ordenes-Aenishanslins, Francisco J. Ossandon, Ignacio Varas, Patricia Vera-Wolf, Donna Marie B. Hongo, Laurens Kraal, Nathaniel A. Walton, Amanda Morton, Juan P. Bustamante, Kwasi Addae, Graham Gass, Katia Soto-Liebe, Juan A. Ugalde, Eduardo H. Morales, Daniel Almonacid, Jessica Richman
  • Patent number: 11004542
    Abstract: Techniques for generating therapy biomarker scores and visualizing same. The techniques include determining, using a patient's sequence data and distributions of biomarker values across one or more reference populations, a first set of normalized scores for a first set of biomarkers associated with a first therapy, and a second set of normalized scores for a second set of biomarkers associated with a second therapy, generating a graphical user interface (GUI) including a first portion associated with the first therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the first set of normalized scores; and a second portion associated with a second therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the second set of normalized scores; and displaying the generated GUI.
    Type: Grant
    Filed: April 23, 2020
    Date of Patent: May 11, 2021
    Assignee: BostonGene Corporation
    Inventors: Alexander Bagaev, Feliks Frenkel, Ravshan Ataullakhanov
  • Patent number: 10996214
    Abstract: Methods and systems for use in sperm analysis are described. A method for processing measured data comprising at least interferometric phase data of label-free sperm cell(s), the processing comprising determining topographic optical phase delay map of the label-free sperm, determining at least one physical parameter of the label-free sperm, and generating data indicative of sperm quality for the label-free sperm. A device comprising a flow channel comprising an inlet for receiving fluid containing cells, a selection zone and at least two outlets at said selection zone; and a flow-driving mechanism comprising a flow-driving unit configured and operable to generate flow of said fluid from said inlet towards at least first of said at least two outlets, and a collecting driving unit selectively operating along the direction of a second outlet of said at least two outlets to direct a portion of interest of said fluid towards said second outlet.
    Type: Grant
    Filed: January 31, 2017
    Date of Patent: May 4, 2021
    Assignee: TECHNOLOGY INNOVATION MOMENTUM FUND (ISRAEL) LIMITED PARTNERSHIP
    Inventors: Natan Tzvi Shaked, Pinhas Girshovitz, Itay Barnea, Michal Balberg, Simcha Mirsky, Pinkie Jacob Eravuchira
  • Patent number: 10991453
    Abstract: Disclosed are new and improved methods and systems for nucleic acid sequence analysis that can analyze data indicative of natural by-products of nucleotide incorporation events without the need for exogenous labels or dyes to identify nucleic acid sequences of interest. In particular, the methods and systems of the present teachings can process such data and various forms thereof to align fragments of the nucleic acid(s) of interest, particularly those analyzed using an addition sequencing technique, for example, as occurs with the use of nucleotide flows.
    Type: Grant
    Filed: November 15, 2017
    Date of Patent: April 27, 2021
    Assignee: Life Technologies Corporation
    Inventor: Nils Homer
  • Patent number: 10982286
    Abstract: The present invention relates to methods of using cell-free DNA analysis for guiding treatment of advanced prostate cancer. In particular, liquid biopsies are collected from urine and/or plasma of patients for measuring copy number variation in cell-free DNA associated with metastatic prostate cancer. In particular, urine genomic abnormality (UGA) and plasma genomic abnormality (PGA) values are contemplated for use in predicting treatment responses in advanced prostate cancer patients and for use in making decisions related to androgen deprivation therapy (ADT) treatment outcomes in hormone sensitive stage and for starting or changing chemotherapy treatments in castrate resistant advanced cancer stage.
    Type: Grant
    Filed: January 20, 2017
    Date of Patent: April 20, 2021
    Assignees: Mayo Foundation for Medical Education and Research, The Medical College of Wisconsin, Inc., UWM Research Foundation, Inc.
    Inventors: Manish Kohli, Liang Wang, Chiang-Ching Huang
  • Patent number: 10976324
    Abstract: The application relates to hepatic fibrosis, specifically to hepatic fibrosis that may appear in a patient infected with one or more hepatitis viruses and/or who is suffering from hepatitis, specifically chronic hepatitis. The application provides methods and means for determining the stage (or degree) of hepatic fibrosis of such a patient. Specifically, the methods and means of the application make it possible to determine whether or not the stage (or degree) of hepatic fibrosis of the patient has exceeded the stage of light fibrosis. The methods and means of the invention use a combination of biomarkers such as, in particular, the CXCL10 protein and hyaluronic acid (HA).
    Type: Grant
    Filed: June 9, 2015
    Date of Patent: April 13, 2021
    Inventors: Nadine Lambert, Benedicte Watelet, Isabelle Catherine Batxelli, Tarik Asselah
  • Patent number: 10966689
    Abstract: Disclosed is a method for predicting an in vivo concentration of an analyte, including: estimating an in vivo intrinsic spectrum of the analyte; and predicting the in vivo concentration of the analyte by using a concentration predicting algorithm based on the estimated in vivo intrinsic spectrum and an in vivo spectrum obtained during a section in which the in vivo concentration of the analyte is not substantially changed.
    Type: Grant
    Filed: May 9, 2017
    Date of Patent: April 6, 2021
    Assignee: SAMSUNG ELECTRONICS CO., LTD.
    Inventors: Seonmyeong Choi, Woochang Lee, June Young Lee
  • Patent number: 10966651
    Abstract: An information processing method is executed by a computer having a control unit, wherein the control unit executes: acquiring a plurality of biological signals; detecting for each predetermined time unit a peak part of the respective biological signals; attaching identical identification information to one or a plurality of peak parts forming an identical peak when attaching peak identification information to each of the biological signals; and extracting a combination of corresponding peaks from at least two biological signals on the basis of the identification information of each time unit of the at least two biological signals.
    Type: Grant
    Filed: November 12, 2015
    Date of Patent: April 6, 2021
    Assignee: JINS HOLDINGS Inc.
    Inventor: Taiki Komoda
  • Patent number: 10963601
    Abstract: A system and method for molecular design and simulation is disclosed. In one aspect, a system for simulating a molecular structure includes a processor configured to simulate the molecular structure, a head-mounted display (HMD) configured to display the molecular structure, and at least one handheld input device. The input device may be configured to: receive input from a user, the input being indicative of movement of the handheld input device in 6 degrees-of-freedom (DoF), and selectively map, based on additional user input and at least one property of the molecular structure, one of the DoF to one of a plurality of defined techniques for altering the molecular structure. The processor may be configured to modify the molecular structure based on the received input as mapped to the selected defined technique.
    Type: Grant
    Filed: May 24, 2017
    Date of Patent: March 30, 2021
    Assignees: Nanome, Inc., The Regents of the University of California
    Inventors: Steven Robert McCloskey, Taylor Philip Horwood, Keita William Funakawa, Benjamin Hugh Bratton
  • Patent number: 10962548
    Abstract: A method determines an amino acid sequence that binds to a target molecule or a base sequence encoding the same. The method pans for bringing a library constructed by a display method, followed by incubation. The method sequences for analyzing a base sequence before panning step and the polypeptide group of the library after panning by a next-generation sequencer, or determining an amino acid sequence based on a base sequence obtained by analyzing the base sequence of a nucleic acid encoding all the polypeptides by a next-generation sequencer. The method scores for evaluating and scoring, based on the results of the sequencing step, an amplification ratio. The method determines a sequence for selecting a polypeptide with a high score and determines an amino acid sequence of the polypeptide or a base sequence as an amino acid sequence that binds to the target molecule or as a base sequence of a nucleic acid encoding the polypeptide.
    Type: Grant
    Filed: November 21, 2014
    Date of Patent: March 30, 2021
    Assignee: MOLCURE, INC.
    Inventor: Ryu Ogawa