Patents by Inventor Zachary Apte

Zachary Apte 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: 10787714
    Abstract: A method for at least one of characterizing, diagnosing, and treating a condition associated with microbiome functional features in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.
    Type: Grant
    Filed: August 17, 2017
    Date of Patent: September 29, 2020
    Assignee: PSOMAGEN, INC.
    Inventors: Zachary Apte, Daniel Almonacid, Jessica Richman
  • Patent number: 10786195
    Abstract: A method for at least one of characterizing, diagnosing, and treating a condition associated with microbiome taxonomic features in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.
    Type: Grant
    Filed: August 17, 2017
    Date of Patent: September 29, 2020
    Assignee: Psomagen, Inc.
    Inventors: Zachary Apte, Daniel Almonacid, Jessica Richman
  • Publication number: 20200303070
    Abstract: Embodiments of a method and/or system, such as for improving a microorganism-related characterization process, can include: preparing a set of control samples (e.g., from an individual specimen); determining one or more reference microorganism-related parameters (e.g., cutoff reference ranges of relative abundance for a set of microorganism taxa) based on one or more control samples of the set of control samples; and determining one or more variability parameters for the microorganism-related characterization based on the one or more reference microorganism-related parameters and one or more control sample characterizations for one or more control samples of the set of control samples.
    Type: Application
    Filed: November 6, 2018
    Publication date: September 24, 2020
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid, Patricia Vera, Elisabeth M. Bik, Amanda Morton, Tomas Norambuena, Rodrigo Ortiz
  • Publication number: 20200299763
    Abstract: Embodiments of a method and/or system (e.g., for improved single molecule sequencing, etc.) can include preparing a set of unique molecular identifier (UMI)-based molecules associated with a set of target nucleic acid sequences; facilitating generation of (e.g., generating, etc.) a set of tagged nucleic acid molecules based on the set of UMI-based molecules and a set of nucleic acid molecules corresponding to (e.g., including, etc.) the set of target nucleic acid sequences; and/or facilitating (e.g., performing, etc.) single molecule sequencing with the set of tagged nucleic acid molecules.
    Type: Application
    Filed: October 9, 2018
    Publication date: September 24, 2020
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid, Eduardo Morales, Luis Leon, Sara W. Bird, Juan Ugalde
  • Patent number: 10777320
    Abstract: A method for at least one of characterizing, diagnosing, and treating a mental health associated condition in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the mental health associated condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the mental health associated condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.
    Type: Grant
    Filed: April 13, 2016
    Date of Patent: September 15, 2020
    Assignee: PSOMAGEN, INC.
    Inventors: Zachary Apte, Daniel Almonacid, Jessica Richman, Siavosh Rezvan Behbahani
  • Publication number: 20200286623
    Abstract: Embodiments of a method and/or system, such as for characterizing at least one microorganism-related condition, can include: determining a set of associations (e.g., positive associations such as positive correlations, negative associations such as negative correlations, non-associations such as no correlation or minimal correlation, etc.) between a set of microorganism taxa and at least one microorganism-related condition; determining a set of reference features (e.g., reference abundance ranges, etc.) for the set of microorganism taxa; and determining one or more significance index metrics based on the set of associations and the set of reference features.
    Type: Application
    Filed: September 14, 2018
    Publication date: September 10, 2020
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid, Patricio Lagos, Ricardo Castro, Paz Tapia
  • Patent number: 10755800
    Abstract: A method for at least one of characterizing, diagnosing, and treating an endocrine system condition in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the endocrine system condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the endocrine system condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.
    Type: Grant
    Filed: July 12, 2016
    Date of Patent: August 25, 2020
    Assignee: PSOMAGEN, INC.
    Inventors: Zachary Apte, Daniel Almonacid, Jessica Richman, Siavosh Rezvan Behbahani
  • Publication number: 20200263171
    Abstract: Embodiments of a method and/or system, such as for preparation of a normalized library for sequencing such as next-generation sequencing, can include one or more of: generating one or more normalized amplicon libraries; generating one or more normalized microbial community-associated libraries; and/or generating one or more normalized combined sequence libraries associated with amplicon-associated sequencing and microbial community-associated sequencing.
    Type: Application
    Filed: September 7, 2018
    Publication date: August 20, 2020
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid, Eduardo Morales, Rodrigo Ortiz, Nicolas Ordenes, Juan Jimenez, Cristian Bravo, Natalia Scioscia, Eduardo Olivares, Luis Leon, Paulo Covarrubias, Felipe Sepulveda, Felipe Melis
  • Publication number: 20200202979
    Abstract: Embodiments of a method and/or system (e.g., for nasal-related characterization) can include determining a microorganism dataset associated with a set of subjects; and/or performing a characterization process based on the microorganism dataset, where performing the characterization process can additionally or alternatively include performing a nasal-related characterization process, and/or determining one or more therapies, such as for one or more nasal-related conditions.
    Type: Application
    Filed: September 6, 2018
    Publication date: June 25, 2020
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid, Juan Ugalde, Patricia Vera-Wolf, Sandro Valenzuela
  • Publication number: 20200123539
    Abstract: Embodiments of a method 100 and/or system 200 or library preparation for sequencing associated with microorganisms can include: preparing a set of unique molecular identifier (UMI)-based molecules associated with one or more targets; preparing a set of sequencing-based primers; generating a set of tagged target molecules based on the set of UMI-based molecules and one or more samples associated with the one or more targets; and/or generating a set of sequencing-ready tagged target molecules based on the tagged target molecules and the set of sequencing-based primers.
    Type: Application
    Filed: June 20, 2018
    Publication date: April 23, 2020
    Inventors: Zachary APTE, Jessica RICHMAN, Daniel AL-MONACID, Juan JIMINEZ, Rodrigo ORTIZ, Eduardo MORALES, Paulo COVARRUBIAS, Eduardo OLIVARES, Nicolas ORDENES, Luis LEON
  • Publication number: 20190367968
    Abstract: Methods, compositions, and systems are provided for detecting one or more a bacterial vaginosis issues by characterizing the microbiome of an individual, monitoring such effects, and/or determining, displaying, or promoting a therapy for the bacterial vaginosis issue. Methods, compositions, and systems are also provided for generating and comparing microbiome composition and/or functional diversity datasets. Methods, compositions, and systems are also provided for generating a characterization model and/or therapy model for bacterial vaginosis.
    Type: Application
    Filed: September 9, 2016
    Publication date: December 5, 2019
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid, Siavosh Rezvan Behbahani
  • Patent number: 10415105
    Abstract: An embodiment of a method for diagnostic testing includes: providing a sampling kit to a subject, the sampling kit including a sample container for reception of a sample from a collection site of the subject; receiving the sample from the subject; generating a microbiome sequence dataset based upon sequencing nucleic acid content of a microorganism portion of the sample; detecting a presence of a set of microbiome targets; generating a diagnostic analysis based on the detected set of microbiome targets; generating a therapy recommendation based on the set of microbiome targets; and promoting the therapy recommendation in coordination with presenting information derived from the diagnostic analysis.
    Type: Grant
    Filed: June 30, 2016
    Date of Patent: September 17, 2019
    Assignee: uBiome, Inc.
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid
  • Patent number: 10409955
    Abstract: A method for at least one of characterizing, diagnosing, and treating a locomotor system condition in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the locomotor system condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the locomotor system condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.
    Type: Grant
    Filed: April 13, 2016
    Date of Patent: September 10, 2019
    Assignee: uBiome, Inc.
    Inventors: Zachary Apte, Daniel Almonacid, Jessica Richman, Siavosh Rezvan Behbahani
  • Patent number: 10410749
    Abstract: A method for at least one of characterizing, diagnosing, and treating a cutaneous condition in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the cutaneous condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the cutaneous condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.
    Type: Grant
    Filed: April 13, 2016
    Date of Patent: September 10, 2019
    Assignee: uBiome, Inc.
    Inventors: Zachary Apte, Daniel Almonacid, Jessica Richman, Siavosh Rezvan Behbahani
  • Patent number: 10395777
    Abstract: Embodiments of a method and/or system for characterizing one or more sleep-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 sleep-related conditions, based on the microorganism dataset, where performing the characterization process can additionally or alternatively include performing a sleep-related characterization process for the one or more sleep-related conditions, and/or determining one or more therapies S140.
    Type: Grant
    Filed: June 4, 2018
    Date of Patent: August 27, 2019
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid, Inti Pedroso, Catalina Valdivia, Rodrigo Ortiz, Paz Tapia
  • Patent number: 10388407
    Abstract: Embodiments of a method and/or system for characterizing a headache-related condition for a user can include one or more of: generating a microbiome dataset for each of an aggregate set of biological samples associated with a population of subjects, based on sample processing of the biological samples; processing a supplementary dataset associated with one or more headache-related conditions for the set of users; and performing a characterization process for the one or more headache-related conditions, based on the supplementary dataset and microbiome features extracted from the microbiome dataset.
    Type: Grant
    Filed: November 21, 2017
    Date of Patent: August 20, 2019
    Assignee: uBiome, Inc.
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid, Rodrigo Ortiz, Catalina Valdivia, Inti Pedroso, Paz Tapia
  • Patent number: 10383519
    Abstract: A method for at least one of characterizing, diagnosing, and treating a condition associated with microbiome-derived functional features in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.
    Type: Grant
    Filed: November 16, 2017
    Date of Patent: August 20, 2019
    Assignee: uBiome, Inc.
    Inventors: Zachary Apte, Daniel Almonacid, Jessica Richman
  • Patent number: 10381117
    Abstract: A method for at least one of characterizing, diagnosing, and treating a cutaneous condition in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the cutaneous condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the cutaneous condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.
    Type: Grant
    Filed: December 20, 2017
    Date of Patent: August 13, 2019
    Assignee: uBiome, Inc.
    Inventors: Zachary Apte, Daniel Almonacid, Jessica Richman
  • Patent number: 10380325
    Abstract: A method for diagnosing and treating an immune microbial dysfunction in a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the immune microbial dysfunction based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset, wherein the characterization is diagnostic of at least one of Crohn's disease, inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), ulcerative colitis, and celiac disease; based upon the characterization, generating a therapy model configured to correct the immune microbial dysfunction; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.
    Type: Grant
    Filed: May 26, 2017
    Date of Patent: August 13, 2019
    Assignee: uBiome, Inc.
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid
  • Patent number: 10381112
    Abstract: Embodiments of a method and/or system for characterizing an allergy-related condition for a user can include one or more of: generating a microbiome dataset for each of an aggregate set of biological samples associated with a population of subjects, based on sample processing of the biological samples; processing a supplementary dataset associated with one or more allergy-related conditions for the set of users; and performing an allergy-related characterization process for the one or more allergy-related conditions, based on the supplementary dataset and/or microbiome features extracted from the microbiome dataset.
    Type: Grant
    Filed: December 15, 2017
    Date of Patent: August 13, 2019
    Assignee: uBiome, Inc.
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid, Catalina Valdivia, Rodrigo Ortiz, Inti Pedroso, Victoria Dumas, Paz Tapia, Eduardo Morales