Ubiome, Inc.

Psomagen, Inc.

Other

Zachary Apte

Jessica Richman

Daniel Almonacid

Siavosh Rezvan Behbahani

Rodrigo Ortiz

Eduardo Morales

Catalina Valdivia

Paz Tapia

Inti Pedroso

Sara W Bird

Victoria Dumas

Audrey Goddard

Francisco J Ossandon

Juan Ugalde

Ingrid Araya

Valeria Marquez

Laurens Kraal

Javier Gimpel

Melissa Alegria

Nathan Saichek

Elisabeth Bik

Luis Fernando Gomez

Paulo Covarrubias

Nicolas Ordenes-Aenishanslins

Ignacio Varas

Sarah L Gupta

Patricia Vera-Wolf

Pamela A Nieto

Kira Harman

Donna Marie B Hongo

Mario Saavedra

Victor Alegria-Mera

Juan Jimenez

Amanda Morton

Janyra Espinoza

Ricardo Castro

Kwasi Addae

Pamela Nieto

Nicolas Ordenes

Camila F Navas

Katia Soto-Liebe

Luis Leon

Nathaniel A Walton

Patricio Lagos

Juan P Bustamante

Constance Norris

Felipe Melis-Arcos

Graham Gass

Juan A Ugalde

Juan Pablo Cardenas

Cristian Bravo

Harold Nunez

Eduardo H Morales

Luis E Leon

Juan P Cardenas

Eduardo Olivares

Janet Torres

Natalia Scioscia

Felipe Sepulveda

Felipe Melis

A system and method for sample droplet processing, the system including a substrate, an electrode array network coupled to the substrate and configured to provide a pattern of controlled electric fields for manipulation of the set of sample droplets; a first layer in communication with the electrode array network, the first layer separating the electrode array network from fluid of the set of sample droplets; and a second layer opposing the first layer and displaced from the first layer to define a region wherein droplets of the set of sample droplets can reside. In some variations, the system can additionally include an electronics subsystem coupled to at least one of the substrate and the electrode array network, and a control module in communication with the electronics subsystem, wherein the control module generates and manipulates the pattern of controlled electric fields.

Manipulation of sample droplets with an electrode system

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.

Method and system for microbiome-derived diagnostics and therapeutics for bacterial vaginosis

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.

Single molecule sequencing and unique molecular identifiers to characterize nucleic acid sequences

Therapeutic compositions and an associated method for improving a Toll-like receptor (TLR)-related condition, including determining a set of peptide sequences associated with a microorganism-related modulator of a TLR, determining a first set of binding parameters for the set of peptide sequences in relation to the TLR, selecting a target subset of peptide sequences from the set of peptide sequences based on the first set of binding parameters, reengineering the target subset of peptide sequences based on mutating amino acid residues of the target subset of peptide sequences, determining a second set of binding parameters for the reengineered target subset of peptide sequences in relation to the TLR, and identifying a first peptide for use in a therapeutic composition for improving the TLR-related condition, based on the second set of binding parameters for the reengineered target subset of peptide sequences.

Therapeutic and diagnostics compositions targeting toll-like receptors and methods thereof

Embodiments of a system and method for characterizing a panel of conditions associated with a set of taxa related to microorganisms can include a taxonomic database including reference microbiome features for the set of taxa associated with the panel of conditions; a handling operable to collect a container including biological material from a user, the handling system comprising a sequencer system operable to determine a microorganism sequence dataset; and a panel characterization system operable to: determine user microbiome features for the set of taxa for the user based on the microorganism sequence dataset, generate a comparison between the user microbiome features and the reference microbiome features, and determine a panel characterization for the panel of conditions for the user based on the comparison; and a treatment system operable to promote a therapy for a condition of the panel of conditions based on the panel characterization.

Method and system for panel characterizations

Methods, compositions, and systems are provided for detecting one or more effects of antibiotic usage for an infectious disease or other health condition on the microbiome of an individual, monitoring such effects, and/or determining, displaying, or promoting a therapy for such an effect. 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 for antibiotic usage.

Method and system for microbiome-derived diagnostics and therapeutics infectious disease and other health conditions associated with antibiotic usage

Embodiments of the system and/or method can include and/or apply a magnetic device for facilitating a magnetic field for isolating the nucleic acid material from a sample, the magnetic device including a support component; and a set of magnetic pins attached to the support component and movable with at least three degrees of freedom when attached to the support component, where the set of magnetic pins provide adaptability to shapes of sample compartments of a sample container.

Method and system for high-throughput particle handling by use of magnetic fields and device

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.

Microorganism-related significance index metrics

Embodiments of a method and system for improved microbiome sequencing can include: generating guide RNA complexes for a set of targets corresponding to a set of taxa associated with the microorganism-related condition; processing the biological sample with the gRNA complexes to generate microorganism nucleic acid fragments comprising a set of end regions associated with the set of targets; ligating the set of end regions with a set of adapters sharing an adapter sequence; and amplifying the set of targets based on the ligated set of end regions and a set of primers sharing a primer sequence associated with the adapter sequence.

Method and system for CRISPR-based library preparation and sequencing

Embodiments of a method and/or system can include administering, to a patient with one or more conditions associated with at least one of TMA, TMAO, and/or derivatives thereof, a therapeutically effective amount of a compound for affecting inhibiting one or more CutC enzymes and/or CntA enzymes associated with microorganisms from at least one taxon from a set of microorganism taxa.

Targeted drugs associated with trimethylamine and/or trimeihylamine-n-oxide

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.

Method and system for characterization for female reproductive system-related conditions associated with microorganisms

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.

Method and system for microbiome-derived diagnostics and therapeutics for endocrine system conditions

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.

Method and system for microbiome-derived diagnostics and therapeutics

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.

Method and system for microbiome-derived diagnostics and therapeutics for locomotor system conditions

Growing community of inventors

San Francisco, CA, United States of America

Zachary Apte