Allen Institute, DBA Allen Institute for Brain Science; Allen Institute for Cell Science

United States of America

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C12N 15/86 - Viral vectors 30
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1.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN THE CEREBELLUM AND A SECONDARY CELL TYPE

      
Application Number 18698499
Status Pending
Filing Date 2022-10-05
First Publication Date 2025-07-24
Owner Allen Institute (USA)
Inventor
  • Daigle, Tanya
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui
  • Mich, John K.

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in a cerebellar cell type and a secondary cell type.

IPC Classes  ?

  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • A61K 9/00 - Medicinal preparations characterised by special physical form
  • C12N 5/0797 - Stem cellsProgenitor cells
  • C12N 15/86 - Viral vectors

2.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN EXCITATORY CORTICAL NEURONS

      
Application Number 19007263
Status Pending
Filing Date 2024-12-31
First Publication Date 2025-07-24
Owner Allen Institute (USA)
Inventor
  • Graybuck, Lucas T.
  • Tasic, Bosiljka
  • Daigle, Tanya
  • Ting, Jonathan
  • Zeng, Hongkui
  • Kalmbach, Brian Edward
  • Mich, John K.
  • Hess, Erik
  • Lein, Edward Sebastian
  • Levi, Boaz P.

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in excitatory cortical neurons, such as primarily within cortical layers 2/3, 4, 5, and 6 and including those with extratelencephalic (ET) projections, intratelencephalic (IT) projections, and pyramidal tract (PT) projections, among others.

IPC Classes  ?

3.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN INTERNEURONS

      
Application Number 19007152
Status Pending
Filing Date 2024-12-31
First Publication Date 2025-07-10
Owner
  • Allen Institute (USA)
  • Seattle Children's Hospital d/b/a Seattle Children's Research Institute (USA)
Inventor
  • Ting, Jonathan
  • Levi, Boaz P.
  • Mich, John K.
  • Lein, Edward Sebastian
  • Kalume, Franck

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in GABAergic interneurons.

IPC Classes  ?

  • C12N 15/86 - Viral vectors
  • A01K 67/0278 - Knock-in vertebrates, e.g. humanised vertebrates
  • A61K 35/30 - NervesBrainEyesCorneal cellsCerebrospinal fluidNeuronal stem cellsNeuronal precursor cellsGlial cellsOligodendrocytesSchwann cellsAstrogliaAstrocytesChoroid plexusSpinal cord tissue
  • C12N 5/0793 - Neurons

4.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN SEROTONERGIC NEURONS

      
Application Number US2024061435
Publication Number 2025/137554
Status In Force
Filing Date 2024-12-20
Publication Date 2025-06-26
Owner ALLEN INSTITUTE (USA)
Inventor
  • Ben-Simon, Yoav
  • Opitz-Araya, Ximena
  • Lein, Edward Sebastian
  • Tasic, Bosiljka
  • Thomas, Emma
  • Ting, Jonathan

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in serotonergic neurons within the dorsal raphe nucleus and/or the median raphe nucleus.

IPC Classes  ?

  • C12N 15/67 - General methods for enhancing the expression
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells

5.

SYSTEMS AND METHODS FOR REPRODUCIBILITY VERIFICATION

      
Application Number US2024059360
Publication Number 2025/128556
Status In Force
Filing Date 2024-12-10
Publication Date 2025-06-19
Owner ALLEN INSTITUTE (USA)
Inventor Meijer, Paul

Abstract

A computer implemented method of auditing a data analysis process is provided. The method includes generating a certificate of reproducibility that permits a user or auditor to exactly duplicate the various steps involved in the data analysis process, including data ingestion, data processing, and data output. The certificate of reproducibility may include a directed reproducibility graph of events that contribute to the output. The certificate of reproducibility and directed reproducibility graph may be published.

IPC Classes  ?

  • G06F 16/23 - Updating
  • G06F 21/64 - Protecting data integrity, e.g. using checksums, certificates or signatures
  • G06F 16/90 - Details of database functions independent of the retrieved data types

6.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN DOPAMINERGIC NEURONS

      
Application Number 18841086
Status Pending
Filing Date 2023-02-24
First Publication Date 2025-05-22
Owner Allen Institute (USA)
Inventor
  • Daigle, Tanya
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in dopaminergic neurons of the central nervous system. Wherein, an artificial expression construct comprising (i) an enhancer is eHGT 888m.

IPC Classes  ?

  • C12N 15/86 - Viral vectors
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy

7.

BIOMARKERS TO PREDICT ONSET OF CLINICAL RHEUMATOID ARTHRITIS

      
Application Number US2024055169
Publication Number 2025/101929
Status In Force
Filing Date 2024-11-08
Publication Date 2025-05-15
Owner
  • ALLEN INSTITUTE (USA)
  • THE REGENTS OF THE UNIVERSITY OF COLORADO, A BODY CORPORATE (USA)
  • BOARD OF REGENTS OF THE UNIVERSITY OF NEBRASKA (USA)
  • UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES (USA)
Inventor
  • Gillespie, Mark, Andrew
  • Li, Xiaojun
  • Savage, Adam, Kenneth
  • Zaim, Samir, Rachid
  • Deane, Kevin, Dale
  • Holers, Vernon, Michael
  • Mikuls, Ted, Richard
  • Edison, Jess, David

Abstract

Biomarkers to predict progression from at-risk of developing rheumatoid arthritis (pre-RA) to physician-confirmed rheumatoid arthritis (i.e., Clinical RA) within defined time periods are described. The described biomarkers can be used to identify interventions to prevent, delay, or modulate future Clinical RA and to identify potential stage-specific targets for preventive interventions.

IPC Classes  ?

  • G01N 33/564 - ImmunoassayBiospecific binding assayMaterials therefor for pre-existing immune complex or autoimmune disease
  • G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation

8.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN NEURONS AND ASTROCYTES FOR THE ASSESSMENT AND/OR TREATMENT OF SLC6A1-RELATED DISORDERS

      
Application Number US2024047232
Publication Number 2025/064516
Status In Force
Filing Date 2024-09-18
Publication Date 2025-03-27
Owner ALLEN INSTITUTE (USA)
Inventor
  • Gore, Bryan
  • Guo, Rong
  • Hage, Travis
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Martinez, Refugio
  • Mich, John K.
  • Opitz-Araya, Ximena
  • Ting, Jonathan

Abstract

Artificial expression constructs for modulating gene expression in neurons and astrocytes are described. Particular artificial expression constructs modulate gene expression in pan-brain GABAergic neurons and forebrain GABAergic neurons. The artificial expression constructs can be used in the assessment and/or treatment of SLC6A1-related disorders, such as epilepsy, seizures, autism spectrum disorder, and related disorders.

IPC Classes  ?

  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 15/864 - Parvoviral vectors
  • C12N 5/00 - Undifferentiated human, animal or plant cells, e.g. cell linesTissuesCultivation or maintenance thereofCulture media therefor

9.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN THE BASAL GANGLIA

      
Application Number US2024046735
Publication Number 2025/059552
Status In Force
Filing Date 2024-09-13
Publication Date 2025-03-20
Owner ALLEN INSTITUTE (USA)
Inventor
  • Bakken, Trygve
  • Daigle, Tanya
  • Levi, Boaz P.
  • Tasic, Bosiljka
  • Ting, Jonathan

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in basal ganglia neurons including striatal neurons, globus pallidus neurons, and substantia nigra neurons.

IPC Classes  ?

  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 15/86 - Viral vectors
  • A01K 67/0275 - Genetically modified vertebrates, e.g. transgenic
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C12N 5/00 - Undifferentiated human, animal or plant cells, e.g. cell linesTissuesCultivation or maintenance thereofCulture media therefor

10.

MOLECULAR SIGNATURES FOR CELL TYPING AND MONITORING IMMUNE HEALTH

      
Application Number 18721154
Status Pending
Filing Date 2022-12-19
First Publication Date 2025-02-20
Owner ALLEN INSTITUTE (USA)
Inventor
  • Bumol, Thomas F.
  • Li, Xiao-Jun
  • Savage, Adam
  • Skene, Peter
  • Torgerson, Troy
  • Vasaikar, Suhas

Abstract

Provided herein are methods, devices, and systems comprising identification of a panel of gene markers useful for immune cell typing and identifying, detecting, and/or monitoring disease conditions in a subject in need thereof, including infections, cancer and autoimmune conditions. The methods also provide for assays for determining the levels of said markers prior to and after treatment of a condition in the subject, wherein the condition is impacted by one or more factors including age, occupation or environment of the subject.

IPC Classes  ?

  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
  • C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage
  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

11.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN NEOCORTICAL LAYER 4 OR LAYER 5 INTRATELENCEPHALIC NEURONS

      
Application Number 18717907
Status Pending
Filing Date 2022-12-07
First Publication Date 2025-02-06
Owner Allen Institute (USA)
Inventor
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Ting, Jonathan

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in neocortical layer 4 (L4) intratelencephalic (IT) neurons and/or neocortical L5 IT neurons.

IPC Classes  ?

  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C12N 15/86 - Viral vectors

12.

RESCUING VOLTAGE-GATED SODIUM CHANNEL FUNCTION IN INHIBITORY NEURONS

      
Application Number 18920747
Status Pending
Filing Date 2024-10-18
First Publication Date 2025-02-06
Owner
  • Allen Institute (USA)
  • Seattle Children's Hospital d/b/a Seattle Children's Research Institute (USA)
Inventor
  • Mich, John K.
  • Lein, Edward Sebastian
  • Ting, Jonathan
  • Levi, Boaz P.
  • Hess, Erik
  • Kalume, Franck

Abstract

Selectively providing voltage-gated sodium channel function sufficient to rescue impaired Nav1.1 function to inhibitory neurons is described. Provided voltage-gated sodium channel function sufficient to rescue impaired Nav1.1 function in inhibitory neurons can be used to treat disorders such as epilepsy, and more particularly, Dravet Syndrome.

IPC Classes  ?

  • A61K 38/17 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans
  • A61K 9/00 - Medicinal preparations characterised by special physical form
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C07K 14/705 - ReceptorsCell surface antigensCell surface determinants
  • C12N 15/86 - Viral vectors

13.

ANTISENSE OLIGONUCLEOTIDES AND ARTIFICIAL EXPRESSION CONSTRUCTS FOR EXPRESSING RNA IN INHIBITORY NEURONS

      
Application Number US2024038566
Publication Number 2025/019685
Status In Force
Filing Date 2024-07-18
Publication Date 2025-01-23
Owner ALLEN INSTITUTE (USA)
Inventor
  • Gore, Bryan
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Liu, Jiatai
  • Martinez, Refugio
  • Mich, John K.
  • Ting, Jonathan

Abstract

Antisense oligonucleotides and artificial expression constructs for modulating RNA expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express RNA in GABAergic neurons. Antisense oligonucleotides and artificial expression constructs can be used to rescue sodium voltage-gated channel function to treat disorders such as epilepsy, and more particularly, Dravet Syndrome, among many other uses.

IPC Classes  ?

  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof
  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 15/79 - Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • C12N 15/861 - Adenoviral vectors

14.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN CARDIOMYOCYTES

      
Application Number US2024035977
Publication Number 2025/006852
Status In Force
Filing Date 2024-06-28
Publication Date 2025-01-02
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Johansen, Nelson
  • Lein, Edward Sebastian

Abstract

Artificial expression constructs for modulating gene expression in cardiomyocytes within targeted anatomical regions are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in cardiomyocytes within targeted anatomical regions including the heart atria and/or heart ventricles.

IPC Classes  ?

15.

METHODS OF PREPARING AND FREEZING BIOLOGICAL SAMPLES FOR ANALYTICAL USE AND ASSOCIATED COMPOSITIONS

      
Application Number US2024014861
Publication Number 2024/168076
Status In Force
Filing Date 2024-02-07
Publication Date 2024-08-15
Owner ALLEN INSTITUTE (USA)
Inventor
  • Skene, Peter
  • Reading, Julian

Abstract

Provided herein are methods of preparing a biological sample for analysis. In some embodiments, the methods comprise cryopreserving the cells and assessing biological features. Also provided are methods of analyzing biological samples which have been prepared according to the steps of the present technology. In some embodiments, the methods of the present technology preserve native cell structures of biological samples relative to samples prepared by other methods.

IPC Classes  ?

  • G01N 1/28 - Preparing specimens for investigation
  • C12N 5/0787 - Granulocytes, e.g. basophils, eosinophils, neutrophils or mast cells
  • G01N 1/10 - Devices for withdrawing samples in the liquid or fluent state

16.

INTEIN-MEDIATED RECONSTITUTION OF VOLTAGE-GATED SODIUM CHANNEL FUNCTION

      
Application Number US2024014080
Publication Number 2024/163796
Status In Force
Filing Date 2024-02-01
Publication Date 2024-08-08
Owner
  • ALLEN INSTITUTE (USA)
  • SEATTLE CHILDREN'S HOSPITAL D/B/A SEATTLE CHILDREN'S RESEARCH INSTITUTE (USA)
Inventor
  • Gore, Bryan
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Martinez, Refugio
  • Mich, John K.
  • Kalume, Franck

Abstract

Artificial expression constructs for the rescue of voltage-gated sodium channel function using intein-mediated reconstitution of the SCN1A encoded protein, voltage-gated sodium channel alpha subunit 1 (Nav1.1) are described. Rescued voltage-gated sodium channel function can be used to treat disorders such as epilepsy, and more particularly, Dravet Syndrome.

IPC Classes  ?

  • C12N 15/86 - Viral vectors
  • A61K 9/00 - Medicinal preparations characterised by special physical form
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C07K 14/47 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans from vertebrates from mammals
  • C07K 14/70 - Enkephalins
  • A61P 25/08 - AntiepilepticsAnticonvulsants

17.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN CELLS WITHIN THE SPINAL CORD

      
Application Number US2024014276
Publication Number 2024/163914
Status In Force
Filing Date 2024-02-02
Publication Date 2024-08-08
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Gao, Yuan
  • Johansen, Nelson
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Yao, Zizhen
  • Zeng, Hongkui

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in the spinal cord spinal motor neurons including Spp1 spinal motor neurons, Parg spinal motor neurons, Ogdh1 spinal motor neurons, or ChAT spinal motor neurons; alpha motor neurons including Chodl spinal motor neurons; gamma motor neurons; spinal excitatory motor neurons including Mafa excitatory neurons, Esrrg Trhr excitatory neurons, Slc17a6 spinal cord excitatory neurons; spinal inhibitory neurons including Slc6a5 spinal cord inhibitory neurons; pan spinal neurons including Esrrg spinal motor neurons and pan spinal cord types; cerebrospinal fluid-contacting neurons including Poln spinal motor neurons; and spinal non-neuronal cells including astrocytes and oligodendrocytes.

IPC Classes  ?

  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C12N 15/86 - Viral vectors
  • A61K 9/00 - Medicinal preparations characterised by special physical form
  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof

18.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN NEURONS WITHIN THE THALAMUS

      
Application Number 18563252
Status Pending
Filing Date 2022-05-20
First Publication Date 2024-08-01
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Mitchell, Amanda
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Weed, Natalie
  • Zeng, Hongkui

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in GABAergic or glutamatergic neurons within the thalamus. In some cases, the artificial constructs can also be used to express synthetic genes or modify gene expression in neurons within the thalamus as well as a secondary cell type.

IPC Classes  ?

19.

MOLECULAR SIGNATURES OF LONG-TERM COVID-19 AND TREATMENT THEREOF

      
Application Number 18557406
Status Pending
Filing Date 2022-04-28
First Publication Date 2024-07-04
Owner
  • ALLEN INSTITUTE (USA)
  • FRED HUTCHINSON CANCER CENTER (USA)
Inventor
  • Bumol, Thomas F.
  • Li, Xiaojun
  • Skene, Peter
  • Szeto, Gregory Lee
  • Talla, Aarthi
  • Torgerson, Troy
  • Pebworth, Mark-Phillip
  • Vasaikar, Suhas
  • Mcelrath, Juliana M.

Abstract

In various embodiments, provided are immune response signatures that can be used for the diagnosis, monitoring, and treatment of long-term diseases and inflammatory disorders caused by viral infections. In some embodiments, the viral infection is SARS-CoV-2 infection. In some embodiments, the long-term disease is post-acute sequelae of SARS-CoV-2 infection (PASC).

IPC Classes  ?

  • G01N 33/569 - ImmunoassayBiospecific binding assayMaterials therefor for microorganisms, e.g. protozoa, bacteria, viruses

20.

SELECTIVE-PLANE ILLUMINATION MICROSCOPY WITH HIGH ÉTENDUE AND LONG WORKING DISTANCE OBJECTIVE LENSES

      
Application Number US2023083330
Publication Number 2024/129575
Status In Force
Filing Date 2023-12-11
Publication Date 2024-06-20
Owner ALLEN INSTITUTE (USA)
Inventor
  • Glaser, Adam
  • Chandrashekar, Jayaram
  • Svoboda, Karel

Abstract

An expansion-assisted selective plane illumination microscope (ExA-SPIM) has diffraction- limited and aberration-free performance over a large field of view (e.g., 85 mm2) and working distance (e.g., 35 mm). ExA-SPIM enables molecular imaging across three- dimensional samples with high imaging throughput for applications in biology and neuroscience. Combined with new tissue clearing and expansion methods, ExA-SPIM allows nanoscale imaging of centimeter-scale samples, including entire mouse brains, with diffraction-limited resolutions and high contrast without sectioning. ExA-SPIM can be used to reconstruct individual neurons across the mouse brain, image cortico-spinal neurons in the macaque motor cortex, and trace axons in human white matter.

IPC Classes  ?

  • G01N 21/63 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
  • G01N 21/64 - FluorescencePhosphorescence
  • G02B 21/06 - Means for illuminating specimen
  • G01N 21/62 - Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
  • G02B 21/00 - Microscopes

21.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN CLAUSTRUM NEURONS

      
Application Number 18285188
Status Pending
Filing Date 2022-03-30
First Publication Date 2024-06-06
Owner Allen Institute (USA)
Inventor
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Sedeño Cortés, Adriana Estela
  • Tasic, Bosiljka
  • Ting, Jonathan

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in claustrum neurons including L6 IT Car3 neurons.

IPC Classes  ?

  • C12N 15/86 - Viral vectors
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C07K 14/47 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans from vertebrates from mammals

22.

Removing independent noise using DeepInterpolation

      
Application Number 17772971
Grant Number 12367557
Status In Force
Filing Date 2020-10-07
First Publication Date 2024-05-16
Grant Date 2025-07-22
Owner Allen Institute (USA)
Inventor
  • Lecoq, Jerome Anthony-Jean
  • Oliver, Michael David
  • Siegle, Joshua Handman
  • Koch, Christof

Abstract

A facility for transforming a subject data item sequence is described. The facility accesses a trained relationship model. For each of a plurality of subject items of the subject data item sequence, the facility: selects a first contiguous series of items of the subject data item sequence immediately before the subject data item; selects a second contiguous series of items of the subject data item sequence immediately after the subject data item; and applies the trained relationship model to the selected first and second contiguous series of data items to obtain a denoised version of the subject data item. The facility then assembles the obtained denoised subject data items into a denoised data item sequence.

IPC Classes  ?

  • G06T 5/70 - DenoisingSmoothing
  • G06T 5/50 - Image enhancement or restoration using two or more images, e.g. averaging or subtraction

23.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN GABAERGIC NEURONS AND ASTROCYTES

      
Application Number 18263930
Status Pending
Filing Date 2022-02-02
First Publication Date 2024-04-11
Owner Allen Institute (USA)
Inventor
  • Gore, Bryan
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Machen, Deja
  • Martinez, Refugio
  • Mich, John K.
  • Ting, Jonathan

Abstract

Artificial expression constructs for modulating gene expression in GABAergic neurons and astrocytes are described. The artificial expression constructs can be used to express SLC6A1 for the treatment of SLC6A1-associated disorders, among other uses.

IPC Classes  ?

  • C12N 15/86 - Viral vectors
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy

24.

ELECTRICAL STIMULATION ENTRAINMENT OF TARGETED NEURONAL CELL TYPES

      
Application Number 18255813
Status Pending
Filing Date 2021-12-02
First Publication Date 2024-03-28
Owner Allen Institute (USA)
Inventor
  • Anastassiou, Constantinos
  • Lee, Soo Yeun

Abstract

Electrostimulating waveforms offering simultaneous and controllable cell-type-specific entrainment are described. The waveforms selectively entrain excitatory versus inhibitory cortical and hippocampal neurons including pyramidal neurons, parvalbumin neurons, and somatostatin neurons. The embodiment provides targeted electrical stimulation (ES) entrainment of excitatory versus inhibitory neurons. For example, the current disclosure provides methods of selectively entraining excitatory neurons with ES frequencies below 30 Hertz (Hz) and in particular embodiments to frequencies below 15 Hz, such as 8 Hz and 4 Hz. The current disclosure also provides methods of selectively entraining inhibitory neurons to ES frequencies of at least 30 Hz and depending on the type of inhibitory neuron, utilizing a frequency that is 30-60 Hz or a frequency that is greater than 100 Hz.

IPC Classes  ?

  • A61N 1/36 - Applying electric currents by contact electrodes alternating or intermittent currents for stimulation, e.g. heart pace-makers
  • A61N 1/05 - Electrodes for implantation or insertion into the body, e.g. heart electrode

25.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN CHANDELIER CELLS

      
Application Number 18252498
Status Pending
Filing Date 2021-11-10
First Publication Date 2024-01-18
Owner Allen Institute (USA)
Inventor
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Kalmbach, Brian Edward
  • Lein, Edward Sebastian
  • Mich, John K.
  • Levi, Boaz P.
  • Sedeño Cortés, Adriana Estela
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in chandelier cells. Chandelier cells are a subtype of GABAergic interneurons that that have been implicated in disorders such as epilepsy and schizophrenia.

IPC Classes  ?

26.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN NON-NEURONAL CENTRAL NERVOUS SYSTEM CELLS

      
Document Number 03259293
Status Pending
Filing Date 2023-06-13
Open to Public Date 2023-12-21
Owner ALLEN INSTITUTE (USA)
Inventor
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Martinez, Refugio
  • Mich, John K.
  • Opitz-Araya, Ximena
  • Ting, Jonathan

IPC Classes  ?

  • A01K 67/027 - New or modified breeds of vertebrates
  • A61P 25/28 - Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
  • C12N 5/0735 - Embryonic stem cellsEmbryonic germ cells
  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
  • C12N 15/86 - Viral vectors

27.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN NON-NEURONAL CENTRAL NERVOUS SYSTEM CELLS

      
Application Number US2023068369
Publication Number 2023/245013
Status In Force
Filing Date 2023-06-13
Publication Date 2023-12-21
Owner ALLEN INSTITUTE (USA)
Inventor
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Martinez, Refugio
  • Mich, John K.
  • Opitz-Araya, Ximena
  • Ting, Jonathan

Abstract

To fully understand the biology of the brain, different cell types need to be distinguished and defined and, to further study them, artificial expression constructs that can label and perturb them need to be identified, in mouse, recombinase driver lines have been used to great effect to label cell populations that share marker gene expression. However, the creation, maintenance, and use of such lines that label cell types with high specificity can be costly, frequently requiring triple transgenic crosses, which yield a low frequency of experimental animals. Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in non-neuronal cells including oligodendrocytes, microglia, astrocytes, or endothelial cells.

IPC Classes  ?

  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
  • A01K 67/027 - New or modified breeds of vertebrates
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 15/86 - Viral vectors
  • A61P 25/28 - Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
  • C12N 5/0735 - Embryonic stem cellsEmbryonic germ cells

28.

SYSTEMS, DEVICES, AND METHODS FOR COMPOUND SCREENING USING PREDICTIVE TAGGING

      
Application Number 18005077
Status Pending
Filing Date 2021-07-28
First Publication Date 2023-10-26
Owner ALLEN INSTITUTE (USA)
Inventor
  • Johnson, Gregory
  • Ounkomol, Chawin
  • Collman, Forrest
  • Seshamani, Sharmishtaa
  • Gaudreault, Nathalie
  • Yan, Calysta
  • Chen, Jianxu
  • Rafelski, Susanne

Abstract

The present invention provides various methods for screening one or more compounds, suitably using non-invasive visual methods and neural networks for generating predicted fluorescence images of cells, to assess an effect of the compound on the cell, as well as to classify a compound or to determine an activity of a compound. Also provided are systems and methods for carrying out such assessments.

IPC Classes  ?

29.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN STRIATAL NEURONS

      
Application Number 18040961
Status Pending
Filing Date 2021-08-13
First Publication Date 2023-09-28
Owner Allen Institute (USA)
Inventor
  • Daigle, Tanya
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui

Abstract

Artificial expression constructs for modulating gene expression in striatal neurons are described. The artificial expression constructs can be used to express heterologous genes in striatal neurons including in striatal medium spiny neuron-pan, striatal medium spiny neuron-indirect pathway, striatal medium spiny neuron-direct pathway, striatal interneuron-cholinergic, and Drd3+ medium spiny neurons in olfactory tubercle. The artificial expression constructs can be used for many purposes, including to research and treat movement disorders such as Parkinson's disease and Huntington's disease.

IPC Classes  ?

  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C12N 9/88 - Lyases (4.)
  • C12N 15/86 - Viral vectors
  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides

30.

Systems, devices, and methods for image processing to generate an image having predictive tagging

      
Application Number 18170076
Grant Number 12008764
Status In Force
Filing Date 2023-02-16
First Publication Date 2023-09-07
Grant Date 2024-06-11
Owner ALLEN INSTITUTE (USA)
Inventor
  • Johnson, Gregory
  • Ounkomol, Chawin
  • Collman, Forrest
  • Seshamani, Sharmishtaa

Abstract

A computing device, method, system, and instructions in a non-transitory computer-readable medium for performing image analysis on 3D microscopy images to predict localization and/or labeling of various structures or objects of interest, by predicting the location in such images at which a dye or other marker associated with such structures would appear. The computing device, method, and system receives sets of 3D images that include unlabeled images, such as transmitted light images or electron microscope images, and labeled images, such as images captured with fluorescence tagging. The computing device trains a statistical model to associate structures in the labeled images with the same structures in the unlabeled light images. The processor further applies the statistical model to a new unlabeled image to generate a predictive labeled image that predicts the location of a structure of interest in the new image.

IPC Classes  ?

  • G06T 7/11 - Region-based segmentation
  • G02B 21/00 - Microscopes
  • G06N 3/045 - Combinations of networks
  • G06N 3/08 - Learning methods
  • G06N 20/20 - Ensemble learning
  • G06T 7/174 - SegmentationEdge detection involving the use of two or more images
  • G06T 7/187 - SegmentationEdge detection involving region growingSegmentationEdge detection involving region mergingSegmentationEdge detection involving connected component labelling
  • G06V 10/25 - Determination of region of interest [ROI] or a volume of interest [VOI]
  • G06V 10/50 - Extraction of image or video features by performing operations within image blocksExtraction of image or video features by using histograms, e.g. histogram of oriented gradients [HoG]Extraction of image or video features by summing image-intensity valuesProjection analysis
  • G06V 10/764 - Arrangements for image or video recognition or understanding using pattern recognition or machine learning using classification, e.g. of video objects
  • G06V 20/69 - Microscopic objects, e.g. biological cells or cellular parts

31.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN DOPAMINERGIC NEURONS

      
Document Number 03244907
Status Pending
Filing Date 2023-02-24
Open to Public Date 2023-08-31
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Tasic, Bosiljka
  • Zeng, Hongkui
  • Ting, Jonathan
  • Levi, Boaz P.
  • Lein, Edward Sebastian

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in dopaminergic neurons of the central nervous system. Wherein, an artificial expression construct comprising (i) an enhancer is eHGT 888m.

IPC Classes  ?

  • C12N 15/79 - Vectors or expression systems specially adapted for eukaryotic hosts

32.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN DOPAMINERGIC NEURONS

      
Application Number US2023063259
Publication Number 2023/164643
Status In Force
Filing Date 2023-02-24
Publication Date 2023-08-31
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in dopaminergic neurons of the central nervous system. Wherein, an artificial expression construct comprising (i) an enhancer is eHGT 888m.

IPC Classes  ?

  • C12N 15/79 - Vectors or expression systems specially adapted for eukaryotic hosts

33.

SYSTEMS, DEVICES, AND METHODS FOR QUALITY CONTROL OF CELL PRODUCTION USING PREDICTIVE TAGGING

      
Application Number 18041086
Status Pending
Filing Date 2021-08-11
First Publication Date 2023-08-24
Owner ALLEN INSTITUTE (USA)
Inventor
  • Johnson, Gregory
  • Ounkomol, Chawin
  • Collman, Forrest
  • Seshamani, Sharmishtaa
  • Kranda, Michael

Abstract

The present invention provides various methods for easily assessing cell quality of a cell production process, suitably using non-invasive visual methods and neural networks for generating predictive fluorescence images of cells to assess quality attributes. Also provided are systems and methods for carrying out such processes.

IPC Classes  ?

  • G01N 15/02 - Investigating particle size or size distribution
  • G01N 15/14 - Optical investigation techniques, e.g. flow cytometry

34.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN INHIBITORY NEOCORTICAL NEURONS

      
Application Number 18000574
Status Pending
Filing Date 2021-06-04
First Publication Date 2023-07-06
Owner Allen Institute (USA)
Inventor
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Sedeño Cortés, Adriana Estela
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Walker, Miranda
  • Zeng, Hongkui

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in inhibitory neocortical GABAergic neurons including somatostatin GABAergic neurons, parvalbumin GABAergic neurons, vasointestinal peptide GABAergic neurons, Lamp5 GABAergic neurons, and in some instances astrocytes.

IPC Classes  ?

  • C12N 15/86 - Viral vectors
  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof
  • A61K 9/00 - Medicinal preparations characterised by special physical form

35.

MOLECULAR SIGNATURES FOR CELL TYPING AND MONITORING IMMUNE HEALTH

      
Application Number US2022081977
Publication Number 2023/115065
Status In Force
Filing Date 2022-12-19
Publication Date 2023-06-22
Owner ALLEN INSTITUTE (USA)
Inventor
  • Bumol, Thomas F.
  • Li, Xiao-Jun
  • Savage, Adam
  • Skene, Peter
  • Torgerson, Troy
  • Vasaikar, Suhas

Abstract

Provided herein are methods, devices, and systems comprising identification of a panel of gene markers useful for immune cell typing and identifying, detecting, and/or monitoring disease conditions in a subject in need thereof, including infections, cancer and autoimmune conditions. The methods also provide for assays for determining the levels of said markers prior to and after treatment of a condition in the subject, wherein the condition is impacted by one or more factors including age, occupation or environment of the subject.

IPC Classes  ?

  • C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
  • G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
  • C12Q 1/689 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
  • C12Q 1/6893 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for protozoa
  • C12Q 1/37 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving hydrolase involving peptidase or proteinase

36.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN NEOCORTICAL LAYER 4 OR LAYER 5 INTRATELENCEPHALIC NEURONS

      
Application Number US2022081114
Publication Number 2023/108021
Status In Force
Filing Date 2022-12-07
Publication Date 2023-06-15
Owner ALLEN INSTITUTE (USA)
Inventor
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Ting, Jonathan

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in neocortical layer 4 (L4) intratelencephalic (IT) neurons and/or neocortical L5 IT neurons.

IPC Classes  ?

  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
  • G01N 33/569 - ImmunoassayBiospecific binding assayMaterials therefor for microorganisms, e.g. protozoa, bacteria, viruses
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • A61P 25/28 - Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia

37.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN NEOCORTICAL LAYER 5 GLUTAMATERGIC NEURONS

      
Application Number 17996910
Status Pending
Filing Date 2021-04-21
First Publication Date 2023-05-25
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Kalmbach, Brian Edward
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Sedeño Cortés, Adriana Estela
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. Particularly, the artificial expression constructs can be used to selectively express synthetic genes and/or modify gene expression in neocortical glutamatergic layer 5 neurons, such as glutamatergic layer 5 extratelencephalic-projecting (L5 ET) neurons.

IPC Classes  ?

38.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN NON-NEURONAL BRAIN CELLS

      
Application Number 17907385
Status Pending
Filing Date 2021-03-26
First Publication Date 2023-04-20
Owner ALLEN INSTITUTE (USA)
Inventor
  • Ting, Jonathan
  • Tasic, Bosiljka
  • Levi, Boaz P.
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Lein, Edward Sebastian
  • Mich, John K.
  • Sedeño Cortés, Adriana Estela
  • Zeng, Hongkui

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in astrocytes, oligodendrocytes, microglia, pericytes, SMC, or endothelial cells.

IPC Classes  ?

  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells

39.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN THE CEREBELLUM AND A SECONDARY CELL TYPE

      
Document Number 03233342
Status Pending
Filing Date 2022-10-05
Open to Public Date 2023-04-13
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui
  • Mich, John K.

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in a cerebellar cell type and a secondary cell type.

IPC Classes  ?

  • A61K 35/76 - VirusesSubviral particlesBacteriophages
  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 15/67 - General methods for enhancing the expression

40.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN THE CEREBELLUM AND A SECONDARY CELL TYPE

      
Application Number US2022077586
Publication Number 2023/060112
Status In Force
Filing Date 2022-10-05
Publication Date 2023-04-13
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui
  • Mich, John K.

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in a cerebellar cell type and a secondary cell type.

IPC Classes  ?

  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 15/67 - General methods for enhancing the expression
  • A61K 35/76 - VirusesSubviral particlesBacteriophages

41.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN NEURONS WITHIN THE THALAMUS

      
Document Number 03219142
Status Pending
Filing Date 2022-05-20
Open to Public Date 2022-11-24
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Mitchell, Amanda
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Weed, Natalie
  • Zeng, Hongkui

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in GABAergic or glutamatergic neurons within the thalamus. In some cases, the artificial constructs can also be used to express synthetic genes or modify gene expression in neurons within the thalamus as well as a secondary cell type.

IPC Classes  ?

  • C12N 15/79 - Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N 15/86 - Viral vectors

42.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN NEURONS WITHIN THE THALAMUS

      
Application Number US2022030371
Publication Number 2022/246276
Status In Force
Filing Date 2022-05-20
Publication Date 2022-11-24
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Mitchell, Amanda
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Weed, Natalie
  • Zeng, Hongkui

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in GABAergic or glutamatergic neurons within the thalamus. In some cases, the artificial constructs can also be used to express synthetic genes or modify gene expression in neurons within the thalamus as well as a secondary cell type.

IPC Classes  ?

  • C12N 15/79 - Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N 15/86 - Viral vectors

43.

MOLECULAR SIGNATURES OF LONG-TERM COVID-19 AND TREATMENT THEREOF

      
Application Number US2022026841
Publication Number 2022/232463
Status In Force
Filing Date 2022-04-28
Publication Date 2022-11-03
Owner
  • ALLEN INSTITUTE (USA)
  • FRED HUTCHINSON CANCER CENTER (USA)
Inventor
  • Bumol, Thomas F.
  • Li, Xiaojun
  • Skene, Peter
  • Szeto, Gregory Lee
  • Talla, Aarthi
  • Torgerson, Troy
  • Pebworth, Mark-Phillip
  • Vasaikar, Suhas
  • Mcelrath, M. Juliana

Abstract

In various embodiments, provided are immune response signatures that can be used for the diagnosis, monitoring, and treatment of long-term diseases and inflammatory disorders caused by viral infections. In some embodiments, the viral infection is SARS-CoV-2 infection. In some embodiments, the long-term disease is post-acute sequelae of SARS-CoV-2 infection (PASC).

IPC Classes  ?

  • A61K 39/215 - Coronaviridae, e.g. avian infectious bronchitis virus
  • C07K 14/165 - Coronaviridae, e.g. avian infectious bronchitis virus
  • C07K 14/52 - CytokinesLymphokinesInterferons
  • C07K 14/525 - Tumour necrosis factor [TNF]
  • C07K 14/54 - Interleukins [IL]
  • C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material

44.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN CLAUSTRUM NEURONS

      
Application Number US2022022656
Publication Number 2022/212585
Status In Force
Filing Date 2022-03-30
Publication Date 2022-10-06
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Sedeno Cortes, Adriana Estela
  • Tasic, Bosiljka
  • Ting, Jonathan

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in claustrum neurons including L6 IT Car3 neurons.

IPC Classes  ?

  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C12N 15/09 - Recombinant DNA-technology
  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof
  • C12N 15/12 - Genes encoding animal proteins

45.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN GABAERGIC NEURONS AND ASTROCYTES

      
Document Number 03207224
Status Pending
Filing Date 2022-02-02
Open to Public Date 2022-08-11
Owner ALLEN INSTITUTE (USA)
Inventor
  • Gore, Bryan
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Machen, Deja
  • Martinez, Refugio
  • Mich, John K.
  • Ting, Jonathan

Abstract

Artificial expression constructs for modulating gene expression in GABAergic neurons and astrocytes are described. The artificial expression constructs can be used to express SLC6A1 for the treatment of SLC6A1-associated disorders, among other uses.

IPC Classes  ?

  • A61K 31/7088 - Compounds having three or more nucleosides or nucleotides
  • A61K 31/7105 - Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
  • A61K 31/7115 - Nucleic acids or oligonucleotides having modified bases, i.e. other than adenine, guanine, cytosine, uracil or thymine
  • A61K 31/712 - Nucleic acids or oligonucleotides having modified sugars, i.e. other than ribose or 2'-deoxyribose
  • A61K 31/7125 - Nucleic acids or oligonucleotides having modified internucleoside linkage, i.e. other than 3'-5' phosphodiesters

46.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN SELECTED NEURONAL CELL POPULATIONS

      
Application Number 17431079
Status Pending
Filing Date 2020-02-14
First Publication Date 2022-08-11
Owner Allen Institute (USA)
Inventor
  • Ting, Jonathan
  • Levi, Boaz P.
  • Tasic, Bosiljka
  • Mich, John K.
  • Hess, Erik
  • Lein, Edward Sebastian
  • Graybuck, Lucas T.
  • Daigle, Tanya
  • Zeng, Hongkui

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in GABAergic neurons generally; and/or GABAergic neuron cell types such as lysosomal associated membrane protein 5 (Lamp5) neurons; vasoactive intestinal polypeptide-expressing (Vip) neurons; somatostatin (Sst) neurons; and/or parvalbumin (Pvalb) neuron cell types. Certain artificial expression constructs additionally drive selective gene expression in Layer 4 and/or layer 5 intratelencephalic (IT) neurons, deep cerebellar nuclear neurons or cerebellar Purkinje cells.

IPC Classes  ?

  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C12N 5/0793 - Neurons
  • C12N 7/00 - Viruses, e.g. bacteriophagesCompositions thereofPreparation or purification thereof
  • C12N 15/86 - Viral vectors
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
  • C12N 9/22 - Ribonucleases
  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof
  • A01K 67/027 - New or modified breeds of vertebrates

47.

Systems and methods for using an ontology to generate database entries and access and search a database

      
Application Number 17617514
Grant Number 11914631
Status In Force
Filing Date 2020-07-15
First Publication Date 2022-08-11
Grant Date 2024-02-27
Owner Allen Institute (USA)
Inventor Acharya, Gautham Bhat

Abstract

A system, apparatus and methods for generating database entries and tools for accessing and searching a database from an Ontology. Starting with an Ontology used to represent data and relationships between data, the system and methods described enable that data to be stored in a desired type of database and accessed using an API and search query generated from the Ontology. Embodiments provide a structure and process to implement a data access system or framework that can be used to unify and better understand information across an organization's entire set of data. Such a framework can help enable and improve the organization and discovery of knowledge, increase the value of existing data, and reduce complexity when developing next-generation applications.

IPC Classes  ?

  • G06F 16/36 - Creation of semantic tools, e.g. ontology or thesauri
  • G06F 16/25 - Integrating or interfacing systems involving database management systems
  • G06F 16/242 - Query formulation
  • G06F 16/901 - IndexingData structures thereforStorage structures

48.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN GABAERGIC NEURONS AND ASTROCYTES

      
Application Number US2022014956
Publication Number 2022/169884
Status In Force
Filing Date 2022-02-02
Publication Date 2022-08-11
Owner ALLEN INSTITUTE (USA)
Inventor
  • Gore, Bryan
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Machen, Deja
  • Martinez, Refugio
  • Mich, John K.
  • Ting, Jonathan

Abstract

Artificial expression constructs for modulating gene expression in GABAergic neurons and astrocytes are described. The artificial expression constructs can be used to express SLC6A1 for the treatment of SLC6A1-associated disorders, among other uses.

IPC Classes  ?

  • A61K 31/7088 - Compounds having three or more nucleosides or nucleotides
  • A61K 31/712 - Nucleic acids or oligonucleotides having modified sugars, i.e. other than ribose or 2'-deoxyribose
  • A61K 31/7105 - Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
  • A61K 31/7125 - Nucleic acids or oligonucleotides having modified internucleoside linkage, i.e. other than 3'-5' phosphodiesters
  • A61K 31/7115 - Nucleic acids or oligonucleotides having modified bases, i.e. other than adenine, guanine, cytosine, uracil or thymine

49.

ELECTRICAL STIMULATION ENTRAINMENT OF TARGETED NEURONAL CELL TYPES

      
Application Number US2021061592
Publication Number 2022/120035
Status In Force
Filing Date 2021-12-02
Publication Date 2022-06-09
Owner ALLEN INSTITUTE (USA)
Inventor
  • Anastassiou, Constantinos
  • Lee, Soo Yeun

Abstract

Electrostimulating waveforms offering simultaneous and controllable cell-type-specific entrainment are described. The waveforms selectively entrain excitatory versus inhibitory cortical and hippocampal neurons including pyramidal neurons, parvalbumin neurons, and somatostatin neurons. The embodiment provides targeted electrical stimulation (ES) entrainment of excitatory versus inhibitory neurons. For example, the current disclosure provides methods of selectively entraining excitatory neurons with ES frequencies below 30 Hertz (Hz) and in particular embodiments to frequencies below 15 Hz, such as 8 Hz and 4 Hz. The current disclosure also provides methods of selectively entraining inhibitory neurons to ES frequencies of at least 30 Hz and depending on the type of inhibitory neuron, utilizing a frequency that is 30-60 Hz or a frequency that is greater than 100 Hz.

IPC Classes  ?

  • A61N 1/36 - Applying electric currents by contact electrodes alternating or intermittent currents for stimulation, e.g. heart pace-makers
  • A61M 21/00 - Other devices or methods to cause a change in the state of consciousnessDevices for producing or ending sleep by mechanical, optical, or acoustical means, e.g. for hypnosis
  • A61N 1/00 - ElectrotherapyCircuits therefor
  • A61N 1/18 - Applying electric currents by contact electrodes

50.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN CHANDELIER CELLS

      
Document Number 03197041
Status Pending
Filing Date 2021-11-10
Open to Public Date 2022-05-19
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Kalmbach, Brian Edward
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Sedeno Cortes, Adriana Estela
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in chandelier cells. Chandelier cells are a subtype of GABAergic interneurons that that have been implicated in disorders such as epilepsy and schizophrenia.

IPC Classes  ?

51.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN CHANDELIER CELLS

      
Application Number US2021058812
Publication Number 2022/103859
Status In Force
Filing Date 2021-11-10
Publication Date 2022-05-19
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Kalmbach, Brian Edward
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Sedeno Cortes, Adriana Estela
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui

Abstract

Artificial expression constructs for modulating gene expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express synthetic genes or modify gene expression in chandelier cells. Chandelier cells are a subtype of GABAergic interneurons that that have been implicated in disorders such as epilepsy and schizophrenia.

IPC Classes  ?

52.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN STRIATAL NEURONS

      
Document Number 03186367
Status Pending
Filing Date 2021-08-13
Open to Public Date 2022-02-17
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui

Abstract

Artificial expression constructs for modulating gene expression in striatal neurons are described. The artificial expression constructs can be used to express heterologous genes in striatal neurons including in striatal medium spiny neuron-pan, striatal medium spiny neuron-indirect pathway, striatal medium spiny neuron-direct pathway, striatal interneuron-cholinergic, and Drd3+ medium spiny neurons in olfactory tubercle. The artificial expression constructs can be used for many purposes, including to research and treat movement disorders such as Parkinson's disease and Huntington's disease.

IPC Classes  ?

  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof
  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 15/67 - General methods for enhancing the expression
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells

53.

SYSTEMS, DEVICES, AND METHODS FOR QUALITY CONTROL OF CELL PRODUCTION USING PREDICTIVE TAGGING

      
Application Number US2021045561
Publication Number 2022/035973
Status In Force
Filing Date 2021-08-11
Publication Date 2022-02-17
Owner ALLEN INSTITUTE (USA)
Inventor
  • Johnson, Gregory
  • Ounkomol, Chawin
  • Collman, Forrest
  • Seshamani, Sharmishtaa
  • Kranda, Michael

Abstract

The present invention provides various methods for easily assessing cell quality of a cell production process, suitably using non-invasive visual methods and neural networks for generating predictive fluorescence images of cells to assess quality attributes. Also provided are systems and methods for carrying out such processes.

IPC Classes  ?

54.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR MODULATING GENE EXPRESSION IN STRIATAL NEURONS

      
Application Number US2021045995
Publication Number 2022/036255
Status In Force
Filing Date 2021-08-13
Publication Date 2022-02-17
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui

Abstract

Artificial expression constructs for modulating gene expression in striatal neurons are described. The artificial expression constructs can be used to express heterologous genes in striatal neurons including in striatal medium spiny neuron-pan, striatal medium spiny neuron-indirect pathway, striatal medium spiny neuron-direct pathway, striatal interneuron-cholinergic, and Drd3+ medium spiny neurons in olfactory tubercle. The artificial expression constructs can be used for many purposes, including to research and treat movement disorders such as Parkinson's disease and Huntington's disease.

IPC Classes  ?

  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof
  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 15/67 - General methods for enhancing the expression
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells

55.

SYSTEMS, DEVICES, AND METHODS FOR COMPOUND SCREENING USING PREDICTIVE TAGGING

      
Application Number US2021043430
Publication Number 2022/026532
Status In Force
Filing Date 2021-07-28
Publication Date 2022-02-03
Owner ALLEN INSTITUTE (USA)
Inventor
  • Johnson, Gregory
  • Ounkomol, Chawin
  • Collman, Forrest
  • Seshamani, Sharmishtaa
  • Gaudreault, Nathalie
  • Yan, Calysta
  • Chen, Jianxu
  • Rafelski, Susanne

Abstract

The present invention provides various methods for screening one or more compounds, suitably using non-invasive visual methods and neural networks for generating predicted fluorescence images of cells, to assess an effect of the compound on the cell, as well as to classify a compound or to determine an activity of a compound. Also provided are systems and methods for carrying out such assessments.

IPC Classes  ?

56.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN EXCITATORY CORTICAL NEURONS

      
Application Number 17291584
Status Pending
Filing Date 2019-11-05
First Publication Date 2021-12-23
Owner Allen Institute (USA)
Inventor
  • Graybuck, Lucas T.
  • Tasic, Bosiljka
  • Daigle, Tanya
  • Ting, Jonathan
  • Zeng, Hongkui
  • Kalmbach, Brian Edward
  • Mich, John K.
  • Hess, Erik
  • Lein, Edward Sebastian
  • Levi, Boaz P.

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in excitatory cortical neurons, such as primarily within cortical layers 2/3, 4, 5, and 6 and including those with extratelencephalic (ET) projections, intratelencephalic (IT) projections, and pyramidal tract (PT) projections, among others.

IPC Classes  ?

57.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN INHIBITORY NEOCORTICAL NEURONS

      
Document Number 03180017
Status Pending
Filing Date 2021-06-04
Open to Public Date 2021-12-09
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Sedeno Cortes, Adriana Estela
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Walker, Miranda
  • Zeng, Hongkui

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in inhibitory neocortical GABAergic neurons including somatostatin GABAergic neurons, parvalbumin GABAergic neurons, vasointestinal peptide GABAergic neurons, Lamp5 GABAergic neurons, and in some instances astrocytes.

IPC Classes  ?

  • C12N 15/09 - Recombinant DNA-technology
  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof
  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 15/67 - General methods for enhancing the expression

58.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN INHIBITORY NEOCORTICAL NEURONS

      
Application Number US2021036028
Publication Number 2021/248085
Status In Force
Filing Date 2021-06-04
Publication Date 2021-12-09
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Sedeno Cortes, Adriana Estela
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Walker, Miranda
  • Zeng, Hongkui

Abstract

Lamp5Lamp5 GABAergic neurons, and in some instances astrocytes.

IPC Classes  ?

  • C12N 15/09 - Recombinant DNA-technology
  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof
  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 15/67 - General methods for enhancing the expression

59.

Miscellaneous Design

      
Serial Number 97151186
Status Registered
Filing Date 2021-12-01
Registration Date 2023-01-03
Owner Allen Institute, DBA ALLEN INSTITUTE FOR BRAIN SCIENCE; ALLEN INSTITUTE FOR CELL SCIENCE; ALLEN INSTITUTE FOR IMMUNOLOGY; ALLEN INSTITUTE FOR NEURAL DYNAMICS; PAUL G. ALLEN FRONTIERS GROUP ()
NICE Classes  ? 41 - Education, entertainment, sporting and cultural services

Goods & Services

Educational services, namely, providing classes, seminars, workshops and conferences in the fields of neuroscience and cell biology research, and distribution of informational materials therewith

60.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN INTERNEURONS

      
Application Number 17283232
Status Pending
Filing Date 2019-10-03
First Publication Date 2021-11-11
Owner
  • Allen Institute (USA)
  • Seattle Children's Hospital d/b/a Seattle Children's Research Institute (USA)
Inventor
  • Ting, Jonathan
  • Levi, Boaz P.
  • Mich, John K.
  • Lein, Edward Sebastian
  • Kalume, Franck

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in GABAergic interneurons.

IPC Classes  ?

  • C12N 15/86 - Viral vectors
  • C12N 5/0793 - Neurons
  • A01K 67/027 - New or modified breeds of vertebrates
  • A61K 35/30 - NervesBrainEyesCorneal cellsCerebrospinal fluidNeuronal stem cellsNeuronal precursor cellsGlial cellsOligodendrocytesSchwann cellsAstrogliaAstrocytesChoroid plexusSpinal cord tissue

61.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN NEOCORTICAL LAYER 5 GLUTAMATERGIC NEURONS

      
Application Number US2021028489
Publication Number 2021/216778
Status In Force
Filing Date 2021-04-21
Publication Date 2021-10-28
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Kalmbach, Brian Edward
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Sedeno Cortes, Adriana Estela
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. Particularly, the artificial expression constructs can be used to selectively express synthetic genes and / or modify gene expression in neocortical glutamatergic layer 5 neurons, such as glutamatergic layer 5 extratelencephalic-projecting (L5 ET) neurons.

IPC Classes  ?

62.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN NEOCORTICAL LAYER 5 GLUTAMATERGIC NEURONS

      
Document Number 03175993
Status Pending
Filing Date 2021-04-21
Open to Public Date 2021-10-28
Owner ALLEN INSTITUTE (USA)
Inventor
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Kalmbach, Brian Edward
  • Lein, Edward Sebastian
  • Levi, Boaz P.
  • Mich, John K.
  • Sedeno Cortes, Adriana Estela
  • Tasic, Bosiljka
  • Ting, Jonathan
  • Zeng, Hongkui

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. Particularly, the artificial expression constructs can be used to selectively express synthetic genes and / or modify gene expression in neocortical glutamatergic layer 5 neurons, such as glutamatergic layer 5 extratelencephalic-projecting (L5 ET) neurons.

IPC Classes  ?

63.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN NON-NEURONAL BRAIN CELLS

      
Document Number 03173609
Status Pending
Filing Date 2021-03-26
Open to Public Date 2021-09-30
Owner ALLEN INSTITUTE (USA)
Inventor
  • Ting, Jonathan
  • Tasic, Bosiljka
  • Levi, Boaz P.
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Lein, Edward Sebastian
  • Mich, John K.
  • Sedeno Cortes, Adriana Estela
  • Zeng, Hongkui

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in astrocytes, oligodendrocytes, microglia, pericytes, SMC, or endothelial cells.

IPC Classes  ?

  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C12N 15/67 - General methods for enhancing the expression
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells

64.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN NON-NEURONAL BRAIN CELLS

      
Application Number US2021024525
Publication Number 2021/195591
Status In Force
Filing Date 2021-03-26
Publication Date 2021-09-30
Owner ALLEN INSTITUTE (USA)
Inventor
  • Ting, Jonathan
  • Tasic, Bosiljka
  • Levi, Boaz P.
  • Daigle, Tanya
  • Graybuck, Lucas T.
  • Lein, Edward Sebastian
  • Mich, John K.
  • Sedeno Cortes, Adriana Estela
  • Zeng, Hongkui

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in astrocytes, oligodendrocytes, microglia, pericytes, SMC, or endothelial cells.

IPC Classes  ?

  • C12N 15/67 - General methods for enhancing the expression
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy

65.

Systems, devices, and methods for image processing to generate an image having predictive tagging

      
Application Number 17148192
Grant Number 11614610
Status In Force
Filing Date 2021-01-13
First Publication Date 2021-06-10
Grant Date 2023-03-28
Owner ALLEN INSTITUTE (USA)
Inventor
  • Johnson, Gregory
  • Ounkomol, Chawin
  • Collman, Forrest
  • Seshamani, Sharmishtaa

Abstract

A computing device, method, system, and instructions in a non-transitory computer-readable medium for performing image analysis on 3D microscopy images to predict localization and/or labeling of various structures or objects of interest, by predicting the location in such images at which a dye or other marker associated with such structures would appear. The computing device, method, and system receives sets of 3D images that include unlabeled images, such as transmitted light images or electron microscope images, and labeled images, such as images captured with fluorescence tagging. The computing device trains a statistical model to associate structures in the labeled images with the same structures in the unlabeled light images. The processor further applies the statistical model to a new unlabeled image to generate a predictive labeled image that predicts the location of a structure of interest in the new image.

IPC Classes  ?

  • G02B 21/00 - Microscopes
  • G06T 7/187 - SegmentationEdge detection involving region growingSegmentationEdge detection involving region mergingSegmentationEdge detection involving connected component labelling
  • G06T 7/11 - Region-based segmentation
  • G06T 7/174 - SegmentationEdge detection involving the use of two or more images
  • G06N 20/20 - Ensemble learning
  • G06N 3/04 - Architecture, e.g. interconnection topology
  • G06N 3/08 - Learning methods

66.

REMOVING INDEPENDENT NOISE USING DEEPINTERPOLATION

      
Application Number US2020054605
Publication Number 2021/086562
Status In Force
Filing Date 2020-10-07
Publication Date 2021-05-06
Owner ALLEN INSTITUTE (USA)
Inventor
  • Lecoq, Jerome, Anthony-Jean
  • Oliver, Michael, David
  • Siegle, Joshua, Handman
  • Koch, Christof

Abstract

A facility for transforming a subject data item sequence is described. The facility accesses a trained relationship model. For each of a plurality of subject items of the subject data item sequence, the facility: selects a first contiguous series of items of the subject data item sequence immediately before the subject data item; selects a second contiguous series of items of the subject data item sequence immediately after the subject data item; and applies the trained relationship model to the selected first and second contiguous series of data items to obtain a denoised version of the subject data item. The facility then assembles the obtained denoised subject data items into a denoised data item sequence.

IPC Classes  ?

  • H04N 5/21 - Circuitry for suppressing or minimising disturbance, e.g. moire or halo
  • H04N 7/01 - Conversion of standards
  • G06N 20/00 - Machine learning
  • G06T 5/00 - Image enhancement or restoration

67.

BUILDING COMPUTATIONAL TRANSFER FUNCTIONS ON 3D LIGHT MICROSCOPY IMAGES USING DEEP LEARNING

      
Application Number US2020053644
Publication Number 2021/067507
Status In Force
Filing Date 2020-09-30
Publication Date 2021-04-08
Owner
  • ALLEN INSTITUTE (USA)
  • UNIVERSITY OF NOTRE DAME DU LAC (USA)
Inventor
  • Chen, Jianxu
  • Viana, Matheus Palhares
  • Rafelski, Susanne Marie
  • Wang, Hongxiao
  • Chen, Danny Ziyi
  • Frick, Christopher Lee
  • Sluzewski, Filip

Abstract

An image transformation facility is described. The facility accesses a machine learning model trained to transform three-dimensional microscopy images in an imaging domain of a source image type into three-dimensional images in an imaging domain of a target image type. The facility also accesses a subject microscopy image in the imaging domain of the source image type. The facility applies the trained machine learning model to the subject microscopy image to obtain a transfer result image in the imaging domain of the target image type.

IPC Classes  ?

  • G06T 3/00 - Geometric image transformations in the plane of the image
  • G06T 7/30 - Determination of transform parameters for the alignment of images, i.e. image registration
  • G06T 15/50 - Lighting effects
  • G06N 3/08 - Learning methods

68.

Rescuing voltage-gated sodium channel function in inhibitory neurons

      
Application Number 17044232
Grant Number 12121563
Status In Force
Filing Date 2019-04-09
First Publication Date 2021-01-21
Grant Date 2024-10-22
Owner
  • Allen Institute (USA)
  • Seattle Children's Hospital (USA)
Inventor
  • Mich, John K.
  • Lein, Edward Sebastian
  • Ting, Jonathan
  • Levi, Boaz P.
  • Hess, Erik
  • Kalume, Franck

Abstract

Selectively providing voltage-gated sodium channel function sufficient to rescue impaired Nav1.1 function to inhibitory neurons is described. Provided voltage-gated sodium channel function sufficient to rescue impaired Nav1.1 function in inhibitory neurons can be used to treat disorders such as epilepsy, and more particularly, Dravet Syndrome.

IPC Classes  ?

  • A61K 38/17 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans
  • A61K 9/00 - Medicinal preparations characterised by special physical form
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C07K 14/705 - ReceptorsCell surface antigensCell surface determinants
  • C12N 15/86 - Viral vectors

69.

SYSTEMS AND METHODS FOR USING AN ONTOLOGY TO GENERATE DATABASE ENTRIES AND ACCESS AND SEARCH A DATABASE

      
Application Number US2020042186
Publication Number 2021/011691
Status In Force
Filing Date 2020-07-15
Publication Date 2021-01-21
Owner ALLEN INSTITUTE (USA)
Inventor Acharya, Gautham Bhat

Abstract

A system, apparatus and methods for generating database entries and tools for accessing and searching a database from an Ontology. Starting with an Ontology used to represent data and relationships between data, the system and methods described enable that data to be stored in a desired type of database and accessed using an API and search query generated from the Ontology. Embodiments provide a structure and process to implement a data access system or framework that can be used to unify and better understand information across an organization's entire set of data. Such a framework can help enable and improve the organization and discovery of knowledge, increase the value of existing data, and reduce complexity when developing next-generation applications.

IPC Classes  ?

  • G06F 7/00 - Methods or arrangements for processing data by operating upon the order or content of the data handled
  • G06F 16/00 - Information retrievalDatabase structures thereforFile system structures therefor

70.

Systems, apparatuses and methods for simultaneous multi-plane imaging

      
Application Number 16900279
Grant Number 11307143
Status In Force
Filing Date 2020-06-12
First Publication Date 2020-10-01
Grant Date 2022-04-19
Owner Allen Institute (USA)
Inventor
  • Tsyboulski, Dmitri
  • Orlova, Natalia
  • Lecoq, Jerome Anthony
  • Saggau, Peter

Abstract

A system includes a light source to generate an optical signal having a set of pulses at a first repetition rate. The system also includes a multiplexer circuit to generate a multiplexed optical signal from the optical signal n sets of pulses at a second repetition rate, where the n sets of pulses have different polarization states and are at the first repetition rate. The system also includes a focusing unit to split the multiplexed optical signal into n excitation signals to excite a sample. The system also includes an objective to receive the n excitation signals and to illuminate the sample. The objective and the focusing unit collectively focus each excitation signal of the n excitation signals on a different focal plane of the sample to generate a response signal. The system also includes a demultiplexer circuit to generate n emission signals based on the response signal.

IPC Classes  ?

  • G01N 21/64 - FluorescencePhosphorescence
  • G02B 21/00 - Microscopes
  • G02B 21/36 - Microscopes arranged for photographic purposes or projection purposes

71.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN SELECTED NEURONAL CELL POPULATIONS

      
Document Number 03142948
Status Pending
Filing Date 2020-02-14
Open to Public Date 2020-08-20
Owner ALLEN INSTITUTE (USA)
Inventor
  • Ting, Jonathan
  • Levi, Boaz P.
  • Tasic, Bosiljka
  • Mich, John K.
  • Hess, Erik
  • Lein, Edward Sebastian
  • Graybuck, Lucas T.
  • Daigle, Tanya
  • Zeng, Hongkui

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in GABAergic neurons generally; and/or GABAergic neuron cell types such as lysosomal associated membrane protein 5 (Lamp5) neurons; vasoactive intestinal polypeptide-expressing (Vip) neurons; somatostatin (Sst) neurons; and/or parvalbumin (Pvalb) neuron cell types. Certain artificial expression constructs additionally drive selective gene expression in Layer 4 and/or layer 5 intratelencephalic (IT) neurons, deep cerebellar nuclear neurons or cerebellar Purkinje cells.

IPC Classes  ?

  • C12N 5/0793 - Neurons
  • C12N 5/10 - Cells modified by introduction of foreign genetic material, e.g. virus-transformed cells
  • C12N 15/09 - Recombinant DNA-technology
  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof
  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 15/67 - General methods for enhancing the expression
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
  • C12N 15/861 - Adenoviral vectors

72.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN SELECTED NEURONAL CELL POPULATIONS

      
Application Number US2020018416
Publication Number 2020/168279
Status In Force
Filing Date 2020-02-14
Publication Date 2020-08-20
Owner ALLEN INSTITUTE (USA)
Inventor
  • Ting, Jonathan
  • Levi, Boaz P.
  • Tasic, Bosiljka
  • Mich, John K.
  • Hess, Erik
  • Lein, Edward Sebastian
  • Graybuck, Lucas T.
  • Daigle, Tanya
  • Zeng, Hongkui

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in GABAergic neurons generally; and/or GABAergic neuron cell types such as lysosomal associated membrane protein 5 (Lamp5) neurons; vasoactive intestinal polypeptide-expressing (Vip) neurons; somatostatin (Sst) neurons; and/or parvalbumin (Pvalb) neuron cell types. Certain artificial expression constructs additionally drive selective gene expression in Layer 4 and/or layer 5 intratelencephalic (IT) neurons, deep cerebellar nuclear neurons or cerebellar Purkinje cells.

IPC Classes  ?

  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C12N 15/09 - Recombinant DNA-technology
  • C12N 15/11 - DNA or RNA fragmentsModified forms thereof
  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 15/67 - General methods for enhancing the expression
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells

73.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN EXCITATORY CORTICAL NEURONS

      
Document Number 03118689
Status Pending
Filing Date 2019-11-05
Open to Public Date 2020-05-14
Owner ALLEN INSTITUTE (USA)
Inventor
  • Graybuck, Lucas T.
  • Tasic, Bosiljka
  • Daigle, Tanya
  • Ting, Jonathan
  • Zeng, Hongkui
  • Kalmbach, Brian Edward
  • Mich, John K.
  • Hess, Erik
  • Lein, Edward Sebastian
  • Levi, Boaz P.

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in excitatory cortical neurons, such as primarily within cortical layers 2/3, 4, 5, and 6 and including those with extratelencephalic (ET) projections, intratelencephalic (IT) projections, and pyramidal tract (PT) projections, among others.

IPC Classes  ?

  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C12N 5/0793 - Neurons
  • C12N 15/67 - General methods for enhancing the expression
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells

74.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN EXCITATORY CORTICAL NEURONS

      
Application Number US2019059927
Publication Number 2020/097121
Status In Force
Filing Date 2019-11-05
Publication Date 2020-05-14
Owner ALLEN INSTITUTE (USA)
Inventor
  • Graybuck, Lucas T.
  • Tasic, Bosiljka
  • Daigle, Tanya
  • Ting, Jonathan
  • Zeng, Hongkui
  • Kalmbach, Brian Edward
  • Mich, John K.
  • Hess, Erik
  • Lein, Edward Sebastian
  • Levi, Boaz P.

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in excitatory cortical neurons, such as primarily within cortical layers 2/3, 4, 5, and 6 and including those with extratelencephalic (ET) projections, intratelencephalic (IT) projections, and pyramidal tract (PT) projections, among others.

IPC Classes  ?

  • C12N 15/67 - General methods for enhancing the expression
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
  • C12N 5/0793 - Neurons
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy

75.

SEGMENTING 3D INTRACELLULAR STRUCTURES IN MICROSCOPY IMAGES USING AN ITERATIVE DEEP LEARNING WORKFLOW THAT INCORPORATES HUMAN CONTRIBUTIONS

      
Application Number US2019058894
Publication Number 2020/092590
Status In Force
Filing Date 2019-10-30
Publication Date 2020-05-07
Owner ALLEN INSTITUTE (USA)
Inventor
  • Chen, Jianxu
  • Ding, Liya
  • Viana, Matheus Palhares
  • Rafelski, Susanne Marie

Abstract

A facility for identifying the boundaries of 3-dimensional structures in 3-dimensional images is described. For each of multiple 3-dimensional images, the facility receives results of a first attempt to identify boundaries of structures in the 3-dimensional image, and causes the results of the first attempt to be presented to a person. For each of a number of 3-dimensional images, the facility receives input generated by the person providing feedback on the results of the first attempt. The facility then uses the following to train a deep-learning network to identify boundaries of 3-dimensional structures in 3-dimensional images: at least a portion of the plurality of 3-dimensional images, at least a portion of the received results, and at least a portion of provided feedback.

IPC Classes  ?

  • G06T 7/11 - Region-based segmentation
  • G06T 3/00 - Geometric image transformations in the plane of the image
  • G06T 5/00 - Image enhancement or restoration
  • G06T 5/20 - Image enhancement or restoration using local operators

76.

SEGMENTING 3D INTRACELLULAR STRUCTURES IN MICROSCOPY IMAGES USING AN ITERATIVE DEEP LEARNING WORKFLOW THAT INCORPORATES HUMAN CONTRIBUTIONS

      
Document Number 03117959
Status Pending
Filing Date 2019-10-30
Open to Public Date 2020-05-07
Owner ALLEN INSTITUTE (USA)
Inventor
  • Chen, Jianxu
  • Ding, Liya
  • Viana, Matheus Palhares
  • Rafelski, Susanne Marie

Abstract

A facility for identifying the boundaries of 3-dimensional structures in 3-dimensional images is described. For each of multiple 3-dimensional images, the facility receives results of a first attempt to identify boundaries of structures in the 3-dimensional image, and causes the results of the first attempt to be presented to a person. For each of a number of 3-dimensional images, the facility receives input generated by the person providing feedback on the results of the first attempt. The facility then uses the following to train a deep-learning network to identify boundaries of 3-dimensional structures in 3-dimensional images: at least a portion of the plurality of 3-dimensional images, at least a portion of the received results, and at least a portion of provided feedback.

IPC Classes  ?

77.

Segmenting 3D intracellular structures in microscopy images using an iterative deep learning workflow that incorporates human contributions

      
Application Number 16669089
Grant Number 11501446
Status In Force
Filing Date 2019-10-30
First Publication Date 2020-04-30
Grant Date 2022-11-15
Owner Allen Institute (USA)
Inventor
  • Chen, Jianxu
  • Ding, Liya
  • Viana, Matheus Palhares
  • Rafelski, Susanne Marie

Abstract

A facility for identifying the boundaries of 3-dimensional structures in 3-dimensional images is described. For each of multiple 3-dimensional images, the facility receives results of a first attempt to identify boundaries of structures in the 3-dimensional image, and causes the results of the first attempt to be presented to a person. For each of a number of 3-dimensional images, the facility receives input generated by the person providing feedback on the results of the first attempt. The facility then uses the following to train a deep-learning network to identify boundaries of 3-dimensional structures in 3-dimensional images: at least a portion of the plurality of 3-dimensional images, at least a portion of the received results, and at least a portion of provided feedback.

IPC Classes  ?

78.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN INTERNEURONS

      
Document Number 03115652
Status Pending
Filing Date 2019-10-03
Open to Public Date 2020-04-16
Owner
  • ALLEN INSTITUTE (USA)
  • SEATTLE CHILDREN'S HOSPITAL (D/B/A SEATTLE CHILDREN'S RESEARCH INSTITUTE) (USA)
Inventor
  • Ting, Jonathan
  • Levi, Boaz P.
  • Mich, John K.
  • Lein, Edward Sebastian
  • Kalume, Franck

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in GABAergic interneurons.

IPC Classes  ?

  • C12N 15/09 - Recombinant DNA-technology
  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 15/86 - Viral vectors
  • C12N 15/864 - Parvoviral vectors

79.

ARTIFICIAL EXPRESSION CONSTRUCTS FOR SELECTIVELY MODULATING GENE EXPRESSION IN INTERNEURONS

      
Application Number US2019054539
Publication Number 2020/076614
Status In Force
Filing Date 2019-10-03
Publication Date 2020-04-16
Owner
  • ALLEN INSTITUTE (USA)
  • SEATTLE CHILDREN'S HOSPITAL (D/B/A SEATTLE CHILDREN'S RESEARCH INSTITUTE) (USA)
Inventor
  • Ting, Jonathan
  • Levi, Boaz P.
  • Mich, John K.
  • Lein, Edward Sebastian
  • Kalume, Franck

Abstract

Artificial expression constructs for selectively modulating gene expression in selected central nervous system cell types are described. The artificial expression constructs can be used to selectively express synthetic genes or modify gene expression in GABAergic interneurons.

IPC Classes  ?

  • C12N 15/09 - Recombinant DNA-technology
  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 15/86 - Viral vectors
  • C12N 15/864 - Parvoviral vectors

80.

Systems, devices, and methods for image processing to generate an image having predictive tagging

      
Application Number 16304021
Grant Number 10935773
Status In Force
Filing Date 2018-08-08
First Publication Date 2019-12-19
Grant Date 2021-03-02
Owner Allen Institute (USA)
Inventor
  • Johnson, Gregory
  • Ounkomol, Chawin
  • Collman, Forrest
  • Seshamani, Sharmishtaa

Abstract

A computing device, method, system, and instructions in a non-transitory computer-readable medium for performing image analysis on 3D microscopy images to predict localization and/or labeling of various structures or objects of interest, by predicting the location in such images at which a dye or other marker associated with such structures would appear. The computing device, method, and system receives sets of 3D images that include unlabeled images, such as transmitted light images or electron microscope images, and labeled images, such as images captured with fluorescence tagging. The computing device trains a statistical model to associate structures in the labeled images with the same structures in the unlabeled light images. The processor further applies the statistical model to a new unlabeled image to generate a predictive labeled image that predicts the location of a structure of interest in the new image.

IPC Classes  ?

  • G02B 21/00 - Microscopes
  • G06T 7/187 - SegmentationEdge detection involving region growingSegmentationEdge detection involving region mergingSegmentationEdge detection involving connected component labelling
  • G06T 7/11 - Region-based segmentation
  • G06T 7/174 - SegmentationEdge detection involving the use of two or more images
  • G06N 20/20 - Ensemble learning
  • G06N 3/04 - Architecture, e.g. interconnection topology
  • G06N 3/08 - Learning methods

81.

STEM CELL LINES CONTAINING ENDOGENOUS, DIFFERENTIALLY-EXPRESSED TAGGED PROTEINS, METHODS OF PRODUCTION, AND USE THEREOF

      
Application Number US2019035852
Publication Number 2019/236893
Status In Force
Filing Date 2019-06-06
Publication Date 2019-12-12
Owner ALLEN INSTITUTE (USA)
Inventor Roberts, Brock

Abstract

The present invention provides stably tagged cells, including stem cells and methods for producing such cells comprising one or more tagged, differentially-expressed proteins using a gene editing system. The methods described herein enable the insertion of large fluorescent tags into a plurality of genomic loci to generate stem cells that are phenotypically and functional similar to the un-modified parent population. Stem cells produced by the methods described herein additionally retain the capacity to self-renew and differentiate into specialized cell types and can be used in assays and visualization of three-dimensional live cell imaging.

IPC Classes  ?

  • C12N 15/63 - Introduction of foreign genetic material using vectorsVectorsUse of hosts thereforRegulation of expression
  • C12N 9/22 - Ribonucleases
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy

82.

RESCUING VOLTAGE-GATED SODIUM CHANNEL FUNCTION IN INHIBITORY NEURONS

      
Document Number 03096407
Status Pending
Filing Date 2019-04-09
Open to Public Date 2019-10-17
Owner
  • SEATTLE CHILDREN'S HOSPITAL D/B/A SEATTLE CHILDREN'S RESEARCH INSTITUTE (USA)
  • ALLEN INSTITUTE (USA)
Inventor
  • Mich, John K.
  • Lein, Edward Sebastian
  • Ting, Jonathan
  • Levi, Boaz P.
  • Hess, Erik
  • Kalume, Franck

Abstract

Selectively providing voltage-gated sodium channel function sufficient to rescue impaired Nav1.1 function to inhibitory neurons is described. Provided voltage-gated sodium channel function sufficient to rescue impaired Nav1.1 function in inhibitory neurons can be used to treat disorders such as epilepsy, and more particularly, Dravet Syndrome.

IPC Classes  ?

  • A01K 67/00 - Rearing or breeding animals, not otherwise provided forNew or modified breeds of animals
  • A61K 35/76 - VirusesSubviral particlesBacteriophages
  • A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseasesGene therapy
  • C07K 14/705 - ReceptorsCell surface antigensCell surface determinants
  • C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
  • C12N 15/12 - Genes encoding animal proteins
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
  • C12N 15/86 - Viral vectors
  • C12N 15/864 - Parvoviral vectors

83.

RESCUING VOLTAGE-GATED SODIUM CHANNEL FUNCTION IN INHIBITORY NEURONS

      
Application Number US2019026638
Publication Number 2019/199867
Status In Force
Filing Date 2019-04-09
Publication Date 2019-10-17
Owner
  • ALLEN INSTITUTE (USA)
  • SEATTLE CHILDREN'S HOSPITAL D/B/A SEATTLE CHILDREN'S RESEARCH INSTITUTE (USA)
Inventor
  • Mich, John K.
  • Lein, Edward Sebastian
  • Ting, Jonathan
  • Levi, Boaz P.
  • Hess, Erik
  • Kalume, Franck

Abstract

Selectively providing voltage-gated sodium channel function sufficient to rescue impaired Nav1.1 function to inhibitory neurons is described. Provided voltage-gated sodium channel function sufficient to rescue impaired Nav1.1 function in inhibitory neurons can be used to treat disorders such as epilepsy, and more particularly, Dravet Syndrome.

IPC Classes  ?

  • A61K 31/7088 - Compounds having three or more nucleosides or nucleotides
  • A61K 31/7105 - Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
  • A61K 31/7115 - Nucleic acids or oligonucleotides having modified bases, i.e. other than adenine, guanine, cytosine, uracil or thymine
  • A61K 31/712 - Nucleic acids or oligonucleotides having modified sugars, i.e. other than ribose or 2'-deoxyribose
  • A61K 31/7125 - Nucleic acids or oligonucleotides having modified internucleoside linkage, i.e. other than 3'-5' phosphodiesters

84.

Miscellaneous Design

      
Serial Number 88657292
Status Registered
Filing Date 2019-10-16
Registration Date 2020-07-28
Owner Allen Institute, DBA Allen Institute for Brain Science; Allen Institute for Cell Science; Allen Institute for Immunology; Paul G. Allen Frontiers Group ()
NICE Classes  ?
  • 09 - Scientific and electric apparatus and instruments
  • 41 - Education, entertainment, sporting and cultural services

Goods & Services

Downloadable computer software for accessing medical and scientific research results Educational services, namely, providing classes, seminars, workshops and conferences in the fields of neuroscience and cell biology research, and distribution of informational materials therewith

85.

Miscellaneous Design

      
Serial Number 88657295
Status Registered
Filing Date 2019-10-16
Registration Date 2020-03-31
Owner Allen Institute, DBA ALLEN INSTITUTE FOR BRAIN SCIENCE; ALLEN INSTITUTE FOR CELL SCIENCE; ALLEN INSTITUTE FOR IMMUNOLOGY; PAUL G. ALLEN FRONTIERS GROUP ()
NICE Classes  ? 41 - Education, entertainment, sporting and cultural services

Goods & Services

Educational services, namely, providing classes, seminars, workshops and conferences in the fields of neuroscience and cell biology research, and distribution of informational materials therewith

86.

Miscellaneous Design

      
Serial Number 88605850
Status Registered
Filing Date 2019-09-05
Registration Date 2020-07-28
Owner Allen Institute, DBA Allen Institute for Brain Science; Allen Institute for Cell Science; Allen Institute for Immunology; Paul G. Allen Frontiers Group ()
NICE Classes  ?
  • 41 - Education, entertainment, sporting and cultural services
  • 42 - Scientific, technological and industrial services, research and design

Goods & Services

Educational services, namely, providing training, classes, workshops, seminars, symposia and conferences in the fields of human and animal biology research, and distributing informational materials in connection therewith Scientific and technological services, namely, science research information in the fields of science and medicine

87.

SYSTEMS, APPARATUSES AND METHODS FOR SIMULTANEOUS MULTI-PLANE IMAGING

      
Document Number 03083287
Status In Force
Filing Date 2018-12-11
Open to Public Date 2019-06-20
Grant Date 2024-02-20
Owner ALLEN INSTITUTE (USA)
Inventor
  • Tsyboulski, Dmitri
  • Orlova, Natalia
  • Lecoq, Jerome Anthony
  • Saggau, Peter

Abstract

A system includes a light source to generate an optical signal having a set of pulses at a first repetition rate. The system also includes a multiplexer circuit to generate a multiplexed optical signal from the optical signal n sets of pulses at a second repetition rate, where the n sets of pulses have different polarization states and are at the first repetition rate. The system also includes a focusing unit to split the multiplexed optical signal into n excitation signals to excite a sample. The system also includes an objective to receive the n excitation signals and to illuminate the sample. The objective and the focusing unit collectively focus each excitation signal of the n excitation signals on a different focal plane of the sample to generate a response signal. The system also includes a demultiplexer circuit to generate n emission signals based on the response signal.

IPC Classes  ?

  • G02B 21/00 - Microscopes
  • G02B 21/18 - Arrangements with more than one light-path, e.g. for comparing two specimens
  • G02B 27/28 - Optical systems or apparatus not provided for by any of the groups , for polarising

88.

SYSTEMS, APPARATUSES, AND METHODS FOR SIMULTANEOUS MULTI-PLANE IMAGING

      
Application Number US2018064909
Publication Number 2019/118433
Status In Force
Filing Date 2018-12-11
Publication Date 2019-06-20
Owner ALLEN INSTITUTE (USA)
Inventor
  • Tsyboulski, Dmitri
  • Orlova, Natalia
  • Lecoq, Jérôme, Anthony
  • Saggau, Peter

Abstract

A system includes a light source to generate an optical signal having a set of pulses at a first repetition rate. The system also includes a multiplexer circuit to generate a multiplexed optical signal from the optical signal n sets of pulses at a second repetition rate, where the n sets of pulses have different polarization states and are at the first repetition rate. The system also includes a focusing unit to split the multiplexed optical signal into n excitation signals to excite a sample. The system also includes an objective to receive the n excitation signals and to illuminate the sample. The objective and the focusing unit collectively focus each excitation signal of the n excitation signals on a different focal plane of the sample to generate a response signal. The system also includes a demultiplexer circuit to generate n emission signals based on the response signal.

IPC Classes  ?

  • G02B 21/00 - Microscopes
  • G02B 21/18 - Arrangements with more than one light-path, e.g. for comparing two specimens
  • G02B 27/28 - Optical systems or apparatus not provided for by any of the groups , for polarising

89.

SYSTEMS, DEVICES, AND METHODS FOR IMAGE PROCESSING TO GENERATE AN IMAGE HAVING PREDICTIVE TAGGING

      
Document Number 03071685
Status In Force
Filing Date 2018-08-08
Open to Public Date 2019-02-14
Grant Date 2023-11-21
Owner ALLEN INSTITUTE (USA)
Inventor
  • Johnson, Gregory
  • Ounkomol, Chawin
  • Collman, Forrest
  • Seshamani, Sharmishtaa

Abstract

A computing device, method, system, and instructions in a non-transitory computerreadable medium for performing image analysis on 3D microscopy images to predict localization and/or labeling of various structures or objects of interest, by predicting the location in such images at which a dye or other marker associated with such structures would appear. The computing device, method, and system receives sets of 3D images that include unlabeled images, such as transmitted light images or electron microscope images, and labeled images, such as images captured with fluorescence tagging. The computing device trains a statistical model to associate structures in the labeled images with the same structures in the unlabeled light images. The processor further applies the statistical model to a new unlabeled image to generate a predictive labeled image that predicts the location of a structure of interest in the new image.

IPC Classes  ?

  • A61B 5/0275 - Measuring blood flow using tracers, e.g. dye dilution
  • G06N 3/02 - Neural networks
  • G06T 7/10 - SegmentationEdge detection
  • G06V 20/69 - Microscopic objects, e.g. biological cells or cellular parts

90.

SYSTEMS, DEVICES, AND METHODS FOR IMAGE PROCESSING TO GENERATE AN IMAGE HAVING PREDICTIVE TAGGING

      
Application Number US2018045840
Publication Number 2019/032723
Status In Force
Filing Date 2018-08-08
Publication Date 2019-02-14
Owner ALLEN INSTITUTE (USA)
Inventor
  • Johnson, Gregory
  • Ounkomol, Chawin
  • Collman, Forrest
  • Seshamani, Sharmishtaa

Abstract

A computing device, method, system, and instructions in a non-transitory computerreadable medium for performing image analysis on 3D microscopy images to predict localization and/or labeling of various structures or objects of interest, by predicting the location in such images at which a dye or other marker associated with such structures would appear. The computing device, method, and system receives sets of 3D images that include unlabeled images, such as transmitted light images or electron microscope images, and labeled images, such as images captured with fluorescence tagging. The computing device trains a statistical model to associate structures in the labeled images with the same structures in the unlabeled light images. The processor further applies the statistical model to a new unlabeled image to generate a predictive labeled image that predicts the location of a structure of interest in the new image.

IPC Classes  ?

  • A61B 5/0275 - Measuring blood flow using tracers, e.g. dye dilution
  • G06K 9/66 - Methods or arrangements for recognition using electronic means using simultaneous comparisons or correlations of the image signals with a plurality of references, e.g. resistor matrix references adjustable by an adaptive method, e.g. learning

91.

SYSTEMS, DEVICES, AND METHODS FOR IMAGE PROCESSING TO GENERATE AN IMAGE HAVING PREDICTIVE TAGGING

      
Document Number 03213179
Status Pending
Filing Date 2018-08-08
Open to Public Date 2019-02-14
Owner ALLEN INSTITUTE (USA)
Inventor
  • Johnson, Gregory
  • Ounkomol, Chawin
  • Collman, Forrest
  • Seshamani, Sharmishtaa

Abstract

A computing device, method, system, and instructions in a non-transitory computer-readable medium for performing image analysis on 3D microscopy images to predict localization and/or labeling of various structures or objects of interest, by predicting the location in such images at which a dye or other marker associated with such structures would appear. The computing device, method, and system receives sets of 3D images that include unlabeled images, such as transmitted light images or electron microscope images, and labeled images, such as images captured with fluorescence tagging. The computing device trains a statistical model to associate structures in the labeled images with the same structures in the unlabeled light images. The processor further applies the statistical model to a new unlabeled image to generate a predictive labeled image that predicts the location of a structure of interest in the new image.

IPC Classes  ?

  • A61B 5/0275 - Measuring blood flow using tracers, e.g. dye dilution
  • G06T 15/50 - Lighting effects
  • G06V 10/82 - Arrangements for image or video recognition or understanding using pattern recognition or machine learning using neural networks
  • G06V 20/69 - Microscopic objects, e.g. biological cells or cellular parts

92.

GENETICALLY-TAGGED STEM CELL LINES AND METHODS OF USE

      
Application Number US2018017708
Publication Number 2018/148603
Status In Force
Filing Date 2018-02-09
Publication Date 2018-08-16
Owner ALLEN INSTITUTE (USA)
Inventor
  • Gunawardane, Ruwanthi
  • Roberts, Brock
  • Haupt, Amanda
  • Horwitz, Rick
  • Wiegraebe, Winfried
  • Gaudreault, Nathalie
  • Bialy, Nikki
  • Rafelski, Susanne
  • Johnson, Graham
  • Mueller, Irina
  • Hookway, Caroline
  • Tucker, Andrew

Abstract

The present invention provides stably tagged stem cells and methods for producing stem cells comprising one or more tagged proteins using a gene editing system. The methods described herein enable the insertion of large fluorescent tags into a plurality of genomic loci to generate stem cells that are phenotypically and functional similar to the un-modified parent population. Stem cells produced by the methods described herein additionally retain the capacity to self-renew and differentiate into specialized cell types and can be used in assays and visualization of three- dimensional live cell imaging.

IPC Classes  ?

  • A61K 38/46 - Hydrolases (3)
  • C12N 9/22 - Ribonucleases
  • C12N 15/85 - Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
  • C12N 15/90 - Stable introduction of foreign DNA into chromosome

93.

Miscellaneous Design

      
Serial Number 87264037
Status Registered
Filing Date 2016-12-09
Registration Date 2018-02-27
Owner Allen Institute, DBA Allen Institute for Brain Science; Allen Institute for Cell Science ()
NICE Classes  ?
  • 09 - Scientific and electric apparatus and instruments
  • 41 - Education, entertainment, sporting and cultural services
  • 42 - Scientific, technological and industrial services, research and design

Goods & Services

Computer software for accessing medical and scientific research results downloadable via the internet Educational services, namely, providing training, classes, workshops, seminars and conferences in the field of cell biology research, and distributing informational materials in connection therewith Medical and scientific research, namely, providing temporary use of non-downloadable computer software for accessing medical and scientific research results

94.

ALLEN INSTITUTE FOR CELL SCIENCE

      
Serial Number 87264025
Status Registered
Filing Date 2016-12-09
Registration Date 2018-02-27
Owner Allen Institute, DBA Allen Institute for Brain Science, Allen Institute for Cell Science ()
NICE Classes  ?
  • 09 - Scientific and electric apparatus and instruments
  • 41 - Education, entertainment, sporting and cultural services
  • 42 - Scientific, technological and industrial services, research and design

Goods & Services

Computer software for accessing medical and scientific research results downloadable via the internet Educational services, namely, providing training, classes, workshops, seminars and conferences in the field of cell biology research, and distributing informational materials in connection therewith Medical and scientific research, namely, providing temporary use of non-downloadable computer software for accessing medical and scientific research results

95.

ALLEN INSTITUTE

      
Serial Number 87264038
Status Registered
Filing Date 2016-12-09
Registration Date 2017-08-08
Owner Allen Institute, DBA Allen Institute for Brain Science; Allen Institute for Cell Science ()
NICE Classes  ?
  • 09 - Scientific and electric apparatus and instruments
  • 41 - Education, entertainment, sporting and cultural services
  • 42 - Scientific, technological and industrial services, research and design

Goods & Services

Computer software for accessing medical and scientific research results downloadable via the internet Educational services, namely, providing classes, seminars, workshops and conferences in the fields of neuroscience and cell biology research, and distribution of informational materials therewith Medical and scientific research, namely, providing temporary use of non-downloadable software for accessing medical and scientific results

96.

METHODS TO ISOLATE HIGH QUALITY RNA FROM FIXED SAMPLES

      
Application Number US2016025077
Publication Number 2016/161023
Status In Force
Filing Date 2016-03-30
Publication Date 2016-10-06
Owner
  • PRESIDENT AND FELLOWS OF HARVARD COLLEGE (USA)
  • ALLEN INSTITUTE (USA)
Inventor
  • Jang, Sumin
  • Thomsen, Elliot, R.
  • Doyle, Adele, M.
  • Levi, Boaz, P.
  • Ramanathan, Sharad

Abstract

Some aspects of this disclosure provide compositions, methods, and kits for isolating RNA from fixed biological samples. Such compositions, methods, and kits are useful for isolating intact (e.g., not degraded or fragmented) RNA, for example, RNA having an RNA integrity number (RIN) ≥ 8.0.

IPC Classes  ?

  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
  • G01N 1/28 - Preparing specimens for investigation
  • G01N 1/30 - StainingImpregnating

97.

Miscellaneous Design

      
Serial Number 85582032
Status Registered
Filing Date 2012-03-28
Registration Date 2012-11-13
Owner ALLEN INSTITUTE, DBA ALLEN INSTITUTE FOR BRAIN SCIENCE; ALLEN INSTITUTE FOR CELL SCIENCE; ALLEN INSTITUTE FOR IMMUNOLOGY; ALLEN INSTITUTE FOR NEURAL DYNAMICS; PAUL G. ALLEN FRONTIERS GROUP ()
NICE Classes  ?
  • 09 - Scientific and electric apparatus and instruments
  • 42 - Scientific, technological and industrial services, research and design

Goods & Services

Computer software for accessing medical and scientific research results downloadable via the internet Medical and scientific research, namely, providing temporary use of non-downloadable software for accessing medical and scientific results

98.

ALLEN

      
Serial Number 77809537
Status Registered
Filing Date 2009-08-20
Registration Date 2010-03-02
Owner ALLEN INSTITUTE, DBA ALLEN INSTITUTE FOR BRAIN SCIENCE; ALLEN INSTITUTE FOR CELL SCIENCE ()
NICE Classes  ? 42 - Scientific, technological and industrial services, research and design

Goods & Services

A house mark for medical and scientific research, namely, providing temporary use of non-downloadable computer software for accessing medical and scientific research results

99.

ALLEN

      
Serial Number 77807910
Status Registered
Filing Date 2009-08-19
Registration Date 2010-03-02
Owner ALLEN INSTITUTE, DBA ALLEN INSTITUTE FOR BRAIN SCIENCE; ALLEN INSTITUTE FOR CELL SCIENCE ()
NICE Classes  ? 42 - Scientific, technological and industrial services, research and design

Goods & Services

A house mark for medical and scientific research, namely, providing temporary use of non-downloadable computer software for accessing medical and scientific research results

100.

ALLEN INSTITUTE FOR BRAIN SCIENCE

      
Serial Number 77789337
Status Registered
Filing Date 2009-07-24
Registration Date 2010-03-02
Owner ALLEN INSTITUTE, DBA ALLEN INSTITUTE FOR BRAIN SCIENCE; ALLEN INSTITUTE FOR CELL SCIENCE; ALLEN INSTITUTE FOR IMMUNOLOGY; PAUL G. ALLEN FRONTIERS GROUP ()
NICE Classes  ?
  • 09 - Scientific and electric apparatus and instruments
  • 42 - Scientific, technological and industrial services, research and design

Goods & Services

Computer software for accessing medical and scientific research results downloadable via the internet Medical and scientific research, namely, providing temporary use of non-downloadable software for accessing medical and scientific results
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