公开(公告)号：US20240355417A1

公开(公告)日：2024-10-24

申请号：US18618412

申请日：2024-03-27

申请人： BioNTech SE ,  InstaDeep Ltd

发明人： Alexander Muik ,  Ugur Sahin ,  Asaf Poran ,  Alexandra Walls ,  Yunguan Fu ,  Rafal Okuniewski ,  Nicolas Winfried Pfeuffer

IPC分类号： G16B20/50 ,  G16B40/20 ,  G16B45/00 ,  G16B50/30 ,  G16H50/80

CPC分类号： G16B20/50 ,  G16B40/20 ,  G16B45/00 ,  G16B50/30 ,  G16H50/80

摘要： The present disclosure, among other things, provides technologies for identifying, characterizing, and/or monitoring variant sequences of a particular reference infections agent. Among other things, systems, methods, and architectures described herein provide visualization and decision support tools that can, e.g., facilitate decision making processes by local authorities and improve pandemic response in terms of, e.g., resource allocation, policy making, and speed tailored vaccine development. The present disclosure also provides tools for analyzing circulating variants to predict mutations likely to increase immune evasion of infectious agents.

公开(公告)号：US20240117365A1

公开(公告)日：2024-04-11

申请号：US18454343

申请日：2023-08-23

申请人： The Broad Institute, Inc. ,  Massachusetts Institute of Technology

发明人： Feng Zhang

IPC分类号： C12N15/74 ,  C12N9/22 ,  C12N15/113 ,  C12N15/63 ,  C12N15/70 ,  C12N15/85 ,  C12N15/90 ,  G16B20/00 ,  G16B20/20 ,  G16B20/30 ,  G16B20/50 ,  G16B30/10

CPC分类号： C12N15/746 ,  C12N9/22 ,  C12N15/113 ,  C12N15/63 ,  C12N15/70 ,  C12N15/74 ,  C12N15/85 ,  C12N15/8509 ,  C12N15/907 ,  G16B20/00 ,  G16B20/20 ,  G16B20/30 ,  G16B20/50 ,  G16B30/10 ,  C12N15/102 ,  C12N2310/20 ,  C12N2310/3519 ,  C12N2310/531

摘要： The invention provides for systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for selecting specific cells by introducing precise mutations utilizing the CRISPR/Cas system.

公开(公告)号：US20240047011A1

公开(公告)日：2024-02-08

申请号：US18488691

申请日：2023-10-17

申请人： The Broad Institute, Inc. ,  Massachusetts Institute of Technology

发明人： Feng Zhang ,  David Arthur Scott

IPC分类号： G16B40/00 ,  G16B20/00 ,  G16B20/50 ,  G16B40/30 ,  G16B20/30 ,  G06F18/231 ,  G06F18/20 ,  G06F18/2413

CPC分类号： G16B40/00 ,  G16B20/00 ,  G16B20/50 ,  G16B40/30 ,  G16B20/30 ,  G06F18/231 ,  G06F18/295 ,  G06F18/2413 ,  G06N3/088

摘要： Embodiments disclosed herein provide methods for identifying new CRISPR loci and effectors, as well as different CRISPR loci combinations found in various organisms. Class-II CRISPR systems contain single-gene effectors that have been engineered for transformative biological discovery and biomedical applications. Discovery of additional single-gene or multicomponent CRISPR effectors may enhance existing CRISPR applications, such as precision genome engineering. Comprehensive characterization of CRISPR-loci may identify novel functional roles of CRISPR loci enabling new tools for biomedicine and biological discovery. CRISPR loci have enormous feature complexity, but classification of CRISPR loci has been focused on a small fraction of highly abundant features. Increased genome sequencing has enhanced the sampling of this feature complexity.

公开(公告)号：US20230343412A1

公开(公告)日：2023-10-26

申请号：US18058611

申请日：2022-11-23

申请人： Beijing Youzhuju Network Technology Co., Ltd ,  Lemon Inc.

发明人： Fei YE ,  Danqing WANG

IPC分类号： G16B20/30 ,  G16B20/50

CPC分类号： G16B20/30 ,  G16B20/50

摘要： Systems and methods directed to providing a method for determining a prediction result related to an antibody sequence. The method comprises obtaining an antibody sequence comprising a plurality of amino acids, and obtaining a germline sequence of the antibody sequence. The method further comprises determining a prediction result related to the antibody sequence based on at least one of: evolution information between the antibody sequence and the germline sequence, or a mutation position on the antibody sequence, wherein an amino acid of the plurality of amino acids mutates on the mutation position.

公开(公告)号：US20230298694A1

公开(公告)日：2023-09-21

申请号：US17722528

申请日：2022-04-18

申请人： Subhadra Dravida ,  Samhita B L N

发明人： Subhadra Dravida ,  Samhita B L N

IPC分类号： G16B20/50 ,  G16B40/00 ,  G16C20/30 ,  C12Q1/6827 ,  C12Q1/70 ,  C12N5/074

CPC分类号： G16B20/50 ,  C12N5/0696 ,  C12Q1/6827 ,  C12Q1/70 ,  G16B40/00 ,  G16C20/30

摘要： A system and method for test predicting human neurovirulence and neurotoxicity risks is disclosed. The system comprises a real-time platform or TRANS-MSC (Configured Human induced Pluripotent Stem Cells) unit and a trained digital platform. The TRANS-MSC incubates the vaccine/biologic, drug/API, cosmetic/ingredient, anti-venom aliquots collected from the produced batches in the manufacturing system. The digital platform is embedded with artificial intelligence (AI) and machine learning (ML) modules, augmented with a robotic process automation framework. The AI modules predict human neurovirulence, human neurotoxicity patterns along with any adventitious microbial contaminants in the process. The AI and ML modules are trained with a plurality of TRANS-MSC acquired phenotype micrographs and a plurality of neurotoxic genes involved in viral, bacterial, fungal infections. Further, the test is customized to a genetically distinct population, user’s library of research-grade, ingredients, intermittents, final products, etc. that are at the risk of causing neurovirulence or neurotoxicity in the clinics.

公开(公告)号：US20230227534A1

公开(公告)日：2023-07-20

申请号：US17631640

申请日：2020-07-24

申请人： ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (EPFL)

发明人： Patrick BARTH

IPC分类号： C07K14/72 ,  G16B15/20 ,  G16B15/30 ,  G16B20/50

CPC分类号： C07K14/723 ,  G16B15/20 ,  G16B15/30 ,  G16B20/50

摘要： The present disclosure relates to a method for generating variants of a protein based on a native protein regulated by allosteric pathway, the method comprising:

i) providing 3D structures of the native protein;
ii) identifying at least one pair of coupled allosteric sites within the amino acid sequence of the native protein named microswitch;
iii) generating in silico mutations of said identified microswitch to generate a pool of variants;
iv) computing at least one score reflecting the variation in allosteric coupling; and/or the variation in the relative stability
v) predicting the activity of each variant compared to the native protein based on the computed score.

The disclosure also concern a computer implemented program to carry out said method, and a variant of a protein or an active fragment thereof, a polynucleotide.

公开(公告)号：US11636920B2

公开(公告)日：2023-04-25

申请号：US16230149

申请日：2018-12-21

申请人： Deep Genomics Incorporated

发明人： Hui Yuan Xiong ,  Brendan Frey

IPC分类号： G16B20/20 ,  G06N3/08 ,  G06N3/04 ,  G16B40/00 ,  G16B20/00 ,  G16B40/20 ,  G16B30/00 ,  G16H10/40 ,  G16H50/30 ,  G16H50/70 ,  G16H50/20 ,  G16B5/00 ,  G16B40/30 ,  G16B50/20 ,  G16B20/40 ,  G16B20/50 ,  G06N3/084 ,  G06N3/082

摘要： We describe systems and methods for generating and training convolutional neural networks using biological sequences and relevance scores derived from structural, biochemical, population and evolutionary data. The convolutional neural networks take as input biological sequences and additional information and output molecular phenotypes. Biological sequences may include DNA, RNA and protein sequences. Molecular phenotypes may include protein-DNA interactions, protein-RNA interactions, protein-protein interactions, splicing patterns, polyadenylation patterns, and microRNA-RNA interactions, which may be described using numerical, categorical or ordinal attributes. Intermediate layers of the convolutional neural networks are weighted using relevance score sequences, for example, conservation tracks. The resulting molecular phenotype convolutional neural networks may be used in genetic testing, to identify drug targets, to identify patients that respond similarly to a drug, to ascertain health risks, or to connect patients that have similar molecular phenotypes.

公开(公告)号：US20220409725A1

公开(公告)日：2022-12-29

申请号：US17395400

申请日：2021-08-05

申请人： Genentech, Inc.

发明人： Paul CARTER ,  Christoph SPIESS ,  Yiyuan YIN ,  Jianhui ZHOU ,  Wendy SANDOVAL ,  Jacob CORN ,  Michael DILLON

IPC分类号： A61K39/44 ,  C07K16/46 ,  G16B20/50 ,  G16B20/30 ,  A61K39/395

摘要： Provided are, inter alia, multispecific antigen binding proteins, or antigen-binding fragments thereof, comprising one or more mutations in the VH/VL domains and/or CH1/CL domains, pharmaceutical compositions comprising same, isolated nucleic acids, vectors, and host cells encoding/expressing same, method of making the multispecific antigen binding proteins, computer readable media for evaluating multispecific antigen binding proteins, and libraries.

公开(公告)号：US20220361428A1

公开(公告)日：2022-11-17

申请号：US17874203

申请日：2022-07-26

申请人： MONSANTO TECHNOLOGY LLC

发明人： David Vincent BUTRUILLE ,  Lex Evan FLAGEL

IPC分类号： A01H1/04 ,  G16B20/00 ,  G16B40/00 ,  C12Q1/6895 ,  C12N15/82 ,  G16B20/50

摘要： Methods are provided for genome editing. On example method includes editing a genome sequence of an organism with multiple edits simultaneously without precise knowledge of a phenotypic effect of each individual one of the multiple edits, wherein the multiple edits are selected based on a prediction of an aggregate phenotypic effect of the multiple edits on a phenotypic trait. The method also includes aggregating the multiple edits into multi-dimensional pools, whereby phenotypic effects of contrasting pools of edits are compared to ascertain which of the multiple edits are most likely to be causing large phenotypic effects while eliminating need to evaluate each edit separately. The organism may include one of: maize, soybean, wheat, sorghum, rice, cotton, rapeseed, sunflower, bean, tomato, squash, cucumber, melon, pepper, watermelon, eggplant, okra, pea, chickpea, lentil, peanut, onion, carrot, celery, beet, cauliflower, broccoli, cabbage, Brussels sprout, radish, black-eyed pea, potato, sweet-potato, sugar cane, cassava, and banana.

公开(公告)号：US20220246240A1

公开(公告)日：2022-08-04

申请号：US17719431

申请日：2022-04-13

申请人： President and Fellows of Harvard College

发明人： Gleb Kuznetsov ,  Marc J. Lajoie ,  Matthieu M. Landon ,  Michael G. Napolitano ,  Daniel Bryan Goodman ,  Christopher J. Gregg ,  George M. Church ,  Nili Ostrov

IPC分类号： G16B35/10 ,  G16B20/50 ,  C07K14/245 ,  C12N15/10 ,  C12P21/00

摘要： Methods and systems for designing, testing, and validating genome designs based on rules or constraints or conditions or parameters or features and scoring are described herein. A computer-implemented method includes receiving data for a known genome and a list of alleles, identifying and removing occurrences of each allele in the known genome, determining a plurality of allele choices with which to replace occurrences in the known genome, generating a plurality of alternative gene sequences for a genome design based on the known genome, wherein each alternative gene sequence comprises a different allele choice, applying a plurality of rules or constraints or conditions or parameters or features to each alternative gene sequence by assigning a score for each rule or constraint or condition or parameter or feature in each alternative gene sequence, resulting in scores for the applied plurality of rules or constraints or conditions or parameters or features, scoring each alternative gene sequence based on a weighted combination of the scores for the plurality of rules or constraints or conditions or parameters or features, and selecting at least one alternative gene sequence as the genome design based on the scoring.