JP7602484B2 - 収束抗体特異性配列パターンの識別 - Google Patents

収束抗体特異性配列パターンの識別 Download PDF

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JP7602484B2
JP7602484B2 JP2021561675A JP2021561675A JP7602484B2 JP 7602484 B2 JP7602484 B2 JP 7602484B2 JP 2021561675 A JP2021561675 A JP 2021561675A JP 2021561675 A JP2021561675 A JP 2021561675A JP 7602484 B2 JP7602484 B2 JP 7602484B2
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amino acid
antigen
sequences
sequence
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JP2022530941A (ja
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シモン フリーデンソン
サイ レッディ
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Eidgenoessische Technische Hochschule Zurich ETHZ
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    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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    • G06N3/0895—Weakly supervised learning, e.g. semi-supervised or self-supervised learning
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    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
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    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N7/00—Computing arrangements based on specific mathematical models
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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/30—Detection of binding sites or motifs
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/30—Unsupervised data analysis

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JP2021561675A 2019-05-03 2020-05-02 収束抗体特異性配列パターンの識別 Active JP7602484B2 (ja)

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JP2024155436A JP2024167413A (ja) 2019-05-03 2024-09-10 収束抗体特異性配列パターンの識別

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US201962843010P 2019-05-03 2019-05-03
US62/843,010 2019-05-03
PCT/IB2020/054171 WO2020225693A1 (en) 2019-05-03 2020-05-02 Identification of convergent antibody specificity sequence patterns

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CA (1) CA3132181A1 (https=)
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JP7648099B2 (ja) 2019-05-19 2025-03-18 ジャスト－エヴォテック バイオロジクス，インコーポレイテッド 機械学習法によるタンパク質配列の生成
CA3160429A1 (en) * 2019-12-06 2021-06-10 Philip M. KIM System and method for generating a protein sequence
US11388356B1 (en) * 2021-04-12 2022-07-12 Tetramem Inc. AI fusion pixel sensor using memristors
CN113393900B (zh) * 2021-06-09 2022-08-02 吉林大学 基于改进Transformer模型的RNA状态推断研究方法
US20250191674A1 (en) * 2022-02-28 2025-06-12 Genentech, Inc. Protein design with segment preservation
US12587274B2 (en) 2023-03-28 2026-03-24 Quantum Generative Materials Llc Satellite optimization management system based on natural language input and artificial intelligence
CN116895350B (zh) * 2023-08-04 2024-01-16 辽宁工业大学 一种在复合位移加载下波纹管的多轴疲劳寿命预测方法
WO2025074981A1 (ja) * 2023-10-04 2025-04-10 国立大学法人大阪大学 抗体選別方法、コンピュータプログラム及び情報処理装置
US12368503B2 (en) 2023-12-27 2025-07-22 Quantum Generative Materials Llc Intent-based satellite transmit management based on preexisting historical location and machine learning
US12603701B2 (en) 2023-12-27 2026-04-14 Quantum Generative Materials Llc Distributed satellite constellation management and control system

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2012097107A (ja) 2005-11-14 2012-05-24 Bioren Inc 推定成熟ｃｄｒのブラスティングならびにコホートライブラリの作製およびスクリーニングによる抗体の超ヒト化
CN108138244A (zh) 2015-09-18 2018-06-08 纽约市哥伦比亚大学理事会 病毒组捕获测序平台、设计和构建方法以及使用方法

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US20230019590A1 (en) * 2010-03-23 2023-01-19 Iogenetics, Llc Bioinformatic processes for determination of peptide binding
US11573239B2 (en) * 2017-07-17 2023-02-07 Bioinformatics Solutions Inc. Methods and systems for de novo peptide sequencing using deep learning
EP3486816A1 (en) * 2017-11-16 2019-05-22 Institut Pasteur Method, device, and computer program for generating protein sequences with autoregressive neural networks
CN108549794B (zh) * 2018-03-29 2021-05-25 中国林业科学研究院资源昆虫研究所 一种蛋白质二级结构预测方法
US20220180975A1 (en) * 2019-01-28 2022-06-09 The Broad Institute, Inc. Methods and systems for determining gene expression profiles and cell identities from multi-omic imaging data

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2012097107A (ja) 2005-11-14 2012-05-24 Bioren Inc 推定成熟ｃｄｒのブラスティングならびにコホートライブラリの作製およびスクリーニングによる抗体の超ヒト化
CN108138244A (zh) 2015-09-18 2018-06-08 纽约市哥伦比亚大学理事会 病毒组捕获测序平台、设计和构建方法以及使用方法

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AU2020269607B2 (en) 2025-12-11
JP2024167413A (ja) 2024-12-03
IL287237A (en) 2021-12-01
US20220164627A1 (en) 2022-05-26
CN114026645A (zh) 2022-02-08
EP3963590A1 (en) 2022-03-09
JP2022530941A (ja) 2022-07-05
WO2020225693A1 (en) 2020-11-12
CN120526845A (zh) 2025-08-22
AU2020269607A1 (en) 2021-10-28
CA3132181A1 (en) 2020-11-12

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