AU2014212432B2 - Methods, systems, and software for identifying bio-molecules using models of multiplicative form - Google Patents

Methods, systems, and software for identifying bio-molecules using models of multiplicative form Download PDF

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AU2014212432B2
AU2014212432B2 AU2014212432A AU2014212432A AU2014212432B2 AU 2014212432 B2 AU2014212432 B2 AU 2014212432B2 AU 2014212432 A AU2014212432 A AU 2014212432A AU 2014212432 A AU2014212432 A AU 2014212432A AU 2014212432 B2 AU2014212432 B2 AU 2014212432B2
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Nicholas John Agard
Gregory Allan Cope
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Codexis Inc
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    • C12N15/1034Isolating an individual clone by screening libraries
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    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
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    • G16B5/00ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
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AU2014212432A 2013-01-31 2014-01-29 Methods, systems, and software for identifying bio-molecules using models of multiplicative form Active AU2014212432B2 (en)

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US201361759276P 2013-01-31 2013-01-31
US61/759,276 2013-01-31
US201361799377P 2013-03-15 2013-03-15
US61/799,377 2013-03-15
PCT/US2014/013668 WO2014120821A1 (en) 2013-01-31 2014-01-29 Methods, systems, and software for identifying bio-molecules using models of multiplicative form

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EP (4) EP4414988A3 (https=)
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CN (3) CN109360608B (https=)
AU (2) AU2014212432B2 (https=)
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Families Citing this family (76)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9665694B2 (en) 2013-01-31 2017-05-30 Codexis, Inc. Methods, systems, and software for identifying bio-molecules with interacting components
EP3597772A1 (en) 2013-04-17 2020-01-22 Agency For Science, Technology And Research Method for generating extended sequence reads
EP2911075A1 (de) * 2014-02-25 2015-08-26 LTS LOHMANN Therapie-Systeme AG System zur Bestimmung einer Eignung eines Wirkstoffs für die transdermale oder transmukosale Applikation sowie entsprechendes Verfahren
US10370648B2 (en) 2014-11-25 2019-08-06 Codexis, Inc. Engineered imine reductases and methods for the reductive amination of ketone and amine compounds
US20170372005A1 (en) * 2014-12-22 2017-12-28 Board Of Regents Of The University Of Texas System Systems and methods for processing sequence data for variant detection and analysis
LT3237621T (lt) 2014-12-22 2023-09-25 Codexis, Inc. Žmogaus alfa-galaktozidazės variantai
EP3298524A4 (en) 2015-05-22 2019-03-20 CSTS Health Care Inc. THERMODYNAMIC MEASURES ON PROTEIN-PROTEIN INTERACTION NETWORKS FOR CANCER THERAPY
FR3047013A1 (fr) * 2016-01-22 2017-07-28 Univ Montpellier Procede de classification d'un echantillon biologique.
WO2017190211A1 (en) * 2016-05-04 2017-11-09 Deep Genomics Incorporated Methods and systems for producing an expanded training set for machine learning using biological sequences
WO2017213758A1 (en) 2016-06-09 2017-12-14 Codexis, Inc. Biocatalysts and methods for hydroxylation of chemical compounds
MX2018015534A (es) 2016-06-15 2019-03-14 Codexis Inc Beta-glucosidasas dise?adas y metodos de glucosilacion.
IL264686B2 (en) 2016-08-26 2024-07-01 Codexis Inc Engineered imine reductases and methods for reversible amination of ketone and amine compounds
US10118610B2 (en) * 2016-08-31 2018-11-06 Ford Global Technologies, Llc Autonomous vehicle using path prediction
CA3175070A1 (en) 2017-02-03 2018-08-09 Codexis, Inc. Engineered glycosyltransferases and steviol glycoside glucosylation methods
MX2019009615A (es) 2017-02-13 2019-10-14 Codexis Inc Polipeptidos dise?ados de fenilalanina amonio liasa.
CN108693787A (zh) * 2017-03-29 2018-10-23 株式会社东芝 模型构建系统以及模型构建方法
KR20250028535A (ko) 2017-06-30 2025-02-28 코덱시스, 인코포레이티드 T7 rna 폴리머라제 변이체
EP3645712A4 (en) 2017-06-30 2021-07-07 Codexis, Inc. T7 RNA POLYMERASE VARIANTS
CN107677997B (zh) * 2017-09-28 2021-06-29 杭州电子科技大学 基于GLMB滤波和Gibbs采样的扩展目标跟踪方法
US20190108311A1 (en) * 2017-10-06 2019-04-11 Grail, Inc. Site-specific noise model for targeted sequencing
US11462299B2 (en) 2017-10-17 2022-10-04 Invitae Corporation Molecular evidence platform for auditable, continuous optimization of variant interpretation in genetic and genomic testing and analysis
JP2021506252A (ja) 2017-12-13 2021-02-22 コデクシス, インコーポレイテッド アミドカップリングのためのカルボキシエステラーゼポリペプチド
CN108281192B (zh) * 2017-12-29 2022-03-22 一诺仪器(中国)有限公司 基于集成学习算法的人体成分预测方法及系统
WO2020028039A1 (en) 2018-07-30 2020-02-06 Codexis, Inc. Engineered glycosyltransferases and steviol glycoside glucosylation methods
WO2020077274A1 (en) * 2018-10-11 2020-04-16 Berkeley Lights, Inc. Systems and methods for identification of optimized protein production and kits therefor
US11398297B2 (en) * 2018-10-11 2022-07-26 Chun-Chieh Chang Systems and methods for using machine learning and DNA sequencing to extract latent information for DNA, RNA and protein sequences
AU2019373208A1 (en) 2018-10-29 2021-05-13 Codexis, Inc. Engineered DNA polymerase variants
CA3122524A1 (en) 2018-12-14 2020-06-18 Codexis, Inc. Engineered tyrosine ammonia lyase
AU2019403323B2 (en) 2018-12-20 2026-02-26 Codexis, Inc. Human alpha-galactosidase variants
CA3127602A1 (en) * 2019-01-22 2020-07-30 EMULATE, Inc. High-content imaging of microfluidic devices
WO2020168286A1 (en) * 2019-02-14 2020-08-20 University Of Washington Systems and methods for improved nanopore-based analysis of nucleic acids
CN109902389B (zh) * 2019-03-01 2021-01-01 厦门大学 基于改进通用似然估计的不确定性有限元模型修正方法
CN109979539B (zh) * 2019-04-10 2020-10-02 电子科技大学 基因序列优化方法、装置及数据处理终端
KR20240033101A (ko) 2019-05-02 2024-03-12 더 보드 오브 리젠츠 오브 더 유니버시티 오브 텍사스 시스템 합성 단백질 안정성을 증가시키기 위한 시스템 및 방법
JP7298284B2 (ja) * 2019-05-09 2023-06-27 富士通株式会社 演算処理装置、演算処理プログラム、及び演算処理方法
CN114375448A (zh) * 2019-06-07 2022-04-19 徕卡显微系统Cms有限公司 用于处理生物学相关数据的系统和方法、用于控制显微镜的系统和方法及显微镜
KR20220019778A (ko) * 2019-06-12 2022-02-17 퀀텀-에스아이 인코포레이티드 머신 학습을 이용한 단백질 식별을 위한 기법들 및 관련된 시스템들 및 방법들
EP4501403A3 (en) 2019-08-30 2025-05-14 Société des Produits Nestlé S.A. Engineered lipase variants
JP7438693B2 (ja) * 2019-09-02 2024-02-27 キヤノンメディカルシステムズ株式会社 診療支援装置
EP4004200A4 (en) * 2019-09-13 2023-08-02 The University of Chicago METHOD AND APPARATUS USING MACHINE LEARNING FOR EVOLUTIONARY DATA-DRIVEN DESIGN OF PROTEINS AND OTHER SEQUENCE-DEFINED BIOMOLECULES
US20220390438A1 (en) * 2019-11-04 2022-12-08 Oxford University Innovation Limited Identification and Characterisation of Herbicides and Plant Growth Regulators
CA3160429A1 (en) * 2019-12-06 2021-06-10 Philip M. KIM System and method for generating a protein sequence
WO2021119261A1 (en) * 2019-12-10 2021-06-17 Homodeus, Inc. Generative machine learning models for predicting functional protein sequences
JP2023507575A (ja) 2019-12-20 2023-02-24 コデクシス, インコーポレイテッド 操作された酸性アルファ-グルコシダーゼバリアント
JP2023512683A (ja) 2020-02-04 2023-03-28 コデクシス, インコーポレイテッド 操作されたロイシンデカルボキシラーゼ
JP7747337B2 (ja) 2020-04-10 2025-10-01 コデクシス, インコーポレイテッド 速度論的光学分割のためのカルボキシエステラーゼポリペプチド
US11188778B1 (en) 2020-05-05 2021-11-30 Illumina, Inc. Equalization-based image processing and spatial crosstalk attenuator
AU2021303778A1 (en) * 2020-07-06 2023-02-09 Basf Se Media, methods, and systems for protein design and optimization
CN116897205A (zh) 2020-08-28 2023-10-17 科德克希思公司 工程化淀粉酶变体
AU2021334371A1 (en) 2020-08-28 2023-03-09 Codexis, Inc. Engineered protease variants
US11361194B2 (en) 2020-10-27 2022-06-14 Illumina, Inc. Systems and methods for per-cluster intensity correction and base calling
WO2022133289A2 (en) 2020-12-18 2022-06-23 Codexis, Inc. Engineered uridine phosphorylase variant enzymes
JP7577002B2 (ja) * 2021-03-19 2024-11-01 日本放送協会 特徴抽出装置およびプログラム
US11439159B2 (en) 2021-03-22 2022-09-13 Shiru, Inc. System for identifying and developing individual naturally-occurring proteins as food ingredients by machine learning and database mining combined with empirical testing for a target food function
CN112735535B (zh) * 2021-04-01 2021-06-25 腾讯科技(深圳)有限公司 预测模型训练、数据预测方法、装置和存储介质
US12180483B2 (en) 2021-04-02 2024-12-31 Codexis, Inc. Engineered cyclic GMP-AMP synthase (cGAS) variant enzymes
EP4314262A1 (en) 2021-04-02 2024-02-07 Codexis, Inc. Engineered guanylate kinase variant enzymes
IL305919A (en) 2021-04-02 2023-11-01 Codexis Inc Engineered adenylate kinase variant enzymes
CA3215105A1 (en) 2021-04-02 2022-10-06 Codexis, Inc. Engineered acetate kinase variant enzymes
US12100486B2 (en) * 2021-05-14 2024-09-24 International Business Machines Corporation Identification of unknown genomes and closest known genomes
CA3220735A1 (en) 2021-05-21 2022-11-24 Codexis, Inc. Engineered methionine gamma lyase variants
EP4374343B1 (en) 2021-07-19 2025-12-03 Illumina, Inc. Intensity extraction with interpolation and adaptation for base calling
US11455487B1 (en) 2021-10-26 2022-09-27 Illumina Software, Inc. Intensity extraction and crosstalk attenuation using interpolation and adaptation for base calling
US20230052080A1 (en) * 2021-08-10 2023-02-16 International Business Machines Corporation Application of deep learning for inferring probability distribution with limited observations
US12129495B2 (en) 2021-10-15 2024-10-29 Codexis, Inc. Engineered DNA polymerase variants
JP2024540358A (ja) 2021-11-01 2024-10-31 シンティス バイオ,インコーポレイティド 工学操作ロイシン脱炭酸酵素
JP2024540281A (ja) * 2021-11-02 2024-10-31 トリナミクス ゲゼルシャフト ミット ベシュレンクテル ハフツング 近赤外分光法による皮膚年齢の測定
CN114913939B (zh) * 2022-07-19 2022-11-15 北京科技大学 高通量平台和机器学习优化的药物组合设计方法及装置
JP7775162B2 (ja) * 2022-08-10 2025-11-25 株式会社東芝 情報処理装置、情報処理方法およびコンピュータプログラム
US12587274B2 (en) 2023-03-28 2026-03-24 Quantum Generative Materials Llc Satellite optimization management system based on natural language input and artificial intelligence
CN116884503B (zh) * 2023-09-06 2023-12-26 北京齐碳科技有限公司 序列和后验矩阵的处理方法、装置和计算设备
US12603701B2 (en) 2023-12-27 2026-04-14 Quantum Generative Materials Llc Distributed satellite constellation management and control system
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
CN117935934B (zh) * 2024-03-25 2024-07-02 中国科学院天津工业生物技术研究所 一种基于机器学习预测磷酸酶最佳催化温度的方法
WO2025235589A1 (en) 2024-05-08 2025-11-13 Codexis, Inc. Dna polymerase variants
CN120910531B (zh) * 2025-07-23 2026-02-10 上海交通大学 一种摩擦系数波动性与均值指标分层建模预测方法

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20110257023A1 (en) * 2002-03-01 2011-10-20 Codexis Mayflower Holdings, Llc Methods, systems, and software for identifying functional biomolecules

Family Cites Families (49)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5837458A (en) 1994-02-17 1998-11-17 Maxygen, Inc. Methods and compositions for cellular and metabolic engineering
US5834252A (en) 1995-04-18 1998-11-10 Glaxo Group Limited End-complementary polymerase reaction
US5605793A (en) 1994-02-17 1997-02-25 Affymax Technologies N.V. Methods for in vitro recombination
US20060257890A1 (en) 1996-05-20 2006-11-16 Maxygen, Inc. Methods and compositions for cellular and metabolic engineering
US6117679A (en) 1994-02-17 2000-09-12 Maxygen, Inc. Methods for generating polynucleotides having desired characteristics by iterative selection and recombination
US6335160B1 (en) 1995-02-17 2002-01-01 Maxygen, Inc. Methods and compositions for polypeptide engineering
US6537776B1 (en) 1999-06-14 2003-03-25 Diversa Corporation Synthetic ligation reassembly in directed evolution
US6171820B1 (en) 1995-12-07 2001-01-09 Diversa Corporation Saturation mutagenesis in directed evolution
US6153410A (en) 1997-03-25 2000-11-28 California Institute Of Technology Recombination of polynucleotide sequences using random or defined primers
US6537746B2 (en) 1997-12-08 2003-03-25 Maxygen, Inc. Method for creating polynucleotide and polypeptide sequences
US7315786B2 (en) 1998-10-16 2008-01-01 Xencor Protein design automation for protein libraries
US20020048772A1 (en) 2000-02-10 2002-04-25 Dahiyat Bassil I. Protein design automation for protein libraries
US6376246B1 (en) 1999-02-05 2002-04-23 Maxygen, Inc. Oligonucleotide mediated nucleic acid recombination
US6917882B2 (en) 1999-01-19 2005-07-12 Maxygen, Inc. Methods for making character strings, polynucleotides and polypeptides having desired characteristics
ES2341217T3 (es) 1999-01-19 2010-06-17 Maxygen, Inc. Recombinacion de acidos nucleicos mediada por oligonucleotidos.
US20070065838A1 (en) 1999-01-19 2007-03-22 Maxygen, Inc. Oligonucleotide mediated nucleic acid recombination
US7024312B1 (en) 1999-01-19 2006-04-04 Maxygen, Inc. Methods for making character strings, polynucleotides and polypeptides having desired characteristics
CA2391987A1 (en) * 1999-11-22 2001-05-31 Yissum Research Development Company Of The Hebrew University Of Jerusalem System and method for searching a combinatorial space
US20010051855A1 (en) * 2000-02-17 2001-12-13 California Institute Of Technology Computationally targeted evolutionary design
AU2001241939A1 (en) 2000-02-28 2001-09-12 Maxygen, Inc. Single-stranded nucleic acid template-mediated recombination and nucleic acid fragment isolation
EP1272967A2 (en) 2000-03-30 2003-01-08 Maxygen, Inc. In silico cross-over site selection
EP1283877A2 (en) 2000-05-23 2003-02-19 California Institute Of Technology Gene recombination and hybrid protein development
US20030032059A1 (en) 2000-05-23 2003-02-13 Zhen-Gang Wang Gene recombination and hybrid protein development
AU2002211624A1 (en) 2000-10-10 2002-04-22 Genencor International, Inc. Information rich libraries
JP2004536819A (ja) * 2001-06-11 2004-12-09 トランジション・セラピューティックス・インコーポレーテッド ウイルス性、増殖性および炎症性の疾患の治療のためにビタミンb12および治療薬を用いた複合治療
US20050084907A1 (en) * 2002-03-01 2005-04-21 Maxygen, Inc. Methods, systems, and software for identifying functional biomolecules
JP5319865B2 (ja) 2002-03-01 2013-10-16 コデクシス メイフラワー ホールディングス, エルエルシー 機能的生体分子を同定する方法、システム、およびソフトウェア
KR20040111456A (ko) 2002-04-04 2004-12-31 이시하라 산교 가부시끼가이샤 데이터 해석 장치 및 방법
WO2003099999A2 (en) * 2002-05-20 2003-12-04 Abmaxis, Inc. Generation and selection of protein library in silico
JP4042492B2 (ja) * 2002-08-07 2008-02-06 トヨタ自動車株式会社 エンジン制御パラメータの適合方法及び適合システム
JP2004355174A (ja) * 2003-05-28 2004-12-16 Ishihara Sangyo Kaisha Ltd データ解析方法及びそのシステム
JP2008500269A (ja) * 2003-10-08 2008-01-10 イーバイオサイエンス 天然免疫グロブリン結合試薬とその作製及び使用方法
US7529714B2 (en) * 2004-12-14 2009-05-05 International Business Machines Corporation Cost management of software application portfolio
CN1763227A (zh) * 2005-09-01 2006-04-26 南京工业大学 一种提高蛋白质生物学功能的方法
EP3124497B1 (en) 2007-09-14 2020-04-15 Adimab, LLC Rationally designed, synthetic antibody libraries and uses therefor
CN101889074A (zh) 2007-10-04 2010-11-17 哈尔西恩莫尔丘勒公司 采用电子显微镜对核酸聚合物测序
US8383346B2 (en) 2008-06-13 2013-02-26 Codexis, Inc. Combined automated parallel synthesis of polynucleotide variants
US20090312196A1 (en) 2008-06-13 2009-12-17 Codexis, Inc. Method of synthesizing polynucleotide variants
CN101353372A (zh) * 2008-08-04 2009-01-28 林峻 一种新型蛋白质分子定向进化方法
AU2009325069B2 (en) * 2008-12-11 2015-03-19 Pacific Biosciences Of California, Inc. Classification of nucleic acid templates
US8551096B2 (en) * 2009-05-13 2013-10-08 Boston Scientific Scimed, Inc. Directional delivery of energy and bioactives
CN101792934A (zh) * 2009-08-26 2010-08-04 青岛科技大学 一种基于组合原理和pcr建立超大容量基因文库的新方法
JP5649424B2 (ja) * 2010-02-03 2015-01-07 大和ハウス工業株式会社 防水シート診断方法および診断装置
US20120115734A1 (en) * 2010-11-04 2012-05-10 Laura Potter In silico prediction of high expression gene combinations and other combinations of biological components
JP4839416B1 (ja) 2011-01-06 2011-12-21 アクアエンタープライズ株式会社 移動過程予測システム、移動過程予測方法、移動過程予測装置及びコンピュータプログラム
US20120231447A1 (en) * 2011-02-15 2012-09-13 Howard Hughes Medical Institute Surface Passivation Methods for Single Molecule Imaging of Biochemical Reactions
CN102206625A (zh) * 2011-03-04 2011-10-05 东华大学 易错pcr/卡那霉素筛选系统定向进化蛋白质内含子
US20130017540A1 (en) * 2011-06-07 2013-01-17 Yun Yen Identification of mutation types associated with acquired resistance and methods for using same
US9665694B2 (en) 2013-01-31 2017-05-30 Codexis, Inc. Methods, systems, and software for identifying bio-molecules with interacting components

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20110257023A1 (en) * 2002-03-01 2011-10-20 Codexis Mayflower Holdings, Llc Methods, systems, and software for identifying functional biomolecules

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