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• FluxRETAP: a REaction TArget Prioritization genome-scale modeling technique for selecting genetic targets.
  Metabolic engineering is rapidly evolving as a result of new advances in synthetic biology tools and automation platforms that enable high throughput strain construction, as well as the development of machine learning tools (ML) for biology. However, selecting…
  pubmed Czajka JJ, Kim J, Tang YJ, Pomraning KR 等 2025 Sep 1 置信度 0.82
• Strong Translation Elongation Factor 1-Alpha (tef1α) Promoter Reporter Systems for Aspergillus niger.
  Strong promoters are crucial for microbial metabolic engineering and synthetic biology, enabling high-level gene expression and pathway optimization. In this study, we have identified the translation elongation factor 1-α gene promoter ( tef1 p) with its…
  pubmed Yuan G, Serrano-Zayas T, Dai Z, DeMers EI 等 2025 Sep 19 置信度 0.82
• Modulation of Gut Microbiota by Red Ginseng Extract Powder and Dietary Fiber in Obese Mice: Identification of Key Microbial Candidates.
  Red ginseng extract powder (RGEP) and red ginseng dietary fiber (RGDF) contain bioactive components with potential prebiotic effects. As gut microbiota plays a critical role in obesity and is influenced by prebiotics, we investigated the effects of RGEP and RG…
  pubmed Shin J, Jin DY, Seo SH, Yu HY 等 2025 Aug 18 置信度 0.82
• A High-Sensitivity Genetically Encoded Biosensor for Terephthalic Acid Detection in PET Degradation.
  The accumulation of polyethylene terephthalate (PET) waste poses a serious environmental challenge due to its durability and resistance to degradation. Enzymatic PET hydrolysis offers a sustainable solution, but efficient high-throughput screening tools for PE…
  pubmed Oh SJ, An JU, Park JH, Choi EW 等 2025 Sep 19 置信度 0.82
• Optimized Ribonucleoprotein Complexes Enhance Prime Editing Efficiency in Zebrafish.
  Prime editing (PE) has emerged as a transformative genome editing technology, enabling precise base substitutions, insertions, and deletions without inducing double-strand DNA breaks (DSBs). However, its application in zebrafish remains limited by low efficien…
  pubmed Qin L, Lin Q 2025 Aug 6 置信度 0.82
• Building a Synthetic Cell Together.
  Synthetic cells (SynCells) are artificial constructs designed to mimic cellular functions, offering insights into fundamental biology, as well as promising impact in the fields of medicine, biotechnology, and bioengineering. Achieving a functional SynCell from…
  pubmed Giaveri S, Abil Z, Kohyama S, Fu M 等 2025 Aug 12 置信度 0.82
• Determination of the transcription unit landscape and associated regulatory elements in Methylosinus sporium 5.
  Methanotrophic bacteria show significant promise for methane bioconversion. Despite their ecological and biotechnological importance, the understanding of their transcriptional regulation and genetic regulatory elements remains limited. Here, we applied high-t…
  pubmed Bae J, Song D-U, Lee H, Lee S-G 等 2025 Sep 2 置信度 0.82
• Nitrogen limitation causes a seismic shift in redox state and phosphorylation of proteins implicated in carbon flux and lipidome remodeling in Rhodotorula toruloides.
  Oleaginous yeast are prodigious producers of oleochemicals, offering alternative and secure sources for applications in foodstuff, skincare, biofuels, and bioplastics. Nitrogen starvation is the primary strategy used to induce oil accumulation in oleagino…
  pubmed Gluth A, Czajka JJ, Li X, Bloodsworth KJ 等 2025 Jul 21 置信度 0.82
• The Future of a Myriad of Accelerated Biodiscoveries Lies in AI-Powered Mass Spectrometry and Multiomics Integration.
  The intersection of modern artificial intelligence (AI) and mass spectrometry (MS) is set to transform the MS-based "omics" research fields, particularly proteomics, metabolomics, lipidomics, and glycomics, enabling advancements across a wide range of domains,…
  pubmed Bilbao A 2025 Aug 置信度 0.82
• Genetic characteristics of novel extreme alkaline-inducible promoter located in five prime upstream region of peptidyl-prolyl cis/trans isomerase from Vibrio anguillarum.
  This study presents the identification and characterization of the promoter region of Vibrio anguillarum NB10, which enhances the expression of FK506-binding protein (FKBP)-type peptidyl-prolyl cis/trans isomerase (PPIase; FklB), capable of binding to the immu…
  pubmed Kim DG, Kim GM, Oh DN, Kim YS 等 2025 Jul 1 置信度 0.82
• A generalized platform for artificial intelligence-powered autonomous enzyme engineering.
  Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a ge…
  pubmed Singh N, Lane S, Yu T, Lu J 等 2025 Jul 1 置信度 0.82
• Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications.
  Lack of standardization in biofoundries limits the scalability and efficiency of synthetic biology research. Here, we propose an abstraction hierarchy that organizes biofoundry activities into four interoperable levels: Project, Service/Capability, Workflow, a…
  pubmed Kim H, Hillson NJ, Cho BK, Sung BH 等 2025 Jul 1 置信度 0.82
• Merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis.
  Synthetic biology offers the promise of manufacturing chemicals more sustainably than petrochemistry. Yet, both the rate at which biomanufacturing can synthesize these molecules and the net chemical accessible space are limited by existing pathway discovery me…
  pubmed Chainani Y, Diaz J, Guilarte-Silva M, Blay V 等 2025 Jul 1 置信度 0.82
• Mass Spectrometric Screening for Improving Enzymatic Conversion of Formaldehyde into C2 and C3 Products.
  One-carbon biomanufacturing offers a sustainable route for producing value-added chemicals. Glycolaldehyde synthase (GALS), an engineered enzyme from Pseudomonas putida , catalyzes a key step by condensing formaldehyde (FALD) into carbohydrate molecules, such …
  pubmed Luo Y, Fu L, Chen J, Xu H 等 2025 Jul 18 置信度 0.82
• From bench to biofactory: high-throughput technologies and automated workflows to accelerate biomanufacturing.
  Microbial production of target molecules has advanced significantly in recent years driven by innovations in enzyme engineering, DNA synthesis, and genomic editing. However, to access the massive potential of microbial production, a vast parametric space remai…
  pubmed Petzold CJ, Mukhopadhyay A 2025 Aug 置信度 0.82
• Modular and signal-responsive transcriptional regulation using CRISPRi-aided genetic switches in Escherichia coli.
  Precise and dynamic transcriptional regulation is a cornerstone of synthetic biology, enabling the construction of robust genetic circuits and programmable cellular systems. However, existing regulatory tools are often limited by issues such as leaky transcrip…
  pubmed Kim SK, Woo SG, Park JH, Lee SG 等 2025 Jun 6 置信度 0.82
• Enabling quantification of 2'-fucosyllactose via ligand-dependent thermal stabilization of BoGT6a.
  2'-Fucosyllactose (2'-FL) is a major component of Human Milk Oligosaccharides (HMOs) that plays a crucial role in developing the neonatal immune system and modulating gut microbiota. Due to its health benefits, 2'-FL has gained industrial importance as a key i…
  pubmed Kim N, Shin J, Kim JS, Kweon DH 2025 Sep 置信度 0.82
• Can protein expression be 'solved'?
  Recombinant protein expression is central to biotechnology's application. However, not all proteins can be expressed in all organisms, and, given the vast experimental space, it can be challenging to identify the conditions that will yield successful protein e…
  pubmed Baranowski C, Martin HG, Oyarzún DA, Spinner A 等 2025 Nov 置信度 0.82
• Enabling malic acid production from corn-stover hydrolysate in Lipomyces starkeyi via metabolic engineering and bioprocess optimization.
  Lipomyces starkeyi is an oleaginous yeast with a native metabolism well-suited for production of lipids and biofuels from complex lignocellulosic and waste feedstocks. Recent advances in genetic engineering tools have facilitated the development of L. starkeyi…
  pubmed Czajka JJ, Dai Z, Radivojević T, Kim J 等 2025 May 21 置信度 0.82
• The knowledge driven DBTL cycle provides mechanistic insights while optimising dopamine production in Escherichia coli.
  Dopamine is a promising organic compound with several key applications in emergency medicine, diagnosis and treatment of cancer, production of lithium anodes, and wastewater treatment. Since studies on in vivo dopamine production are limited, this study demons…
  pubmed Hägele L, Trachtmann N, Takors R 2025 May 16 置信度 0.82
• Converging quality by design, artificial intelligence, and biofoundry automation: A new paradigm for scalable circular biomanufacturing
  Synthetic biology applies engineering principles to the rational design of biological systems with the aim of producing predictable and tunable behaviour. Although the field's conceptual foundations and core technologies are well established, the recent simult…
  pubmed Carlos Belloch-Molina, Francisco Vitor Santos da Silva, John P. Morrissey, Maria Sousa Gallagher 等 2026 置信度 0.82
• Artificial Intelligence-Driven Enzyme Engineering from Structural Prediction to De Novo Design
  The rapid maturation of artificial intelligence (AI) has catalyzed a fundamental transition in biocatalysis, moving from structural analysis toward the prescriptive design of bespoke enzymes. This review synthesizes this AI-driven revolution, evaluating breakt…
  openalex Hongling Shi, Xueyang Bai, Fangyuan Tian, Yangwan Li 等 2026-03-18 置信度 0.72 BespokeComputer scienceRational designArtificial intelligenceProtein design
• An AI-Native Biofoundry for Autonomous Enzyme Engineering: Integrating Active Learning with Automated Experimentation
  Abstract The engineering of enzymes with novel functions is a cornerstone of synthetic biology but remains bottlenecked by the fragmentation between computational design and physical execution. While “self-driving” laboratories promise to resolve this, existin…
  openalex Chuwen Zhang, Lixiang Yang, Yanjia Qin, Danjing Li 等 2026-02-01 置信度 0.72 Computer scienceSynthetic biologyScripting languageArtificial intelligenceContext (archaeology)
• Building a global alliance of biofoundries
  Biofoundries provide an integrated infrastructure to enable the rapid design, construction, and testing of genetically reprogrammed organisms for biotechnology applications and research. Many biofoundries are being built and a Global Biofoundry Alliance has re…
  openalex Nathan J. Hillson, Mark X. Caddick, Yizhi Cai, José A. Carrasco 等 2019-05-09 置信度 0.72 AllianceGenetically engineeredBiotechnologyBusinessComputer science
• Engineering biological systems using automated biofoundries
  openalex Ran Chao, Shekhar Mishra, Tong Si, Huimin Zhao 2017-06-07 置信度 0.72 ObstacleBiochemical engineeringComputer scienceEngineeringSynthetic biology
• Building a biofoundry
  A biofoundry provides automation and analytics infrastructure to support the engineering of biological systems. It allows scientists to perform synthetic biology and aligned experimentation on a high-throughput scale, massively increasing the solution space th…
  openalex Maciej B. Holowko, Emma Frow, Janet C. Reid, Michelle Rourke 等 2020-12-16 置信度 0.72 OperationalizationInteroperabilityComputer scienceContext (archaeology)Outreach
• Integrating protein language models and automatic biofoundry for enhanced protein evolution.
  europepmc 2025 置信度 0.80
• A role for Biofoundries in rapid development and validation of automated SARS-CoV-2 clinical diagnostics
  The SARS-CoV-2 pandemic has shown how a rapid rise in demand for patient and community sample testing can quickly overwhelm testing capability globally. With most diagnostic infrastructure dependent on specialized instruments, their exclusive reagent supplies …
  openalex Michael A. Crone, Miles Priestman, Marta Ciechonska, Kirsten Jensen 等 2020-09-08 置信度 0.72 WorkflowSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2)Computer scienceLoop-mediated isothermal amplificationCoronavirus disease 2019 (COVID-19)
• AutoBioTech─A Versatile Biofoundry for Automated Strain Engineering
  High Resolution Image Download MS PowerPoint Slide The inevitable transition from petrochemical production processes to renewable alternatives has sparked the emergence of biofoundries in recent years. Manual engineering of microbes will not be sufficient to m…
  openalex Tobias Michael Rosch, Julia Tenhaef, Tim Stoltmann, Till Redeker 等 2024-07-08 置信度 0.72 WorkflowModular designCorynebacterium glutamicumGenome engineeringToolbox
• Biofoundries are a nucleating hub for industrial translation
  Contemporary synthetic biology embraces the entire innovation pipeline; it is a transformative technology platform impacting new applications and improving existing industrial products and processes. However, challenges still emerge at the interface of upstrea…
  openalex Tabasum Farzaneh, Paul S. Freemont 2021-05-20 置信度 0.72 Transformative learningDownstream (manufacturing)Key (lock)WorkflowUpstream (networking)
• Biofoundry-assisted expression and characterization of plant proteins
  Abstract Many goals in synthetic biology, including the elucidation and refactoring of biosynthetic pathways and the engineering of regulatory circuits and networks, require knowledge of protein function. In plants, the prevalence of large gene families means …
  openalex Quentin M. Dudley, Yaomin Cai, Kalyani Kallam, Hubert Debreyne 等 2021-09-11 置信度 0.72 Synthetic biologyCell-free protein synthesisProtein engineeringComputational biologyProtein expression
• RoboMoClo: A Robotics-Assisted Modular Cloning Framework for Multiple Gene Assembly in Biofoundry
  Efficient and versatile DNA assembly frameworks have had an impact on promoting synthetic biology to build complex biological systems. To accelerate system development, laboratory automation (or biofoundry) provides an opportunity to construct organisms and DN…
  openalex Dong Hun Kang, Sung Cheon Ko, Yu Been Heo, Hyun Jeong Lee 等 2022-02-15 置信度 0.72 Synthetic biologyModular designCorynebacterium glutamicumComputational biologyComputer science
• Biofoundry Palette: Planning-Assistant Software for Liquid Handler-Based Experimentation and Operation in the Biofoundry Workflow
  Lab automation has facilitated synthetic biology applications in an automated workflow, and biofoundry facilities have enabled automated high-throughput experiments of gene cloning and genome engineering to be conducted following a precise experimental design …
  openalex Sung Cheon Ko, Mingu Cho, Hyun Jeong Lee, Han Min Woo 2022-09-29 置信度 0.72 WorkflowPalette (painting)Computer sciencePython (programming language)Software
• Biofoundries: Bridging Automation and Biomanufacturing in Synthetic Biology
  openalex Dae‐Hee Lee, Haseong Kim, Bong Hyun Sung, Byung‐Kwan Cho 等 2023-12-01 置信度 0.72 BiomanufacturingAutomationSynthetic biologyBioproductsSystems engineering
• Enabling the Advanced Bioeconomy through Public Policy Supporting Biofoundries and Engineering Biology
  openalex R.I. Kitney, Michael Adeogun, Yoshiyuki Fujishima, Ángel Goñi‐Moreno 等 2019-04-26 置信度 0.72 CommercializationSynthetic biologyBiotechnologyBusinessEngineering management
• Advancing high-throughput screening systems for synthetic biology and biofoundry
  High-throughput (HT) methodologies are extensively applied in synthetic biology for the rapid enrichment and selection of desired properties from a wide range of genetic diversity. In order to effectively analyze these vast variants, HT tools must offer parall…
  openalex Kil Koang Kwon, Jinju Lee, Haseong Kim, Dae‐Hee Lee 等 2023-11-20 置信度 0.72 ThroughputSynthetic biologyComputer scienceSelection (genetic algorithm)High-throughput screening
• Artificial intelligence–powered biofoundries for protein engineering and metabolic engineering
  Synthetic biology is rapidly evolving through the integration of artificial intelligence (AI) and automated biofoundries. This convergence accelerates the design–build–test–learn cycle, shifting protein engineering and metabolic engineering from labor-intensiv…
  europepmc Junyu Chen, Nilmani Singh, Jingxia Lu, Stephan Lane 等 2025 置信度 0.80 Metabolic engineeringWorkflowSynthetic biologyProtein engineeringComputer science
• Building Better Bacteriophage with Biofoundries to Combat Antibiotic-Resistant Bacteria
  Resistance to antibiotics is an escalating global crisis, presenting a major health, social, and economic burden. An underexplored alternative to antibiotic treatment is phage therapy whereby bacteriophages are used to infect and kill pathogenic multidrug-resi…
  openalex Karen D. Weynberg, Paul R. Jaschke 2019-11-20 置信度 0.72 Phage therapyBacteriophageAntibiotic resistanceAntibioticsMicrobiology
• A biofoundry workflow for the identification of genetic determinants of microbial growth inhibition
  Abstract Biofoundries integrate high-throughput software and hardware platforms with synthetic biology approaches to enable the design, execution and analyses of large-scale experiments. The unique and powerful combination of laboratory infrastructure and expe…
  openalex Alaster D. Moffat, Adam Elliston, Nicola J. Patron, Andrew W. Truman 等 2021-01-01 置信度 0.72 WorkflowTransposon mutagenesisComputational biologyIdentification (biology)Synthetic biology
• Pandemic preparedness: synthetic biology and publicly funded biofoundries can rapidly accelerate response time
  Synthetic biology has played a key role in responding to the current pandemic. Biofoundries are critical synthetic biology infrastructure which should be available to all nations as a part of their independent bioengineering, biosecurity, and countermeasure re…
  openalex Claudia E. Vickers, Paul S. Freemont 2022-01-21 置信度 0.72 BiosecurityPreparednessPandemicCoronavirus disease 2019 (COVID-19)2019-20 coronavirus outbreak
• Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications.
  europepmc 2025 置信度 0.80
• Advancing biofoundry development: strategies and challenges
  openalex Aporva Gupta, Seung‐Goo Lee, Bong Hyun Sung, Dae‐Hee Lee 等 2024-07-02 置信度 0.72 Industrial and production engineeringManagement scienceEngineeringRisk analysis (engineering)Business
• Public biofoundries as innovation intermediaries: the integration of translation, sustainability, and responsibility
  The emergence and evolution of engineering biology, and its potential to address multiple global challenges is associated with the rise of biofoundries. These innovation intermediaries are facilities that employ advanced automation and computational analytics …
  openalex Andrew Watkins, Adam McCarthy, Claire Holland, Philip Shapira 2023-11-06 置信度 0.72 IntermediaryCommercializationSustainabilityBusinessBusiness model
• Biofoundry-Scale DNA Assembly Validation Using Cost-Effective High-Throughput Long-Read Sequencing
  Biofoundries are automated high-throughput facilities specializing in the design, construction, and testing of engineered/synthetic DNA constructs (plasmids), often from genetic parts. A critical step of this process is assessing the fidelity of the assembled …
  openalex Péter Végh, Sophie Donovan, Susan J. Rosser, Giovanni Stracquadanio 等 2024-02-08 置信度 0.72 Nanopore sequencingDNA sequencingComputational biologyComputer scienceSequence assembly
• Automated Construction of a Yeast-Based Multigene Library via Homologous Recombination in a Biofoundry Workflow
  Efficiently building metabolic pathways via multigene assembly has long been constrained by the limitations of traditional cloning techniques, necessitating a breakthrough in gene assembly methods. Notably, various in vitro gene assembly methods have been deve…
  openalex Min-Jun Seong, Y YOON, Kil Koang Kwon, Haseong Kim 等 2025-05-07 置信度 0.72 Homologous recombinationWorkflowYeastRecombinationComputational biology
• Biofoundries and citizen science can accelerate disease surveillance and environmental monitoring
  A biofoundry is a highly automated facility for processing of biological samples. In that capacity it has a major role in accelerating innovation and product development in engineering biology by implementing design, build, test and learn (DBTL) cycles. Biofou…
  openalex Martin Holub, Ethan Agena 2023-01-12 置信度 0.72 BiosecurityScope (computer science)Citizen scienceBusinessProduct (mathematics)
• Building Biofoundry India: challenges and path forward
  Biofoundry is a place where biomanufacturing meets automation. The highly modular structure of a biofoundry helps accelerate the design-build-test-learn workflow to deliver products fast and in a streamlined fashion. In this perspective, we describe our effort…
  openalex Binay Panda, Pawan K. Dhar 2021-06-24 置信度 0.72 BiomanufacturingWorkflowModular designComputer scienceKey (lock)
• A Procedural Framework for Benchmarking Biofoundry Capabilities
  Benchmarking compares the performance of a product or service with a competitor. In a biofoundry context, capability benchmarking enables more effective use of development resources and furthering business development efforts. Biofoundries considering benchmar…
  openalex Nathan J. Hillson 2023-11-09 置信度 0.72 BenchmarkingAgile software developmentContext (archaeology)Process (computing)Process management
• Operate a Cell-Free Biofoundry using Large Language Models
  europepmc 2024 置信度 0.80
• Author Correction: Building a global alliance of biofoundries
  The original version of this Comment contained errors in the legend of Figure 2, in which the locations of the fifteenth and sixteenth GBA members were incorrectly given as '(15) Australian Genome Foundry, Macquarie University; (16) Australian Foundry for Adva…
  openalex Nathan J. Hillson, Mark X. Caddick, Yizhi Cai, José A. Carrasco 等 2019-07-11 置信度 0.72 BiomanufacturingFifteenthLegendAllianceLibrary science
• A new role for Biofoundries in rapid prototyping, development, and validation of automated clinical diagnostic tests for SARS-CoV-2
  Abstract The SARS-CoV-2 pandemic has shown how the rapid rise in demand for patient and community sample testing, required for tracing and containing a highly infectious disease, has quickly overwhelmed testing capability globally. With most diagnostic infrast…
  openalex Michael A. Crone, Miles Priestman, Marta Ciechonska, Kirsten Jensen 等 2020-05-06 置信度 0.72 WorkflowComputer scienceTurnaround timeSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2)Sample (material)
• Progress and challenges in the biofoundry of immunosuppressants: From process to practice
  Abstract Microorganisms are known to produce pharmaceutically important secondary metabolites that are used as drug moieties in the treatment of various disorders. Discovery of one such class of drugs called immunosuppressants led the way for new and improved …
  crossref Ananta Ganjoo, Nitika Sharma, Haseena Shafeeq, Nargis A. Bhat 等 2022-09-16T02:20:21Z 置信度 0.70
• Introduction to the Special Issue on BioFoundries and Cloud Laboratories
  No abstract available.
  openalex Douglas Densmore, Nathan J. Hillson, Eric Klavins, Chris J. Myers 等 2023-07-31 置信度 0.72 Cloud computingComputer scienceOperating system
• Automated and Programmable Cell-Free Systems for Scalable Synthetic Biology with a Focus on Biofoundry Integration.
  europepmc 2025 置信度 0.80
• Frontiers in biofoundry: opportunities and challenges
  Synthetic biology, with its vast potential applications in diverse fields such as biomanufacturing, agriculture, pharmaceuticals, medicine, environment and food industries, is increasingly recognized for its transformative solutions and sustainability potentia…
  openalex Choo Yee Yu, Geik Yong Ang, Nurulfiza Mat Isa, Kok‐Gan Chan 2025-10-03 置信度 0.72 PaceTransformative learningSustainabilitySynthetic biologyEngineering
• Biofoundry-Assisted Golden Gate Cloning with AssemblyTron.
  europepmc 2025 置信度 0.80
• High-throughput yeast engineering in biofoundries: towards autonomous and scalable synthetic biology.
  europepmc 2026 置信度 0.80
• Challenges and opportunities for establishing biofoundries in Latin America.
  europepmc 2026 置信度 0.80
• Biofoundries for plant-derived bioactive compounds
  openalex Lihang Xie 2024-01-01 置信度 0.72 Computer scienceChemistry
• Architectures of emerging biofoundry platforms for synthetic biology.
  europepmc 2025 置信度 0.80
• Efficient exploration of terpenoid biosynthetic gene clusters in filamentous fungi
  Terpenoids, critical components of human medicine, are the largest family of natural products. Fungi are an important source of terpenoids, but many of the corresponding biosynthetic gene clusters (BGCs) are silent in laboratory conditions. Strategies such as …
  openalex Yujie Yuan, Shu Cheng, Guangkai Bian, Pan Yan 等 2022-04-26 置信度 0.72 TerpenoidAspergillus oryzaeChassisBiologyGene cluster
• Recent advances in AI-enabled automation of DNA assembly in biofoundries.
  europepmc 2025 置信度 0.80
• Semi-automated biofoundry workflows for sequence coevolution-guided isoprene synthase engineering.
  europepmc 2026 置信度 0.80
• Kraft lignin biofoundry: A comprehensive review of innovations in thermochemical and biochemical strategies for industrial biorefinery applications
  openalex Jesús J. Ascencio, Mónica María Cruz-Santos, Fabrício B. Ferreira, Andre Luis Ferraz 等 2026-01-01 置信度 0.72 BiorefineryLigninBiochemical engineeringCommodity chemicalsBiorefining
• Techno-economic assessment-guided biofoundry for microbial strain development.
  europepmc 2026 置信度 0.80
• Biofoundry-assisted expression and characterisation of plant proteins
  Abstract Many goals in synthetic biology, including the elucidation and refactoring of biosynthetic pathways and the engineering of regulatory circuits and networks, require knowledge of protein function. In plants, the prevalence of large gene families means …
  openalex Quentin M. Dudley, Yaomin Cai, Kalyani Kallam, Hubert Debreyne 等 2021-03-11 置信度 0.72 Synthetic biologyComputational biologyCell-free protein synthesisWorkflowProtein expression
• Streamlining the Design‐Build‐Test‐Learn Process in Automated Biofoundries
  Bioengineering is increasingly contributing to solving societal challenges in biomedical, environmental, agricultural, and industrial setups. To facilitate standardization of bioengineering, the field has adopted the concept of design-build-test-learn cycles (…
  openalex Enrico Orsi, Nicolás Gurdo, Pablo I. Nikel 2026-01-09 置信度 0.72 WorkflowStandardizationProcess (computing)Modular designComputer science
• Connector-enabled integration of Golden Gate Assembly and yeast recombination for streamlined multigene pathway construction in the biofoundry workflow.
  europepmc 2026 置信度 0.80
• Improving Reproducibility in Synthetic Biology
  Synthetic biology holds great promise to deliver transformative technologies to the world in the coming years. However, several challenges still remain to be addressed before it can deliver on its promises. One of the most important issues to address is the la…
  openalex Mathew M. Jessop-Fabre, Nikolaus Sonnenschein 2019-02-11 置信度 0.72 Transformative learningSynthetic biologyData scienceComputer sciencePerspective (graphical)
• 2nd symposium on engineering biology and BioFoundry
  openalex Yuanli Gao, Chang Dong, Jiazhang Lian, Baojun Wang 2023-01-01 置信度 0.72 Engineering ethicsEngineeringBiologyComputational biology
• Accelerating strain engineering in biofuel research via build and test automation of synthetic biology
  openalex Jianzhi Zhang, Yongcan Chen, Lihao Fu, Erpeng Guo 等 2021-01-25 置信度 0.72 Synthetic biologyChassisBiofuelAutomationComputer science
• Merging automation and fundamental discovery into the design–build–test–learn cycle of nontraditional microbes
  Major advances toward a bio-based industry enabled cost-efficient bioproduction of multiple chemicals, yet successful industrial processes are relatively scarce and limited to the use of few workhorse microbes as hosts. An in-depth understanding of the physiol…
  openalex Nicolás Gurdo, Daniel C. Volke, Pablo I. Nikel 2022-04-08 置信度 0.72 AutomationTest (biology)Computer scienceBiochemical engineeringComputational biology
• Author Correction: A role for Biofoundries in rapid development and validation of automated SARS-CoV-2 clinical diagnostics
  An amendment to this paper has been published and can be accessed via a link at the top of the paper.
  openalex Michael A. Crone, Miles Priestman, Marta Ciechonska, Kirsten Jensen 等 2020-09-17 置信度 0.72 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)Coronavirus disease 2019 (COVID-19)2019-20 coronavirus outbreakComputer scienceVirology
• Bio‐informational futures
  openalex Thomas A. Dixon, Natalie C. Curach, Isak S. Pretorius 2020-02-11 置信度 0.72 ExcellenceLibrary sciencePolitical scienceLawComputer science
• Build a Sustainable Vaccines Industry with Synthetic Biology
  openalex R.I. Kitney, Jennifer Bell, Jim Philp 2021-01-11 置信度 0.72 Synthetic biologyBiologyComputational biologyBiotechnologyBusiness
• <i>In silico</i> design and automated learning to boost next-generation smart biomanufacturing
  Abstract The increasing demand for bio-based compounds produced from waste or sustainable sources is driving biofoundries to deliver a new generation of prototyping biomanufacturing platforms. Integration and automation of the design, build, test and learn (DB…
  openalex Pablo Carbonell, Rosalind Le Feuvre, Eriko Takano, Nigel S. Scrutton 2020-01-01 置信度 0.72 BiomanufacturingComputer scienceSystems engineeringAutomationWorkflow
• Potential use of microbial engineering in single-cell protein production
  openalex Balaji Balagurunathan, Hua Ling, Won Jae Choi, Matthew Wook Chang 2022-06-02 置信度 0.72 CommercializationSynthetic biologyBiotechnologyBiochemical engineeringProduction (economics)
• Enabling technology and core theory of synthetic biology
  openalex Xian‐En Zhang, Chenli Liu, Junbiao Dai, Ying‐Jin Yuan 等 2023-02-06 置信度 0.72 Synthetic biologySystems biologyComputational biologyRational designBiology
• A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology
  Centralized facilities for genetic engineering, or "biofoundries", offer the potential to design organisms to address emerging needs in medicine, agriculture, industry, and defense. The field has seen rapid advances in technology, but it is difficult to gauge …
  openalex Arturo Casini, Fangyuan Chang, Raissa Eluere, Andrew King 等 2018-02-26 置信度 0.72 Streptomyces coelicolorChemistryComputational biologyStreptomycesBiochemical engineering
• Selenzyme: enzyme selection tool for pathway design
  Summary: Synthetic biology applies the principles of engineering to biology in order to create biological functionalities not seen before in nature. One of the most exciting applications of synthetic biology is the design of new organisms with the ability to p…
  openalex Pablo Carbonell, Jerry Wong, Neil Swainston, Eriko Takano 等 2018-02-06 置信度 0.72 BespokePipeline (software)WorkflowComputer scienceSynthetic biology
• Advances in analytical tools for high throughput strain engineering
  openalex Esteban Marcellin, Lars K. Nielsen 2018-02-12 置信度 0.72 AutomationComputer scienceAnalyticsSynthetic biologyExploit
• Automated high-throughput DNA synthesis and assembly
  DNA synthesis and assembly primarily revolve around the innovation and refinement of tools that facilitate the creation of specific genes and the manipulation of entire genomes. This multifaceted process encompasses two fundamental steps: the synthesis of leng…
  openalex Yuxin Ma, Zhaoyang Zhang, Bin Jia, Ying‐Jin Yuan 2024-02-25 置信度 0.72 WorkstationThroughputSynthetic biologyComputer scienceOligonucleotide
• Pathway Evolution Through a Bottlenecking‐Debottlenecking Strategy and Machine Learning‐Aided Flux Balancing
  Abstract The evolution of pathway enzymes enhances the biosynthesis of high‐value chemicals, crucial for pharmaceutical, and agrochemical applications. However, unpredictable evolutionary landscapes of pathway genes often hinder successful evolution. Here, the…
  openalex Huaxiang Deng, Han Yu, Y. Deng, Yulan Qiu 等 2024-02-06 置信度 0.72 Flux (metallurgy)Computer scienceBiochemical engineeringComputational biologyBiology
• Consolidated Bioprocessing: Synthetic Biology Routes to Fuels and Fine Chemicals
  The long road from emerging biotechnologies to commercial "green" biosynthetic routes for chemical production relies in part on efficient microbial use of sustainable and renewable waste biomass feedstocks. One solution is to apply the consolidated bioprocessi…
  openalex Alec Banner, Helen S. Toogood, Nigel S. Scrutton 2021-05-18 置信度 0.72 BioprocessBiochemical engineeringSynthetic biologyBiomass (ecology)Commodity chemicals
• Aquarium: open-source laboratory software for design, execution and data management
  Automation has been shown to improve the replicability and scalability of biomedical and bioindustrial research. Although the work performed in many labs is repetitive and can be standardized, few academic labs can afford the time and money required to automat…
  openalex Justin D. Vrana, Orlando de Lange, Yaoyu Yang, Garrett Newman 等 2021-01-01 置信度 0.72 WorkflowComputer scienceAutomationScalabilitySoftware engineering
• Automation in synthetic biology using biological foundries
  Synthetic biology applies engineering principles for the deliberate design, engineering, and de novo creation of artificial biological systems with certain functions. Due to the complexity of living systems and lack of rational design principles, iterative tri…
  openalex Ting Tang, Lihao Fu, Erpeng Guo, Zhenkun Zhang 等 2020-07-16 置信度 0.72 Synthetic biologyWorkflowAutomationBiomanufacturingComputer science
• Future trends in synthetic biology in Asia
  Synthetic biology research and technology translation has garnered increasing interest from the governments and private investors in Asia, where the technology has great potential in driving a sustainable bio-based economy. This Perspective reviews the latest …
  openalex Ning Mao, Nikhil Aggarwal, Chueh Loo Poh, Byung‐Kwan Cho 等 2021-03-01 置信度 0.72 BiosecurityGovernment (linguistics)Synthetic biologyCorporate governancePrivate sector
• SynBiopython: an open-source software library for <i>Synthetic Biology</i>
  Abstract Advances in hardware automation in synthetic biology laboratories are not yet fully matched by those of their software counterparts. Such automated laboratories, now commonly called biofoundries, require software solutions that would help with many sp…
  openalex Jing Wui Yeoh, Neil Swainston, Péter Végh, Valentin Zulkower 等 2021-01-01 置信度 0.72 Python (programming language)Computer scienceSoftware engineeringSoftwareSynthetic biology
• New approaches to secondary metabolite discovery from anaerobic gut microbes.
  europepmc 2025 置信度 0.80
• An engineering biology approach to automated workflow and biodesign
  The paper addresses the application of engineering biology strategies and techniques to the automation of laboratory workflow-primarily in the context of biofoundries and biodesign applications based on the Design, Build, Test and Learn paradigm. The trend tow…
  pubmed Alexis Casas, Matthieu Bultelle, R.I. Kitney, Casas A 等 2024 置信度 0.82 WorkflowBiomanufacturingComputer scienceAutomationWorkflow technology
• Reconstitution and optimization of complex plant natural product biosynthetic pathways in microbial expression systems
  openalex Jucan Gao, Yuanwei Gou, Lei Huang, Jiazhang Lian 2024-05-04 置信度 0.72 Synthetic biologyBiochemical engineeringNatural productSystems biologyModular design
• The Construction of a Microbial Synthesis System for Rare Earth Enrichment and Material Applications
  Rare earth materials play an irreplaceable role in biomedical and high technology fields. However, typical mining and extraction approaches to rare earth elements (REEs) often lead to severe environmental problems and resource wastage due to the involvement of…
  openalex Huijing Cui, Xin Zhang, Jing Chen, Xining Qian 等 2023-05-27 置信度 0.72 BioproductsRare earthNanotechnologyMaterials scienceBiochemical engineering
• Plaque Size Tool: An automated plaque analysis tool for simplifying and standardising bacteriophage plaque morphology measurements
  openalex Ellina Trofimova, Paul R. Jaschke 2021-05-27 置信度 0.72 BacteriophageBiologyWorkflowPetri dishLytic cycle
• Congo red protects bacteriophages against UV irradiation and allows for the simultaneous use of phages and UV for membrane sterilization
  Congo red dye protects bacteriophages from the adverse effects of UV radiation, allowing for simultaneous membrane surface cleaning from biofoundries.
  openalex Mateusz Wdowiak, Patryk A. Mierzejewski, Rafał Zbonikowski, Bartłomiej Bończak 等 2023-01-01 置信度 0.72 Sterilization (economics)Congo redIrradiationMicrobiologyMembrane
• Growing a circular economy with fungal biotechnology: a white paper
  Fungi have the ability to transform organic materials into a rich and diverse set of useful products and provide distinct opportunities for tackling the urgent challenges before all humans. Fungal biotechnology can advance the transition from our petroleum-bas…
  openalex Vera Meyer, Evelina Y. Basenko, J. Philipp Benz, Gerhard H. Braus 等 2020-04-02 置信度 0.72 White (mutation)Circular economyBiotechnologyWhite rotBiology
• Enhancing lipid production in plant cells through automated high-throughput genome engineering and phenotyping.
  europepmc 2025 置信度 0.80
• CRISPR–dCas13a system for programmable small RNAs and polycistronic mRNA repression in bacteria
  Bacterial small RNAs (sRNAs) function in post-transcriptional regulatory responses to environmental changes. However, the lack of eukaryotic RNA interference-like machinery in bacteria has limited the systematic engineering of RNA repression. Here, we report t…
  openalex Sung Cheon Ko, Han Min Woo 2023-11-28 置信度 0.72 CRISPRTrans-activating crRNABiologyArgonauteCas9
• Rapid Prototyping Platform for Saccharomyces cerevisiae Using Computer-Aided Genetic Design Enabled by Parallel Software and Workcell Platform Development
  Biofoundries have enabled the ability to automate the construction of genetic constructs using computer-aided design. In this study, we have developed the methodology required to abstract and automate the construction of yeast-compatible designs. We demonstrat…
  openalex Priscilla D. Rajakumar, Glen-Oliver F. Gowers, Lorna Suckling, Alexander J. Foster 等 2018-08-30 置信度 0.72 SoftwareCoding (social sciences)Software engineeringComputer scienceRapid prototyping
• Prototyping of microbial chassis for the biomanufacturing of high-value chemical targets
  Metabolic engineering technologies have been employed with increasing success over the last three decades for the engineering and optimization of industrial host strains to competitively produce high-value chemical targets. To this end, continued reductions in…
  openalex Christopher Robinson, Jonathan Tellechea‐Luzardo, Pablo Carbonell, Adrian J. Jervis 等 2021-06-08 置信度 0.72 BiomanufacturingWorkflowSynthetic biologyBiochemical engineeringChassis
• Towards next-generation model microorganism chassis for biomanufacturing
  openalex Yanfeng Liu, Anqi Su, Jianghua Li, Rodrigo Ledesma‐Amaro 等 2020-09-24 置信度 0.72 BiomanufacturingSynthetic biologyChassisMetabolic engineeringCorynebacterium glutamicum