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• Biotechnological domestication of pseudomonads using synthetic biology
  openalex Pablo I. Nikel, Esteban Martínez‐García, Vı́ctor de Lorenzo 2014-04-16 置信度 0.72 Synthetic biologyBiologyBiochemical engineeringComputational biologyDomestication
• Engineering genetic circuit interactions within and between synthetic minimal cells
  openalex Katarzyna P. Adamala, Daniel A. Martin-Alarcon, Katriona R. Guthrie-Honea, Edward S. Boyden 2016-11-14 置信度 0.72 Synthetic biologyModular designChemistryScalabilityModularity (biology)
• Engineering living therapeutics with synthetic biology
  openalex Andrés Cubillos-Ruiz, Tingxi Guo, Anna Sokolovska, Paul Miller 等 2021-10-06 置信度 0.72 Synthetic biologyComputational biologyBiologyFlexibility (engineering)Function (biology)
• Control theory meets synthetic biology
  The past several years have witnessed an increased presence of control theoretic concepts in synthetic biology. This review presents an organized summary of how these control design concepts have been applied to tackle a variety of problems faced when building…
  openalex Domitilla Del Vecchio, Aaron J. Dy, Yili Qian 2016-07-01 置信度 0.72 Synthetic biologyComputer scienceRobustness (evolution)Control (management)Field (mathematics)
• Engineering Molecular Circuits Using Synthetic Biology in Mammalian Cells
  Synthetic biology has made significant leaps over the past decade, and it now enables rational and predictable reprogramming of cells to conduct complex physiological activities. The bases for cellular reprogramming are mainly genetic control components affect…
  openalex Markus Wieland, Martin Fussenegger 2012-06-13 置信度 0.72 Synthetic biologyReprogrammingBiologyComputational biologyGene regulatory network
• Synchronous long-term oscillations in a synthetic gene circuit
  openalex Laurent Potvin-Trottier, Nathan D. Lord, Glenn Vinnicombe, Johan Paulsson 2016-10-01 置信度 0.72 Synthetic biologyElectronic circuitLaboratory flaskCoupling (piping)Biological system
• Synthetic Biology and Metabolic Engineering
  Metabolic engineering emerged 20 years ago as the discipline occupied with the directed modification of metabolic pathways for the microbial synthesis of various products. As such, it deals with the engineering (design, construction, and optimization) of nativ…
  openalex Gregory Stephanopoulos 2012-11-01 置信度 0.72 Synthetic biologyMetabolic engineeringContext (archaeology)Systems biologyBiochemical engineering
• Adaptive circuits in synthetic biology
  One of the most remarkable features of biological systems is their ability to adapt to the constantly changing environment. By harnessing principles of control theory, synthetic biologists are starting to mimic this adaptation in regulatory gene circuits. Doin…
  openalex Timothy Frei, Mustafa Khammash 2021-10-19 置信度 0.72 Synthetic biologyAdaptation (eye)Computer scienceImperfectGene regulatory network
• Foundations for the design and implementation of synthetic genetic circuits
  openalex Adrian L. Slusarczyk, Allen Yilun Lin, Ron Weiss 2012-05-18 置信度 0.72 Synthetic biologyScope (computer science)Context (archaeology)Computer scienceElectronic circuit
• Cell-free synthetic biology: Thinking outside the cell
  openalex C. Eric Hodgman, Michael C. Jewett 2011-09-18 置信度 0.72 Synthetic biologyBiochemical engineeringCell-free protein synthesisSystems biologyMetabolic engineering
• Synthetic biology devices for in vitro and in vivo diagnostics
  There is a growing need to enhance our capabilities in medical and environmental diagnostics. Synthetic biologists have begun to focus their biomolecular engineering approaches toward this goal, offering promising results that could lead to the development of …
  openalex Shimyn Slomovic, Keith Pardee, James J. Collins 2015-11-23 置信度 0.72 Synthetic biologyComputer scienceNanotechnologyMolecular diagnosticsComputational biology
• Synthetic biology devices and circuits for RNA-based ‘smart vaccines’: a propositional review
  Nucleic acid vaccines have been gaining attention as an alternative to the standard attenuated pathogen or protein based vaccine. However, an unrealized advantage of using such DNA or RNA based vaccination modalities is the ability to program within these nucl…
  openalex Oliwia Andries, Tasuku Kitada, Katie Bodner, Niek N. Sanders 等 2015-01-07 置信度 0.72 Synthetic biologyRNAComputational biologyBiologyNucleic acid
• Reconstruction of genetic circuits
  openalex David Sprinzak, Michael B. Elowitz 2005-11-23 置信度 0.72 Synthetic biologyModularity (biology)Electronic circuitConstruct (python library)Computer science
• Synthetic analog computation in living cells
  openalex Ramiz Daniel, Jacob R. Rubens, Rahul Sarpeshkar, Timothy K. Lu 2013-05-14 置信度 0.72 Synthetic biologyComputer scienceComputationElectronic circuitDigital electronics
• Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology
  openalex Heinz Koeppl, Douglas Densmore, Gianluca Setti, Mario di Bernardo 2011-05-30 置信度 0.72 Synthetic biologyAbstractionComputer scienceSystems biologyKey (lock)
• Synthetic Biology and Personalized Medicine
  Synthetic biology, application of synthetic chemistry to biology, is a broad term that covers the engineering of biological systems with structures and functions not found in nature to process information, manipulate chemicals, produce energy, maintain cell en…
  openalex Kanika Jain 2012-08-16 置信度 0.72 Synthetic biologyComputational biologyFlexibility (engineering)Systems biologyComputer science
• Co-culture systems and technologies: taking synthetic biology to the next level
  Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecol…
  openalex Lisa Goers, Paul S. Freemont, Karen M. Polizzi 2014-05-14 置信度 0.72 Synthetic biologySystems biologySet (abstract data type)Natural (archaeology)Biochemical engineering
• A synchronized quorum of genetic clocks
  openalex Tal Danino, Octavio Mondragón-Palomino, Lev S. Tsimring, Jeff Hasty 2010-01-01 置信度 0.72 Synchronization (alternating current)Synthetic biologyComputer scienceCoupling (piping)Population
• Application of combinatorial optimization strategies in synthetic biology
  In the first wave of synthetic biology, genetic elements, combined into simple circuits, are used to control individual cellular functions. In the second wave of synthetic biology, the simple circuits, combined into complex circuits, form systems-level functio…
  openalex Gita Naseri, Mattheos Koffas 2020-05-15 置信度 0.72 Synthetic biologyComputer scienceSimple (philosophy)Electronic circuitConstruct (python library)
• Gene-Expressing Liposomes as Synthetic Cells for Molecular Communication Studies
  The bottom-up branch of synthetic biology includes – among others – innovative studies that combine cell-free protein synthesis with liposome technology to generate cell-like systems of minimal complexity, often referred to as synthetic cells. The functions of…
  openalex Giordano Rampioni, Francesca D’Angelo, Livia Leoni, Pasquale Stano 2019-01-17 置信度 0.72 Synthetic biologyComputational biologyArtificial cellModular designComputer science
• Synthetic biology: applying biological circuits beyond novel therapies
  Synthetic biology, an engineering, circuit-driven approach to biology, has developed whole new classes of therapeutics. Unfortunately, these advances have thus far been undercapitalized upon by basic researchers. As discussed herein, using synthetic circuits, …
  openalex Anton Dobrin, Pratik Saxena, Martin Fussenegger 2015-12-24 置信度 0.72 Synthetic biologyBiologyComputational biology
• Synthetic cooperation in engineered yeast populations
  Cooperative interactions are key to diverse biological phenomena ranging from multicellularity to mutualism. Such diversity makes the ability to create and control cooperation desirable for potential applications in areas as varied as agriculture, pollutant tr…
  openalex Wenying Shou, Sri Ram, José M. G. Vilar 2007-02-02 置信度 0.72 BiologySynthetic biologyMulticellular organismPopulationBiochemical engineering
• Applications of synthetic biology in medical and pharmaceutical fields
  Synthetic biology aims to design or assemble existing bioparts or bio-components for useful bioproperties. During the past decades, progresses have been made to build delicate biocircuits, standardized biological building blocks and to develop various genomic/…
  openalex Xu Yan, Xu Liu, Cuihuan Zhao, Guo‐Qiang Chen 2023-05-11 置信度 0.72 Synthetic biologyComputational biologyBiologySystems biologyMetabolic engineering
• New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering
  Cyanobacteria are promising microorganisms for sustainable biotechnologies, yet unlocking their potential requires radical re-engineering and application of cutting-edge synthetic biology techniques. In recent years, the available devices and strategies for mo…
  openalex María Santos‐Merino, Amit Kumar Singh, Daniel C. Ducat 2019-02-27 置信度 0.72 BioproductionSynthetic biologyMetabolic engineeringCyanobacteriaComputational biology
• The Next Generation of Synthetic Biology Chassis: Moving Synthetic Biology from the Laboratory to the Field
  Escherichia coli (E. coli) has played a pivotal role in the development of genetics and molecular biology as scientific fields. It is therefore not surprising that synthetic biology (SB) was built upon E. coli and continues to dominate the field. However, scie…
  openalex Bryn L. Adams 2016-09-26 置信度 0.72 Synthetic biologyChassisBiologyField (mathematics)Computer science
• Transcriptional regulatory circuits controlling mitochondrial biogenesis and function
  We are witnessing a period of renewed interest in the biology of the mitochondrion. The mitochondrion serves a critical function in the maintenance of cellular energy stores, thermogenesis, and apoptosis. Moreover, alterations in mitochondrial function contrib…
  openalex Daniel P. Kelly, Richard C. Scarpulla 2004-02-15 置信度 0.72 BiologyCell biologyFunction (biology)BiogenesisMitochondrial biogenesis
• Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology
  openalex Lukas Buecherl, Chris J. Myers 2022-05-16 置信度 0.72 Synthetic biologyWorkflowField (mathematics)AutomationBiology
• Emerging biomedical applications of synthetic biology
  openalex Wilfried Weber, Martin Fussenegger 2011-11-29 置信度 0.72 Synthetic biologySystems biologyInfectious disease (medical specialty)Computational biologyComputer science
• Protocols for Implementing an <em>Escherichia coli</em> Based TX-TL Cell-Free Expression System for Synthetic Biology
  Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform. This is useful for expressing proteins and genetic circuits in a controlled manner as well as for providing a prototyping environmen…
  openalex Zachary Z. Sun, Clarmyra A. Hayes, Jonghyeon Shin, Filippo Caschera 等 2013-09-16 置信度 0.72 Synthetic biologyT7 RNA polymeraseTranscription (linguistics)BiologyEscherichia coli
• A Synthetic Optogenetic Transcription Device Enhances Blood-Glucose Homeostasis in Mice
  Synthetic biology has advanced the design of genetic devices that can be used to reprogram metabolic activities in mammalian cells. By functionally linking the signal transduction of melanopsin to the control circuit of the nuclear factor of activated T cells,…
  openalex Haifeng Ye, Marie Daoud‐El Baba, Ren‐Wang Peng, Martin Fussenegger 2011-06-24 置信度 0.72 Cell biologyBiologyOptogeneticsTransgeneTranscription factor
• Emergent genetic oscillations in a synthetic microbial consortium
  A challenge of synthetic biology is the creation of cooperative microbial systems that exhibit population-level behaviors. Such systems use cellular signaling mechanisms to regulate gene expression across multiple cell types. We describe the construction of a …
  openalex Ye Chen, Jae Kyoung Kim, Andrew J. Hirning, Krešimir Josić́ 等 2015-08-27 置信度 0.72 Synthetic biologyPopulationRepressorBiologyStrain (injury)
• Genetic circuits in synthetic biology: broadening the toolbox of regulatory devices
  Devices sensing inputs and generating outputs are fundamental regulatory units, and as such are the basis of more complex regulatory networks. We provide an overview of regulatory devices used as fundamental regulatory building blocks in synthetic biology, and…
  openalex Marik M. Müller, Katja M. Arndt, Stefan A. Hoffmann 2025-03-07 置信度 0.72 ToolboxSynthetic biologyComputational biologyElectronic circuitBiology
• Amyloid beta: structure, biology and structure-based therapeutic development
  openalex Guo-fang Chen, Ting-Hai Xu, Yan Yan, Yu-ren Zhou 等 2017-07-17 置信度 0.72 DementiaAmyloid precursor protein secretaseProteasesAlzheimer's diseaseAmyloid precursor protein
• Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an <i>Escherichia coli</i> Based TX-TL Cell-Free System
  Accelerating the pace of synthetic biology experiments requires new approaches for rapid prototyping of circuits from individual DNA regulatory elements. However, current testing standards require days to weeks due to cloning and in vivo transformation. In thi…
  openalex Zachary Z. Sun, Enoch Yeung, Clarmyra A. Hayes, Vincent Noireaux 等 2013-11-22 置信度 0.72 Synthetic biologyDNAComputational biologyEscherichia coliPlasmid
• GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology
  Plant synthetic biology aims to apply engineering principles to plant genetic design. One strategic requirement of plant synthetic biology is the adoption of common standardized technologies that facilitate the construction of increasingly complex multigene st…
  openalex Alejandro Sarrion‐Perdigones, Marta Vázquez‐Vilar, Jorge Palaci, Bas Castelijns 等 2013-05-13 置信度 0.72 Synthetic biologyModular designComputational biologyIn silicoComputer science
• The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology
  openalex Michal Galdzicki, Kevin Clancy, Ernst Oberortner, Matthew Pocock 等 2014-06-01 置信度 0.72 Synthetic biologyWorkflowDocumentationComputer scienceSoftware
• Parameterized quantum circuits as machine learning models
  Abstract Hybrid quantum–classical systems make it possible to utilize existing quantum computers to their fullest extent. Within this framework, parameterized quantum circuits can be regarded as machine learning models with remarkable expressive power. This Re…
  openalex Marcello Benedetti, Erika Lloyd, Stefan Sack, Mattia Fiorentini 2019-10-17 置信度 0.72 Parameterized complexityComputer scienceVariety (cybernetics)Field (mathematics)Quantum
• The Systems Biology Graphical Notation
  openalex Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie 等 2009-08-01 置信度 0.72 Computer scienceNotationSBMLSystems biologyRepresentation (politics)
• Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology
  Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation process…
  openalex Shweta Jaiswal, Pratyoosh Shukla 2020-05-19 置信度 0.72 BioremediationBiochemical engineeringSynthetic biologyEnvironmental remediationBiology
• Genetic switchboard for synthetic biology applications
  A key next step in synthetic biology is to combine simple circuits into higher-order systems. In this work, we expanded our synthetic riboregulation platform into a genetic switchboard that independently controls the expression of multiple genes in parallel. F…
  openalex Jarred M. Callura, Charles R. Cantor, James J. Collins 2012-03-27 置信度 0.72 Synthetic biologyBiologyPentose phosphate pathwayMetabolomeGene
• A synthetic mammalian gene circuit reveals antituberculosis compounds
  Synthetic biology provides insight into natural gene-network dynamics and enables assembly of engineered transcription circuitries for production of difficult-to-access therapeutic molecules. In Mycobacterium tuberculosis EthR binds to a specific operator (O(e…
  openalex Wilfried Weber, Ronald G. Schoenmakers, Bettina Keller, Marc Gitzinger 等 2008-07-09 置信度 0.72 EthionamideDerepressionBiologyGeneReporter gene
• Toehold Switches: De-Novo-Designed Regulators of Gene Expression
  openalex Alexander A. Green, Pamela A. Silver, James J. Collins, Peng Yin 2014-10-24 置信度 0.72 BiologySynthetic biologyCrosstalkComputational biologyOrthogonality
• Droplet microfluidics for synthetic biology
  Synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in…
  openalex Philip C. Gach, Kosuke Iwai, Peter W. Kim, Nathan J. Hillson 等 2017-01-01 置信度 0.72 MicrofluidicsSynthetic biologyNanotechnologyField (mathematics)Biochemical engineering
• Understanding Biological Regulation Through Synthetic Biology
  Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry-biochemistry and molecular …
  openalex Caleb J. Bashor, James J. Collins 2018-03-16 置信度 0.72 Synthetic biologyGene regulatory networkSystems biologyFunction (biology)Biological network
• A synthetic biology approach to engineering circuits in immune cells
  A synthetic circuit in a biological system involves the designed assembly of genetic elements, biomolecules, or cells to create a defined function. These circuits are central in synthetic biology, enabling the reprogramming of cellular behavior and the enginee…
  openalex Daniel Hoces, Jesús Miguéns Blanco, Rogelio A. Hernández‐López 2023-07-19 置信度 0.72 Synthetic biologyReprogrammingCancer immunotherapyImmunotherapyCancer cell
• The promise and perils of synthetic biology.
  ver the past fifty years, several pivotal advances have transformed the life sciences, including the discovery of the structure of DNA, the deciphering of the genetic code, the development of recombinant DNA technology, and the mapping of the human genome. Syn…
  openalex Jonathan Β. Tucker, Raymond A. Zilinskas 2006-01-01 置信度 0.72 Synthetic biologyComputational biologyTransformative learningBiologyComputer science
• Synthetic biology of cyanobacteria: unique challenges and opportunities
  Photosynthetic organisms, and especially cyanobacteria, hold great promise as sources of renewably-produced fuels, bulk and specialty chemicals, and nutritional products. Synthetic biology tools can help unlock cyanobacteria's potential for these functions, bu…
  openalex Bertram M. Berla, Rajib Saha, Cheryl M. Immethun, Costas D. Maranas 等 2013-01-01 置信度 0.72 CyanobacteriaBiologySynthetic biologyComputational biologyEcology
• Synthetic genetic circuits for programmable biological functionalities
  openalex Peng‐Fei Xia, Hua Ling, Jee Loon Foo, Matthew Wook Chang 2019-04-30 置信度 0.72 Synthetic biologyElectronic circuitComputer scienceComputational biologyNanotechnology
• Retropath: Automated Pipeline for Embedded Metabolic Circuits
  Metabolic circuits are a promising alternative to other conventional genetic circuits as modular parts implementing functionalities required for synthetic biology applications. To date, metabolic design has been mainly focused on production circuits. Emergent …
  openalex Pablo Carbonell, Pierre Parutto, Claire Baudier, Christophe Junot 等 2013-10-04 置信度 0.72 Synthetic biologyElectronic circuitPipeline (software)ChassisComputer science
• Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture
  To support an ever-increasing population, modern agriculture faces numerous challenges that pose major threats to global food and energy security. Plant-associated microbes, with their many plant growth-promoting (PGP) traits, have enormous potential in helpin…
  openalex Ke Jing, Bing Wang, Yasuo Yoshikuni 2020-08-13 置信度 0.72 MicrobiomeBiologyComputational biologyAgricultureMetagenomics
• Synergies between synthetic biology and metabolic engineering
  openalex Jens Nielsen, Jay D. Keasling 2011-08-01 置信度 0.72 Synthetic biologyMetabolic engineeringBiologyComputational biologyBiotechnology
• Advances in synthetic biology: on the path from prototypes to applications
  openalex Ryan McDaniel, Ron Weiss 2005-07-13 置信度 0.72 Synthetic biologyMulticellular organismComputer scienceComputational biologySystems biology
• CaMV35S promoter – A plant biology and biotechnology workhorse in the era of synthetic biology
  Transgene over-expression has fueled many important plant biology discoveries in the last 40 years, as well as the development of economically important transgenic crop varieties. The 35S promoter from the plant pathogen Cauliflower Mosaic Virus (CaMV) has bee…
  openalex Stephanie C. Amack, Mauricio S. Antunes 2020-10-07 置信度 0.72 Cauliflower mosaic virusBiologyTransgenePromoterGenetically modified crops
• Analog synthetic biology
  We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed t…
  openalex Rahul Sarpeshkar 2014-02-25 置信度 0.72 Analogue electronicsAnalog computerComputationComputer scienceElectronic circuit
• NF-κB in biology and targeted therapy: new insights and translational implications
  NF-κB signaling has been discovered for nearly 40 years. Initially, NF-κB signaling was identified as a pivotal pathway in mediating inflammatory responses. However, with extensive and in-depth investigations, researchers have discovered that its role can be e…
  openalex Qing Guo, Yizi Jin, Xinyu Chen, Xiaomin Ye 等 2024-03-04 置信度 0.72 Signal transductionWnt signaling pathwayBiologyNF-κBCancer research
• Creating small transcription activating RNAs
  openalex James Chappell, Melissa K. Takahashi, Julius B. Lucks 2015-02-02 置信度 0.72 Terminator (solar)BiologySynthetic biologyRNAUpstream activating sequence
• A split-Cas9 architecture for inducible genome editing and transcription modulation
  openalex Bernd Zetsche, Sara E. Volz, Feng Zhang 2015-02-01 置信度 0.72 Genome editingCas9Transcription (linguistics)ArchitectureBiology
• Petri Nets for Systems and Synthetic Biology
  openalex Monika Heiner, David Gilbert, Robin Donaldson 2008-05-30 置信度 0.72 Rotation formalisms in three dimensionsPetri netComputer scienceComplement (music)Stochastic Petri net
• Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology
  openalex Barbara Jusiak, Sara Cleto, Pablo Pérez‐Piñera, Timothy K. Lu 2016-01-22 置信度 0.72 CRISPRSynthetic biologyComputational biologyBiologyGene regulatory network
• Synthetic gene circuits for the detection, elimination and prevention of disease
  openalex Ferdinand Sedlmayer, Dominique Aubel, Martin Fussenegger 2018-06-04 置信度 0.72 Synthetic biologyRepurposingComputational biologyComputer scienceGenetically engineered
• Sense and sensibility: of synthetic biology and the redesign of bioreporter circuits
  It is tempting to speculate that sixty years ago, when Jacob and Monod presented their model of the lac operon (Jacob and Monod, 1961), they already had a glimpse of the future of the lacZ gene, not only as encoding a cleaver of disaccharides, nor as a compone…
  openalex Shimshon Belkin, Baojun Wang 2021-10-24 置信度 0.72 BioreporterOperonBiosensorReporter geneSynthetic biology
• Phage-Based Applications in Synthetic Biology
  Bacteriophage research has been instrumental to advancing many fields of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been adapted for building gene circuits to program biological systems. Phages als…
  openalex Sébastien Lemire, Kevin Yehl, Timothy K. Lu 2018-07-12 置信度 0.72 Synthetic biologyBiologyBacteriophageComputational biologyChemical biology
• De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells
  A grand challenge in synthetic biology is to use our current knowledge of RNA science to perform the automatic engineering of completely synthetic sequences encoding functional RNAs in living cells. We report here a fully automated design methodology and exper…
  openalex Guillermo Rodrigo, Thomas E. Landrain, Alfonso Jaramillo 2012-09-04 置信度 0.72 Synthetic biologyRNAComputational biologyNon-coding RNAElectronic circuit
• Bacterial Quorum Sensing: Signals, Circuits, and Implications for Biofilms and Disease
  Communication between bacteria, belonging to the same species or to different species, is mediated through different chemical signals that are synthesized and secreted by bacteria. These signals can either be cell-density related (autoinducers) or be produced …
  openalex Arul Jayaraman, Thomas K. Wood 2008-07-22 置信度 0.72 Quorum sensingBiofilmAutoinducerBacteriaBiology
• Industry 5.0—The Relevance and Implications of Bionics and Synthetic Biology
  Bionics (the imitation or abstraction of the “inventions of nature) and, to an even greater extent, synthetic biology, will be as relevant to engineering development and industry as the silicon chip was over the last 50 years. Chemical industries already use s…
  openalex Peter Sachsenmeier 2016-06-01 置信度 0.72 BionicsSynthetic biologyCommercializationBiochemical engineeringNanotechnology
• Functional Synthetic Biology
  Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms. However, current paradi…
  arxiv Ibrahim Aldulijan, Jacob Beal, Sonja Billerbeck, Jeff Bouffard 等 2022-07-01T16:44:29Z 置信度 0.78 q-bio.QM
• Synthetic Biology in Leishmaniasis: Design,simulation and validation of constructed Genetic circuit
  Building circuits and studying their behavior in cells is a major goal of systems and synthetic biology. Synthetic biology enables the precise control of cellular states for systems studies, the discovery of novel parts, control strategies, and interactions fo…
  arxiv Dixita Limbachiya 2013-04-01T12:32:52Z 置信度 0.78 q-bio.MN
• Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions
  Background: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time relative to the need…
  arxiv Ian Vernon, Junli Liu, Michael Goldstein, James Rowe 等 2016-07-21T15:10:57Z 置信度 0.78 q-bio.MNq-bio.CBq-bio.QMstat.APstat.ME
• From Physics to Biology by Extending Criticality and Symmetry Breakings
  Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic …
  arxiv Giuseppe Longo, Maël Montévil 2011-03-09T17:08:48Z 置信度 0.78 q-bio.OT
• Analysing control-theoretic properties of nonlinear synthetic biology circuits
  Synthetic biology is a recent area of biological engineering, whose aim is to provide cells with novel functionalities. A number of important results regarding the development of control circuits in synthetic biology have been achieved during the last decade. …
  arxiv Antón Pardo, Sandra Díaz Seoane, Dorin A. Ionescu, Antonis Papachristodoulou 等 2024-11-08T09:55:47Z 置信度 0.78 eess.SYq-bio.QM
• Methods of Information Theory and Algorithmic Complexity for Network Biology
  We survey and introduce concepts and tools located at the intersection of information theory and network biology. We show that Shannon's information entropy, compressibility and algorithmic complexity quantify different local and global aspects of synthetic an…
  arxiv Hector Zenil, Narsis A. Kiani, Jesper Tegnér 2014-01-15T14:34:00Z 置信度 0.78 q-bio.MNq-bio.QM
• Effects of RF Stimulus and Negative Feedback on Nonlinear Circuits
  We investigate the combined effect of rectification and nonlinear dynamics on the behavior of several simple nonlinear circuits. We consider the classic Resistor-Inductor-Diode (RLD) circuit driven by a low frequency source when an operational amplifier with n…
  arxiv Renato Mariz de Moraes, Steven M. Anlage 2002-08-27T21:34:32Z 置信度 0.78 nlin.CD
• Athena: Modular CAM/CAD Software for Synthetic Biology
  Synthetic biology is the engineering of cellular networks. It combines principles of engineering and the knowledge of biological networks to program the behavior of cells. Computational modeling techniques in conjunction with molecular biology techniques have …
  arxiv Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro 2009-02-16T03:31:27Z 置信度 0.78 q-bio.QMq-bio.MN
• The use of information theory in evolutionary biology
  Information is a key concept in evolutionary biology. Information is stored in biological organism's genomes, and used to generate the organism as well as to maintain and control it. Information is also "that which evolves". When a population adapts to a local…
  arxiv Christoph Adami 2011-12-16T15:59:35Z 置信度 0.78 q-bio.PEcs.ITq-bio.NC
• Systems biology beyond degree, hubs and scale-free networks: the case for multiple metrics in complex networks
  Modeling and topological analysis of networks in biological and other complex systems, must venture beyond the limited consideration of very few network metrics like degree, betweenness or assortativity. A proper identification of informative and redundant ent…
  arxiv Soumen Roy 2012-05-10T17:26:02Z 置信度 0.78 q-bio.QMcond-mat.stat-mechcs.SIphysics.soc-ph
• Universally Sloppy Parameter Sensitivities in Systems Biology
  Quantitative computational models play an increasingly important role in modern biology. Such models typically involve many free parameters, and assigning their values is often a substantial obstacle to model development. Directly measuring \emph{in vivo} bioc…
  arxiv Ryan N. Gutenkunst, Joshua J. Waterfall, Fergal P. Casey, Kevin S. Brown 等 2007-01-24T19:12:58Z 置信度 0.78 q-bio.QMq-bio.MN
• Approximation of Intractable Likelihood Functions in Systems Biology via Normalizing Flows
  Systems biology relies on mathematical models that often involve complex and intractable likelihood functions, posing challenges for efficient inference and model selection. Generative models, such as normalizing flows, have shown remarkable ability in approxi…
  arxiv Vincent D. Zaballa, Elliot E. Hui 2023-12-04T23:10:56Z 置信度 0.78 q-bio.QM
• Privacy Measurement in Tabular Synthetic Data: State of the Art and Future Research Directions
  Synthetic data (SD) have garnered attention as a privacy enhancing technology. Unfortunately, there is no standard for quantifying their degree of privacy protection. In this paper, we discuss proposed quantification approaches. This contributes to the develop…
  arxiv Alexander Boudewijn, Andrea Filippo Ferraris, Daniele Panfilo, Vanessa Cocca 等 2023-11-29T08:51:40Z 置信度 0.78 cs.AIcs.CRcs.DBstat.ML
• Virtual-organism toy-model as a tool to develop bioinformatics approaches of Systems Biology for medical-target discovery
  Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human cells. Since the Syste…
  arxiv Albert Pujol, Raquel Valls, Vesna Radovanovic, Emre Guney 等 2013-01-11T16:00:30Z 置信度 0.78 q-bio.MNq-bio.CB
• Non-intrusive data-driven model order reduction for circuits based on Hammerstein architectures
  We demonstrate that system identification techniques can provide a basis for effective, non-intrusive model order reduction (MOR) for common circuits that are key building blocks in microelectronics. Our approach is motivated by the practical operation of thes…
  arxiv Joshua Hanson, Paul Kuberry, Biliana Paskaleva, Pavel Bochev 2024-05-30T15:47:48Z 置信度 0.78 eess.SYcs.LG
• Efficient Uncertainty Quantification for the Periodic Steady State of Forced and Autonomous Circuits
  This brief paper proposes an uncertainty quantification method for the periodic steady-state (PSS) analysis with both Gaussian and non-Gaussian variations. Our stochastic testing formulation for the PSS problem provides superior efficiency over both Monte Carl…
  arxiv Zheng Zhang, Tarek A. El-Moselhy, Paolo Maffezzoni, Ibrahim 等 2014-09-16T22:46:49Z 置信度 0.78 cs.CE
• Synthetic biology: From a word to a world
  Synthetic biology is one of the battlefields where the main countries fight for the supremacy in science. The word synthetic biology hides a big world, ready to be explored by interdisciplinary research collaborations. The purpose of this investigation is to r…
  arxiv Xiaojun Hu, Ronald Rousseau 2014-06-10T14:53:39Z 置信度 0.78 q-bio.OT
• TinkerCell: Modular CAD Tool for Synthetic Biology
  Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has b…
  arxiv Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro 2009-07-23T03:21:21Z 置信度 0.78 q-bio.MNq-bio.QM
• Reversible Logic Circuit Synthesis
  Reversible or information-lossless circuits have applications in digital signal processing, communication, computer graphics and cryptography. They are also a fundamental requirement in the emerging field of quantum computation. We investigate the synthesis of…
  arxiv Vivek V. Shende, Aditya K. Prasad, Igor L. Markov, John P. Hayes 2002-06-28T23:38:19Z 置信度 0.78 quant-ph
• Blind source separation methods for deconvolution of complex signals in cancer biology
  Two blind source separation methods (Independent Component Analysis and Non-negative Matrix Factorization), developed initially for signal processing in engineering, found recently a number of applications in analysis of large-scale data in molecular biology. …
  arxiv Andrei Zinovyev, Ulykbek Kairov, Tatiana Karpenyuk, Erlan Ramanculov 2013-01-11T23:47:16Z 置信度 0.78 q-bio.QMcs.CEq-bio.GN
• Teaching Memory Circuit Elements via Experiment-Based Learning
  The class of memory circuit elements which comprises memristive, memcapacitive, and meminductive systems, is gaining considerable attention in a broad range of disciplines. This is due to the enormous flexibility these elements provide in solving diverse probl…
  arxiv Y. V. Pershin, M. Di Ventra 2011-12-22T19:38:18Z 置信度 0.78 physics.ins-detcond-mat.mes-hallcs.ET
• Landauer in the age of synthetic biology: energy consumption and information processing in biochemical networks
  A central goal of synthetic biology is to design sophisticated synthetic cellular circuits that can perform complex computations and information processing tasks in response to specific inputs. The tremendous advances in our ability to understand and manipulat…
  arxiv Pankaj Mehta, Alex H. Lang, David J. Schwab 2015-05-11T03:25:24Z 置信度 0.78 q-bio.MNcond-mat.stat-mechphysics.bio-ph
• Bayesian Parameter Estimation for Dynamical Models in Systems Biology
  Dynamical systems modeling, particularly via systems of ordinary differential equations, has been used to effectively capture the temporal behavior of different biochemical components in signal transduction networks. Despite the recent advances in experimental…
  arxiv Nathaniel J. Linden, Boris Kramer, Padmini Rangamani 2022-04-11T21:24:10Z 置信度 0.78 q-bio.QMq-bio.MN
• An Evaluation of Large Pre-Trained Models for Gesture Recognition using Synthetic Videos
  In this work, we explore the possibility of using synthetically generated data for video-based gesture recognition with large pre-trained models. We consider whether these models have sufficiently robust and expressive representation spaces to enable "training…
  arxiv Arun Reddy, Ketul Shah, Corban Rivera, William Paul 等 2024-10-03T02:31:14Z 置信度 0.78 cs.CV
• The Convergence of AI and Synthetic Biology: The Looming Deluge
  The convergence of artificial intelligence (AI) and synthetic biology is rapidly accelerating the pace of biological discovery and engineering. AI techniques, such as large language models and biological design tools, are enabling the automated design, build, …
  arxiv Cindy Vindman, Benjamin Trump, Christopher Cummings, Madison Smith 等 2024-04-29T14:17:06Z 置信度 0.78 q-bio.OT
• Deciphering neural circuits for Caenorhabditis elegans behavior by computations and perturbations to genome and connectome
  {\it Caenorhabditis elegans} nematode worms are the only animals with the known detailed neural connectivity diagram, well characterized genomics, and relatively simple quantifiable behavioral output. With this in mind, many researchers view this animal as the…
  arxiv Jan Karbowski 2019-10-16T16:17:33Z 置信度 0.78 q-bio.NCq-bio.GNq-bio.QM
• Perspectives on theory at the interface of physics and biology
  Theoretical physics is the search for simple and universal mathematical descriptions of the natural world. In contrast, much of modern biology is an exploration of the complexity and diversity of life. For many, this contrast is prima facie evidence that theor…
  arxiv William Bialek 2015-12-30T14:47:40Z 置信度 0.78 physics.bio-phcond-mat.dis-nnphysics.hist-phq-bio.QM
• Bistability of an In Vitro Synthetic Autoregulatory Switch
  The construction of synthetic biochemical circuits is an essential step for developing quantitative understanding of information processing in natural organisms. Here, we report construction and analysis of an in vitro circuit with positive autoregulation that…
  arxiv Pakpoom Subsoontorn, Jongmin Kim, Erik Winfree 2011-01-04T14:23:40Z 置信度 0.78 q-bio.MNq-bio.BMq-bio.QM
• Bayesian and Algebraic Strategies to Design in Synthetic Biology
  Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper and safer. But this re…
  arxiv Robyn P. Araujo, Sean T. Vittadello, Michael P. H. Stumpf 2021-08-17T00:43:00Z 置信度 0.78 q-bio.MNq-bio.CB
• Physical Principles of Quantum Biology
  This technical monograph provides a comprehensive overview of the field of quantum biology. It approaches quantum biology from a physical perspective with core quantum mechanical concepts presented foremost to provide a theoretical foundation for the field. An…
  arxiv Nathan S. Babcock, Brandy N. Babcock 2025-03-14T17:12:25Z 置信度 0.78 physics.bio-phq-bio.BMq-bio.CBq-bio.SCq-bio.TO
• Physics of liquid crystals in cell biology
  The last decade has witnessed a rapid growth in understanding of the pivotal roles of mechanical stresses and physical forces in cell biology. As a result an integrated view of cell biology is evolving, where genetic and molecular features are scrutinized hand…
  arxiv Amin Doostmohammadi, Benoit Ladoux 2021-10-07T06:42:11Z 置信度 0.78 cond-mat.softcond-mat.mtrl-sciphysics.bio-ph
• Integration of Omics Data and Systems Biology Modeling: Effect of Cyclosporine A on the Nrf2 Pathway in Human Renal Kidneys Cells
  In a recent paper, Wilmes et al. demonstrated a qualitative integration of omics data streams to gain a mechanistic understanding of cyclosporine A toxicity. One of their major conclusions was that cyclosporine A strongly activates the nuclear factor (erythroi…
  arxiv Jérémy Hamon, Paul Jennings, Frederic Y. Bois 2013-12-17T12:28:58Z 置信度 0.78 q-bio.QMq-bio.MN
• TEDDY: A Family Of Foundation Models For Understanding Single Cell Biology
  Understanding the biological mechanisms of disease is crucial for medicine, and in particular, for drug discovery. AI-powered analysis of genome-scale biological data holds great potential in this regard. The increasing availability of single-cell RNA sequenci…
  arxiv Alexis Chevalier, Soumya Ghosh, Urvi Awasthi, James Watkins 等 2025-03-05T13:24:57Z 置信度 0.78 cs.LGq-bio.QM
• Circuit design in biology and machine learning. I. Random networks and dimensional reduction
  A biological circuit is a neural or biochemical cascade, taking inputs and producing outputs. How have biological circuits learned to solve environmental challenges over the history of life? The answer certainly follows Dobzhansky's famous quote that ``nothing…
  arxiv Steven A. Frank 2024-08-18T22:11:24Z 置信度 0.78 q-bio.PEcs.LGphysics.bio-ph
• Toward a general theory for the universality and scaling in critical thermal responses in biology
  We developed a theory showing that under appropriate normalizations and rescalings, temperature response curves show a remarkably regular behavior and follow a general, universal law. The impressive universality of temperature response curves remained hidden d…
  arxiv Jose Ignacio Arroyo, Pablo A. Marquet, Christopher P. Kempes, Geoffrey West 2025-03-07T04:19:25Z 置信度 0.78 q-bio.OT