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• Complex versus Complicated Systems Biology, Universality versus Detailed Modelling
  Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects of biological system…
  arxiv Kunihiko Kaneko 2026-03-18T01:43:42Z 置信度 0.78 physics.bio-ph
• Circuit-centric Genetic Algorithm (CGA) for Analog and Radio-Frequency Circuit Optimization
  This paper presents an automated method for optimizing parameters in analog/high-frequency circuits, aiming to maximize performance parameters of a radio-frequency (RF) receiver. The design target includes a reduction of power consumption and noise figure and …
  arxiv Mingi Kwon, Yeonjun Lee, Ickhyun Song 2023-11-19T02:33:22Z 置信度 0.78 cs.NEeess.SY
• Synthetic graphs for link prediction benchmarking
  Predicting missing links in complex networks requires algorithms that are able to explore statistical regularities in the existing data. Here we investigate the interplay between algorithm efficiency and network structures through the introduction of suitably-…
  arxiv Alexey Vlaskin, Eduardo G. Altmann 2024-12-04T22:50:26Z 置信度 0.78 cs.SIphysics.soc-ph
• Downstream Task-Oriented Generative Model Selections on Synthetic Data Training for Fraud Detection Models
  Devising procedures for downstream task-oriented generative model selections is an unresolved problem of practical importance. Existing studies focused on the utility of a single family of generative models. They provided limited insights on how synthetic data…
  arxiv Yinan Cheng, Chi-Hua Wang, Vamsi K. Potluru, Tucker Balch 等 2024-01-01T23:33:56Z 置信度 0.78 cs.LGcs.AI
• Quantum Circuit Transformation Based on Simulated Annealing and Heuristic Search
  Quantum algorithm design usually assumes access to a perfect quantum computer with ideal properties like full connectivity, noise-freedom and arbitrarily long coherence time. In Noisy Intermediate-Scale Quantum (NISQ) devices, however, the number of qubits is …
  arxiv Xiangzhen Zhou, Sanjiang Li, Yuan Feng 2019-08-23T14:54:26Z 置信度 0.78 quant-ph
• Multi-strategy Based Quantum Cost Reduction of Quantum Boolean Circuits
  The construction of quantum computers is based on the synthesis of low-cost quantum circuits. The quantum circuit of any Boolean function expressed in a Positive Polarity Reed-Muller $PPRM$ expansion can be synthesized using Multiple-Control Toffoli ($MCT$) ga…
  arxiv Taghreed Ahmed, Ahmed Younes, and Islam Elkabani 2024-07-05T19:25:46Z 置信度 0.78 quant-phcs.ET
• Systems biology: From the cell to the brain
  With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to understanding the se…
  arxiv Sitabhra Sinha, T Jesan, Nivedita Chatterjee 2010-01-27T03:35:20Z 置信度 0.78 q-bio.MNphysics.bio-phq-bio.NC
• Neurobiology and Changing Ecosystems: toward understanding the impact of anthropogenic influences on neurons and circuits
  Rapid anthropogenic environmental changes, including those due to habitat contamination, degradation, and climate change, have far-reaching effects on biological systems that may outpace animals' adaptive responses (Radchuk et al., 2019). Neurobiological syste…
  arxiv Angie Michaiel, Amy Bernard 2022-10-14T16:33:27Z 置信度 0.78 q-bio.NC
• Quantum Biology at the Cellular Level - elements of the research program
  Quantum Biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (Quantum Biology at Cellular Level), a research…
  arxiv Michael Bordonaro, Vasily Ogryzko 2013-04-02T16:38:18Z 置信度 0.78 q-bio.OT
• Biology-Derived Algorithms in Engineering Optimization
  Biology-derived algorithms are an important part of computational sciences, which are essential to many scientific disciplines and engineering applications. Many computational methods are derived from or based on the analogy to natural evolution and biological…
  arxiv Xin-She Yang 2010-03-09T14:53:12Z 置信度 0.78 math.OCcs.CEcs.NEq-bio.QM
• Synthetic to Authentic: Transferring Realism to 3D Face Renderings for Boosting Face Recognition
  In this paper, we investigate the potential of image-to-image translation (I2I) techniques for transferring realism to 3D-rendered facial images in the context of Face Recognition (FR) systems. The primary motivation for using 3D-rendered facial images lies in…
  arxiv Parsa Rahimi, Behrooz Razeghi, Sebastien Marcel 2024-07-10T13:07:39Z 置信度 0.78 cs.CV
• Using Libraries of Approximate Circuits in Design of Hardware Accelerators of Deep Neural Networks
  Approximate circuits have been developed to provide good tradeoffs between power consumption and quality of service in error resilient applications such as hardware accelerators of deep neural networks (DNN). In order to accelerate the approximate circuit desi…
  arxiv Vojtech Mrazek, Lukas Sekanina, Zdenek Vasicek 2020-04-22T10:42:27Z 置信度 0.78 cs.AR
• Sparse Feature Circuits: Discovering and Editing Interpretable Causal Graphs in Language Models
  We introduce methods for discovering and applying sparse feature circuits. These are causally implicated subnetworks of human-interpretable features for explaining language model behaviors. Circuits identified in prior work consist of polysemantic and difficul…
  arxiv Samuel Marks, Can Rager, Eric J. Michaud, Yonatan Belinkov 等 2024-03-28T17:56:07Z 置信度 0.78 cs.LGcs.AIcs.CL
• Ten Simple Rules for Creating Biomolecular Graphics
  One need only compare the number of three-dimensional molecular illustrations in the first (1990) and third (2004) editions of Voet & Voet's "Biochemistry" in order to appreciate this field's profound communicative value in modern biological sciences -- ra…
  arxiv Cameron Mura 2014-07-15T17:48:16Z 置信度 0.78 q-bio.BMcs.HC
• Design and applications of synthetic information processing circuits in mammalian cells
  Mammalian cells represent a challenge and opportunity for synthetic biology. The toolbox of regulators implemented in mammalian cells includes small molecule- or physical stimulus-responsive elements from bacteria, yeast and plants, and designed nucleic acid b…
  crossref Jan Lonzaric, Tina Fink, Roman Jerala 2017-12-18T10:37:25Z 置信度 0.70
• Synthetic biological toggle circuits that respond within seconds and teach us new biology
  Imagine it would take several minutes or even hours for your light bulb to turn on after you hit the switch—not very useful for many daily (and nightly) activities. Light switches are made from the so-called toggle switches; basic and widely used electrical co…
  crossref Sonja Billerbeck 2021-08-28T17:50:55Z 置信度 0.70
• Impact of retroactivity on information flows in engineered synthetic biological circuits
  Abstract In biological networks, retroactivity describes the feedback from downstream components that can influence and alter the behavior of upstream systems. This effect poses a major challenge to the modular design of synthetic circuits, where upstream modu…
  crossref Sailash Moirangthem, Karthik Raman 2026-03-07T05:55:17Z 置信度 0.70
• Generative design of synthetic gene circuits for functional and evolutionary properties
  1 Abstracts In the past decades, a wide suite of design tools for biological systems have been developed, but using these to create biotechnologies that achieve reliable and predictable behaviour remains challenging. Modelling approaches have enabled researche…
  crossref Olivia Gallup, Harrison Steel 2025-09-28T03:30:13Z 置信度 0.70
• Multistable and dynamic CRISPRi-based synthetic circuits
  Abstract Gene expression control based on CRISPRi (clustered regularly interspaced short palindromic repeats interference) has emerged as a powerful tool for creating synthetic gene circuits, both in prokaryotes and in eukaryotes; yet, its lack of cooperativit…
  crossref Javier Santos-Moreno, Eve Tasiudi, Joerg Stelling, Yolanda Schaerli 2019-09-03T17:55:12Z 置信度 0.70
• Design and Mathematical Analysis of Synthetic Inhibitory Circuits that Program Self-Organizing Multicellular Structures
  ABSTRACT Bottom-up approaches are becoming increasingly popular for studying multicellular self-organization and development. In contrast to the classic top-down approach, where parts of the organization/developmental process are broken to understand the proce…
  crossref Calvin Lam 2023-11-19T00:45:10Z 置信度 0.70
• Design and Mathematical Analysis of Activating Amplifiers that Enable Modular Temporal Control in Synthetic Circuits
  ABSTRACT The ability to control mammalian cells such that they self-organize or enact therapeutic effects as desired has incredible implications. Not only would it further our understanding of native processes such as development and the immune response, but i…
  crossref Calvin Lam 2023-03-19T03:46:39Z 置信度 0.70
• Decision letter for "Bacterial degrons in synthetic circuits"
  crossref 2022-08-17T17:00:13Z 置信度 0.70
• A framework for the modular and combinatorial assembly of synthetic gene circuits
  ABSTRACT Synthetic gene circuits emerge from iterative design-build-test cycles. Most commonly, the time-limiting step is the circuit construction process. Here, we present a hierarchical cloning scheme based on the widespread Gibson assembly method and make t…
  crossref Javier Santos-Moreno, Yolanda Schaerli 2019-04-19T02:55:12Z 置信度 0.70
• Identifying competition phenotypes in synthetic biochemical circuits
  Abstract Synthetic gene circuits require cellular resources, which are often limited. This leads to competition for resources by different genes, which alter a synthetic genetic circuit’s behavior. However, the manner in which competition impacts behavior depe…
  crossref M. Ali Al-Radhawi, Domitilla Del Vecchio, Eduardo D. Sontag 2022-03-24T00:10:16Z 置信度 0.70
• Synthetic Circuits for the Detection of Bacteria
  crossref Monisa Anwer, Ajay Kumar 2026-05-17T22:16:55Z 置信度 0.70
• Synthetic Circuits for the Detection of Viruses
  crossref Dharmisha Solanki, Vijai Singh 2026-05-17T22:40:07Z 置信度 0.70
• TXO: Transcription-Only genetic circuits as a novel cell-free approach for Synthetic Biology
  Abstract While synthetic biology represents a promising approach to solve real-world problems, the use of genetically modified organisms is a cause of legal and environmental concerns. Cell-free systems have emerged as a possible solution but much work is need…
  crossref Felipe A. Millacura, Mengxi Li, Marcos Valenzuela-Ortega, Christopher E. French 2019-10-31T23:45:13Z 置信度 0.70
• Modeling Dynamic Transcriptional Circuits with CRISPRi
  Abstract Targeted transcriptional repression with catalytically inactive Cas9 (CRISPRi) promises to reproduce the functions of traditional synthetic transcriptional circuits, but with better orthogonality, programmability, and extensibility. However, CRISPRi l…
  crossref Samuel Clamons, Richard M. Murray 2017-11-28T01:10:12Z 置信度 0.70
• The Synthetic Approach for Regulatory and Metabolic Circuits
  This chapter contains sections titled: Introduction Biological Oscillators Cell–Cell Communication in Bacteria Conclusion References
  crossref Wilson W. Wong, James C. Liao 2009-09-22T20:46:30Z 置信度 0.70
• Using Models to (Re-)Design Synthetic Circuits
  Mathematical models play an important role in the design of synthetic gene circuits, by guiding the choice of biological components and their assembly into novel gene networks. Here, we present a guide for biologists to build and utilize models of gene network…
  crossref Giselle McCallum, Laurent Potvin-Trottier 2021-01-06T14:08:40Z 置信度 0.70
• Tailored synthetic sRNAs dynamically tune multilayer genetic circuits
  Abstract Predictable and controllable tuning of genetic circuits to regulate gene expression, including modulation of existing circuits or constructs without the need for redesign or rebuilding, is a persistent challenge in synthetic biology. Here, we propose …
  crossref Ana K. Velazquez Sanchez, Bjarne Klopprogge, Karl-Heinz Zimmermann, Zoya Ignatova 2022-11-09T22:10:16Z 置信度 0.70
• DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems
  crossref Nathan J. Hillson 2011-05-20T17:49:31Z 置信度 0.70
• Feedback Control and Sensitivity Analysis in Synthetic Gene Circuits.
  Synthetic gene circuits are engineered DNA sequences that control when genes turn on and how much they are expressed, alongside the regulatory machinery of cells. Many gene circuits use feedback, such that the molecules produced by a gene increase or decrease …
  europepmc 2026 置信度 0.80
• Design of CRISPRi-Based Synthetic Gene Circuits in Bacteria.
  Synthetic gene circuits are key elements of engineered biological systems that allow us to control and program cellular behavior. Yet, circuit design can be challenging to newcomers due to the numerous design choices and the abundance and variety of parameters…
  europepmc 2026 置信度 0.80
• Mathematical Modeling of Synthetic Genetic Circuits
  Synthetic genetic circuits are the core research objects in synthetic biology, and the programming of cell behavior is achieved through the combination of engineered gene elements. Mathematical modeling provides crucial support for understanding and designing …
  crossref Haimei Wang 2025-12-05T03:00:02Z 置信度 0.70
• Co-transcriptional RNA strand displacement circuits
  Abstract Engineered molecular circuits that process information in biological systems could address emerging human health and biomanufacturing needs. However, such circuits can be difficult to rationally design and scale. DNA-based strand displacement reaction…
  crossref Samuel W. Schaffter, Elizabeth A. Strychalski 2021-07-21T00:40:12Z 置信度 0.70
• How to model DNA replication in stochastic models of synthetic gene circuits (and why)
  Abstract Biocircuit modeling sometimes requires explicit tracking of a self-replicating DNA species. The most obvious, straightforward way to model a replicating DNA is structurally unstable and leads to pathological model behavior. We describe a simple, stabl…
  crossref Samuel E. Clamons, Richard M. Murray 2021-09-27T12:38:07Z 置信度 0.70
• Scalable dynamic characterization of synthetic gene circuits
  Abstract The dynamic behavior of synthetic gene circuits plays a key role in ensuring their correct function. Although there has been substantial work on modeling dynamic behavior after circuit construction, the forward engineering of dynamic behavior remains …
  crossref Neil Dalchau, Paul K. Grant, Prashant Vaidyanathan, Carlo Spaccasassi 等 2019-05-14T04:25:25Z 置信度 0.70
• An automated model reduction tool to guide the design and analysis of synthetic biological circuits
  Abstract We present an automated model reduction algorithm that uses quasi-steady state approximation to minimize the error between the desired outputs. Additionally, the algorithm minimizes the sensitivity of the error with respect to parameters to ensure rob…
  crossref Ayush Pandey, Richard M. Murray 2019-05-17T16:34:16Z 置信度 0.70
• Synthetic genetic circuits enable reprogramming of plant roots
  Abstract The shape of a plant’s root system influences its ability to reach essential nutrients in the soil and to acquire water during drought. Progress in engineering plant roots to optimize water and nutrient acquisition has been limited by our capacity to …
  crossref Jennifer A. N. Brophy, Katie J. Magallon, Kiril Kniazev, José R. Dinneny 2022-02-03T11:40:50Z 置信度 0.70
• Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits
  Qualitative modeling approaches are promising and still underexploited tools for the analysis and design of synthetic circuits. They can make predictions of circuit behavior in the absence of precise, quantitative information. Moreover, they provide direct ins…
  crossref Madalena Chaves, Hidde de Jong 2021-01-06T14:08:40Z 置信度 0.70
• Gene Synthesis – Enabling Technologies for Synthetic Biology
  crossref Michael Liss, Ralf Wagner 2011-05-20T17:49:31Z 置信度 0.70
• Synthetic gene circuits for higher-order information processing
  crossref Kathakali Sarkar, Sangram Bagh 2022-01-14T22:43:13Z 置信度 0.70
• Growth defects and loss-of-function in synthetic gene circuits
  Abstract Synthetic gene circuits perturb the physiology of their cellular host. The extra load on endogenous processes shifts the equilibrium of resource allocation in the host, leading to slow growth and reduced biosynthesis. Here we built integrated host-cir…
  crossref Evangelos-Marios Nikolados, Andrea Y. Weiße, Francesca Ceroni, Diego A. Oyarzún 2019-05-01T04:35:14Z 置信度 0.70
• Characterizing Optogenetic Tools for Use in Synthetic Gene Circuits.
  Synthetic gene circuits consist of engineered networks of genes and proteins. The function of these circuits can be tuned by regulating the expression levels of key circuit components. Light is an ideal signal for controlling expression levels in these circuit…
  europepmc 2026 置信度 0.80
• A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits
  Abstract Synthetic genes compete among themselves and with the host cell’s genes for expression machinery, exhibiting resource couplings that affect the dynamics of cellular processes. The modeling of such couplings can be facilitated by simplifying the kineti…
  crossref Kirill Sechkar, Giansimone Perrino, Guy-Bart Stan 2023-04-08T23:45:12Z 置信度 0.70
• Data Model Standardization for Synthetic Biomolecular Circuits and Systems
  crossref Michal Galdzicki, Deepak Chandran, John H. Gennari, Herbert M. Sauro 2011-05-20T17:49:31Z 置信度 0.70
• Engineering RNAi Circuits
  Engineered "computing" biological networks are a generalization of endogenous regulatory pathways. They are intended to generate novel biological responses based on preprogrammed processing of multiple molecular signals. We have recently introduced an approach…
  crossref Yaakov Benenson 2012-05-17T10:15:48Z 置信度 0.70
• Modeling Growth-Mediated Dilution in Synthetic Circuits: Effects of Circuit Topology and Phase Separation.
  Growth-mediated dilution is a major source of variability and instability in synthetic gene circuits, influencing both expression dynamics and circuit memory. Our previous work demonstrated that circuit topology plays a critical role in determining how robustl…
  europepmc 2026 置信度 0.80
• Using Computational Modeling and Experimental Synthetic Perturbations to Probe Biological Circuits
  This chapter describes approaches for using computational modeling of synthetic biology perturbations to analyze endogenous biological circuits, with a particular focus on signaling and metabolic pathways. We describe a bottom-up approach in which ordinary dif…
  crossref Joshua R. Porter, Eric Batchelor 2014-12-08T14:39:11Z 置信度 0.70
• Computer-Aided Design for Synthetic Biology
  crossref Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro, Douglas Densmore 2011-05-20T17:49:31Z 置信度 0.70
• Context Dependence of Biological Circuits
  Abstract It has been an ongoing scientific debate whether biological parameters are conserved across experimental setups with different media, pH values, and other experimental conditions. Our work explores this question using Bayesian probability as a rigorou…
  crossref Thomas A. Catanach, Reed McCardell, Ania-Ariadna Baetica, Richard M. Murray 2018-07-03T14:15:08Z 置信度 0.70
• Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits
  Abstract We present a Python-based software package to automatically obtain phenomenological models of input-controlled synthetic biological circuits from descriptive models. From the parts and mechanism description of a synthetic biological circuit, it is eas…
  crossref Ayush Pandey, Richard M. Murray 2020-02-19T04:05:24Z 置信度 0.70
• Bayesian optimization for design of multiscale biological circuits
  Abstract Recent advances in synthetic biology have enabled the construction of molecular circuits that operate across multiple scales of cellular organization, such as gene regulation, signalling pathways and cellular metabolism. Computational optimization can…
  crossref Charlotte Merzbacher, Oisin Mac Aodha, Diego A. Oyarzún 2023-02-03T22:55:14Z 置信度 0.70
• Metabolism
  This chapter focuses on metabolism, specifically carbon and energy metabolism, meaning the processes by which a cell builds all of the molecules necessary to grow and divide. For example, E. coli s metabolic network enables each individual cell to create a nea…
  crossref Markus W. Covert 2019-06-03T08:10:04Z 置信度 0.70
• Synthetic negative feedback circuits using engineered small RNAs
  ABSTRACT Negative feedback is known to endow biological and man-made systems with robust performance in the face of uncertainties and disturbances. To date, synthetic biological feedback circuits have relied upon protein-based, transcriptional regulation to co…
  crossref Ciarán L. Kelly, Andreas W. K. Harris, Harrison Steel, Edward J. Hancock 等 2017-09-06T02:11:01Z 置信度 0.70
• Construction of Synthetic Gene Circuits in the Escherichia coli Genome
  The construction of stable and functional synthetic circuits in bacteria is necessary in the areas of systems and synthetic biology. The common approach using plasmids to carry foreign genetic circuits offers convenience in genetic construction but is poor in …
  crossref Bei-Wen Ying, Yuya Akeno, Tetsuya Yomo 2013-08-30T20:48:21Z 置信度 0.70
• Toward Modularity in Synthetic Biology: Design Patterns and Fan-out
  crossref Kyung Hyuk Kim, Deepak Chandran, Herbert M. Sauro 2011-05-20T17:49:31Z 置信度 0.70
• Automatic Feedback Control for Resource-Aware Characterisation of Genetic Circuits
  Abstract Many applications of engineered cells are enabled by genetic circuits – networks of genes regulating each other to process signals. Complex circuits are built by combining standardised modular components with different functions. Nonetheless, genes in…
  crossref Kirill Sechkar, Harrison Steel 2025-04-01T18:20:13Z 置信度 0.70
• Transcriptional Regulation
  This chapter focuses on transcriptional regulation and introduces this control with the example of a transcription factor that is bound by a small molecule, changing the protein s affinity for its binding site on the DNA. It illustrates the relationship betwee…
  crossref Markus W. Covert 2019-06-03T12:10:04Z 置信度 0.70
• Engineering synthetic CopT/A-based genetic circuits for miRNA imaging and functional gene regulation
  Abstract Synthetic genetic circuits that can operate at the transcriptional and translation levels have been widely applied in the control of cellular behaviors and functions. However, the regulation of genetic circuits is often accompanied by the introduction…
  crossref Chuanxian Zhang, Xiaorui Shi, Chu Tang, Yarong Du 等 2023-01-25T22:50:22Z 置信度 0.70
• Optimal Experimental Design for Systems and Synthetic Biology Using AMIGO2
  Dynamic modeling in systems and synthetic biology is still quite a challenge-the complex nature of the interactions results in nonlinear models, which include unknown parameters (or functions). Ideally, time-series data support the estimation of model unknowns…
  crossref Eva Balsa-Canto, Lucia Bandiera, Filippo Menolascina 2021-01-06T14:08:40Z 置信度 0.70
• Antithetic integral feedback for the robust control of monostable and oscillatory biomolecular circuits
  Abstract Biomolecular feedback systems are now a central application area of interest within control theory. While classical control techniques provide valuable insight into the function and design of both natural and synthetic biomolecular systems, there are …
  crossref Noah Olsman, Fulvio Forni 2019-11-13T20:55:16Z 置信度 0.70
• A Modular Approach to Building Complex Synthetic Circuits
  Efficient assembly of genetic circuits is a critical element in synthetic biology for implementing complex gene expression systems. Here we present an assembly framework that integrates recent developments in DNA recombination technologies and unique nucleotid…
  crossref Yinqing Li, Ron Weiss 2017-08-11T11:54:40Z 置信度 0.70
• Integrated Models
  The idea to separate the total functionality of the cell into smaller pieces that could be modeled individually and then integrated was a critical aspect of our future strategy for modeling entire cells. The development of regulatory flux balance analysis (rFB…
  crossref Markus W. Covert 2019-06-03T12:10:04Z 置信度 0.70
• Structure Determines Function – The Role of Topology in the Functionality of Gene Circuits
  As synthetic biologists, we sometimes forget the toggle switch and the self-activating switch, the foundational advances that launched the entire field of synthetic biology a mere two decades ago. As the first in a long line of increasingly sophisticated gene …
  crossref Daniel Bojar 2020-06-19T16:34:46Z 置信度 0.70
• Synthetic Gene Circuits
  crossref 2021-01-06T14:08:40Z 置信度 0.70
• <i>In situ</i> generation of RNA complexes for synthetic molecular strand displacement circuits in autonomous systems
  Abstract Synthetic molecular circuits implementing DNA or RNA strand-displacement reactions can be used to build complex systems such as molecular computers and feedback control systems. Despite recent advances, application of nucleic acid-based circuits in vi…
  crossref Wooli Bae, Guy-Bart V. Stan, Thomas E. Ouldridge 2020-07-16T06:27:14Z 置信度 0.70
• Predicting Composition of Genetic Circuits with Resource Competition: Demand and Sensitivity
  Abstract The design of genetic circuits typically relies on characterization of constituent modules in isolation to predict the behavior of modules’ composition. However, it has been shown that the behavior of a genetic module changes when other modules are in…
  crossref Cameron D. McBride, Domitilla Del Vecchio 2021-05-27T20:55:16Z 置信度 0.70
• Signal Transduction
  Signal transduction is the mechanism by which cells sense and react to factors in the external environment. To model signal transduction, authors must mathematically describe three new aspects of the underlying networks: the binding of ligands to receptors, th…
  crossref Markus W. Covert 2019-06-03T08:10:04Z 置信度 0.70
• Computational characterization of recombinase circuits for periodic behaviors
  Abstract In nature, recombinases are site-specific proteins capable of rearranging DNA, and they are expanding the repertoire of gene editing tools used in synthetic biology. The on/off response of recombinases, achieved by inverting the direction of a promote…
  crossref Judith Landau, Christian Cuba Samaniego, Giulia Giordano, Elisa Franco 2021-11-07T00:00:16Z 置信度 0.70
• Guest Editorial—Special Issue on Synthetic Biology
  The 10 papers in this special section on synthetic biology bring together information that both reviews and presents original work aimed at addressing these challenges. These papers incorporate advances and insights from analog circuit design, control theory, …
  crossref Rahul Sarpeshkar 2015-09-23T20:00:03Z 置信度 0.70
• Design Principles for Polymerase Strand Recycling Circuits
  Cell-free biosensing systems are being engineered as versatile and programmable diagnostic technologies. A core component of cell-free biosensors are programmable molecular circuits that improve biosensor speed, sensitivity and specificity by performing molecu…
  crossref Yueyi Li, Arno E. Gundlach, Andrew D. Ellington, Julius B. Lucks 2025-03-19T17:10:02Z 置信度 0.70
• Programming the elongation of mammalian cell aggregates with synthetic gene circuits
  Abstract A key goal of synthetic morphogenesis is the identification and implementation of methods to control morphogenesis. One line of research is the use of synthetic genetic circuits guiding the self-organization of cell ensembles. This approach has led to…
  crossref Josquin Courte, Christian Chung, Naisargee Jain, Catcher Salazar 等 2024-12-12T22:51:24Z 置信度 0.70
• A model for the spatio-temporal design of gene regulatory circuits
  Abstract The design of increasingly complex gene regulatory networks relies upon mathematical modelling to link the gap that goes from conceptualisation to implementation. An overarching challenge is to update modelling abstractions and assumptions as new mech…
  crossref Ruud Stoof, Alexander Wood, Ángel Goñi-Moreno 2019-01-17T23:25:23Z 置信度 0.70
• Distributed implementation of Boolean functions by transcriptional synthetic circuits
  Abstract Starting in the early 2000s, a sophisticated technology has been developed for the rational construction of synthetic genetic networks that implement specified logical functionalities. Despite impressive progress, however, the scaling necessary in ord…
  crossref M. Ali Al-Radhawi, Anh Phong Tran, Elizabeth A. Ernst, Tianchi Chen 等 2020-04-22T08:25:19Z 置信度 0.70
• Variation: Numerical Integration
  Numerical integration is the most common way to solve sets of ordinary differential equations (ODEs), in particular when more than a few ODEs need to be solved simultaneously. This chapter considers the Euler method, begins with a set of initial conditions and…
  crossref Markus W. Covert 2019-06-03T12:10:04Z 置信度 0.70
• Transcriptional interference in toehold switch-based RNA circuits
  ABSTRACT Gene regulation based on regulatory RNA is an important mechanism in cells and is increasingly used for regulatory circuits in synthetic biology. Toehold switches are rationally designed post-transcriptional riboregulators placed in the 5’ untranslate…
  crossref Elisabeth Falgenhauer, Andrea Mückl, Matthaeus Schwarz-Schilling, Friedrich C. Simmel 2021-09-30T00:51:04Z 置信度 0.70
• Variation: Graphical Analysis
  Graphical analysis lead us to deeper intuition about ordinary differential equations (ODEs) by enabling us to identify stable and unstable states, to plot dynamics, and to consider the effects of varying initial conditions and parameter values, rapidly and wit…
  crossref Markus W. Covert 2019-06-03T08:10:04Z 置信度 0.70
• Generating effective models and parameters for RNA genetic circuits
  RNA genetic circuitry is emerging as a powerful tool to control gene expression. However, little work has been done to create a theoretical foundation for RNA circuit design. A prerequisite to this is a quantitative modeling framework that accurately describes…
  crossref Chelsea Y Hu, Jeffrey D Varner, Julius B Lucks 2015-04-22T01:06:44Z 置信度 0.70
• Variation: Stochastic Simulation
  This chapter explains the relationship between rate parameters based on ordinary differential equations (ODEs) and those based on stochastic simulation. Stochastic methods differ from ODEs in a number of ways. In general, ODEs are the best choice when the syst…
  crossref Markus W. Covert 2019-06-03T08:10:04Z 置信度 0.70
• dCas12a:Pre-crRNA: A New Tool to Induce mRNA Degradation in Saccharomyces cerevisiae Synthetic Gene Circuits
  We describe a new way to trigger mRNA degradation in Saccharomyces cerevisiae synthetic gene circuits. Our method demands to modify either the 5'- or the 3'-UTR that flanks a target gene with elements from the pre-crRNA of type V Cas12a proteins and expresses …
  crossref Lifang Yu, Mario Andrea Marchisio 2024-03-11T22:02:42Z 置信度 0.70
• On the Construction of Minimal Cell Models in Synthetic Biology and Origins of Life Studies
  crossref Pasquale Stano, Pier Luigi Luisi 2011-05-20T17:49:31Z 置信度 0.70
• Programming Cell-Free Biosensors with DNA Strand Displacement Circuits
  Cell-free biosensors are powerful platforms for monitoring human and environmental health. Here, we expand their capabilities by interfacing them with toehold-mediated strand displacement circuits, a dynamic DNA nanotechnology that enables molecular computatio…
  openalex Jaeyoung K. Jung, Khalid K. Alam, Julius B. Lucks, Chloé M. Archuleta 2021-03-16T23:20:12Z 置信度 0.72 InterfacingBiosensorElectronic circuitSynthetic biologyComputer science
• Analysis of Circuits for Dosage Control in Microbial Populations
  Designing genetic circuits to control the behaviors of microbial populations is an ongoing challenge in synthetic biology. Here we analyze circuits which implement dosage control by controlling levels of a global signal in a microbial population in face of var…
  crossref Sophie J. Walton, Samuel E. Clamons, Richard M. Murray 2020-12-22T14:41:01Z 置信度 0.70
• Introduction to RNA-Based Circuits and Devices
  RNA synthetic biology advances the engineering of RNA molecules for therapeutics and biotechnology. Synthetic systems, through RNA’s ability to modulate gene expression and its interaction with proteins, metabolites, and nucleic acids, offering precise and spa…
  crossref Dharmisha Solanki, Vijai Singh 2026-02-07T04:06:10Z 置信度 0.70
• Variation: Boolean Representations
  This chapter presents the exploration of the negatively autoregulated circuit using a classical Boolean approach that relies on work performed by Rene Thomas at the Universite Libre de Bruxelles in Belgium. The idea behind the Boolean approach is that to ident…
  crossref Markus W. Covert 2019-06-03T12:10:04Z 置信度 0.70
• Length and time scales of cell-cell signaling circuits in agar
  Abstract A community of genetically heterogeneous cells embedded in an unmixed medium allows for sophisticated operations by retaining spatial differentiation and coordinating division-of-labor. To establish the principles of engineering reliable cell-cell com…
  crossref Joy Doong, James Parkin, Richard M. Murray 2017-11-19T01:10:22Z 置信度 0.70
• Synthetic mammalian signaling circuits for robust cell population control
  Summary In multicellular organisms, cells actively sense and control their own population density. Synthetic mammalian quorum sensing circuits could provide insight into principles of population control and extend cell therapies. However, a key challenge is re…
  crossref Yitong Ma, Mark W. Budde, Michaëlle N. Mayalu, Junqin Zhu 等 2020-09-03T08:20:14Z 置信度 0.70
• From Circuits to Symphonies: A Systems-Engineering Blueprint for Multimicrobial Synthetic Biology.
  Synthetic biology is expanding from single-species engineering toward the design of synthetic microbial consortia capable of distributed metabolism, coordinated behavior, and enhanced functional robustness. However, engineering frameworks derived from intracel…
  europepmc 2026 置信度 0.80
• Towards interoperable modeling of toehold-mediated strand exchange circuits across DNA nanotechnology and engineering biology
  Originally developed for DNA nanotechnology, toehold-mediated strand exchange (TMSE) circuits are gaining traction in synthetic biology due to their high programmability, seamless integration with biological components, and robust operation across diverse envi…
  europepmc 2026 置信度 0.80
• Modular Scalable Synthetic Gene Circuits for Complex Functions Within Minimal Computational Layers in Human Cells.
  Engineering mammalian cells to execute complex genetic programs remains a significant challenge in synthetic biology. Synthetic gene circuits typically implement sophisticated programs through cascaded computational layers. However, these architectures require…
  europepmc 2026 置信度 0.80
• Programmable regenerative tissues: Converging mammalian synthetic biology and tissue engineering.
  Synthetic biology can program cellular behavior but remains underused in regenerative medicine. This commentary argues that integrating synthetic biology with tissue engineering should target vascularization and immune integration through compact, context-awar…
  europepmc 2026 置信度 0.80
• Synthetic gene circuits in tumor immunotherapy: design principles and applications.
  Tumor immunotherapy has revolutionized cancer treatment by harnessing the immune system to recognize and eliminate malignant cells. However, limited response rates, systemic toxicity, and tumor heterogeneity remain major challenges. Synthetic gene circuits - e…
  europepmc 2026 置信度 0.80
• Synthetic DNA circuits for programming cell functions.
  Synthetic biology aims to re-engineer living cells into autonomous computational chassis capable of executing sophisticated biological tasks. Within this framework, programmable nucleic acid-based logic networks have emerged as a versatile molecular control la…
  europepmc 2026 置信度 0.80
• The Promise of Synthetic Biology for Redesigning Plant Architecture.
  Ensuring global food security under accelerating climate change requires transformative approaches to crop improvement that extend beyond the limits of traditional breeding and gene editing. While domestication and modern agriculture have delivered substantial…
  europepmc 2026 置信度 0.80
• Toward predictable and programmable genetic circuits in plants.
  Predictable design is central to realizing the potential of plant genetic circuits by linking regulatory architecture to phenotypic outcomes. Despite rapid advances in genetic parts and circuit construction, most plant circuits are still developed through empi…
  europepmc 2026 置信度 0.80
• A Linear Mixed Effects Model for Evaluating Synthetic Gene Circuits.
  One significant advancement in synthetic biology is the development of synthetic gene circuits with predictive Boolean logic. However, there is no universally accepted or applied statistical test to analyze the performance of these circuits. Many basic statist…
  europepmc 2024 置信度 0.80
• An orthogonal mammalian gene circuit for selective sensing of taurine-conjugated bile acids.
  Beyond their traditional role as dietary lipid emulsifiers, bile acids (BAs) function as pleiotropic signaling molecules that regulate metabolism, inflammation, and diverse disease processes. Taurine-conjugated bile acids (Tau-BAs) and the glycine-to-taurine c…
  europepmc 2026 置信度 0.80
• Can Cells Be Fully Programmed and Engineered?
  Since its inception, synthetic biology has relied on linear genetic modifications to treat living cells as biological counterparts to silicon microchips and computer-aided manufacturing. This paradigm is deeply rooted in the historical frameworks of Turing, Bo…
  europepmc 2026 置信度 0.80