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代表性文献（按质量分排序，前 60 条）

• VU Bioinformatics/NGS Suite: GO Term Enrichment Bubble Plot Generator
  2026 · 生物计算 · VU Bioinformatics/NGS Suite: GO Term Enrichment Bubble Plot Generator What is this work about? This work is part of a research project that investigates the biological processes associated with genes identified through n…
• Mathematical Modeling Of Substrate And Product Inhibition Kinetics With Diffusion Limitation In The Amperometric Biosensor At Spherical Micro Reactions
  2026 · 生物计算 · This study presents a mathematical model of a non-steady-state amperometric biosensor with combined enzyme kinetics and diffusion restrictions, under substrate and product inhibition. An enzymatic reaction with non-Micha…
• Information elicitation mechanisms for Bayesian auctions
  2025 · AI Agent 生态 · Abstract In this paper we design information elicitation mechanisms for Bayesian auctions. While in Bayesian mechanism design the distributions of the players’ private types are often assumed to be common knowledge, info…
• Wireless sensor network using nRF24L01+ for precision agriculture
  2025 · 智慧农业 · Precision agriculture is a strategy for varying inputs and cultivation methods to suit varying soil conditions and agricultural crops. In order to optimize precision agriculture, wireless sensor network (WSN) is suitable…
• Automatic phenotyping using exhaustive projection pursuit
  2025 · AI 驱动科学发现 · Abstract One of the most common objectives in the analysis of flow cytometry data is the identification and delineation of phenotypes, distinct populations of cells with shared characteristics in the measurement dimensio…
• Synthetic Aptamer Mechanoreceptors Enable Cell-Specific Force Sensing and Temporal Control via DNA Circuits
  2025 · 生物计算 · Abstract Cells interpret mechanical cues from their microenvironment with spatiotemporal precision to guide adaptive behaviors. However, engineering synthetic mechanosensing systems with both cell-specificity and program…
• Design Principles for Polymerase Strand Recycling Circuits
  2025 · 生物计算 · 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, sensitiv…
• Engineering Coupled Consortia-Based Biosensors for Diagnostic
  2025 · 生物计算 · Abstract Synthetic multicellular systems have great potential for performing complex tasks, including multi-signal detection and computation through cell-to-cell communication. However, engineering these systems is chall…
• Error propagation in agricultural models
  2024 · 智慧农业 · Spatially distributed agricultural models rely for their operation on a number of value surfaces representing their various input parameters. Each of these surfaces will contain some error, due in part to the sampling an…
• Optimal treatment placement for on-farm experiments: pseudo-Bayesian optimal designs with a linear response plateau model
  2024 · 智慧农业 · On-farm experiments are increasingly being used as their costs have decreased with technological advances in collecting, storing, and processing geospatial data. A question that has not been well addressed is what spatia…
• Accurate Prediction of Protein-Binding Residues in Protein Sequences Using SCRIBER
  2024 · AI 驱动科学发现 · Deciphering molecular-level mechanisms that govern protein-protein interactions (PPIs) relies in part on the accurate prediction of protein-binding partners and protein-binding residues. These predictions can be used to …
• Synthetic dosage-compensating miRNA circuits for quantitative gene therapy
  2024 · 生物计算 · A longstanding challenge in gene therapy is expressing a dosage-sensitive gene within a tight therapeutic window. For example, loss of MECP2 function causes Rett syndrome, while its duplication causes MECP2 duplication s…
• Programming the elongation of mammalian cell aggregates with synthetic gene circuits
  2024 · 生物计算 · 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 …
• A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits
  2023 · 生物计算 · 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 …
• Engineering synthetic CopT/A-based genetic circuits for miRNA imaging and functional gene regulation
  2023 · 生物计算 · 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 …
• Synthetic Biology: A Scientific Review of Current Developments Synthetic Biology: A Scientific Review of Current Developments and Future Perspectives
  2023 · 生物计算 · The field of synthetic biology combines principles from biology, engineering, and computer science to create novel biological systems with specific functions. It has made significant advances in engineering genetic circu…
• Approaches to Evaluating Human–AI Interaction
  2026 · AI 安全与对齐 · Abstract How can human–AI interaction be evaluated? This chapter provides a high-level overview of three main approaches to evaluating human–AI interaction: empirical, analytical, and model based. Empirical methods are b…
• The Mechanism of Dissolution of Sparingly Soluble Salts—Application of a Novel Electrochemical Theory
  2026 · 地外矿物 · Although the dissolution of sparingly soluble salts is of interest to many fields, such as material science, dentistry, and geochemistry, the simplicity of these reactions provides its own motivation for study. Three fea…
• Impact of retroactivity on information flows in engineered synthetic biological circuits
  2026 · 生物计算 · 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…
• Introduction to RNA-Based Circuits and Devices
  2026 · 生物计算 · 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…
• Mixed positive and negative feedback loops drive diverse single-cell gene expression dynamics
  2026 · 生物计算 · Genetic circuits with only a few components can generate complex gene regulatory dynamics. Here, we combine stochastic modelling and single-cell time-lapse microscopy to map how a common circuit motif, the mixed positive…
• Mathematical Modeling of Synthetic Genetic Circuits
  2025 · 生物计算 · 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 …
• Automatic Feedback Control for Resource-Aware Characterisation of Genetic Circuits
  2025 · 生物计算 · 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 di…
• Developing a Generalizable Two-Input Genetic AND Logic Gate in Arabidopsis thaliana for Multi-Signal Processing
  2025 · 生物计算 · With effective engineering using synthetic biology approaches, plant-based platforms could conceivably be designed to minimize the production costs and wastes of high-value products such as medicines, biofuels, and chemi…
• Identifying competition phenotypes in synthetic biochemical circuits
  2022 · 生物计算 · 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…
• Tailored synthetic sRNAs dynamically tune multilayer genetic circuits
  2022 · 生物计算 · 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…
• Synthetic genetic circuits enable reprogramming of plant roots
  2022 · 生物计算 · 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 acquisit…
• Engineering <scp>DNA</scp> Switches for <scp>DNA</scp> Computing Applications
  2021 · 生物计算 · The deoxyribonucleic acid (DNA) is a convenient molecule for the rational design of molecular switches and is ideally suitable for the development of molecular computing systems. Throughout this chapter, we discuss how o…
• Optimal Experimental Design for Systems and Synthetic Biology Using AMIGO2
  2021 · 生物计算 · 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 …
• Transcriptional interference in toehold switch-based RNA circuits
  2021 · 生物计算 · 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 rib…
• Mathematical model of broadly reactive plasma cell production
  2020 · AI 驱动科学发现 · Abstract Strain-specific plasma cells are capable of producing neutralizing antibodies that are essential for clearance of challenging pathogens. These neutralizing antibodies also function as a main defense against dise…
• Analysis of Circuits for Dosage Control in Microbial Populations
  2020 · 生物计算 · 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 …
• Human–AI Agent Team Architectural Patterns
  2024 · AI Agent 生态 · This chapter reviews the literature on human–AI agent teams (HATs), discussing patterns to aid system design. The chapter then discusses the concept of, and example, design patterns that include human–AI agent dyads, as …
• Multi-Local-Worlds economic and management complex adaptive system with agent behavior and local configuration
  2024 · AI Agent 生态 · &lt;abstract&gt; &lt;p&gt;The central focus of our investigation revolved around the convergence of agents' behavior toward a particular invariant distribution and determining the characteristics of the optimal strategie…
• Design of Compliant Mechanisms Approximating Straight and Circular Paths
  2024 · 智慧农业 · Abstract Compliant mechanisms are extensively employed in many fields due to their advantages over their rigid-body counterparts. They transmit force, motion, and energy through the elastic deformations of their flexible…
• Biosensor based detection of tuberculosis biomarkers
  2024 · 生物计算 · Chapter 2Biosensor-based detection of tuberculosis 15 Chapter 3 16 kDa heat shock protein from heat-inactivated Mycobacterium tuberculosis is a homodimer -suitability for diagnostic applications with specific llama VHH m…
• Use of geographic information systems (GIS) in crop protection warning service
  2023 · 智慧农业 · One of the important aims of the Governmental Crop Protection Services (GCPS) in Germany is to reduce spraying intensity and to guarantee an environmentally friendly and economical crop protection strategy. ZEPP is the c…
• Structure prediction of alternative protein conformations
  2023 · AI 驱动科学发现 · Abstract Proteins are dynamic molecules whose movements result in different conformations with different functions. Neural networks such as AlphaFold2 can predict the structure of single-chain proteins in the conformatio…
• Design and Mathematical Analysis of Synthetic Inhibitory Circuits that Program Self-Organizing Multicellular Structures
  2023 · 生物计算 · 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 pr…
• Design and Mathematical Analysis of Activating Amplifiers that Enable Modular Temporal Control in Synthetic Circuits
  2023 · 生物计算 · 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 de…
• Multistable and dynamic CRISPRi-based synthetic circuits
  2019 · 生物计算 · 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 e…
• Scalable dynamic characterization of synthetic gene circuits
  2019 · 生物计算 · 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 …
• Growth defects and loss-of-function in synthetic gene circuits
  2019 · 生物计算 · 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 biosynt…
• A model for the spatio-temporal design of gene regulatory circuits
  2019 · 生物计算 · 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 …
• Context Dependence of Biological Circuits
  2018 · 生物计算 · 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…
• Design and applications of synthetic information processing circuits in mammalian cells
  2017 · 生物计算 · 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…
• Synthetic negative feedback circuits using engineered small RNAs
  2017 · 生物计算 · 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…
• Generating effective models and parameters for RNA genetic circuits
  2015 · 生物计算 · 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 mode…
• DOCK/PIERR: Web Server for Structure Prediction of Protein–Protein Complexes
  2014 · AI 驱动科学发现 · In protein docking we aim to find the structure of the complex formed when two proteins interact. Protein-protein interactions are crucial for cell function. Here we discuss the usage of DOCK/PIERR. In DOCK/PIERR, a unif…
• Construction of Synthetic Gene Circuits in the Escherichia coli Genome
  2013 · 生物计算 · 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…
• Identification of Relevant Genes with a Multi-Agent System using Gene Expression Data
  2012 · AI Agent 生态 · In recent years, technology for information extraction from gene activity in cells, has made an important breakthrough with the DNA microarrays. With this technology it is possible for researchers to know which genes are…
• &lt;title&gt;Modular Alignment System For Spacecraft&lt;/title&gt;
  2012 · AI 安全与对齐 · A modular alignment system has been designed and built at the Institut d'Astrophysique, Lige. Based on the multiple-beam autocollimation principle, it is composed of two collimators, a series of beam splitters and mirror…
• Rapid hierarchical assembly of medium-size DNA cassettes
  2012 · 生物计算 · Synthetic biology applications call for efficient methods to generate large gene cassettes that encode complex gene circuits in order to avoid simultaneous delivery of multiple plasmids encoding individual genes. Multipl…
• Arduino for Robotics
  2011 · 智慧农业 · With some of the basics of electricity, Arduino, and general robot building out of the way, we jump right in to some of the specific interfacing tasks that are needed to complete the projects in this book. In Chapter 1, …
• Multilevel Regulation in RNA-Protein Hybrid Incoherent Feed-Forward Loop Circuits for Tunable Pulse Dynamics in &lt;i&gt;Escherichia coli&lt;/i&gt;.
  2026 · 智慧农业 · Regulating gene expression with precision is essential for cellular engineering and biosensing applications, where rapid, programmable, and sensitive control is desired. Current approaches to regulatory circuit design of…
• Learning stochastic cellular dynamics from snapshots through bidirectional causal neural stochastic differential equations.
  2026 · AI 安全与对齐 · Due to cell destruction in sequencing, time-series data yield unpaired snapshots, obscuring lineages and gene dynamics in individual cells. Current data-driven methods rely on single-variate expression, ignoring cell typ…
• AOP Network Box: An Integrative Framework for Bridging Adverse Outcome Pathways and Biological Networks.
  2026 · AI 驱动科学发现 · Adverse outcome pathways (AOPs) are biological mechanism-based models that connect chemical exposures to adverse outcomes (AOs) through molecular initiating events (MIEs) and key events (KEs). However, there is a notable…
• Using experimental results of protein design to guide biomolecular energy-function development.
  2026 · AI 驱动科学发现 · Computational models of macromolecules have many applications in biochemistry, but physical inaccuracies limit their utility. One class of models uses energy functions rooted in classical mechanics. The standard datasets…
• OMNI-P2x universal neural network potential for excited-state simulations.
  2026 · AI 驱动科学发现 · Photo-active molecular systems play an essential role in modern science and technology, finding applications in solar cells, organic light-emitting diodes, reaction catalysis, photodynamic therapy, and beyond. The ration…
• Ultrafast solvent-modulated roaming mechanism in bromoform revealed by femtosecond X-ray solution scattering.
  2026 · AI 驱动科学发现 · Roaming-mediated isomerization is a universal reaction mechanism in photochemistry, yet solvent-dependent pathways of roaming intermediates remain poorly understood, particularly for environmentally relevant halogen comp…

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