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• Cell-Free Synthetic Biology: Engineering Beyond the Cell
  Cell-free protein synthesis (CFPS) technologies have enabled inexpensive and rapid recombinant protein expression. Numerous highly active CFPS platforms are now available and have recently been used for synthetic biology applications. In this review, we focus …
  openalex Jessica G. Perez, Jessica C. Stark, Michael C. Jewett 2016-10-14 置信度 0.72 BiologyLibrary scienceSynthetic biologyEnvironmental ethicsComputational biology
• Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production
  In the wake of the uprising global energy crisis, microalgae have emerged as an alternate feedstock for biofuel production. In addition, microalgae bear immense potential as bio-cell factories in terms of producing key chemicals, recombinant proteins, enzymes,…
  openalex Sheeja Jagadevan, Avik Banerjee, Chiranjib Banerjee, Chandan Guria 等 2018-06-30 置信度 0.72 Synthetic biologyBiorefineryBiochemical engineeringBiofuelMetabolic engineering
• 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)
• TinkerCell: modular CAD tool for synthetic biology
  BACKGROUND: 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. Using a CAD application, …
  openalex Deepak Chandran, Frank Bergmann, Herbert M. Sauro 2009-01-01 置信度 0.72 Synthetic biologyPython (programming language)Computer scienceModular designRobustness (evolution)
• A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells
  openalex Yutetsu Kuruma, Pasquale Stano, Takuya Ueda, Pier Luigi Luisi 2008-11-08 置信度 0.72 Lysophosphatidic acidPhosphatidic acidLiposomeSynthetic biologyArtificial cell
• 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
• Advancing secondary metabolite biosynthesis in yeast with synthetic biology tools
  Secondary metabolites are an important source of high-value chemicals, many of which exhibit important pharmacological properties. These valuable natural products are often difficult to synthesize chemically and are commonly isolated through inefficient extrac…
  openalex Michael S. Siddiqui, Kate Thodey, Isis J. Trenchard, Christina D. Smolke 2011-12-03 置信度 0.72 Synthetic biologyBiologySaccharomyces cerevisiaeYeastMetabolic engineering
• Predicting Translation Initiation Rates for Designing Synthetic Biology
  In synthetic biology, precise control over protein expression is required in order to construct functional biological systems. A core principle of the synthetic biology approach is a model-guided design and based on the biological understanding of the process,…
  openalex Benjamin Reeve, Thomas Hargest, Charlie Gilbert, Tom Ellis 2014-01-01 置信度 0.72 Synthetic biologyTranslation (biology)Protein biosynthesisMessenger RNAComputational biology
• Tuning Response Curves for Synthetic Biology
  Synthetic biology may be viewed as an effort to establish, formalize, and develop an engineering discipline in the context of biological systems. The ability to tune the properties of individual components is central to the process of system design in all fiel…
  openalex Jordan Ang, Edouard A. Harris, Brendan J. Hussey, Richard Kil 等 2013-08-01 置信度 0.72 Synthetic biologySystems biologyContext (archaeology)Set (abstract data type)Process (computing)
• Building-in biosafety for synthetic biology
  As the field of synthetic biology develops, real-world applications are moving from the realms of ideas and laboratory-confined research towards implementation. A pressing concern, particularly with microbial systems, is that self-replicating re-engineered cel…
  openalex Oliver Wright, Guy‐Bart Stan, Tom Ellis 2013-03-22 置信度 0.72 BiosafetySynthetic biologyBiologyBiochemical engineeringComputational biology
• Setting the standard in synthetic biology
  openalex Adam P. Arkin 2008-07-01 置信度 0.72 Synthetic biologyComputational biologyBiology
• Cascade catalysis – strategies and challenges en route to preparative synthetic biology
  Nature's smartness and efficient assembling cascade type reactions inspired biologists and chemists all around the world. Tremendous effort has been directed towards the understanding and mimicking of such networks. In recent years considerable progress has be…
  openalex Jan Muschiol, Christin Peters, Nikolin Oberleitner, Marko D. Mihovilovič 等 2014-12-10 置信度 0.72 CascadeCatalysisSynthetic biologyNanotechnologyCombinatorial chemistry
• A synthetic biology approach to transform <i>Yarrowia lipolytica</i> into a competitive biotechnological producer of β‐carotene
  The increasing market demands of β-carotene as colorant, antioxidant and vitamin precursor, requires novel biotechnological production platforms. Yarrowia lipolytica, is an industrial organism unable to naturally synthesize carotenoids but with the ability to …
  openalex Macarena Larroudé, Ewelina Celińska, Alexandre Back, T. Stephan 等 2017-10-07 置信度 0.72 YarrowiaSynthetic biologyBiologyCaroteneBiotechnology
• Reinvigorating natural product combinatorial biosynthesis with synthetic biology
  openalex Eunji Kim, Bradley S Moore, Yeo Joon Yoon 2015-08-18 置信度 0.72 Synthetic biologyNatural productDrug discoveryChemical biologyBiosynthesis
• Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology
  openalex James M. Clomburg, Ramón González 2010-02-08 置信度 0.72 BiofuelMetabolic engineeringBiochemical engineeringSynthetic biologyBiotechnology
• Synthetic biology approaches to engineering the nitrogen symbiosis in cereals
  Nitrogen is abundant in the earth's atmosphere but, unlike carbon, cannot be directly assimilated by plants. The limitation this places on plant productivity has been circumvented in contemporary agriculture through the production and application of chemical f…
  openalex Christian Rogers, Giles Oldroyd 2014-03-31 置信度 0.72 Reactive nitrogenNitrogen fixationNitrogenaseNitrogenAgriculture
• Engineering yeast for the production of breviscapine by genomic analysis and synthetic biology approaches
  Abstract The flavonoid extract from Erigeron breviscapus , breviscapine, has increasingly been used to treat cardio- and cerebrovascular diseases in China for more than 30 years, and plant supply of E. breviscapus is becoming insufficient to satisfy the growin…
  openalex Xiaonan Liu, Jian Cheng, Guanghui Zhang, Wentao Ding 等 2018-01-25 置信度 0.72 ScutellarinSynthetic biologyMetabolic engineeringYeastFermentation
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Perspectives for self-driving labs in synthetic biology
  Self-driving labs (SDLs) combine fully automated experiments with artificial intelligence (AI) that decides the next set of experiments. Taken to their ultimate expression, SDLs could usher a new paradigm of scientific research, where the world is probed, inte…
  arxiv Hector Garcia Martin, Tijana Radivojevic, Jeremy Zucker, Kristofer Bouchard 等 2022-10-14T16:58:27Z 置信度 0.78 q-bio.OT
• A systems biology approach to COVID-19 progression in a population
  A number of models in mathematical epidemiology have been developed to account for control measures such as vaccination or quarantine. However, COVID-19 has brought unprecedented social distancing measures, with a challenge on how to include these in a manner …
  arxiv Magdalena Djordjevic, Andjela Rodic, Igor Salom, Dusan Zigic 等 2020-05-19T17:57:41Z 置信度 0.78 q-bio.PEphysics.soc-ph
• New Approaches in Synthetic Biology: Abiotic Organelles and Artificial Cells Powered and Controlled by Light
  One of the major goals of nanobionics and bottom-up synthetic biology is the development of artificial cell organelles for the creation of cell-like structures operating similar to biological systems with a minimalistic set of building blocks. In the present c…
  arxiv Günther Knör 2019-11-15T15:07:27Z 置信度 0.78 q-bio.SCq-bio.BMq-bio.MNq-bio.TO
• Biology and Physics
  This article frames the relation between biology and physics by characterizing the former as a subdiscipline rather than a special case of the latter. To do this, we posit biological physics as the science of living matter in contrast to classic biophysics, th…
  arxiv Stuart A. Newman, Sahotra Sarkar 2026-03-11T19:00:05Z 置信度 0.78 physics.bio-phcond-mat.softq-bio.TO
• 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
• High-Throughput Biologically Optimized Search Engineering Approach to Synthetic Biology
  Synthetic Biology is the new engineering-based approach to biology that includes applications of designing complex biological devices. At present, it is not yet clear what will emerge as the defining principles of Synthetic Biology. One proposed approach is to…
  arxiv A. X. C. N. Valente, Stephen S. Fong 2011-03-28T21:17:25Z 置信度 0.78 q-bio.QM
• Silicon is the next frontier in plant synthetic biology
  Silicon has striking similarity with carbon and is found in plant cells. However, there is no specific role that has been assigned to silicon in the life cycle of plants. The amount of silicon in plant cells is species specific and can reach levels comparable …
  arxiv Aniruddha Acharya, Kaitlin Hopkins, Tatum Simms 2025-03-13T02:33:29Z 置信度 0.78 q-bio.BM
• ART: A machine learning Automated Recommendation Tool for synthetic biology
  Biology has changed radically in the last two decades, transitioning from a descriptive science into a design science. Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or anticancer drugs. Howev…
  arxiv Tijana Radivojević, Zak Costello, Kenneth Workman, Hector Garcia Martin 2019-11-25T17:46:36Z 置信度 0.78 q-bio.QMstat.ML
• BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology
  Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of parameter estimation (model calibration) and optim…
  arxiv Alejandro F Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard 等 2014-07-22T13:31:05Z 置信度 0.78 q-bio.QMcs.CEq-bio.MN
• For principled model fitting in mathematical biology
  The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them. This invalidates th…
  arxiv Thomas House 2014-04-21T20:32:28Z 置信度 0.78 q-bio.QM
• Computer-aided whole-cell design: taking a holistic approach by integrating synthetic with systems biology
  Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design, and software and tools…
  arxiv Lucia Marucci, Matteo Barberis, Jonathan Karr, Oliver Ray 等 2020-06-04T09:19:52Z 置信度 0.78 q-bio.QMq-bio.MN
• Cancer systems biology in the genome sequencing era: Part 1, dissecting and modeling of tumor clones and their networks
  Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has been viewed as a wh…
  arxiv Edwin Wang, Jinfeng Zou, Naif Zaman, Lenore K. Beitel 等 2014-09-06T02:38:11Z 置信度 0.78 q-bio.MN
• 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
• 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
• 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
• Cancer systems biology in the genome sequencing era: Part 2, evolutionary dynamics of tumor clonal networks and drug resistance
  A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor reoccurs. Genome sequencing and computational analysis allow…
  arxiv Edwin Wang, Jinfeng Zou, Naif Zaman, Lenore K. Beitel 等 2014-09-06T02:48:08Z 置信度 0.78 q-bio.MN
• Inverse problems for coupled nonlocal nonlinear systems arising in mathematical biology
  In this paper, we propose and study several inverse problems of determining unknown parameters in nonlocal nonlinear coupled PDE systems, including the potentials, nonlinear interaction functions and time-fractional orders. In these coupled systems, we enforce…
  arxiv Ming-Hui Ding, Hongyu Liu, Catharine W. K. Lo 2024-07-22T15:20:04Z 置信度 0.78 math.APq-bio.PE
• 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
• From Prediction to Simulation: AlphaFold 3 as a Differentiable Framework for Structural Biology
  AlphaFold 3 represents a transformative advancement in computational biology, enhancing protein structure prediction through novel multi-scale transformer architectures, biologically informed cross-attention mechanisms, and geometry-aware optimization strategi…
  arxiv Alireza Abbaszadeh, Armita Shahlaee 2025-08-25T19:49:28Z 置信度 0.78 q-bio.BMcs.LG
• Towards the Recapitulation of Ancient History in the Laboratory: Combining Synthetic Biology with Experimental Evolution
  One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs. Combining ancestral …
  arxiv Betul Kacar, Eric Gaucher 2012-09-23T02:15:22Z 置信度 0.78 q-bio.PEq-bio.MN
• Energy flow in biological system: Bioenergy transduction of V1-ATPase molecular rotary motor from E. hirae
  We classify research fields in biology into those on flows of materials, energy, and information. As a representative energy transducing machinery in biology, our research target, V1-ATPase from a bacterium Enterococcus hirae, a typical molecular rotary motor …
  arxiv Ichiro Yamato, Takeshi Murata, Andrei Khrennikov 2017-05-27T21:31:53Z 置信度 0.78 q-bio.BMquant-ph
• The whack-a-mole governance challenge for AI-enabled synthetic biology: literature review and emerging frameworks
  AI-enabled synthetic biology has tremendous potential but also significantly increases biorisks and brings about a new set of dual use concerns. The picture is complicated given the vast innovations envisioned to emerge by combining emerging technologies, as A…
  arxiv Trond Arne Undheim 2024-02-01T03:53:13Z 置信度 0.78 q-bio.OTcs.AI
• Synthetic Data in MR Spectroscopy: Current Practices, Applications, and Considerations
  The use of synthetic data has emerged as an essential tool in Magnetic Resonance Spectroscopy (MRS) research and applications, providing advantages for optimization of acquisition, software validation, deep learning applications, and enhanced reproducibility. …
  arxiv John T. LaMaster, Aaron T. Gudmundson, Alireza Abaei, Seyma Alcicek 等 2026-02-26T19:42:14Z 置信度 0.78 physics.med-ph
• How to address cellular heterogeneity by distribution biology
  Cellular heterogeneity is an immanent property of biological systems that covers very different aspects of life ranging from genetic diversity to cell-to-cell variability driven by stochastic molecular interactions, and noise induced cell differentiation. Here…
  arxiv Niko Komin, Alexander Skupin 2021-09-13T16:46:58Z 置信度 0.78 q-bio.QM
• Synthetic Biology meets Neuromorphic Computing: Towards a bio-inspired Olfactory Perception System
  In this study, we explore how the combination of synthetic biology, neuroscience modeling, and neuromorphic electronic systems offers a new approach to creating an artificial system that mimics the natural sense of smell. We argue that a co-design approach off…
  arxiv Kevin Max, Larissa Sames, Shimeng Ye, Jan Steinkühler 等 2025-04-14T09:57:20Z 置信度 0.78 cs.NEcs.ETq-bio.NC
• A review of DNA restriction-free overlapping sequence cloning techniques for synthetic biology
  DNA cloning methods are fundamental tools in molecular biology, synthetic biology, and genetic engineering that enable precise DNA manipulation for various scientific and biotechnological applications. This review systematically summarizes the major restrictio…
  arxiv Isabella Frighetto Bomfiglio, Isabelli Seiler de Medeiros Mendes, Diego Bonatto 2025-05-06T16:27:42Z 置信度 0.78 q-bio.BM
• The role of CRKL in Breast Cancer Metastasis: Insights from Systems Biology
  MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally. They are involved in key biological processes and then may play a major role in the development of human diseases including cancer, in particular their involveme…
  arxiv Abderrahim Chafik 2016-08-09T10:29:39Z 置信度 0.78 q-bio.MN
• Simulations meet Machine Learning in Structural Biology
  Classical molecular dynamics (MD) simulations will be able to reach sampling in the second timescale within five years, producing petabytes of simulation data at current force field accuracy. Notwithstanding this, MD will still be in the regime of low-throughp…
  arxiv Adrià Pérez, Gerard Martínez-Rosell, Gianni De Fabritiis 2018-10-19T10:39:23Z 置信度 0.78 q-bio.BMphysics.comp-ph
• A synthetic biology approach for the design of genetic algorithms with bacterial agents
  Bacteria have been a source of inspiration for the design of evolutionary algorithms. At the beginning of the 20th century synthetic biology was born, a discipline whose goal is the design of biological systems that do not exist in nature, for example, program…
  arxiv A. Gargantilla Becerra, M. Gutiérrez, R. Lahoz-Beltra 2021-01-19T09:59:33Z 置信度 0.78 cs.NEcs.MA
• Developing an NLP-based Recommender System for the Ethical, Legal, and Social Implications of Synthetic Biology
  Synthetic biology is an emerging field that involves the engineering and re-design of organisms for purposes such as food security, health, and environmental protection. As such, it poses numerous ethical, legal, and social implications (ELSI) for researchers …
  arxiv Damien Dablain, Lilian Huang, Brandon Sepulvado 2022-07-10T20:18:53Z 置信度 0.78 cs.IRcs.AIcs.CY
• Borges Dilemma, Fundamental Laws, and Systems Biology
  I reason here that the known folk law in biology that there is no general law in biology because of exceptions is false. The (quantitative) systems biology offers the potential to solve the Borges Dilemma, by transcending it. There have already a plenty of ind…
  arxiv P Ao 2007-09-01T00:16:45Z 置信度 0.78 q-bio.QMq-bio.OT
• Population-expression models of immune response
  The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an initial naive phenoty…
  arxiv Sean P Stromberg, Rustom Antia, Ilya Nemenman 2012-09-18T00:46:26Z 置信度 0.78 q-bio.PEq-bio.QM
• Origin of life from a maker's perspective -- focus on protocellular compartments in bottom-up synthetic biology
  The origin of life is shrouded in mystery, with few surviving clues, obscured by evolutionary competition. Previous reviews have touched on the complementary approaches of top-down and bottom-up synthetic biology to augment our understanding of living systems.…
  arxiv Ivan Ivanov, Stoyan K. Smoukov, Ehsan Nourafkan, Katharina Landfester 等 2022-07-14T23:00:09Z 置信度 0.78 q-bio.PEcond-mat.softcs.ROnlin.AOphysics.bio-ph
• Are Synthetic Corruptions A Reliable Proxy For Real-World Corruptions?
  Deep learning (DL) models are widely used in real-world applications but remain vulnerable to distribution shifts, especially due to weather and lighting changes. Collecting diverse real-world data for testing the robustness of DL models is resource-intensive,…
  arxiv Shashank Agnihotri, David Schader, Nico Sharei, Mehmet Ege Kaçar 等 2025-05-07T22:19:55Z 置信度 0.78 cs.CV
• Control systems for synthetic biology and a case-study in cell fate reprogramming
  This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other applications is the abili…
  arxiv Domitilla Del Vecchio 2026-01-27T23:53:33Z 置信度 0.78 eess.SYq-bio.MN
• The case for algebraic biology: from research to education
  Though it goes without saying that linear algebra is fundamental to mathematical biology, polynomial algebra is less visible. In this article, we will give a brief tour of four diverse biological problems where multivariate polynomials play a central role -- a…
  arxiv Matthew Macauley, Nora Youngs 2020-02-29T18:06:29Z 置信度 0.78 q-bio.NCq-bio.OT
• Foundations of biology
  It is often stated that there are no laws in biology, where everything is contingent and could have been otherwise, being solely the result of historical accidents. Furthermore, the customary introduction of fundamental biological entities such as individual o…
  arxiv Jean-Louis Sikorav, Alan Braslau, Arach Goldar 2014-01-13T14:12:10Z 置信度 0.78 q-bio.OT
• Practical Resources for Enhancing the Reproducibility of Mechanistic Modeling in Systems Biology
  Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been extensive standardization…
  arxiv Michael L. Blinov, John H. Gennari, Jonathan R. Karr, Ion I. Moraru 等 2021-04-09T21:09:27Z 置信度 0.78 q-bio.QMq-bio.CBq-bio.MN
• A Molecular Implementation of the Least Mean Squares Estimator
  In order to function reliably, synthetic molecular circuits require mechanisms that allow them to adapt to environmental disturbances. Least mean squares (LMS) schemes, such as commonly encountered in signal processing and control, provide a powerful means to …
  arxiv Christoph Zechner, Mustafa Khammash 2017-01-03T08:55:23Z 置信度 0.78 q-bio.MN
• Insights from Synthetic Star-forming Regions: I. Reliable Mock Observations from SPH Simulations
  Through synthetic observations of a hydrodynamical simulation of an evolving star-forming region, we assess how the choice of observational techniques affects the measurements of properties which trace star formation. Testing and calibrating observational meas…
  arxiv Christine M. Koepferl, Thomas P. Robitaille, James E. Dale, Francesco Biscani 2016-03-07T21:00:00Z 置信度 0.78 astro-ph.SRastro-ph.GAastro-ph.IM
• Integral feedback in synthetic biology: Negative-equilibrium catastrophe
  A central goal of synthetic biology is the design of molecular controllers that can manipulate the dynamics of intracellular networks in a stable and accurate manner. To address the fact that detailed knowledge about intracellular networks is unavailable, inte…
  arxiv Tomislav Plesa, Alex Dack, Thomas E. Ouldridge 2021-02-21T19:28:43Z 置信度 0.78 q-bio.MN
• On LLMs-Driven Synthetic Data Generation, Curation, and Evaluation: A Survey
  Within the evolving landscape of deep learning, the dilemma of data quantity and quality has been a long-standing problem. The recent advent of Large Language Models (LLMs) offers a data-centric solution to alleviate the limitations of real-world data with syn…
  arxiv Lin Long, Rui Wang, Ruixuan Xiao, Junbo Zhao 等 2024-06-14T07:47:09Z 置信度 0.78 cs.CL
• Atomic Biology, Electrostatics, and Ionic Channels
  I believe an atomic biology is needed to supplement present day molecular biology, if we are to design and understand proteins, as well as define, make, and use them. Topics in the paper are molecular biology and atomic biology. Electrodiffusion in the open ch…
  arxiv R. S. Eisenberg 2008-07-04T10:35:06Z 置信度 0.78 q-bio.BMphysics.bio-phq-bio.QM
• 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
• Improve Fidelity and Utility of Synthetic Credit Card Transaction Time Series from Data-centric Perspective
  Exploring generative model training for synthetic tabular data, specifically in sequential contexts such as credit card transaction data, presents significant challenges. This paper addresses these challenges, focusing on attaining both high fidelity to actual…
  arxiv Din-Yin Hsieh, Chi-Hua Wang, Guang Cheng 2024-01-01T22:34:14Z 置信度 0.78 cs.LG
• 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
• 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
• Context in Synthetic Biology: Memory Effects of Environments with Mono-molecular Reactions
  Synthetic biology aims at designing modular genetic circuits that can be assembled according to the desired function. When embedded in a cell, a circuit module becomes a small subnetwork within a larger environmental network, and its dynamics is therefore affe…
  arxiv Johannes Falk, Leo Bronstein, Maleen Hanst, Barbara Drossel 等 2018-09-25T15:39:23Z 置信度 0.78 q-bio.MNcond-mat.stat-mechphysics.bio-phphysics.chem-ph
• 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
• 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 &amp; 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
• Towards Synthetic Data Generation for Improved Pain Recognition in Videos under Patient Constraints
  Recognizing pain in video is crucial for improving patient-computer interaction systems, yet traditional data collection in this domain raises significant ethical and logistical challenges. This study introduces a novel approach that leverages synthetic data t…
  arxiv Jonas Nasimzada, Jens Kleesiek, Ken Herrmann, Alina Roitberg 等 2024-09-24T18:33:57Z 置信度 0.78 cs.CV
• Ensembles of GANs for synthetic training data generation
  Insufficient training data is a major bottleneck for most deep learning practices, not least in medical imaging where data is difficult to collect and publicly available datasets are scarce due to ethics and privacy. This work investigates the use of synthetic…
  arxiv Gabriel Eilertsen, Apostolia Tsirikoglou, Claes Lundström, Jonas Unger 2021-04-23T19:38:48Z 置信度 0.78 cs.CVcs.LGeess.IV
• Everything to the Synthetic: Diffusion-driven Test-time Adaptation via Synthetic-Domain Alignment
  Test-time adaptation (TTA) aims to improve the performance of source-domain pre-trained models on previously unseen, shifted target domains. Traditional TTA methods primarily adapt model weights based on target data streams, making model performance sensitive …
  arxiv Jiayi Guo, Junhao Zhao, Chaoqun Du, Yulin Wang 等 2024-06-06T17:39:09Z 置信度 0.78 cs.CV
• MicroRNA Systems Biology
  Recently, microRNAs (miRNAs) have emerged as central posttranscriptional regulators of gene expression. miRNAs regulate many key biological processes, including cell growth, death, development and differentiation. This discovery is challenging the central dogm…
  arxiv Edwin Wang 2007-12-20T21:02:28Z 置信度 0.78 q-bio.MNq-bio.GN
• The contribution of statistical physics to evolutionary biology
  Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent develop…
  arxiv Harold P. de Vladar, Nick H. Barton 2011-04-14T18:14:50Z 置信度 0.78 q-bio.PEnlin.AOnlin.PSq-bio.QM
• Going Beyond Nouns With Vision &amp; Language Models Using Synthetic Data
  Large-scale pre-trained Vision &amp; Language (VL) models have shown remarkable performance in many applications, enabling replacing a fixed set of supported classes with zero-shot open vocabulary reasoning over (almost arbitrary) natural language prompts. How…
  arxiv Paola Cascante-Bonilla, Khaled Shehada, James Seale Smith, Sivan Doveh 等 2023-03-30T17:57:43Z 置信度 0.78 cs.CVcs.CL