The second wave of synthetic biology: from modules to systems

Purnick, Priscilla E. M., Weiss, Ron·2009·Nature Reviews Molecular Cell Biology
DOI 10.1038/nrm2698

Cited by (999)

Items 701–800 of 999

  1. Understanding Nobel Prize-Winning Articles:A Bibliometric Analysis
    Guoqiang Liang, Haiyan Hou, Peili Ren, Yi Bu, Xiangjie Kong, Zhigang Hu · 2019 · Current Science
  2. A mechanistic model of the BLADE platform predicts performance characteristics of 256 different synthetic DNA recombination circuits
    Jack E. Bowyer, Chloe Ding, Benjamin H. Weinberg, Wilson W. Wong, Declan G. Bates · 2020 · PLoS Computational Biology
  3. Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems
    Leonardo Giannantoni, Roberta Bardini, Alessandro Savino, Stefano Di Carlo · 2024 · BMC Bioinformatics
  4. Life by design: Philosophical perspectives on synthetic biology
    Bernadette Bensaude‐Vincent · 2015 · BIO Web of Conferences
  5. Design tradeoffs in a synthetic gene control circuit for metabolic networks
    Diego A. Oyarzún, G-B Stan · 2012 · Proceedings of the ... American Control Conference/Proceedings of the American Control Conference
  6. Integral action with time scale separation: A mechanism for modularity in biological systems
    Phillip M. Rivera, Domitilla Del Vecchio · 2014 · IEEE Conference on Decision and Control (CDC)
  7. Synthetic Biology: opportunities for Chilean bioindustry and education
    Fernán Federici, Timothy J. Rudge, Bernardo Pollak, Jim P. Haseloff, Rodrigo A. Gutiérrez · 2013 · Biological Research
  8. Open Source Platforms Beyond Software: From ICT to Biotechnology
    Joel West · 2017 · Emerald Group Publishing Limited eBooks
  9. Modular assembling process of an in-silico protocell
    Eugenia Schneider, Michael Mangold · 2017 · Biosystems
  10. Tuning RGD Motif and Hyaluronan Density to Study Integrin Binding
    Cornelia Zapp, Burcu Baykal Minsky, Heike Boehm · 2018 · Frontiers in Physiology
  11. Developing a graduate training program in Synthetic Biology: SynBioCDT
    Idil Cazimoglu, Alexander P. S. Darlington, Aurelija Grigonyte, Charlotte E G Hoskin, Juntai Liu, Robert J. Oppenheimer, Jesús A. Siller‐Farfán, Claire Suzanne Grierson, Antonis Papachristodoulou · 2019 · Synthetic Biology
  12. Daisy Chain Topology Based Mammalian Synthetic Circuits for RNA-Only Delivery
    Kaiyu Liu, Jiong Yang, Shigang Ding, Yi Gao · 2020 · ACS Synthetic Biology
  13. Time-scale separation based design of biomolecular feedback controllers
    Theodore W. Grunberg, Domitilla Del Vecchio · 2019 · IEEE Conference on Decision and Control (CDC)
  14. Function by Agreement
    Pablo Schyfter · 2014 · Social Epistemology
  15. A Comparative Analysis of Variations in Synthetic Biology Regulation
    Benjamin D. Trump · 2016 · Deep Blue (University of Michigan)
  16. Computational haplotype recovery and long-read validation identifies novel isoforms of industrially relevant enzymes from natural microbial communities
    Samuel M. Nicholls, Wayne Aubrey, Arwyn Edwards, Kurt De Grave, Sharon Huws, Leander Schietgat, André Soares, Christopher J. Creevey, Amanda J. Clare · 2018 · Research Portal (Queen's University Belfast)
  17. Supercoiling-mediated feedback rapidly couples and tunes transcription
    Christopher P. Johnstone, Kate E. Galloway · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  18. Recent Advances in Cellular and Molecular Bioengineering for Building and Translation of Biological Systems
    Guohao Dai, Adam W. Feinberg, Leo Q. Wan · 2021 · Cellular and Molecular Bioengineering
  19. Analysis of Gene Regulatory Networks under Positive Feedback
    Mehmet Eren Ahsen, Hitay Özbay, Silviu‐Iulian Niculescu · 2013 · Advances in delays and dynamics
  20. Characterization of Hsp17, a Novel Small Heat Shock Protein, in Sphingomonas melonis TY under Heat Stress
    Yihan Wang, Xiaoyu Wang, Hao Wu, Lvjing Wang, Haixia Wang, Zhenmei Lü · 2023 · Microbiology Spectrum
  21. Commands of Synthetic Biology to Modernize and Re-design the Biological Systems
    Hina Ilyas, Aimen Afzal, Zaheer Abbas, Sabahat Noor, Irfan Ullah, Raja Sheraz Rafique, Zeeshan Abbas, Muhammad Ishaq · 2024 · Advancements in Life Sciences
  22. Mitigating Winner-Take-All Resource Competition through Antithetic Control Mechanism
    Suchana Chakravarty, Rishabh Guttal, Rong Zhang, Xiao‐Jun Tian · 2024 · ACS Synthetic Biology
  23. Integrating recombinase-based feedback and feedforward control for optimal resource decoupling
    Rixin Zhang, Rong Zhang, Xiao‐Jun Tian · 2025 · Nucleic Acids Research
  24. Molecular Communication Among Nanomachines
    Barış Atakan · 2014 · Springer eBooks
  25. Computing with Synthetic Protocells
    Alexis Courbet, Franck Molina, Patrick Amar · 2015 · Acta Biotheoretica
  26. Speculative Life: Art, Synthetic Biology and Blueprints for the Unknown
    Jennifer Johung · 2015 · Theory Culture & Society
  27. Regulation of a Class of Continuous Bioreactor under Switching Kinetic Behavior: Modeling and Simulation Approach
    Fernando A. Cuevas-Ortiz, Pablo Antonio López Pérez, Ricardo Femat, Gerardo Lara‐Cisneros, Ricardo Aguilar‐López · 2015 · Industrial & Engineering Chemistry Research
  28. Synthetic Biology: Computational Modeling Bridging the Gap between In Vitro and In Vivo Reactions
    Vilma Gladys Duschak · 2015 · Current Synthetic and Systems Biology
  29. Computational Design and Analysis of Modular Cells for Large Libraries of Exchangeable Product Synthesis Modules
    Sergio Garcia, Cong T. Trinh · 2021 · Metabolic Engineering
  30. Curation Principles Derived from the Analysis of the SBOL iGEM Data Set
    Jeanet V. Mante, Nicholas Roehner, Kevin W. Keating, James Alastair McLaughlin, Eric M. Young, Jacob Beal, Chris John Myers · 2021 · ACS Synthetic Biology
  31. Formulating Engineering Systems Requirements
    Markus N. Zimmermann, Olivier Ladislas De Weck · 2021 · Springer eBooks
  32. Present and future prospects of crop synthetic biology
    Bo Bi, Wei Li, Yushu Jiang, Hao Du · 2022 · Crop Design
  33. Analysis of Adoption and Implementation of International Educational Standers in Primary Schools: A Case Study of Dir Lower Khyber Pakhtunkhwa
    Muhammad Ibrahim Khan, Nouman Khan, Shakir Ullah, Aziz Ullah, Khan Bahadar · 2023 · Journal of Education and Social Studies
  34. Engineering biology and automation–Replicability as a design principle
    Matthieu Bultelle, Alexis Casas, Richard Ian Kitney · 2024 · Engineering Biology
  35. Synthetic biology and genetic causation
    Gry Oftedal, Veli‐Pekka Parkkinen · 2013 · Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences
  36. Model for a population-based microbial oscillator
    Ángel Goñi‐Moreno, Martyn Amos · 2011 · Biosystems
  37. Synthetic multicellular oscillatory systems: controlling protein dynamics with genetic circuits
    Aneta Koseska, Evgenii I. Volkov, Jürgen Kurths · 2011 · Physica Scripta
  38. Noise Tolerance Analysis for Reliable Analog and Digital Computation in Living Cells
    L Rizik, Ram Y · 2016 · Journal of Bioengineering and Biomedical Sciences
  39. Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications
    Matthias Christen, Luca Del Medico, Heinz Christen, Beat Christen · 2017 · PLoS ONE
  40. Robust directional-diffusive hybrid molecular communication with parity-check erasure coding
    Hiroaki Egashira, Junichi Suzuki, Jonathan S. Mitzman, Tadashi Nakano, Hiroaki Fukuda · 2017 · Joint World Congress of International Fuzzy Systems Association and International Conference on Soft Computing and Intelligent Systems (IFSA-SCIS)
  41. Negative Regulation Gene Circuits for Efflux Pump Control
    Daniel A. Charlebois, Junchen Diao, Dmitry Nevozhay, Gábor Balázsi · 2018 · Methods in molecular biology
  42. Molecular Communication
    Nariman Farsad · 2018 · GetMobile Mobile Computing and Communications
  43. Addressing Evolutionary Questions with Synthetic Biology
    Florian Baier, Yolanda Schaerli · 2021 · Springer eBooks
  44. Prospective Applications of Synthetic Biology for Algal Bioproduct Optimization
    Basel Khraiwesh, Kenan Jijakli, Joseph Swift, Amphun Chaiboonchoe, Rasha Abdrabu, Pei-Wen Chao, Laising Yen, Kourosh Salehi‐Ashtiani · 2015 · Biofuel and biorefinery technologies
  45. Computational Protein Design for Synthetic Biology
    Florian Martin Richter, David A. Baker · 2013 · Elsevier eBooks
  46. BLAST
    Arie Meir, Jaijeet Roychowdhury · 2012 · ACM/IEEE Design Automation Conference (DAC)
  47. Creating a locally crowded environment with nanoclay hydrogels for cell-free biosynthesis
    Xinjie Chen, Qi Sun, Yuan Lu · 2020 · Soft Matter
  48. SHARP: genome-scale identification of gene–protein–reaction associations in cyanobacteria
    S. Krishnakumar, Dilip A. Durai, Pramod P. Wangikar, Ganesh A. Viswanathan · 2013 · Photosynthesis Research
  49. Synthetic biocomputation: the possible and the actual
    V. Solé, Ricard, Macia, Javier · 2011 · European Conference on Artificial Life
  50. The impact of antibiotics on bacterial cellulose in vivo
    Alyssa L. Henning, Jeffrey M. Catchmark · 2017 · Cellulose
  51. The Software Crisis of Synthetic Biology
    Sergi Valverde, Manuel Porcar, Juli G. Peretó, Ricard V. Solé · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
  52. Promoter and transcription factor dynamics tune protein mean and noise strength in a quorum sensing-based feedback synthetic circuit
    Yadira Boada, Alejandro Vignoni, Jesús Picó · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  53. Focus Issue Editorial: Synthetic Biology
    Andrew D. Hanson, Julian M. Hibberd, Mattheos A. G. Koffas, Joachim Kopka, Eleanore T. Wurtzel · 2019 · PLANT PHYSIOLOGY
  54. Microbial biotechnology meets ecological theory: a unified framework to design industrial microbial consortia
    Ignacio Belda · 2026 · International Microbiology
  55. Designed to breathe: synthetic biology applications in plant hypoxia
    Mikel Lavilla-Puerta, Beatrice Giuntoli · 2024 · PLANT PHYSIOLOGY
  56. Promoter Reliability in Modular Transcriptional Networks
    Rajat Anand, Navneet Rai, Mukund Thattai · 2011 · Methods in enzymology on CD-ROM/Methods in enzymology
  57. Application of Supervisory Control Theory to Guide Cellular Dynamics
    Fabio Luis Baldissera, José E.R. Cury · 2012 · IFAC Proceedings Volumes
  58. Using topology to tame the complex biochemistry of genetic networks
    Mukund Thattai · 2013 · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
  59. Structurally reconfigurable designer RNA structures for nanomachines
    Jiao Kai, Yaya Hao, Fei Wang, Lihua Wang, Fan Chunhai, Li Jiang · 2021 · Biophysics Reports
  60. Probing patterning in microbial consortia with a cellular automaton for spatial organisation
    Sankalpa Venkatraghavan, Sathvik Anantakrishnan, Karthik Raman · 2022 · Scientific Reports
  61. Tether-free optogenetic control of insulin secretion using an upconversion nanoparticle-doped hydrogel platform
    Akshaya Bansal, Jing Zhang, Qi Lu, Qingsong Mei, Yong Zhang · 2023 · Biomaterials Science
  62. Designing Conservation Relations in Layered Synthetic Biomolecular Networks
    Thomas P. Prescott, Antonis Papachristodoulou · 2015 · IEEE Transactions on Biomedical Circuits and Systems
  63. The impact of synthetic biology in chemical engineering—Educational issues
    George M. Hall, Joe M. Howe · 2012 · Education for Chemical Engineers
  64. Design Principles of a Genetic Alarm Clock
    Jaroslav Albert, Marianne J. Rooman · 2012 · PLoS ONE
  65. Externally Controllable Molecular Communication Systems for Pattern Formation
    Tadashi Nakano, Shouhei Kobayashi, Tatsuya Suda, Yutaka Okaie, Yasushi Hiraoka, Tokuko Haraguchi · 2014 · ACM International Conference on Nanoscale Computing and Communication (NANOCOM)
  66. Synbiological systems for complex natural products biosynthesis
    Jianhua Li, Hailin Meng, Yong Wang · 2016 · Synthetic and Systems Biotechnology
  67. Biocomputers: Problems They Solve, State of the Art, and Prospects
    Pavel M. Gotovtsev, Д. А. Кириллова, Raif G. Vasilov · 2020 · Nanotechnologies in Russia
  68. Control of mammalian cell-based devices with genetic programming
    Kate E. Dray, Hailey I. Edelstein, Kathleen S. Dreyer, Joshua N. Leonard · 2021 · Current Opinion in Systems Biology
  69. Rapid Characterization of Genetic Parts with Cell-free Systems
    John B. McManus, Casey B. Bernhards, Caitlin E. Sharpes, David C. Garcia, Stephanie D. Cole, Richard M. Murray, Peter A. Emanuel, Matthew W. Lux · 2021 · Journal of Visualized Experiments
  70. Ordering the past, envisioning future(s): How review articles in synthetic biology make use of heterogeneous expectations
    Clemens Dietrich Blümel · 2023 · Futures
  71. SYNTHETIC BIOLOGY APPLIED IN THE AGRIFOOD SECTOR: SOCIETAL PRIORITIES AND PITFALLS
    L. Frewer, D. Coles, A. Dijkstra, S. Kuznesof, H. Kendall, G. Kaptan · 2016 · Applied Studies in Agribusiness and Commerce
  72. High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits
    Abhishek Deshpande, Thomas E. Ouldridge · 2017 · Engineering Biology
  73. Biocircuits in synchrony
    Ricard V. Solé, Javier Macía · 2014 · Nature
  74. A Library Approach for the Discovery of Customized Yeast Three‐Hybrid Counter Selections
    Laura M. Wingler, Virginia W. Cornish · 2011 · ChemBioChem
  75. Using Spinach Aptamer to Correlate mRNA and Protein Levels in Escherichia coli
    Georgios Pothoulakis, Tom Ellis · 2015 · Methods in enzymology on CD-ROM/Methods in enzymology
  76. Engineered Cell-Based Therapies: A Vanguard of Design-Driven Medicine
    Rachel M. Hartfield, Yishan Chuang, Joshua N. Leonard · 2014 · Advances in experimental medicine and biology
  77. Length and time scales of cell-cell signaling circuits in agar
    Joy Doong, James M. Parkin, Richard M. Murray · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  78. Nonlinear Control in the Nematode C. elegans
    Megan Morrison, Charles Fieseler, J. Nathan Kutz · 2021 · Frontiers in Computational Neuroscience
  79. Development of Terminator–Promoter Bifunctional Elements for Application in Saccharomyces cerevisiae Pathway Engineering
    Xiaoxia Ni, Zhengyang Liu, Jintang Guo, Genlin Zhang · 2023 · International Journal of Molecular Sciences
  80. Preventing Multimer Formation in Commonly Used Synthetic Biology Plasmids
    Elizabeth Vaisbourd, Anat Bren, Uri S. Alon, David S. Glass · 2025 · ACS Synthetic Biology
  81. Describing function‐based approximations of biomolecular systems
    Abhishek Dey, Shaunak Sen · 2017 · IET Systems Biology
  82. The dynamic-process characterization and prediction of synthetic gene circuits by dynamic delay model
    Yanhong Sun, Fengyu Zhang, Qi Ouyang, Chunxiong Luo · 2024 · iScience
  83. GUBS, a Behaviour-Based Language for Design in Synthetic Biology
    Adrien Basso-Blandin, Franck Delaplace · 2013 · Scientific Annals of Computer Science
  84. Science & fabrications: On synthetic biology
    Anthony Stavrianakis, Gaymon Bennett · 2014 · BioSocieties
  85. Slow growth leads to a switch
    Keith Edward Shearwin · 2009 · Nature Chemical Biology
  86. Making gene circuits sing
    Arthur B. Prindle, Jeff Hasty · 2012 · Proceedings of the National Academy of Sciences
  87. In Vivo Programmed Gene Expression Based on Artificial Quorum Networks
    Teng Chu, Yajun Huang, Mingyu Hou, Qiyao Wang, Jingfan Xiao, Qin Liu, Yuanxing Zhang · 2015 · Applied and Environmental Microbiology
  88. Programming Biology: Expanding the Toolset for the Engineering of Transcription
    Bob Van Hove, Aaron M. Love, Parayil Kumaran Ajikumar, Marjan De Mey · 2015 · Springer eBooks
  89. Synthetic Biology and the Translational Imperative
    Raheleh Heidari, Marcello Ienca, Bernice S. Elger, Marc Folcher · 2017 · Science and Engineering Ethics
  90. Molecular Signaling Design Exploiting Cyclostationary Drift-Diffusion Fluid
    Toshiaki Koike–Akino, Junichi Suzuki, Philip V. Orlik · 2017 · Globecom
  91. Computational Tools for Applying Multi-level Models to Synthetic Biology
    Roberta Bardini, Gianfranco Michele Maria Politano, Alfredo Benso, Stefano Di Carlo · 2018 · Springer eBooks
  92. Resource Sensor Design for Quantifying Resource Competition in Genetic Circuits
    Cameron D. McBride, Domitilla Del Vecchio · 2018 · IEEE Conference on Decision and Control (CDC)
  93. Developing a Transformation-Independent and Unbiased qPCR Assay to Rapidly Evaluate the Determinants of DNA Assembly Efficiency
    Xiaoyan Ma, Xinxin Liang, Yi‐Xin Huo · 2019 · Engineering
  94. Can optimal experimental design serve as a tool to characterize highly non-linear synthetic circuits?
    Maxim A. Kryukov, Arthur Carcano, Grégory Batt, Jakob Ruess · 2019 · European Control Conference (ECC)
  95. Quorum sensing: the microbial linguistic
    Vikas Kumar, Jyoti Rawat · 2020 · Elsevier eBooks
  96. Synthetic minimal cells and their applications
    Ali Yazdizadeh Kharrazi, Amir Zare, Nils Chapin, Seyedkhashayar Ghavami, Amir Pandi · 2022 · Elsevier eBooks
  97. Characterizing Synthetic Biology Through Its Novel and Enhanced Functionalities
    Christian Pade, Bernd Giese, Stefan Koenigstein, Henning Wigger, Arnim von Gleich · 2014 · Risk engineering
  98. Rational Design of Robust Biomolecular Circuits: from Specification to Parameters
    Marc A. Hafner, Tatjana Petrov, James Jian-Qiang Lu, Heinz Koeppl · 2011 · Springer eBooks
  99. Noise-aware evolutionary TDMA optimization for neuronal signaling in medical sensor-actuator networks
    Junichi Suzuki, Pruet Boonma · 2014 · Genetic and Evolutionary Computation Conference Companion (GECCO Companion)
  100. How Cell-to-Cell Heterogeneity and Scarce Resources Shape the Population-Level Stability Profile of Toggle Switches
    András György · 2019 · IEEE Conference on Decision and Control (CDC)