The second wave of synthetic biology: from modules to systems

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Items 301–400 of 999

1. Multiscale mechanobiology: computational models for integrating molecules to multicellular systems
   Michael Mak, Taeyoon Kim, Muhammad Hamid Zaman, Roger Dale Kamm · 2015 · Integrative Biology
2. Development of GRAS strains for nutraceutical production using systems and synthetic biology approaches: advances and prospects
   Long Liu, Ningzi Guan, Jianghua Li, Hyun‐Dong Shin, Guocheng Du, Jian Chen · 2015 · Critical Reviews in Biotechnology
3. Generating Effective Models and Parameters for RNA Genetic Circuits
   Chelsea Y. Hu, Jeffrey D. Varner, Julius B. Lucks · 2015 · ACS Synthetic Biology
4. An Enzyme‐Coated Metal–Organic Framework Shell for Synthetically Adaptive Cell Survival
   Kang Liang, Joseph J. Richardson, Christian J. Doonan, Xavier Mulet, Yi Ju, Jiwei Cui, Frank Caruso, Paolo Falcaro · 2017 · Angewandte Chemie
5. Convergence of regenerative medicine and synthetic biology to develop standardized and validated models of human diseases with clinical relevance
   Dietmar Werner Hutmacher, Boris Michael Holzapfel, Elena M. De‐Juan‐Pardo, Brooke Pereira, Stuart J. Ellem, Daniela Loessner, Gail Petuna Risbridger · 2015 · Current Opinion in Biotechnology
6. Varieties of noise: Analogical reasoning in synthetic biology
   Tarja Knuuttila, Andrea Loettgers · 2014 · Studies in History and Philosophy of Science Part A
7. Programming Cells to Work for Us
   Yili Qian, Cameron D. McBride, Domitilla Del Vecchio · 2017 · Annual Review of Control Robotics and Autonomous Systems
8. Engineered RNA Nanodesigns for Applications in RNA Nanotechnology
   Kirill A. Afonin, Brian Lindsay, Bruce A. Shapiro · 2013 · DNA and RNA Nanotechnology
9. Robust, tunable genetic memory from protein sequestration combined with positive feedback
   Tatenda Shopera, William R. Henson, Andrew H. Ng, Young Je Lee, Kenneth M. Ng, Tae Seok Moon · 2015 · Nucleic Acids Research
10. SBROME: A Scalable Optimization and Module Matching Framework for Automated Biosystems Design
    Linh Ngoc Huynh, Αθανάσιος Τσουκαλάς, Matthias Köppe, Ilias Tagkopoulos · 2013 · ACS Synthetic Biology
11. Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations
    Jonathan Naylor, Harold M. Fellermann, Yuchun Ding, Waleed Khalid Mohammed, Nicholas Stephen Jakubovics, Joy Mukherjee, Catherine Anne Biggs, Phillip Craig Wright, Natalio Krasnogor · 2017 · ACS Synthetic Biology
12. A Cytomorphic Chip for Quantitative Modeling of Fundamental Bio-Molecular Circuits
    Sung Sik Woo, Jaewook Kim, Rahul Sarpeshkar · 2015 · IEEE Transactions on Biomedical Circuits and Systems
13. Synthetic Tunable Amplifying Buffer Circuit in E. coli
    Kayzad Soli Nilgiriwala, José Ignacio Jiménez, Phillip M. Rivera, Domitilla Del Vecchio · 2014 · ACS Synthetic Biology
14. A High-Throughput Microfluidic Platform for Mammalian Cell Transfection and Culturing
    Kristina Woodruff, Sebastian J. Maerkl · 2016 · Scientific Reports
15. Recent advances in the synthesis of rare sugars using DHAP-dependent aldolases
    Aimin Li, Li Cai, Zhou Chen, Mayan Wang, Ning Wang, Hideki Nakanishi, Xiao‐Dong Gao, Zijie Li · 2017 · Carbohydrate Research
16. Designing with living systems in the synthetic yeast project
    Erika Amethyst Szymanski, Jane E Calvert · 2018 · Nature Communications
17. Universal scaling across biochemical networks on Earth
    Hyunju Kim, Harrison B. Smith, Cole Mathis, Jason Raymond, Sara Imari Walker · 2019 · Science Advances
18. Convergence in parameters and predictions using computational experimental design
    Hagen, David R., White, Jacob K., Tidor, Bruce · 2013 · Interface Focus
19. Cooperative assembly confers regulatory specificity and long-term genetic circuit stability
    Meghan D. J. Bragdon, Nikit Patel, James Chuang, Ethan Levien, Caleb J. Bashor, Ahmad S. Khalil · 2023 · Cell
20. Programming a Pavlovian-like conditioning circuit in Escherichia coli
    Haoqian M. Zhang, Min Lin, Handuo Shi, Weiyue Ji, Longwen Huang, Xiaomeng Zhang, Shan Shen, Rencheng Gao, Shuke Wu, Chengzhe Tian et al. · 2014 · Nature Communications
21. The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms
    Gil Alterovitz, TARO M. MUSO, Marco F. Ramoni · 2009 · Briefings in Bioinformatics
22. Engineering repressors with coevolutionary cues facilitates toggle switches with a master reset
    Rey P Dimas, Xianli Jiang, Jose Alberto de la Paz, Faruck Morcos, Clement T. Y. Chan · 2019 · Nucleic Acids Research
23. Research progress and the biotechnological applications of multienzyme complex
    Yi Jiang, Xinyi Zhang, Haibo Yuan, Di Huang, Ruiming Wang, Hongling Liu, Tengfei Wang · 2021 · Applied Microbiology and Biotechnology
24. Limitations and trade-offs in gene expression due to competition for shared cellular resources
    András György, Domitilla Del Vecchio · 2014 · IEEE Conference on Decision and Control (CDC)
25. Positive Autoregulation Shapes Response Timing and Intensity in Two-component Signal Transduction Systems
    Alexander Yu. Mitrophanov, Tricia J. Hadley, Eduardo A. Groisman · 2010 · Journal of Molecular Biology
26. Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality
    Irene Otero‐Muras, Julio R. Banga · 2017 · ACS Synthetic Biology
27. Accurate, Model-Based Tuning of Synthetic Gene Expression Using Introns in S. cerevisiae
    Ido Yofe, Zohar Zafrir, Rachel Blau, Maya Schuldiner, Tamir Tuller, Ehud Y. Shapiro, Tuval Ben-Yehezkel · 2014 · PLoS Genetics
28. From DNA to Targeted Therapeutics: Bringing Synthetic Biology to the Clinic
    Yvonne Y. Chen, Christina D. Smolke · 2011 · Science Translational Medicine
29. mRNA translation and protein synthesis: an analysis of different modelling methodologies and a new PBN based approach
    Yun‐Bo Zhao, J. Krishnan · 2014 · BMC Systems Biology
30. The Conception of Life in Synthetic Biology
    Anna Deplazes‐Zemp · 2011 · Science and Engineering Ethics
31. Programmable T7-based synthetic transcription factors
    Brendan J. Hussey, David R. McMillen · 2018 · Nucleic Acids Research
32. Intracellular Imaging with Genetically Encoded RNA-Based Molecular Sensors
    Zhining Sun, Tony Nguyen, Kathleen McAuliffe, Mingxu You · 2019 · Nanomaterials
33. An Update on Molecular Tools for Genetic Engineering of Actinomycetes—The Source of Important Antibiotics and Other Valuable Compounds
    Lena Mitousis, Yvonne Thoma, Ewa Maria Musiol-Kroll · 2020 · Antibiotics
34. Engineered systems of inducible anti-repressors for the next generation of biological programming
    Thomas M. Groseclose, Ronald E. Rondon, Zachary D. Herde, Carlos A. Aldrete, Corey J. Wilson · 2020 · Nature Communications
35. Molecular switches in animal cells
    Maximilian Hörner, Wilfried Weber · 2012 · FEBS Letters
36. Biology by Design: From Top to Bottom and Back
    Brian R. Fritz, Laura E. Timmerman, Nichole M. Daringer, Joshua N. Leonard, Michael C. Jewett · 2010 · BioMed Research International
37. Thrombin-Mediated Transcriptional Regulation Using DNA Aptamers in DNA-Based Cell-Free Protein Synthesis
    Sukanya Iyer, Mitchel J. Doktycz · 2013 · ACS Synthetic Biology
38. A quantitative framework for the forward design of synthetic miRNA circuits
    Ryan J. Bloom, Sally M. Winkler, Christina D. Smolke · 2014 · Nature Methods
39. Division of logic labour
    Bochong Li, Lingchong You · 2011 · Nature
40. Exploration, iterativity and kludging in synthetic biology
    Maureen A. O’Malley · 2010 · Comptes Rendus Chimie
41. Robustness analysis, prediction, and estimation for uncertain biochemical networks: An overview
    Stefan Streif, Kwang‐Ki K. Kim, Philipp Rumschinski, Masako Kishida, Dongying Erin Shen, Rolf Findeisen, Richard D. Braatz · 2016 · Journal of Process Control
42. Design principles for the analysis and construction of robustly homeostatic biological networks
    Zhe F. Tang, David R. McMillen · 2016 · Journal of Theoretical Biology
43. Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies
    Isaac Núñez, Tamara Matúte, Ilenne Del Valle, Anton Kan, Atri Tushar Choksi, Drew Endy, Jim P. Haseloff, Timothy J. Rudge, Fernán Federici · 2016 · ACS Synthetic Biology
44. Defensive Function of Transposable Elements in Bacteria
    Catherine Fan, Yin-Hu Wu, Christoph M. Decker, Reza Rohani, Manuela Gesell Salazar, Hua Ye, Zhanfeng Cui, Frank Schmidt, Wei E. Huang · 2019 · ACS Synthetic Biology
45. Recent advances in plasmid-based tools for establishing novel microbial chassis
    Luísa Czamanski Nora, Cauã Antunes Westmann, María‐Eugenia Guazzaroni, Chandra Nayaka Siddaiah, Vijai Kumar Gupta, Rafael Silva‐Rocha · 2019 · Biotechnology Advances
46. Holistic engineering of cell-free systems through proteome-reprogramming synthetic circuits
    Luis Eduardo Contreras-Llano, Conary C. Meyer, Yao Liu, Mridul Sarker, Sierin Lim, Marjorie L. Longo, Cheemeng Tan · 2020 · Nature Communications
47. Integration of microfluidics into the synthetic biology design flow.
    Hai-Yao Huang, D. Densmore · 2014 · Lab on a Chip
48. Sigma Factor-Mediated Tuning of Bacterial Cell-Free Synthetic Genetic Oscillators
    Maaruthy Yelleswarapu, Ardjan J. van der Linden, Bob van Sluijs, Pascal A. Pieters, Emilien Dubuc, Tom F. A. de Greef, Wilhelm T. S. Huck · 2018 · ACS Synthetic Biology
49. Engineering programmable material-to-cell pathways via synthetic notch receptors to spatially control differentiation in multicellular constructs
    Mher Garibyan, Tyler Hoffman, Thijs Makaske, Stephanie K. Do, Yifan Wu, Brian A. Williams, Alexander R. March, Nathan Cho, Nicolas Pedroncelli, Ricardo Espinosa Lima et al. · 2024 · Nature Communications
50. Development and fabrication of nanoporous silicon-based bioreactors within a microfluidic chip
    Scott T. Retterer, Piro Siuti, Chang Kyoung Choi, Darrell K. Thomas, Mitchel J. Doktycz · 2010 · Lab on a Chip
51. Expanding the Logic of Bacterial Promoters Using Engineered Overlapping Operators for Global Regulators
    María‐Eugenia Guazzaroni, Rafael Silva‐Rocha · 2014 · ACS Synthetic Biology
52. Experimental Challenges for Reduced Genomes: The Cell Model Escherichia coli
    Masaomi Kurokawa, Bei‐Wen Ying · 2019 · Microorganisms
53. Harnessing synthetic biology to enhance ocean health
    Peter Quoc Nguyen, Xiaoning Huang, Daniel S. Collins, James J. Collins, Ting Lu · 2023 · Trends in biotechnology
54. Synthetic biology approaches to engineer T cells
    Chia‐Yung Wu, Levi J. Rupp, Kole T. Roybal, Wendell A. Lim · 2015 · Current Opinion in Immunology
55. Gemini, a Bifunctional Enzymatic and Fluorescent Reporter of Gene Expression
    Lance Martin, Austin Che, Drew Endy · 2009 · PLoS ONE
56. Global injectivity and multiple equilibria in uni- and bi-molecular reaction networks
    Casian Pantea, Heinz Koeppl, Gheorghe Crăciun · 2012 · Discrete and Continuous Dynamical Systems - B
57. Toward rational design of bacterial genomes.
    G. Cambray, Vivek K. Mutalik, A. Arkin · 2011 · Current Opinion in Microbiology
58. Measuring Retroactivity from Noise in Gene Regulatory Networks
    Kyung Hyuk Kim, Herbert M. Sauro · 2011 · Biophysical Journal
59. Merging machine learning and bioelectronics for closed-loop control of biological systems and homeostasis
    Mohammad Jafari, Giovanny Marquez, Harika Dechiraju, Marcella M. Gomez, Marco Rolandi · 2023 · Cell Reports Physical Science
60. Designing Genetic Feedback Controllers
    Andreas W. K. Harris, James A. Dolan, Ciarán L. Kelly, James Anderson, Antonis Papachristodoulou · 2015 · IEEE Transactions on Biomedical Circuits and Systems
61. Multicriteria global optimization for biocircuit design
    Irene Otero‐Muras, Julio R. Banga · 2014 · BMC Systems Biology
62. Shaping pulses to control bistable systems: Analysis, computation and counterexamples
    Aivar Sootla, Diego A. Oyarzún, David Angeli, Guy-Bart V. Stan · 2015 · Automatica
63. Nano-guided cell networks as conveyors of molecular communication
    Jessica L. Terrell, Hsuan‐Chen Wu, Chen‐Yu Tsao, Nathan B. Barber, Matthew D. Servinsky, Gregory Francis Payne, William E. Bentley · 2015 · Nature Communications
64. A Computational Workflow for the Automated Generation of Models of Genetic Designs
    Göksel Mısırlı, Tramy Nguyen, James Alastair McLaughlin, Prashant Vaidyanathan, Timothy S. Jones, Douglas Michael Densmore, Chris John Myers, Anil Wipat · 2018 · ACS Synthetic Biology
65. Engineering DNA recognition and allosteric response properties of TetR family proteins by using a module-swapping strategy
    Rey P Dimas, Benjamin R. Jordan, Xianli Jiang, Catherine A Martini, Joseph S. Glavy, Dustin P. Patterson, Faruck Morcos, Clement T. Y. Chan · 2019 · Nucleic Acids Research
66. Effective Use of Linear DNA in Cell-Free Expression Systems
    Megan A. McSweeney, Mark P. Styczynski · 2021 · Frontiers in Bioengineering and Biotechnology
67. Rationally Engineered Synthetic Coculture for Improved Biomass and Product Formation
    Suvi Santala, Matti Tapani Karp, Ville P. Santala · 2014 · PLoS ONE
68. Total synthesis of a eukaryotic chromosome: Redesigning and SCRaMbLE‐ing yeast
    Dejana Jovicevic, Benjamin A. Blount, Tom Ellis · 2014 · BioEssays
69. Broadening the signal specificity of prokaryotic promoters by modifying cis -regulatory elements associated with a single transcription factor
    Rafael Silva‐Rocha, Vı́ctor de Lorenzo · 2012 · Molecular BioSystems
70. Fan-out in gene regulatory networks
    Kyung H. Kim, Herbert M. Sauro · 2010 · Journal of Biological Engineering
71. Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory
    Evgeni V. Nikolaev, Eduardo D. Sontag · 2016 · PLoS Computational Biology
72. Advances in riboswitch‐based biosensor as food samples detection tool
    Xiaoze Dong, Shuo Qi, Imran Mahmood Khan, Yuhan Sun, Yin Zhang, Zhouping Wang · 2022 · Comprehensive Reviews in Food Science and Food Safety
73. Allostery in the ferredoxin protein motif does not involve a conformational switch
    Rachel Nechushtai, Heiko Lammert, Dorit Michaeli, Yael Eisenberg-Domovich, John A. Zuris, Maria A. Luca, Dominique T. Capraro, Alex Fish, Odelia Tepper, Melinda Roy et al. · 2011 · Proceedings of the National Academy of Sciences
74. Reflecting trends in the academic landscape of sustainable energy using probabilistic topic modeling
    Manuel W. Bickel · 2019 · Energy Sustainability and Society
75. Seaweed farming: A perspectives of genetic engineering and nano-technology application
    Nida Tabassum Khan, Kumarasamy Sudhakar, Rizalman Mamat · 2023 · Heliyon
76. Toward Engineering Synthetic Microbial Metabolism
    George H. McArthur, Stephen S. Fong · 2009 · BioMed Research International
77. Synthetic biology: lessons from engineering yeast MAPK signalling pathways
    Kentaro Furukawa, Stefan Hohmann · 2013 · Molecular Microbiology
78. Amyloid Assemblies: Protein Legos at a Crossroads in Bottom‐Up Synthetic Biology
    Rafael Giraldo · 2010 · ChemBioChem
79. Design in synthetic biology
    Adrian Mackenzie · 2010 · BioSocieties
80. Ratiometric Gas Reporting: A Nondisruptive Approach To Monitor Gene Expression in Soils
    Hsiao-Ying Cheng, Caroline A. Masiello, Ilenne Del Valle, Xiaodong Gao, George N. Bennett, Jonathan J. Silberg · 2018 · ACS Synthetic Biology
81. Multiobjective Strain Design: A Framework for Modular Cell Engineering
    Sergio Garcia, Cong T. Trinh · 2018 · Metabolic Engineering
82. Genetic switches designed for eukaryotic cells and controlled by serine integrases
    Mayna da Silveira Gomide, Thais Torquato Sales, Luciana Rodrigues Carvalho Barros, Cintia Elisabeth Gomez Limia, Marco A. de Oliveira, Lílian H. Florentino, L. M. G. Barros, Maria L. Robledo, G. Pinheiro Coelho José, Mariana S. M. Almeida et al. · 2020 · Communications Biology
83. Development of a robust Escherichia coli-based cell-free protein synthesis application platform
    Nan Jiang, Xuanwei Ding, Yuan Lu · 2020 · Biochemical Engineering Journal
84. Synthetic Lateral Inhibition in Periodic Pattern Forming Microbial Colonies
    Salva Duran‐Nebreda, Jordi Pla, Blai Vidiella, Jordi Piñero, Núria Conde Pueyo, Ricard V. Solé · 2021 · ACS Synthetic Biology
85. Cell-Free Characterization of Coherent Feed-Forward Loop-Based Synthetic Genetic Circuits
    Pascal A. Pieters, Bryan L. Nathalia, Ardjan J. van der Linden, Peng Yin, Jongmin Kim, Wilhelm T. S. Huck, Tom F. A. de Greef · 2021 · ACS Synthetic Biology
86. Modulating gene regulation function by chemically controlled transcription factor clustering
    Jiegen Wu, Baoqiang Chen, Yadi Liu, Liang Ma, Wen Liang Huang, Yihan Lin · 2022 · Nature Communications
87. Modulating the Lifetime of DNA Motifs Using Visible Light and Small Molecules
    Laura Wimberger, Felix J. Rizzuto, Jonathon E. Beves · 2023 · Journal of the American Chemical Society
88. Synthetic Biology: A Bridge Between Functional and Evolutionary Biology
    Michel Morange · 2009 · Biological Theory
89. Evolved Quorum Sensing Regulator, LsrR, for Altered Switching Functions
    Bryn L. Adams, Karen K. Carter, Min Amy Guo, Hsuan‐Chen Wu, Chen‐Yu Tsao, Herman O. Sintim, James J. Valdés, William E. Bentley · 2013 · ACS Synthetic Biology
90. A gene network engineering platform for lactic acid bacteria
    Wentao Kong, Venkata S. Kapuganti, Ting Lu · 2015 · Nucleic Acids Research
91. Engineering Multicellular Logic in Bacteria with Metabolic Wires
    Rafael Silva‐Rocha, Vı́ctor de Lorenzo · 2013 · ACS Synthetic Biology
92. Repositioning microbial biotechnology against COVID‐19: the case of microbial production of flavonoids
    Tobias Goris, Álvaro Pérez‐Valero, Igor Martínez, Dong Yi, Luis Fernández‐Calleja, David San León, Uwe T. Bornscheuer, Patricia Magadán‐Corpas, Felipe Lombó, Juan Nogales · 2020 · Microbial Biotechnology
93. Design and Connection of Robust Genetic Circuits
    Adrian Randall, Patrick Guye, Saurabh Gupta, Xavier Duportet, Ron Weiss · 2011 · Methods in enzymology on CD-ROM/Methods in enzymology
94. Engineered genetic information processing circuits
    Hao Qi, Andrew E. Blanchard, Ting Lu · 2013 · WIREs Systems Biology and Medicine
95. Plant and bacterial systems biology as platform for plant synthetic bio(techno)logy
    Matias Daniel Zurbriggen, Alina Moor, Wilfried Weber · 2012 · Journal of Biotechnology
96. Stochastic Stabilization of Phenotypic States: The Genetic Bistable Switch as a Case Study
    Marc L Weber, Javier Buceta · 2013 · PLoS ONE
97. Modeling a Minimal Cell
    Michael Louis Shuler, Patricia Foley, Jordan Atlas · 2012 · Methods in molecular biology
98. Automated design of hammerhead ribozymes and validation by targeting the PABPN1 gene transcript
    Nawwaf N. Kharma, Luc Varin, Aida Abu‐Baker, Jonathan Ouellet, Sabrine Najeh, Mohammad-Reza Ehdaeivand, Gabriel Belmonte, Anas Ambri, Guy Armand Rouleau, Jonathan Perreault · 2015 · Nucleic Acids Research
99. The effect of metabolic stress on genome stability of a synthetic biology chassis Escherichia coli K12 strain
    Jillian M. Couto, Anne M. McGarrity, Julie Russell, William T. Sloan · 2018 · Microbial Cell Factories
100. Plant Secondary Metabolism
     María Alejandra Álvarez · 2014 · Springer eBooks