Biology & Life Sciences

Synthetic Biology: Gene Network Engineering

Published January 30, 2017 Curated Collections

Synthetic Biology is an emerging, trans-disciplinary field at the intersection between many engineering and scientific disciplines such as biology, chemical engineering, chemistry, electrical engineering, and computer science. This section of the Synthetic Biology Collection details papers related to Gene Network Engineering.

Image Credit: Ivan Morozov (Virginia Bioinformatics Institute) / PLOS

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Research Articles

Research Articles

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10.1371/journal.pone.0160711

PLOS ONE Comparative Single-Cell Analysis of Different E. coli Expression Systems during Microfluidic Cultivation
August 15, 2016 Dennis Binder, Christopher Probst, Alexander Grünberger, Fabienne Hilgers, Anita Loeschcke, Karl-Erich Jaeger, Dietrich Kohlheyer, Thomas Drepper
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10.1371/journal.pcbi.1004958

PLOS Computational Biology Implementation Considerations, Not Topological Differences, Are the Main Determinants of Noise Suppression Properties in Feedback and Incoherent Feedforward Circuits
June 3, 2016 Gentian Buzi, Mustafa Khammash
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10.1371/journal.pone.0153679

PLOS ONE Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules
May 5, 2016 Bartłomiej Borek, Jeff Hasty, Lev Tsimring
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10.1371/journal.pone.0152146

PLOS ONE Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method
April 20, 2016 Shin-Ming Tien, Chih-Yuan Hsu, Bor-Sen Chen
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10.1371/journal.pcbi.1004744

PLOS Computational Biology MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression
February 4, 2016 Steven W. Paugh, David R. Coss, Ju Bao, Lucas T. Laudermilk, Christy R. Grace, Antonio M. Ferreira, M. Brett Waddell, Granger Ridout, Deanna Naeve, Michael Leuze, Philip F. LoCascio, John C. Panetta, Mark R. Wilkinson, Ching-Hon Pui, Clayton W. Naeve, Edward C. Uberbacher, Erik J. Bonten, William E. Evans
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10.1371/journal.pone.0147494

PLOS ONE Site-Directed Mutagenesis to Improve Sensitivity of a Synthetic Two-Component Signaling System
January 22, 2016 Audrey Olshefsky, Laila Shehata, Natalie Kuldell
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10.1371/journal.pcbi.1003533

PLOS Computational Biology Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems
March 27, 2014 Samanthe Lyons, Wenlong Xu, June Medford, Ashok Prasad
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10.1371/journal.pgen.1003706

PLOS Genetics The Architecture of a Prototypical Bacterial Signaling Circuit Enables a Single Point Mutation to Confer Novel Network Properties
August 22, 2013 Sri Ram, Mark Goulian
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10.1371/journal.pcbi.1003486

PLOS Computational Biology Modular Composition of Gene Transcription Networks
March 13, 2014 Andras Gyorgy, Domitilla Del Vecchio
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10.1371/journal.pone.0068345

PLOS ONE Biological Signal Processing with a Genetic Toggle Switch
July 16, 2013 Patrick Hillenbrand, Georg Fritz, Ulrich Gerland
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10.1371/journal.pone.0057482

PLOS ONE A Formalized Design Process for Bacterial Consortia That Perform Logic Computing
February 28, 2013 Weiyue Ji, Handuo Shi, Haoqian Zhang, Rui Sun, Jingyi Xi, Dingqiao Wen, Jingchen Feng, Yiwei Chen, Xiao Qin, Yanrong Ma, Wenhan Luo, Linna Deng, Hanchi Lin, Ruofan Yu, Qi Ouyang
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10.1371/journal.pone.0065986

PLOS ONE Multicellular Computing Using Conjugation for Wiring
June 20, 2013 Angel Goni-Moreno, Martyn Amos, Fernando de la Cruz
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10.1371/journal.pone.0052280

PLOS ONE Synthetic miRNA-Mowers Targeting miR-183-96-182 Cluster or miR-210 Inhibit Growth and Migration and Induce Apoptosis in Bladder Cancer Cells
December 17, 2012 Yuchen Liu, Yonghua Han, Hu Zhang, Liping Nie, Zhimao Jiang, Pingping Fa, Yaoting Gui, Zhiming Cai
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10.1371/journal.pone.0047795

PLOS ONE Programmable In Vivo Selection of Arbitrary DNA Sequences
November 14, 2012 Tuval Ben Yehezkel, Tamir Biezuner, Gregory Linshiz, Yair Mazor, Ehud Shapiro
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10.1371/journal.pone.0052000

PLOS ONE Quantitative, Non-Disruptive Monitoring of Transcription in Single Cells with a Broad-Host Range GFP-luxCDABE Dual Reporter System
December 28, 2012 Ilaria Benedetti, Victor de Lorenzo, Rafael Silva-Rocha
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10.1371/journal.pgen.1002963

PLOS Genetics Increasing Signal Specificity of the TOL Network of Pseudomonas putida mt-2 by Rewiring the Connectivity of the Master Regulator XylR
October 11, 2012 Aitor de las Heras, Sofia Fraile, Victor de Lorenzo
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10.1371/journal.pone.0046868

PLOS ONE Inducible Control of Subcellular RNA Localization Using a Synthetic Protein-RNA Aptamer Interaction
October 8, 2012 Brian Belmont, Jacquin Niles
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10.1371/journal.pcbi.1002480

PLOS Computational Biology Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit
April 12, 2012 Dmitry Nevozhay, Rhys Adams, Elizabeth Van Itallie, Matthew Bennett, Gabor Balazsi
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10.1371/journal.pcbi.1002331

PLOS Computational Biology A Feedback Quenched Oscillator Produces Turing Patterning with One Diffuser
January 26, 2012 Justin Hsia, William Holtz, Daniel Huang, Murat Arcak, Michel Maharbiz
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10.1371/journal.pone.0027559

PLOS ONE The Bacterial Nanorecorder: Engineering E. coli to Function as a Chemical Recording Device
November 23, 2011 Prasanna Bhomkar, Prasanna Bhomkar, Wayne Materi, David Wishart
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10.1371/journal.pone.0033279

PLOS ONE Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology
March 19, 2012 Benjamin Blount, Tim Weenink, Serge Vasylechko, Tom Ellis
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10.1371/journal.pcbi.1002264

PLOS Computational Biology Stochastic Delay Accelerates Signaling in Gene Networks
November 10, 2011 Kresimir Josic, Jose Lopez, William Ott, LieJune Shiau, Matthew Bennett
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10.1371/journal.pcbi.1002171

PLOS Computational Biology High-Precision, In Vitro Validation of the Sequestration Mechanism for Generating Ultrasensitive Dose-Response Curves in Regulatory Networks
October 6, 2011 Francesco Ricci, Alexis Vallée-Bélisle, Kevin Plaxco
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10.1371/journal.pcbi.1002074

PLOS Computational Biology Construction and Modelling of an Inducible Positive Feedback Loop Stably Integrated in a Mammalian Cell-Line
June 30, 2011 Velia Siciliano, Filippo Menolascina, Lucia Marucci, Chiara Fracassi, Immacolata Garzilli, Maria Nicoletta Moretti, Diego DiBernardo
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10.1371/journal.pcbi.1002085

PLOS Computational Biology Robust Network Topologies for Generating Switch-Like Cellular Responses
June 23, 2011 Najaf Shah, Casim Sarkar
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10.1371/journal.pone.0016292

PLOS ONE Programmable Ligand Detection System in Plants through a Synthetic Signal Transduction Pathway
January 25, 2011 Mauricio Antunes, Kevin Morey, J. Jeff Smith, Kirk Albrecht, Tessa Bowen, Jeffrey Zdunek, Jared Troupe, Matthew Cuneo, Colleen Webb, Homme Hellinga, June Medford
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10.1371/journal.pone.0016140

PLOS ONE A Multi-Functional Synthetic Gene Network: A Frequency Multiplier, Oscillator and Switch
February 17, 2011 Oliver Purcell, Mario di Bernardo, Claire Grierson, Nigel Savery
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10.1371/journal.pone.0011909

PLOS ONE Oscillations by Minimal Bacterial Suicide Circuits Reveal Hidden Facets of Host-Circuit Physiology
July 30, 2010 Philippe Marguet, Yu Tanouchi, Eric Spitz, Cameron Smith, Lingchong You
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10.1371/journal.pone.0010619

PLOS ONE An Environment-Sensitive Synthetic Microbial Ecosystem
May 12, 2010 Bo Hu, Jin Du, Rui-yang Zou, Ying-jin Yuan
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10.1371/journal.pone.0009182

PLOS ONE Reverse Engineering of Bacterial Chemotaxis Pathway via Frequency Domain Analysis
March 9, 2010 Junjie Luo, Jun Wang, Ting Martin Ma, Zhirong Sun
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10.1371/journal.pone.0008083

PLOS ONE How to Turn a Genetic Circuit into a Synthetic Tunable Oscillator, or a Bistable Switch
December 7, 2009 Lucia Marucci, David A. W. Barton, Irene Cantone, Maria Aurelia Ricci, Maria Pia Cosma, Stefania Santini, Diego di Bernardo, Mario di Bernardo
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10.1371/journal.pone.0006946

PLOS ONE Synthetic Morphology Using Alternative Inputs
September 10, 2009 Hiromasa Tanaka, Tau-Mu Yi
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10.1371/journal.pone.0005399

PLOS ONE Monomeric Bistability and the Role of Autoloops in Gene Regulation
April 30, 2009 Stefanie Widder, Javier Macía, Ricard Solé
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10.1371/journal.pone.0004872

PLOS ONE Timing Cellular Decision Making Under Noise via Cell–Cell Communication
March 13, 2009 Aneta Koseska, Alexey Zaikin, Jürgen Kurths, Jordi García-Ojalvo
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10.1371/journal.pone.0002815

PLOS ONE Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory
July 30, 2008 Timothy S. Ham, Sung K. Lee, Jay D. Keasling, Adam P. Arkin
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10.1371/journal.pone.0002372

PLOS ONE Bimodal and Hysteretic Expression in Mammalian Cells from a Synthetic Gene Circuit
June 4, 2008 Tobias May, Lee Eccleston, Sabrina Herrmann, Hansjörg Hauser, Jorge Goncalves, Dagmar Wirth
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10.1371/journal.pone.0001507

PLOS ONE Reconstitution of Mdm2-Dependent Post-Translational Modifications of p53 in Yeast
January 30, 2008 Barbara Di Ventura, Charlotta Funaya, Claude Antony, Michael Knop, Luis Serrano
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10.1371/journal.pone.0000049

PLOS ONE Adaptive Response of a Gene Network to Environmental Changes by Fitness-Induced Attractor Selection
December 20, 2006 Akiko Kashiwagi, Itaru Urabe, Kunihiko Kaneko, Tetsuya Yomo

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