Biology & Life Sciences

Synthetic Biology: Software & Modeling

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 Software & Modeling.

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

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Research Articles

Research Articles

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10.1371/journal.pone.0161522

PLOS ONE Mapping the Emergence of Synthetic Biology
September 9, 2016 Benjamin Raimbault, Jean-Philippe Cointet, Pierre-Benoît Joly
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PLOS

PLOS Synbio Community State of synbio publishing | PLOS Synthetic Biology Community
October 28, 2016 Aaron Dy
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10.1371/journal.pone.0161605

PLOS ONE Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers
August 18, 2016 Francesco Montefusco, Ozgur E. Akman, Orkun S. Soyer, Declan G. Bates
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10.1371/journal.pone.0157851

PLOS ONE Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy
June 23, 2016 Michael Volpers, Nico J. Claassens, Elad Noor, John van der Oost, Willem M. de Vos, Servé W. M. Kengen, Vitor A. P. Martins dos Santos
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10.1371/journal.pcbi.1004508

PLOS Computational Biology Systematic Prediction of Scaffold Proteins Reveals New Design Principles in Scaffold-Mediated Signal Transduction
September 22, 2015 Jianfei Hu, Johnathan Neiswinger, Jin Zhang, Heng Zhu, Jiang Qian
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10.1371/journal.pone.0155038

PLOS ONE Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom
May 6, 2016 Jennifer Levering, Jared Broddrick, Christopher L. Dupont, Graham Peers, Karen Beeri, Joshua Mayers, Alessandra A. Gallina, Andrew E. Allen, Bernhard O. Palsson, Karsten Zengler
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10.1371/journal.pcbi.1004923

PLOS Computational Biology Stochastic Simulation of Biomolecular Networks in Dynamic Environments
June 1, 2016 Margaritis Voliotis, Philipp Thomas, Ramon Grima, Clive G. Bowsher
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10.1371/journal.pcbi.1004918

PLOS Computational Biology Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks
May 10, 2016 Song Feng, Julien F. Ollivier, Orkun S. Soyer
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10.1371/journal.pcbi.1004799

PLOS Computational Biology Conflicting Selection Pressures Will Constrain Viral Escape from Interfering Particles: Principles for Designing Resistance-Proof Antivirals
May 6, 2016 Luke Rast, Igor Rouzine, Ganna Rozhnova, Lisa Bishop, Ariel Weinberger, Leor Weinberger
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10.1371/journal.pcbi.1004891

PLOS Computational Biology The Role of Genome Accessibility in Transcription Factor Binding in Bacteria
April 22, 2016 Antonio L. C. Gomes, Harris H. Wang
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10.1371/journal.pcbi.1004619

PLOS Computational Biology Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
April 28, 2016 Tatiana Maximova, Ryan Moffatt, Buyong Ma, Ruth Nussinov, Amarda Shehu
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10.1371/journal.pone.0153295

PLOS ONE Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels
April 15, 2016 Arno Steinacher, Declan G. Bates, Ozgur E. Akman, Orkun S. Soyer
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10.1371/journal.pcbi.1004781

PLOS Computational Biology Quorum Sensing Desynchronization Leads to Bimodality and Patterned Behaviors
April 12, 2016 David Quan, William Bentley, Chen-Yu Tsao, Hsuan-Chen Wu
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10.1371/journal.pcbi.1004754

PLOS Computational Biology Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis
March 22, 2016 Prakash Rathi, Alexander Fulton, Karl-Erich Jaeger, Holger Gohlke
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10.1371/journal.pcbi.1004793

PLOS Computational Biology Noise Expands the Response Range of the Bacillus subtilis Competence Circuit
March 22, 2016 Andrew Mugler, Mark Kittisopikul, Luke Hayden, Jintao Liu, Chris Wiggins, Gürol Suel, Aleksandra Walczak
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10.1371/journal.pgen.1005926

PLOS Genetics The Selective Advantage of Synonymous Codon Usage Bias in Salmonella
March 10, 2016 Gerrit Brandis, Diarmaid Hughes
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10.1371/journal.pone.0151086

PLOS ONE Promoters Architecture-Based Mechanism for Noise-Induced Oscillations in a Single-Gene Circuit
March 9, 2016 N. Guisoni, D. Monteoliva, Luis Diambra
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10.1371/journal.pcbi.1004678

PLOS Computational Biology Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication
March 3, 2016 Enrico Guarnera, Igor N. Berezovsky
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10.1371/journal.pone.0150369

PLOS ONE Improving Protein Expression Prediction Using Extra Features and Ensemble Averaging
March 2, 2016 Armando Fernandes, Susana Vinga
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10.1371/journal.pone.0147302

PLOS ONE Extracellular Matrix Deposition in Engineered Micromass Cartilage Pellet Cultures: Measurements and Modelling
February 18, 2016 Miranda C. Lewis, Ben D. MacArthur, Rahul S. Tare, Richard O. C. Oreffo, Colin P. Please
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10.1371/journal.pcbi.1004706

PLOS Computational Biology What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast
February 9, 2016 Artémis Llamosi, Andres Gonzalez-Vargas, Cristian Versari, Eugenio Cinquemani, Giancarlo Ferrari-Trecate, Pascal Hersen, Gregory Batt
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10.1371/journal.pone.0145829

PLOS ONE Single Cell Analysis of a Bacterial Sender-Receiver System
January 25, 2016 Tiago Ramalho, Andrea Meyer, Andrea Mückl, Korbinian Kapsner, Ulrich Gerland, Friedrich C. Simmel
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10.1371/journal.pcbi.1004674

PLOS Computational Biology Sources of Variability in a Synthetic Gene Oscillator
December 22, 2015 Alan Veliz-Cuba, Andrew J. Hirning, Adam A. Atanas, Faiza Hussain, Flavia Vancia, Krešimir Josić, Matthew R. Bennett
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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.pcbi.1000529

PLOS Computational Biology Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars
October 9, 2009 Yizhi Cai, Matthew W. Lux, Laura Adam, Jean Peccoud
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10.1371/journal.pone.0007002

PLOS ONE Design Parameters to Control Synthetic Gene Expression in Escherichia coli
September 14, 2009 Mark Welch, Sridhar Govindarajan, Jon E. Ness, Alan Villalobos, Austin Gurney, Jeremy Minshull, Claes Gustafsson
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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.0009376

PLOS ONE Statecharts for Gene Network Modeling
February 23, 2010 Yong-Jun Shin, Mehrdad Nourani
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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.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.0017005

PLOS ONE Standard Biological Parts Knowledgebase
February 24, 2011 Michal Galdzicki, Cesar Rodriguez, Deepak Chandran, Herbert Sauro, John Gennari
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10.1371/journal.pcbi.1002015

PLOS Computational Biology Autonomous Targeting of Infectious Superspreaders Using Engineered Transmissible Therapies
March 17, 2011 Vincent Metzger, James Lloyd-Smith, Leor Weinberger
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10.1371/journal.pone.0018882

PLOS ONE Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems
April 29, 2011 Lesia Bilitchenko, Adam Liu, Sherine Cheung, Emma Weeding, Bing Xia, Mariana Leguia, John Anderson, Douglas Densmore
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10.1371/journal.pone.0021414

PLOS ONE Rate-Independent Constructs for Chemical Computation
June 30, 2011 Phillip Senum, Marc Riedel
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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.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.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.pone.0022490

PLOS ONE Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks
August 5, 2011 Jacob Beal, Ting Lu, Ron Weiss
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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.1002218

PLOS Computational Biology Robust Signal Processing in Living Cells
November 17, 2011 Ralf Steuer, Steffen Waldherr, Victor Sourjik, Markus Kollmann
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10.1371/journal.pcbi.1002340

PLOS Computational Biology Genetic Co-Occurrence Network across Sequenced Microbes
December 29, 2011 Pan-Jun Kim, Nathan Price
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10.1371/journal.pcbi.1002344

PLOS Computational Biology Adjusting Phenotypes by Noise Control
January 12, 2012 Kyung Kim, Herbert Sauro
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10.1371/journal.pone.0031095

PLOS ONE Two Component Systems: Physiological Effect of a Third Component
February 17, 2012 Baldiri Salvado, Ester Vilaprinyo, Hiren Karathia, Albert Sorribas, Rui Alves
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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.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.pone.0034368

PLOS ONE Synthetic Biology: Mapping the Scientific Landscape
April 23, 2012 Paul Oldham, Stephen Hall, Geoff Burton
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10.1371/journal.pcbi.1002583

PLOS Computational Biology Quantifying and Analyzing the Network Basis of Genetic Complexity
July 5, 2012 Ethan Thompson, Timothy Galitski
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10.1371/journal.pcbi.1002579

PLOS Computational Biology Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity
July 19, 2012 Miles Miller, Marc Hafner, Eduardo Sontag, Noah Davidsohn, Sairam Subramanian, Priscilla Purnick, Douglas Lauffenburger, Ron Weiss
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10.1371/journal.pone.0042790

PLOS ONE BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology
August 24, 2012 Thomas Gorochowski, Antoni Matyjaszkiewicz, Thomas Todd, Neeraj Oak, Kira Kowalska, Stephen Reid, Krasimira Tsaneva-Atanasova, Nigel Savery, Claire Grierson, Mario di Bernardo
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10.1371/journal.pone.0047151

PLOS ONE Estimation and Discrimination of Stochastic Biochemical Circuits from Time-Lapse Microscopy Data
November 6, 2012 David Thorsley, Eric Klavins
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10.1371/journal.pcbi.1002888

PLOS Computational Biology Maximizing the Information Content of Experiments in Systems Biology
January 31, 2013 Juliane Liepe, Sarah Fiippi, Michal Komorowski, Michael Stumpf
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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.pcbi.1002934

PLOS Computational Biology Measurements of the Impact of 3′ End Sequences on Gene Expression Reveal Wide Range and Sequence Dependent Effects
March 7, 2013 Ophir Shalem, Lucas Carey, Danny Zeevi, Eilon Sharon, Leeat Keren, Adina Weinberger, Orna Dahan, Yitzhak Pilpel, Eran Segal
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10.1371/journal.pcbi.1002960

PLOS Computational Biology Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology
March 28, 2013 Tina Toni, Bruce Tidor
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10.1371/journal.pone.0060288

PLOS ONE Quantitative Design of Regulatory Elements Based on High-Precision Strength Prediction Using Artificial Neural Network
April 1, 2013 Hailin Meng, Jianfeng Wang, Zhiqiang Xiong, Feng Xu, Guoping Zhao, Yong Wang
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10.1371/journal.pcbi.1003110

PLOS Computational Biology A Design Principle of Group-level Decision Making in Cell Populations
June 27, 2013 Koichi Fujimoto, Satoshi Sawai
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10.1371/journal.pone.0081248

PLOS ONE How to Make a Synthetic Multicellular Computer
February 19, 2014 Javier Macia, Ricard Sole
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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.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.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.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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