Table of Contents: Synthetic Biology Collection: Software & Modeling


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

Articles in the Synthetic Biology Collection are presented in order of publication date and new articles will be added as they are published. PLOS welcome submissions in this field.

PLOS Collections:

Research Articles

Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems

Samanthe M. Lyons, Wenlong Xu, June Medford, Ashok Prasad

Biological Signal Processing with a Genetic Toggle Switch

Patrick Hillenbrand, Georg Fritz, Ulrich Gerland

Measurements of the Impact of 3′ End Sequences on Gene Expression Reveal Wide Range and Sequence Dependent Effects

Ophir Shalem, Lucas Carey, Danny Zeevi, Eilon Sharon, Leeat Keren, Adina Weinberger, Orna Dahan, Yitzhak Pilpel, Eran Segal

A Formalized Design Process for Bacterial Consortia That Perform Logic Computing

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

Maximizing the Information Content of Experiments in Systems Biology

Juliane Liepe, Sarah Filippi, Michał Komorowski, Michael P. H. Stumpf

BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology

Thomas E. Gorochowski, Antoni Matyjaszkiewicz, Thomas Todd, Neeraj Oak, Kira Kowalska, Stephen Reid, Krasimira T. Tsaneva-Atanasova, Nigel J. Savery, Claire S. Grierson, Mario di Bernardo

Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity

Miles Miller, Marc Hafner, Eduardo Sontag, Noah Davidsohn, Sairam Subramanian, Priscilla E. M. Purnick, Douglas Lauffenburger, Ron Weiss

Synthetic Biology: Mapping the Scientific Landscape

Paul Oldham, Stephen Hall, Geoff Burton

Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit

Dmitry Nevozhay, Rhys M. Adams, Elizabeth Van Itallie, Matthew R. Bennett, Gábor Balázsi

Two Component Systems: Physiological Effect of a Third Component

Baldiri Salvado, Ester Vilaprinyo, Hiren Karathia, Albert Sorribas, Rui Alves

A Feedback Quenched Oscillator Produces Turing Patterning with One Diffuser

Justin Hsia, William J. Holtz, Daniel C. Huang, Murat Arcak, Michel M. Maharbiz

Adjusting Phenotypes by Noise Control

Kyung H. Kim, Herbert M. Sauro

Robust Signal Processing in Living Cells

Ralf Steuer, Steffen Waldherr, Victor Sourjik, Markus Kollmann

Stochastic Delay Accelerates Signaling in Gene Networks

Krešimir Josić, José Manuel López, William Ott, LieJune Shiau, Matthew R. Bennett

Construction and Modelling of an Inducible Positive Feedback Loop Stably Integrated in a Mammalian Cell-Line

Velia Siciliano, Filippo Menolascina, Lucia Marucci, Chiara Fracassi, Immacolata Garzilli, Maria Nicoletta Moretti, Diego di Bernardo

Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems

Lesia Bilitchenko, Adam Liu, Sherine Cheung, Emma Weeding, Bing Xia, Mariana Leguia, J. Christopher Anderson, Douglas Densmore

Autonomous Targeting of Infectious Superspreaders Using Engineered Transmissible Therapies

Vincent T. Metzger, James O. Lloyd-Smith, Leor S. Weinberger

Standard Biological Parts Knowledgebase

Michal Galdzicki, Cesar Rodriguez, Deepak Chandran, Herbert M. Sauro, John H. Gennari

Automatic Design of Digital Synthetic Gene Circuits

Mario A. Marchisio, Jörg Stelling

A Multi-Functional Synthetic Gene Network: A Frequency Multiplier, Oscillator and Switch

Oliver Purcell, Mario di Bernardo, Claire S. Grierson, Nigel J. Savery

Programmable Ligand Detection System in Plants through a Synthetic Signal Transduction Pathway

Mauricio S. Antunes, Kevin J. Morey, J. Jeff Smith, Kirk D. Albrecht, Tessa A. Bowen, Jeffrey K. Zdunek, Jared F. Troupe, Matthew J. Cuneo, Colleen T. Webb, Homme W. Hellinga, June I. Medford

Statecharts for Gene Network Modeling

Yong-Jun Shin, Mehrdad Nourani

How to Turn a Genetic Circuit into a Synthetic Tunable Oscillator, or a Bistable Switch

Lucia Marucci, David A. W. Barton, Irene Cantone, Maria Aurelia Ricci, Maria Pia Cosma, Stefania Santini, Diego di Bernardo, Mario di Bernardo

Design Parameters to Control Synthetic Gene Expression in Escherichia coli

Mark Welch, Sridhar Govindarajan, Jon E. Ness, Alan Villalobos, Austin Gurney, Jeremy Minshull, Claes Gustafsson

Monomeric Bistability and the Role of Autoloops in Gene Regulation

Stefanie Widder, Javier Macía, Ricard Solé

Timing Cellular Decision Making Under Noise via Cell–Cell Communication

Aneta Koseska, Alexey Zaikin, Jürgen Kurths, Jordi García-Ojalvo