Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors

G Rodrigo, J Carrera, A Jaramillo - Nucleic acids research, 2011 - academic.oup.com
The engineering of synthetic gene networks has mostly relied on the assembly of few
characterized regulatory elements using rational design principles. It is of outmost …

OptCircuit: an optimization based method for computational design of genetic circuits

MS Dasika, CD Maranas - BMC systems biology, 2008 - Springer
Background Recent years has witnessed an increasing number of studies on constructing
simple synthetic genetic circuits that exhibit desired properties such as oscillatory behavior …

AutoBioCAD: full biodesign automation of genetic circuits

G Rodrigo, A Jaramillo - ACS synthetic biology, 2013 - ACS Publications
Synthetic regulatory networks with prescribed functions are engineered by assembling a
reduced set of functional elements. We could also assemble them computationally if the …

Foundations for the design and implementation of synthetic genetic circuits

AL Slusarczyk, A Lin, R Weiss - Nature Reviews Genetics, 2012 - nature.com
Synthetic gene circuits are designed to program new biological behaviour, dynamics and
logic control. For all but the simplest synthetic phenotypes, this requires a structured …

Design of genetic networks with specified functions by evolution in silico

P François, V Hakim - … of the National Academy of Sciences, 2004 - National Acad Sciences
Recent studies have provided insights into the modular structure of genetic regulatory
networks and emphasized the interest of quantitative functional descriptions. Here, to …

Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression

AAK Nielsen, TH Segall-Shapiro, CA Voigt - Current opinion in chemical …, 2013 - Elsevier
Highlights•We review recent advances in the forward design of genetic circuits.•Advanced
circuit design concepts pave the way for more complex synthetic cellular regulation.•Part …

Designing biological circuits: from principles to applications

D Chakraborty, R Rengaswamy… - ACS Synthetic Biology, 2022 - ACS Publications
Genetic circuit design is a well-studied problem in synthetic biology. Ever since the first
genetic circuits─ the repressilator and the toggle switch─ were designed and implemented …

A comparative analysis of synthetic genetic oscillators

O Purcell, NJ Savery, CS Grierson… - Journal of The …, 2010 - royalsocietypublishing.org
Synthetic biology is a rapidly expanding discipline at the interface between engineering and
biology. Much research in this area has focused on gene regulatory networks that function …

Engineering and applications of genetic circuits

DJ Sayut, PKR Kambam, L Sun - Molecular BioSystems, 2007 - pubs.rsc.org
In the field of synthetic biology, recent genetic engineering efforts have enabled the
construction of novel genetic circuits with diverse functionalities and unique activation …

Strategy revealing phenotypic differences among synthetic oscillator designs

JG Lomnitz, MA Savageau - ACS synthetic biology, 2014 - ACS Publications
Considerable progress has been made in identifying and characterizing the component
parts of genetic oscillators, which play central roles in all organisms. Nonlinear interaction …