The second wave of synthetic biology: from modules to systems

PEM Purnick, R Weiss - Nature reviews Molecular cell biology, 2009 - nature.com
Synthetic biology is a research field that combines the investigative nature of biology with
the constructive nature of engineering. Efforts in synthetic biology have largely focused on …

Computational modeling, formal analysis, and tools for systems biology

E Bartocci, P Lió - PLoS computational biology, 2016 - journals.plos.org
As the amount of biological data in the public domain grows, so does the range of modeling
and analysis techniques employed in systems biology. In recent years, a number of …

[图书][B] Formal methods for discrete-time dynamical systems

C Belta, B Yordanov, EA Gol - 2017 - Springer
In control theory, complex models of physical processes, such as systems of differential or
difference equations, are usually checked against simple specifications, such as stability …

Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels

SK Lee, H Chou, TS Ham, TS Lee… - Current opinion in …, 2008 - Elsevier
The ability to generate microorganisms that can produce biofuels similar to petroleum-based
transportation fuels would allow the use of existing engines and infrastructure and would …

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 …

Setting the standard in synthetic biology

A Arkin - Nature biotechnology, 2008 - nature.com
Setting the standard in synthetic biology | Nature Biotechnology Skip to main content Thank
you for visiting nature.com. You are using a browser version with limited support for CSS. To …

Precise parameter synthesis for stochastic biochemical systems

M Češka, F Dannenberg, N Paoletti, M Kwiatkowska… - Acta Informatica, 2017 - Springer
We consider the problem of synthesising rate parameters for stochastic biochemical
networks so that a given time-bounded CSL property is guaranteed to hold, or, in the case of …

[HTML][HTML] System design of stochastic models using robustness of temporal properties

E Bartocci, L Bortolussi, L Nenzi… - Theoretical Computer …, 2015 - Elsevier
Stochastic models such as Continuous-Time Markov Chains (CTMC) and Stochastic Hybrid
Automata (SHA) are powerful formalisms to model and to reason about the dynamics of …

A general computational method for robustness analysis with applications to synthetic gene networks

A Rizk, G Batt, F Fages, S Soliman - Bioinformatics, 2009 - academic.oup.com
Motivation: Robustness is the capacity of a system to maintain a function in the face of
perturbations. It is essential for the correct functioning of natural and engineered biological …

Formal guarantees in data-driven model identification and control synthesis

S Sadraddini, C Belta - … of the 21st International Conference on Hybrid …, 2018 - dl.acm.org
For many performance-critical control systems, an accurate (simple) model is not available
in practice. Thus, designing controllers with formal performance guarantees is challenging …