Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case

An interactive decision-support system for multi-objective optimization of nonlinear dynamic processes with uncertainty

(2015) Mattia Vallerio et al.   EXPERT SYSTEMS WITH APPLICATIONS

Simplified mechanistic models of gene regulation for analysis and design

(2015) Edward J. Hancock et al.   Journal of the Royal Society Interface

Modelado de sistemas bioquímicos: De la Ley de Acción de Masas a la Aproximación Lineal del Ruido

(2015) Jesús Picó et al.   Revista Iberoamericana de Automatica e Informatica Industrial

Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters

(2014) Austin WT Chiang et al.   BMC Systems Biology

Integrating Biological Redesign: Where Synthetic Biology Came From and Where It Needs to Go

(2014) Jeffrey C. Way et al.   CELL

Controller tuning using evolutionary multi-objective optimisation: Current trends and applications

(2014) Gilberto Reynoso-Meza et al.   CONTROL ENGINEERING PRACTICE

Equilibrium distributions of simple biochemical reaction systems for time-scale separation in stochastic reaction networks

(2014) B. Melykuti et al.   Journal of the Royal Society Interface

Layered decomposition for the model order reduction of timescale separated biochemical reaction networks

(2014) Thomas P. Prescott et al.   JOURNAL OF THEORETICAL BIOLOGY

Dynamic circuit motifs underlying rhythmic gain control, gating and integration

(2014) Thilo Womelsdorf et al.   NATURE NEUROSCIENCE

Realizing the potential of synthetic biology

(2014) George M. Church et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

BioModels: ten-year anniversary

(2014) Vijayalakshmi Chelliah et al.   NUCLEIC ACIDS RESEARCH

Synthetic circuit for exact adaptation and fold-change detection

(2014) Jongmin Kim et al.   NUCLEIC ACIDS RESEARCH

Negative Autoregulation Matches Production and Demand in Synthetic Transcriptional Networks

(2014) Elisa Franco et al.   ACS Synthetic Biology

A Low Cost, Customizable Turbidostat for Use in Synthetic Circuit Characterization

(2014) Chris N. Takahashi et al.   ACS Synthetic Biology

Design and Implementation of a Biomolecular Concentration Tracker

(2014) Victoria Hsiao et al.   ACS Synthetic Biology

Noise Propagation in Synthetic Gene Circuits for Metabolic Control

(2014) Diego A. Oyarzún et al.   ACS Synthetic Biology

An integrated approach to automated innovization for discovering useful design principles: Case studies from engineering

(2013) Kalyanmoy Deb et al.   APPLIED SOFT COMPUTING

A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits

(2013) Austin WT Chiang et al.   BMC BIOINFORMATICS

Dynamics of the quorum sensing switch: stochastic and non-stationary effects

(2013) Marc Weber et al.   BMC Systems Biology

Tuning the dials of Synthetic Biology

(2013) J. A. J. Arpino et al.   MICROBIOLOGY-SGM

Retroactivity Controls the Temporal Dynamics of Gene Transcription

(2013) Shridhar Jayanthi et al.   ACS Synthetic Biology

Ultrasensitive response motifs: basic amplifiers in molecular signalling networks

(2013) Q. Zhang et al.   Open Biology

Model-based design of synthetic, biological systems

(2012) Nathan Crook et al.   CHEMICAL ENGINEERING SCIENCE

Multiobjective evolutionary algorithms for multivariable PI controller design

(2012) Gilberto Reynoso-Meza et al.   EXPERT SYSTEMS WITH APPLICATIONS

Perspectives on the automatic design of regulatory systems for synthetic biology

(2012) Guillermo Rodrigo et al.   FEBS LETTERS

Controller Tuning by Means of Multi-Objective Optimization Algorithms: A Global Tuning Framework

(2012) Gilberto Reynoso-Meza et al.   IEEE TRANSACTIONS ON CONTROL SYSTEMS TECHNOLOGY

Comparison of design concepts in multi-criteria decision-making using level diagrams

(2012) Gilberto Reynoso-Meza et al.   INFORMATION SCIENCES

Computational tools for the synthetic design of biochemical pathways

(2012) Marnix H. Medema et al.   NATURE REVIEWS MICROBIOLOGY

Fine-tuning gene networks using simple sequence repeats

(2012) R. G. Egbert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design principles of cell circuits with paradoxical components

(2012) Y. Hart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Miles Miller et al.   PLoS Computational Biology

Model decomposition and reduction tools for large-scale networks in systems biology

(2011) James Anderson et al.   AUTOMATICA

Structural Discrimination of Robustness in Transcriptional Feedforward Loops for Pattern Formation

(2011) Guillermo Rodrigo et al.   PLoS One

Automatic Design of Digital Synthetic Gene Circuits

(2011) Mario A. Marchisio et al.   PLoS Computational Biology

Standard virtual biological parts: a repository of modular modeling components for synthetic biology

(2010) M. T. Cooling et al.   BIOINFORMATICS

Multi-objective mixed integer strategy for the optimisation of biological networks

(2010) J.O.H. Sendín et al.   IET Systems Biology

Switchable genetic oscillator operating in quasi-stable mode

(2010) N. Strelkowa et al.   Journal of the Royal Society Interface

Considerations for using integral feedback control to construct a perfectly adapting synthetic gene network

(2010) Jordan Ang et al.   JOURNAL OF THEORETICAL BIOLOGY

Editorial scalability of evolutionary algorithms and other metaheuristics for large-scale continuous optimization problems

(2010) M. Lozano et al.   SOFT COMPUTING

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation

(2009) Lea Goentoro et al.   MOLECULAR CELL

Diversity-based, model-guided construction of synthetic gene networks with predicted functions

(2009) Tom Ellis et al.   NATURE BIOTECHNOLOGY

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

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

(2008) Madhukar S Dasika et al.   BMC Systems Biology

Optimization in computational systems biology

(2008) Julio R Banga   BMC Systems Biology

Synthetic biology: discovering new worlds and new words. The new and not so new aspects of this emerging research field

(2008) Víctor de Lorenzo et al.   EMBO REPORTS

A new graphical visualization of n-dimensional Pareto front for decision-making in multiobjective optimization

(2008) X. Blasco et al.   INFORMATION SCIENCES

Refinement and standardization of synthetic biological parts and devices

(2008) Barry Canton et al.   NATURE BIOTECHNOLOGY