Multicriteria global optimization for biocircuit design

Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits

(2013) Mario Marchisio et al.   BMC Systems Biology

SBROME: A Scalable Optimization and Module Matching Framework for Automated Biosystems Design

(2013) Linh Huynh et al.   ACS Synthetic Biology

Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems

(2013) Pablo Szekely et al.   PLoS Computational Biology

Expanding the synthetic biology toolbox: engineering orthogonal regulators of gene expression

(2012) Christopher V Rao   CURRENT OPINION IN BIOTECHNOLOGY

Synthetic two-way communication between mammalian cells

(2012) William Bacchus et al.   NATURE BIOTECHNOLOGY

Computational tools for the synthetic design of biochemical pathways

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

Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming

(2012) Linh Huynh et al.   PLoS One

Multi-Criteria Optimization of Regulation in Metabolic Networks

(2012) Clara Higuera et al.   PLoS One

Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space

(2012) O. Shoval et al.   SCIENCE

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

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

Five hard truths for synthetic biology

(2010) Roberta Kwok   NATURE

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

An evolutionary method for complex-process optimization

(2009) Jose A. Egea et al.   COMPUTERS & OPERATIONS RESEARCH

Next-generation synthetic gene networks

(2009) Timothy K Lu et al.   NATURE BIOTECHNOLOGY

The second wave of synthetic biology: from modules to systems

(2009) Priscilla E. M. Purnick et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Computational design of synthetic gene circuits with composable parts

(2008) M.A. Marchisio et al.   BIOINFORMATICS

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

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

Extended ant colony optimization for non-convex mixed integer nonlinear programming

(2008) Martin Schlüter et al.   COMPUTERS & OPERATIONS RESEARCH

Refinement and standardization of synthetic biological parts and devices

(2008) Barry Canton et al.   NATURE BIOTECHNOLOGY

A Tabu search-based algorithm for mixed-integer nonlinear problems and its application to integrated process and control system design

(2007) Oliver Exler et al.   COMPUTERS & CHEMICAL ENGINEERING