A computational method for the investigation of multistable systems and its application to genetic switches

Genetic circuit design automation

(2016) A. A. K. Nielsen et al.   SCIENCE

A Statistical Approach Reveals Designs for the Most Robust Stochastic Gene Oscillators

(2016) Mae L. Woods et al.   ACS Synthetic Biology

Quantifying cellular capacity identifies gene expression designs with reduced burden

(2015) Francesca Ceroni et al.   NATURE METHODS

Genetic Toggle Switch in the Absence of Cooperative Binding: Exact Results

(2015) Tommaso Biancalani et al.   PHYSICAL REVIEW LETTERS

Modularity, context-dependence, and insulation in engineered biological circuits

(2015) Domitilla Del Vecchio   TRENDS IN BIOTECHNOLOGY

Multistable switches and their role in cellular differentiation networks

(2014) Ahmadreza Ghaffarizadeh et al.   BMC BIOINFORMATICS

Multicriteria global optimization for biocircuit design

(2014) Irene Otero-Muras et al.   BMC Systems Biology

Construction of an Effective Landscape for Multistate Genetic Switches

(2014) Mingyang Lu et al.   PHYSICAL REVIEW LETTERS

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

(2013) Alec AK Nielsen et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Tristability in Cancer-Associated MicroRNA-TF Chimera Toggle Switch

(2013) Mingyang Lu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Precise and reliable gene expression via standard transcription and translation initiation elements

(2013) Vivek K Mutalik et al.   NATURE METHODS

Contextualizing context for synthetic biology - identifying causes of failure of synthetic biological systems

(2012) Stefano Cardinale et al.   Biotechnology Journal

Iterative plug-and-play methodology for constructing and modifying synthetic gene networks

(2012) Kevin D Litcofsky et al.   NATURE METHODS

Small-Number Effects: A Third Stable State in a Genetic Bistable Toggle Switch

(2012) Rui Ma et al.   PHYSICAL REVIEW LETTERS

Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks

(2012) Fusun Yaman et al.   ACS Synthetic Biology

An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications

(2012) Jacob Beal et al.   ACS Synthetic Biology

Hybrid Models and Biological Model Reduction with PyDSTool

(2012) Robert Clewley   PLoS Computational Biology

A genetic bistable switch utilizing nonlinear protein degradation

(2012) Daniel Huang et al.   Journal of Biological Engineering

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

(2011) Guillermo Rodrigo et al.   NUCLEIC ACIDS RESEARCH

Standard Biological Parts Knowledgebase

(2011) Michal Galdzicki et al.   PLoS One

Bayesian design of synthetic biological systems

(2011) C. P. Barnes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch

(2010) Chunbo Lou et al.   Molecular Systems Biology

A tunable synthetic mammalian oscillator

(2009) Marcel Tigges et al.   NATURE

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

Next-generation synthetic gene networks

(2009) Timothy K Lu et al.   NATURE BIOTECHNOLOGY

Synthetic Gene Networks That Count

(2009) A. E. Friedland et al.   SCIENCE

Measuring the activity of BioBrick promoters using an in vivo reference standard

(2009) Jason R Kelly et al.   Journal of Biological Engineering

Bistability, Epigenetics, and Bet-Hedging in Bacteria

(2008) Jan-Willem Veening et al.   Annual Review of Microbiology

LibSBML: an API Library for SBML

(2008) B. J. Bornstein et al.   BIOINFORMATICS

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

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

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

(2008) T. Toni et al.   Journal of the Royal Society Interface

A fast, robust and tunable synthetic gene oscillator

(2008) Jesse Stricker et al.   NATURE

Refinement and standardization of synthetic biological parts and devices

(2008) Barry Canton et al.   NATURE BIOTECHNOLOGY

Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory

(2008) Timothy S. Ham et al.   PLoS One

Multistable Decision Switches for Flexible Control of Epigenetic Differentiation

(2008) Raúl Guantes et al.   PLoS Computational Biology

Engineering BioBrick vectors from BioBrick parts

(2008) Reshma P Shetty et al.   Journal of Biological Engineering