Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

Unrelated toxin–antitoxin systems cooperate to induce persistence

(2015) Rick A. Fasani et al.   Journal of the Royal Society Interface

Design principles of a conditional futile cycle exploited for regulation

(2015) Dean A. Tolla et al.   Molecular BioSystems

Strategy Revealing Phenotypic Differences among Synthetic Oscillator Designs

(2014) Jason G. Lomnitz et al.   ACS Synthetic Biology

Phenotypic deconstruction of gene circuitry

(2013) Jason G. Lomnitz et al.   CHAOS

Molecular mechanisms of multiple toxin-antitoxin systems are coordinated to govern the persister phenotype

(2013) R. A. Fasani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A mechanism for robust circadian timekeeping via stoichiometric balance

(2012) Jae Kyoung Kim et al.   Molecular Systems Biology

Regulatory Design Governing Progression of Population Growth Phases in Bacteria

(2012) Agustino Martínez-Antonio et al.   PLoS One

Python for Scientists and Engineers

(2011) K. Jarrod Millman et al.   COMPUTING IN SCIENCE & ENGINEERING

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Parameter Estimation Using Metaheuristics in Systems Biology: A Comprehensive Review

(2011) Jianyong Sun et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Automated construction and analysis of the design space for biochemical systems

(2010) R. A. Fasani et al.   BIOINFORMATICS

Regulation of Aerobic-to-Anaerobic Transitions by the FNR Cycle in Escherichia coli

(2010) Dean A. Tolla et al.   JOURNAL OF MOLECULAR BIOLOGY

Phenotypic repertoire of the FNR regulatory network in Escherichia coli

(2010) Dean A. Tolla et al.   MOLECULAR MICROBIOLOGY

Qualitatively distinct phenotypes in the design space of biochemical systems

(2009) Michael A. Savageau et al.   FEBS LETTERS

A tunable synthetic mammalian oscillator

(2009) Marcel Tigges et al.   NATURE

Next-generation synthetic gene networks

(2009) Timothy K Lu et al.   NATURE BIOTECHNOLOGY

Synthetic biology: understanding biological design from synthetic circuits

(2009) Shankar Mukherji et al.   NATURE REVIEWS GENETICS

Phenotypes and tolerances in the design space of biochemical systems

(2009) M. A. Savageau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic Gene Networks That Count

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

Quantifying Global Tolerance of Biochemical Systems: Design Implications for Moiety-Transfer Cycles

(2009) Pedro M. B. M. Coelho et al.   PLoS Computational Biology

A fast, robust and tunable synthetic gene oscillator

(2008) Jesse Stricker et al.   NATURE