BioFNet: biological functional network database for analysis and synthesis of biological systems

From Systems to Structure: Bridging Networks and Mechanism

(2013) James S. Fraser et al.   MOLECULAR CELL

Design Principles of Regulatory Networks: Searching for the Molecular Algorithms of the Cell

(2013) Wendell A. Lim et al.   MOLECULAR CELL

Flux module decomposition for parameter estimation in a multiple-feedback loop model of biochemical networks

(2012) Kazuhiro Maeda et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

A model of spatially restricted transcription in opposing gradients of activators and repressors

(2012) Michael A White et al.   Molecular Systems Biology

A Feedback Quenched Oscillator Produces Turing Patterning with One Diffuser

(2012) Justin Hsia et al.   PLoS Computational Biology

Biological Design Principles of Complex Feedback Modules in theE. coliAmmonia Assimilation System

(2011) Koichi Masaki et al.   ARTIFICIAL LIFE

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

Emergence of Switch-Like Behavior in a Large Family of Simple Biochemical Networks

(2011) Dan Siegal-Gaskins et al.   PLoS Computational Biology

Simplified Models of Biological Networks

(2010) Kim Sneppen et al.   Annual Review of Biophysics

Functional Motifs in Biochemical Reaction Networks

(2010) John J. Tyson et al.   Annual Review of Physical Chemistry

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

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

An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks

(2010) Kazuhiro Maeda et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

Positive Autoregulation Shapes Response Timing and Intensity in Two-component Signal Transduction Systems

(2010) Alexander Y. Mitrophanov et al.   JOURNAL OF MOLECULAR BIOLOGY

An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients

(2010) James Cotterell et al.   Molecular Systems Biology

Build life to understand it

(2010) Michael Elowitz et al.   NATURE

Scaling of morphogen gradients by an expansion-repression integral feedback control

(2010) D. Ben-Zvi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bimodal gene expression in noncooperative regulatory systems

(2010) A. Ochab-Marcinek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fold-change detection and scalar symmetry of sensory input fields

(2010) O. Shoval et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population robustness arising from cellular heterogeneity

(2010) P. Paszek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BioModels.net Web Services, a free and integrated toolkit for computational modelling software

(2009) C. Li et al.   BRIEFINGS IN BIOINFORMATICS

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

Stochastic bimodalities in deterministically monostable reversible chemical networks due to network topology reduction

(2009) Maxim N. Artyomov et al.   JOURNAL OF CHEMICAL PHYSICS

Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues

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

The Effects of Reversibility and Noise on Stochastic Phosphorylation Cycles and Cascades

(2008) Clark A. Miller et al.   BIOPHYSICAL JOURNAL

Feedback regulation of opposing enzymes generates robust, all-or-none bistable responses

(2008) James E. Ferrell   CURRENT BIOLOGY

How noise statistics impact models of enzyme cycles

(2008) Aryeh Warmflash et al.   JOURNAL OF CHEMICAL PHYSICS

Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli

(2008) Yousuke Nishio et al.   Molecular Systems Biology

Setting the standard in synthetic biology

(2008) Adam Arkin   NATURE BIOTECHNOLOGY

Feedback Loops Shape Cellular Signals in Space and Time

(2008) O. Brandman et al.   SCIENCE