Constraint and Contingency in Multifunctional Gene Regulatory Circuits

Protein Modularity, Cooperative Binding, and Hybrid Regulatory States Underlie Transcriptional Network Diversification

(2012) Christopher R. Baker et al.   CELL

Gene Regulatory Logic for Reading the Sonic Hedgehog Signaling Gradient in the Vertebrate Neural Tube

(2012) Nikolaos Balaskas et al.   CELL

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks

(2012) Naomi Habib et al.   Molecular Systems Biology

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Predictive computation of genomic logic processing functions in embryonic development

(2012) I. S. Peter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distributed computation: the new wave of synthetic biology devices

(2012) Javier Macía et al.   TRENDS IN BIOTECHNOLOGY

Quantifying and Analyzing the Network Basis of Genetic Complexity

(2012) Ethan G. Thompson et al.   PLoS Computational Biology

Evolution of Gene Regulatory Networks Controlling Body Plan Development

(2011) Isabelle S. Peter et al.   CELL

Functionality and metagraph disintegration in boolean networks

(2011) Jamie X. Luo et al.   JOURNAL OF THEORETICAL BIOLOGY

Genomic Sequence around Butterfly Wing Development Genes: Annotation and Comparative Analysis

(2011) Inês C. Conceição et al.   PLoS One

Motifs emerge from function in model gene regulatory networks

(2011) Z. Burda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epistasis can lead to fragmented neutral spaces and contingency in evolution

(2011) S. Schaper et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology

(2011) Baojun Wang et al.   Nature Communications

Information propagation within the Genetic Network of Saccharomyces cerevisiae

(2010) Sharif Chowdhury et al.   BMC Systems Biology

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

(2010) James Cotterell et al.   Molecular Systems Biology

Distributed biological computation with multicellular engineered networks

(2010) Sergi Regot et al.   NATURE

Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness

(2010) Margarita V. Meer et al.   NATURE

Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’

(2010) Alvin Tamsir et al.   NATURE

Evolution of Boolean networks under selection for a robust response to external inputs yields an extensive neutral space

(2010) Agnes Szejka et al.   PHYSICAL REVIEW E

Genetic flexibility of regulatory networks

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

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

Flexibility of transcription factor target site position in conserved cis-regulatory modules

(2009) R. Andrew Cameron et al.   DEVELOPMENTAL BIOLOGY

The evolution of hierarchical gene regulatory networks

(2009) Douglas H. Erwin et al.   NATURE REVIEWS GENETICS

Multifunctionality and Robustness Trade-Offs in Model Genetic Circuits

(2008) Olivier C. Martin et al.   BIOPHYSICAL JOURNAL

Design flexibility in cis-regulatory control of gene expression: Synthetic and comparative evidence

(2008) Louisa M. Liberman et al.   DEVELOPMENTAL BIOLOGY

Diverse Two-Dimensional Input Functions Control Bacterial Sugar Genes

(2008) Shai Kaplan et al.   MOLECULAR CELL

A fast, robust and tunable synthetic gene oscillator

(2008) Jesse Stricker et al.   NATURE

Evolvability and hierarchy in rewired bacterial gene networks

(2008) Mark Isalan et al.   NATURE

Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback

(2008) Gil Hornung et al.   PLoS Computational Biology

Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms

(2008) Enrique Balleza et al.   PLoS One

Gene expression dynamics in the macrophage exhibit criticality

(2008) M. Nykter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust, Tunable Biological Oscillations from Interlinked Positive and Negative Feedback Loops

(2008) T. Y.-C. Tsai et al.   SCIENCE

Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition

(2008) Andreea Munteanu et al.   PLoS Computational Biology

Robustness and evolvability: a paradox resolved

(2007) A. Wagner   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES