Evolutionary systems biology: What it is and why it matters

Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance

(2013) Adam C. Palmer et al.   NATURE REVIEWS GENETICS

Robustness from flexibility in the fungal circadian clock

(2012) Ozgur E Akman et al.   BMC Systems Biology

On the Pleiotropic Structure of the Genotype-Phenotype Map and the Evolvability of Complex Organisms

(2012) W. G. Hill et al.   GENETICS

The Inheritance of Process: A Dynamical Systems Approach

(2012) Johannes Jaeger et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Bistability in feedback circuits as a byproduct of evolution of evolvability

(2012) Hiroyuki Kuwahara et al.   Molecular Systems Biology

Bet Hedging in Yeast by Heterogeneous, Age-Correlated Expression of a Stress Protectant

(2012) Sasha F. Levy et al.   PLOS BIOLOGY

Ecology and Evolution as Targets: the Need for Novel Eco-Evo Drugs and Strategies To Fight Antibiotic Resistance

(2011) Fernando Baquero et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Evolution of Gene Regulatory Networks Controlling Body Plan Development

(2011) Isabelle S. Peter et al.   CELL

Quantitative Variation in Autocrine Signaling and Pathway Crosstalk in the Caenorhabditis Vulval Network

(2011) Erika Hoyos et al.   CURRENT BIOLOGY

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

The sociobiology of molecular systems

(2011) Kevin R. Foster   NATURE REVIEWS GENETICS

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Systems-biology approaches for predicting genomic evolution

(2011) Balázs Papp et al.   NATURE REVIEWS GENETICS

Impact of gene expression noise on organismal fitness and the efficacy of natural selection

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

Second-Order Selection for Evolvability in a Large Escherichia coli Population

(2011) R. J. Woods et al.   SCIENCE

Bacteria-Phage Antagonistic Coevolution in Soil

(2011) P. Gomez et al.   SCIENCE

Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability

(2011) Kirsten H. ten Tusscher et al.   PLoS Computational Biology

Epistatic Interaction Maps Relative to Multiple Metabolic Phenotypes

(2011) Evan S. Snitkin et al.   PLoS Genetics

Predicting embryonic patterning using mutual entropy fitness and in silico evolution

(2010) P. Francois et al.   DEVELOPMENT

Prediction of putative protein interactions through evolutionary analysis of osmotic stress response in the model yeast Saccharomyces cerevisae

(2010) Thomas W. Thorne et al.   FUNGAL GENETICS AND BIOLOGY

The Evolution of the Phage Shock Protein Response System: Interplay between Protein Function, Genomic Organization, and System Function

(2010) M. Huvet et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

A computational model of teeth and the developmental origins of morphological variation

(2010) Isaac Salazar-Ciudad et al.   NATURE

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Rapid evolution of stability and productivity at the origin of a microbial mutualism

(2010) K. L. Hillesland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic patterns of pleiotropy and the evolution of complexity

(2010) Z. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origins and Diversification of a Complex Signal Transduction System in Prokaryotes

(2010) K. Wuichet et al.   Science Signaling

Unveiling the role of network and systems biology in drug discovery

(2010) Albert Pujol et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Evolution under Fluctuating Environments Explains Observed Robustness in Metabolic Networks

(2010) Orkun S. Soyer et al.   PLoS Computational Biology

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Specialization Can Drive the Evolution of Modularity

(2010) Carlos Espinosa-Soto et al.   PLoS Computational Biology

Shadows of complexity: what biological networks reveal about epistasis and pleiotropy

(2009) Anna L. Tyler et al.   BIOESSAYS

Phylogenetic diversity of stress signaling pathways in fungi

(2009) Elissavet Nikolaou et al.   BMC EVOLUTIONARY BIOLOGY

A framework for evolutionary systems biology

(2009) Laurence Loewe   BMC Systems Biology

Evolution of Stochastic Switching Rates in Asymmetric Fitness Landscapes

(2009) Marcel Salathé et al.   GENETICS

Abundant Indispensable Redundancies in Cellular Metabolic Networks

(2009) Zhi Wang et al.   Genome Biology and Evolution

Positive selection for elevated gene expression noise in yeast

(2009) Zhihua Zhang et al.   Molecular Systems Biology

Experimental evolution of bet hedging

(2009) Hubertus J. E. Beaumont et al.   NATURE

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

The evolution of hierarchical gene regulatory networks

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

A Developmental Systems Perspective on Epistasis: Computational Exploration of Mutational Interactions in Model Developmental Regulatory Networks

(2009) Jayson Gutiérrez   PLoS One

Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species

(2009) Pedro Beltrao et al.   PLOS BIOLOGY

Canalization of Gene Expression in the Drosophila Blastoderm by Gap Gene Cross Regulation

(2009) Manu et al.   PLOS BIOLOGY

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Parasites lead to evolution of robustness against gene loss in host signaling networks

(2008) Marcel Salathé et al.   Molecular Systems Biology

Neutralism and selectionism: a network-based reconciliation

(2008) Andreas Wagner   NATURE REVIEWS GENETICS

Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Evolution of Complex Modular Biological Networks

(2008) Arend Hintze et al.   PLoS Computational Biology

Network Evolution of Body Plans

(2008) Koichi Fujimoto et al.   PLoS One

Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution

(2008) F. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bet-hedging and epigenetic inheritance in bacterial cell development

(2008) J.-W. Veening et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale reconstruction and phylogenetic analysis of metabolic environments

(2008) E. Borenstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Taxis Responses in Virtual Bacteria: Non-Adaptive Dynamics

(2008) Richard A. Goldstein et al.   PLoS Computational Biology

Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments

(2008) Merav Parter et al.   PLoS Computational Biology

Regulatory Control and the Costs and Benefits of Biochemical Noise

(2008) Sorin Tănase-Nicola et al.   PLoS Computational Biology