Microbial evolution in vivo and in silico: methods and applications

Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation

(2012) Vadim Mozhayskiy et al.   BMC BIOINFORMATICS

Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution

(2012) Vadim Mozhayskiy et al.   BMC BIOINFORMATICS

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

In vivo evolutionary engineering of a boron-resistant bacterium: Bacillus boroniphilus

(2011) Mustafa Şen et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

In Silico Evolution of Early Metabolism

(2011) Alexander Ullrich et al.   ARTIFICIAL LIFE

Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations

(2011) Gregory I. Lang et al.   GENETICS

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution

(2011) H. Bachmann et al.   GENOME RESEARCH

Laboratory Evolution and Multi-platform Genome Re-sequencing of the Cellulolytic ActinobacteriumThermobifida fusca

(2011) Yu Deng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Microbial laboratory evolution in the era of genome-scale science

(2011) T. M. Conrad et al.   Molecular Systems Biology

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

Mathematical descriptions of biochemical networks: Stability, stochasticity, evolution

(2011) Simon Rosenfeld   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

The effects of low-impact mutations in digital organisms

(2011) Chase W Nelson et al.   Theoretical Biology and Medical Modelling

Multiple Means to the Same End: The Genetic Basis of Acquired Stress Resistance in Yeast

(2011) David B. Berry et al.   PLoS Genetics

Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol

(2010) D.-H. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Scaling laws in bacterial genomes: A side-effect of selection of mutational robustness?

(2010) G. Beslon et al.   BIOSYSTEMS

Genetic Adaptation: A New Piece for a Very Old Puzzle

(2010) John R. Roth   CURRENT BIOLOGY

Distribution of Fitness Effects Caused by Single-Nucleotide Substitutions in Bacteriophage f1

(2010) J. B. Peris et al.   GENETICS

A Survey on Methods for Modeling and Analyzing Integrated Biological Networks

(2010) N Tenazinha et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Stochasticity Versus Determinism: Consequences for Realistic Gene Regulatory Network Modelling and Evolution

(2010) Dafyd J. Jenkins et al.   JOURNAL OF MOLECULAR EVOLUTION

Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli

(2010) Hani Goodarzi et al.   Molecular Systems Biology

Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli

(2010) Shota Atsumi et al.   Molecular Systems Biology

Mutational robustness can facilitate adaptation

(2010) Jeremy A. Draghi et al.   NATURE

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Experimental evolution of viruses: Microviridae as a model system

(2010) H. A. Wichman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies

(2010) R. Sanjuan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Individual histories and selection in heterogeneous populations

(2010) S. Leibler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

Parallel Evolution in Pseudomonas aeruginosa over 39,000 Generations In Vivo

(2010) H. K. Huse et al.   mBio

Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints

(2010) Masaki E. Tsuda et al.   PLoS Computational Biology

Transition from Positive to Neutral in Mutation Fixation along with Continuing Rising Fitness in Thermal Adaptive Evolution

(2010) Toshihiko Kishimoto et al.   PLoS Genetics

Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene

(2010) Pep Charusanti et al.   PLoS Genetics

A New Model for Investigating the Evolution of Transcription Control Networks

(2009) Dafyd J. Jenkins et al.   ARTIFICIAL LIFE

Antimony: a modular model definition language

(2009) L. P. Smith et al.   BIOINFORMATICS

Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coli

(2009) Mark T Stanek et al.   BMC EVOLUTIONARY BIOLOGY

Evolving concepts in biofilm infections

(2009) Luanne Hall-Stoodley et al.   CELLULAR MICROBIOLOGY

Isolation of cobalt hyper-resistant mutants of Saccharomyces cerevisiae by in vivo evolutionary engineering approach

(2009) Z. Petek Çakar et al.   JOURNAL OF BIOTECHNOLOGY

Generation and characterisation of stable ethanol-tolerant mutants of Saccharomyces cerevisiae

(2009) Dragana Stanley et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Snowdrift game dynamics and facultative cheating in yeast

(2009) Jeff Gore et al.   NATURE

Adaptive prediction of environmental changes by microorganisms

(2009) Amir Mitchell et al.   NATURE

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Stochastic modelling for quantitative description of heterogeneous biological systems

(2009) Darren J. Wilkinson   NATURE REVIEWS GENETICS

Do symbiotic bacteria subvert host immunity?

(2009) Lora V. Hooper   NATURE REVIEWS MICROBIOLOGY

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

Synergy between pathogen release and resource availability in plant invasion

(2009) D. Blumenthal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A feeling for the numbers in biology

(2009) R. Phillips et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Fitness Effects of Random Mutations in Single-Stranded DNA and RNA Bacteriophages

(2009) Pilar Domingo-Calap et al.   PLoS Genetics

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

(2009) Tom M Conrad et al.   GENOME BIOLOGY

TinkerCell: modular CAD tool for synthetic biology

(2009) Deepak Chandran et al.   Journal of Biological Engineering

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

The effect of genetic robustness on evolvability in digital organisms

(2008) Santiago F Elena et al.   BMC EVOLUTIONARY BIOLOGY

EVOLUTION OF EVOLVABILITY IN A DEVELOPMENTAL MODEL

(2008) Jeremy Draghi et al.   EVOLUTION

Genetic Basis of Evolutionary Adaptation by Escherichia coli to Stressful Cycles of Freezing, Thawing and Growth

(2008) S. C. Sleight et al.   GENETICS

The evolutionary dynamics of evolvability in a gene network model

(2008) J. DRAGHI et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Stochastic switching as a survival strategy in fluctuating environments

(2008) Murat Acar et al.   NATURE GENETICS

Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae

(2008) Katy C Kao et al.   NATURE GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Protein Under-Wrapping Causes Dosage Sensitivity and Decreases Gene Duplicability

(2008) Han Liang et al.   PLoS Genetics

Expression Profiles Reveal Parallel Evolution of Epistatic Interactions Involving the CRP Regulon in Escherichia coli

(2008) Tim F. Cooper et al.   PLoS Genetics

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

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

(2008) Z. D. Blount et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stochasticity and Cell Fate

(2008) R. Losick et al.   SCIENCE

Predictive Behavior Within Microbial Genetic Networks

(2008) I. Tagkopoulos et al.   SCIENCE

Modelling Evolution of Regulatory Networks in Artificial Bacteria

(2008) Y. Sanchez-Dehesa et al.   Mathematical Modelling of Natural Phenomena

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

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

Evolution of Evolvability in Gene Regulatory Networks

(2008) Anton Crombach et al.   PLoS Computational Biology

Evolution of gene regulatory networks: Robustness as an emergent property of evolution

(2007) Arun Krishnan et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Robustness and evolvability: a paradox resolved

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