4.2 Review

Microbial evolution in vivo and in silico: methods and applications

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

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

Vadim Mozhayskiy et al.

BMC BIOINFORMATICS (2012)

Article Biochemistry & Molecular Biology

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

Herwig Bachmann et al.

GENOME RESEARCH (2012)

Article Genetics & Heredity

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

Erdal Toprak et al.

NATURE GENETICS (2012)

Article Multidisciplinary Sciences

The Molecular Diversity of Adaptive Convergence

Olivier Tenaillon et al.

SCIENCE (2012)

Article Microbiology

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

Mustafa Sen et al.

ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2011)

Article Computer Science, Artificial Intelligence

In Silico Evolution of Early Metabolism

Alexander Ullrich et al.

ARTIFICIAL LIFE (2011)

Article Genetics & Heredity

Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations

Gregory I. Lang et al.

GENETICS (2011)

Article Biochemical Research Methods

A Survey on Methods for Modeling and Analyzing Integrated Biological Networks

Nuno Tenazinha et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

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

Yu Deng et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2011)

Review Biochemistry & Molecular Biology

Microbial laboratory evolution in the era of genome-scale science

Tom M. Conrad et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Article Biochemistry & Molecular Biology

EcoCyc: a comprehensive database of Escherichia coli biology

Ingrid M. Keseler et al.

NUCLEIC ACIDS RESEARCH (2011)

Review Biochemistry & Molecular Biology

Mathematical descriptions of biochemical networks: Stability, stochasticity, evolution

Simon Rosenfeld

PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY (2011)

Article Mathematical & Computational Biology

The effects of low-impact mutations in digital organisms

Chase W. Nelson et al.

THEORETICAL BIOLOGY AND MEDICAL MODELLING (2011)

Article Genetics & Heredity

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

David B. Berry et al.

PLOS GENETICS (2011)

Correction Biotechnology & Applied Microbiology

Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol (vol 76, pg 4158, 2010)

Dae-Hee Lee et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2010)

Editorial Material Biochemistry & Molecular Biology

Genetic Adaptation: A New Piece for a Very Old Puzzle

John R. Roth

CURRENT BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

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

Dragana Stanley et al.

JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY (2010)

Article Biochemistry & Molecular Biology

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

Dafyd J. Jenkins et al.

JOURNAL OF MOLECULAR EVOLUTION (2010)

Article Biochemistry & Molecular Biology

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

Hani Goodarzi et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Article Biochemistry & Molecular Biology

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

Shota Atsumi et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Article Multidisciplinary Sciences

Mutational robustness can facilitate adaptation

Jeremy A. Draghi et al.

NATURE (2010)

Article Biochemistry & Molecular Biology

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

Ron Milo et al.

NUCLEIC ACIDS RESEARCH (2010)

Review Biology

Experimental evolution of viruses: Microviridae as a model system

Holly A. Wichman et al.

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

Review Biology

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

Rafael Sanjuan

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

Article Multidisciplinary Sciences

Individual histories and selection in heterogeneous populations

Stanislas Leibler et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Review Genetics & Heredity

Evolution of the mutation rate

Michael Lynch

TRENDS IN GENETICS (2010)

Article Biochemical Research Methods

Evolution of Gene Regulatory Networks by Fluctuating Selection and Intrinsic Constraints

Masaki E. Tsuda et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Article Computer Science, Artificial Intelligence

A New Model for Investigating the Evolution of Transcription Control Networks

Dafyd J. Jenkins et al.

ARTIFICIAL LIFE (2009)

Article Biochemical Research Methods

Antimony: a modular model definition language

Lucian P. Smith et al.

BIOINFORMATICS (2009)

Review Cell Biology

Evolving concepts in biofilm infections

Luanne Hall-Stoodley et al.

CELLULAR MICROBIOLOGY (2009)

Article Biotechnology & Applied Microbiology

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

Z. Petek Cakar et al.

JOURNAL OF BIOTECHNOLOGY (2009)

Article Ecology

The evolutionary dynamics of evolvability in a gene network model

J. Draghi et al.

JOURNAL OF EVOLUTIONARY BIOLOGY (2009)

Article Multidisciplinary Sciences

Snowdrift game dynamics and facultative cheating in yeast

Jeff Gore et al.

NATURE (2009)

Article Multidisciplinary Sciences

Adaptive prediction of environmental changes by microorganisms

Amir Mitchell et al.

NATURE (2009)

Article Multidisciplinary Sciences

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

Jeffrey E. Barrick et al.

NATURE (2009)

Review Genetics & Heredity

RNA-Seq: a revolutionary tool for transcriptomics

Zhong Wang et al.

NATURE REVIEWS GENETICS (2009)

Review Genetics & Heredity

ChIP-seq: advantages and challenges of a maturing technology

Peter J. Park

NATURE REVIEWS GENETICS (2009)

Review Genetics & Heredity

Stochastic modelling for quantitative description of heterogeneous biological systems

Darren J. Wilkinson

NATURE REVIEWS GENETICS (2009)

Review Microbiology

OPINION Do symbiotic bacteria subvert host immunity?

Lora V. Hooper

NATURE REVIEWS MICROBIOLOGY (2009)

Article Multidisciplinary Sciences

Synergy between pathogen release and resource availability in plant invasion

Dana Blumenthal et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

A feeling for the numbers in biology

Rob Phillips et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Genetics & Heredity

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

Pilar Domingo-Calap et al.

PLOS GENETICS (2009)

Article Biochemical Research Methods

TinkerCell: modular CAD tool for synthetic biology

Deepak Chandran et al.

Journal of Biological Engineering (2009)

Article Evolutionary Biology

The effect of genetic robustness on evolvability in digital organisms

Santiago F. Elena et al.

BMC EVOLUTIONARY BIOLOGY (2008)

Article Ecology

Evolution of evolvability in a developmental model

Jeremy Draghi et al.

EVOLUTION (2008)

Article Genetics & Heredity

Stochastic switching as a survival strategy in fluctuating environments

Murat Acar et al.

NATURE GENETICS (2008)

Review Cell Biology

Modelling and analysis of gene regulatory networks

Guy Karlebach et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2008)

Article Physics, Multidisciplinary

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

Arun Krishnan et al.

PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS (2008)

Article Genetics & Heredity

Protein under-wrapping causes dosage sensitivity and decreases gene duplicability

Han Liang et al.

PLOS GENETICS (2008)

Article Multidisciplinary Sciences

Bet-hedging and epigenetic inheritance in bacterial cell development

Jan-Willem Veening et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

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

Zachary D. Blount et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biology

Robustness and evolvability: a paradox resolved

Andreas Wagner

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2008)

Review Multidisciplinary Sciences

Stochasticity and cell fate

Richard Losick et al.

SCIENCE (2008)

Article Multidisciplinary Sciences

Predictive behavior within microbial genetic networks

Ilias Tagkopoulos et al.

SCIENCE (2008)

Article Mathematical & Computational Biology

Modelling Evolution of Regulatory Networks in Artificial Bacteria

Y. Sanchez-Dehesa et al.

MATHEMATICAL MODELLING OF NATURAL PHENOMENA (2008)

Article Biochemical Research Methods

Evolution of taxis responses in virtual bacteria: Non-adaptive dynamics

Richard A. Goldstein et al.

PLOS COMPUTATIONAL BIOLOGY (2008)

Article Biochemical Research Methods

Evolution of Evolvability in Gene Regulatory Networks

Anton Crombach et al.

PLOS COMPUTATIONAL BIOLOGY (2008)

Article Multidisciplinary Sciences

Cooperation and conflict in quorum-sensing bacterial populations

Stephen P. Diggle et al.

NATURE (2007)

Article Multidisciplinary Sciences

Innovation and robustness in complex regulatory gene networks

S. Ciliberti et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Varying environments can speed up evolution

Nadav Kashtan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Review Genetics & Heredity

The distribution of fitness effects of new mutations

Adam Eyre-Walker et al.

NATURE REVIEWS GENETICS (2007)

Article Multidisciplinary Sciences

An experimental test of evolutionary trade-offs during temperature adaptation

Albert F. Bennett et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Evolution of complexity in signaling pathways

Orkun S. Soyer et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Review Microbiology

Social evolution theory for microorganisms

Stuart A. West et al.

NATURE REVIEWS MICROBIOLOGY (2006)

Article Biology

Simulating the evolution of signal transduction pathways

Orkun S. Soyer et al.

JOURNAL OF THEORETICAL BIOLOGY (2006)

Article Multidisciplinary Sciences

Tests of parallel molecular evolution in a long-term experiment with Escherichia coli

Robert Woods et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biotechnology & Applied Microbiology

Network motifs: structure does not determine function

Piers J. Ingram et al.

BMC GENOMICS (2006)

Article Biology

Modelling the evolution of genetic regulatory networks

AP Quayle et al.

JOURNAL OF THEORETICAL BIOLOGY (2006)

Review Genetics & Heredity

Digital genetics: unravelling the genetic basis of evolution

C Adami

NATURE REVIEWS GENETICS (2006)

Article Ecology

Limits to adaptation in asexual populations

JAGM De Visser et al.

JOURNAL OF EVOLUTIONARY BIOLOGY (2005)

Review Genetics & Heredity

Stochasticity in gene expression:: From theories to phenotypes

M Kærn et al.

NATURE REVIEWS GENETICS (2005)

Article Biology

A feedforward loop motif in transcriptional regulation: induction and repression

F Hayot et al.

JOURNAL OF THEORETICAL BIOLOGY (2005)

Article Biotechnology & Applied Microbiology

Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae

ZP Çakar et al.

FEMS YEAST RESEARCH (2005)

Article Computer Science, Artificial Intelligence

Avida: A software platform for research in computational evolutionary biology

C Ofria et al.

ARTIFICIAL LIFE (2004)

Review Genetics & Heredity

Network biology:: Understanding the cell's functional organization

AL Barabási et al.

NATURE REVIEWS GENETICS (2004)

Article Multidisciplinary Sciences

Design of genetic networks with specified functions by evolution in silico

P François et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Multidisciplinary Sciences

Bacterial persistence as a phenotypic switch

NQ Balaban et al.

SCIENCE (2004)

Article Genetics & Heredity

Divergent adaptation of Escherichia coli to cyclic ultraviolet light exposures

D Alcántara-Díaz et al.

MUTAGENESIS (2004)

Article Multidisciplinary Sciences

Cooperation and competition in pathogenic bacteria

AS Griffin et al.

NATURE (2004)

Article Multidisciplinary Sciences

The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus

R Sanjuán et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Review Microbiology

Bacterial biofilms: prokaryotic adventures in multicellularity

JS Webb et al.

CURRENT OPINION IN MICROBIOLOGY (2003)

Review Biochemistry & Molecular Biology

Modeling transcriptional regulatory networks

H Bolouri et al.

BIOESSAYS (2002)

Article Multidisciplinary Sciences

Intrinsic and extrinsic contributions to stochasticity in gene expression

PS Swain et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Multidisciplinary Sciences

Stochastic gene expression in a single cell

MB Elowitz et al.

SCIENCE (2002)

Review Biochemical Research Methods

Modeling and simulation of genetic regulatory systems: A literature review

H De Jong

JOURNAL OF COMPUTATIONAL BIOLOGY (2002)

Article Biology

The small world inside large metabolic networks

A Wagner et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2001)

Article Multidisciplinary Sciences

Fitness effects of advantageous mutations in evolving Escherichia coli populations

M Imhof et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

Article Biology

Hypermutation in bacteria and other cellular systems

BA Bridges

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES (2001)

Article Multidisciplinary Sciences

The large-scale organization of metabolic networks

H Jeong et al.

NATURE (2000)

Review Neurosciences

Mathematical modeling of gene networks

P Smolen et al.

NEURON (2000)