A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

Know your neighbor: Microbiota and host epithelial cells interact locally to control intestinal function and physiology

(2016) Felix Sommer et al.   BIOESSAYS

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments

(2015) Elizabeth R Jerison et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Simple Phenotypic Sweeps Hide Complex Genetic Changes in Populations

(2015) Ram P. Maharjan et al.   Genome Biology and Evolution

Elucidating the molecular architecture of adaptation via evolve and resequence experiments

(2015) Anthony Long et al.   NATURE REVIEWS GENETICS

Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria

(2015) João Barroso-Batista et al.   Nature Communications

Where Next for Microbiome Research?

(2015) Matthew K. Waldor et al.   PLOS BIOLOGY

Coordinated Evolution of Influenza A Surface Proteins

(2015) Alexey D. Neverov et al.   PLoS Genetics

The rule of declining adaptability in microbial evolution experiments

(2015) Alejandro Couce et al.   Frontiers in Genetics

The functional basis of adaptive evolution in chemostats

(2014) David Gresham et al.   FEMS MICROBIOLOGY REVIEWS

Mining the Human Gut Microbiota for Effector Strains that Shape the Immune System

(2014) Philip P. Ahern et al.   IMMUNITY

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

More than a Gut Feeling: the Microbiota Regulates Neurodevelopment and Behavior

(2014) John F Cryan et al.   NEUROPSYCHOPHARMACOLOGY

Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli

(2014) J. Plucain et al.   SCIENCE

The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps

(2014) João Barroso-Batista et al.   PLoS Genetics

Mapping the Fitness Landscape of Gene Expression Uncovers the Cause of Antagonism and Sign Epistasis between Adaptive Mutations

(2014) Hsin-Hung Chou et al.   PLoS Genetics

Rates of transposition in Escherichia coli

(2013) A. Sousa et al.   Biology Letters

SIGN EPISTASIS LIMITS EVOLUTIONARY TRADE-OFFS AT THE CONFLUENCE OF SINGLE- AND MULTI-CARBON METABOLISM INMETHYLOBACTERIUM EXTORQUENSAM1

(2013) Sean Michael Carroll et al.   EVOLUTION

The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally

(2013) Dan M. Park et al.   PLoS Genetics

Bacterial Adaptation through Loss of Function

(2013) Alison K. Hottes et al.   PLoS Genetics

Evolution of clonal populations approaching a fitness peak

(2012) I. Gordo et al.   Biology Letters

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

The multiplicity of divergence mechanisms in a single evolving population

(2012) Ram P Maharjan et al.   GENOME BIOLOGY

Anaerobic Respiration of Escherichia coli in the Mouse Intestine

(2011) Shari A. Jones et al.   INFECTION AND IMMUNITY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The causes of epistasis

(2011) J. A. G. M. de Visser et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

Epistasis between Beneficial Mutations and the Phenotype-to-Fitness Map for a ssDNA Virus

(2011) Darin R. Rokyta et al.   PLoS Genetics

Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models

(2010) C. R. Miller et al.   GENETICS

EcoCyc: a comprehensive database of Escherichia coli biology

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

Fluctuation AnaLysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis

(2009) B. M. Hall et al.   BIOINFORMATICS

The Genetic Basis of Phenotypic Adaptation II: The Distribution of Adaptive Substitutions in the Moving Optimum Model

(2009) Michael Kopp et al.   GENETICS

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

(2009) Jeffrey E. Barrick et al.   NATURE

From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation

(2009) Ville Mustonen et al.   TRENDS IN GENETICS

The Properties of Adaptive Walks in Evolving Populations of Fungus

(2009) Sijmen E. Schoustra et al.   PLOS BIOLOGY

Toward the Use of Genomics to Study Microevolutionary Change in Bacteria

(2009) Daniel Falush   PLoS Genetics