Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination

Light and shadow on the mechanisms of integration site selection in yeast Ty retrotransposon families

(2021) Amandine Bonnet et al.   CURRENT GENETICS

Fluctuating Environments Maintain Genetic Diversity through Neutral Fitness Effects and Balancing Selection

(2021) Farah Abdul-Rahman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Species-Wide Transposable Element Repertoires Retrace the Evolutionary History of the Saccharomyces cerevisiae Host

(2021) Claudine Bleykasten-Grosshans et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic impact of stress-induced transposable element mobility in Arabidopsis

(2021) David Roquis et al.   NUCLEIC ACIDS RESEARCH

New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources

(2021) Stacia R Engel et al.   GENETICS

Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination

(2020) Wioletta Czaja et al.   PLoS Genetics

Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy

(2020) Pieter Spealman et al.   NUCLEIC ACIDS RESEARCH

Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective

(2020) Patrick H. Maxwell   Mobile DNA

Stress-driven transposable element de-repression dynamics and virulence evolution in a fungal pathogen

(2019) Simone Fouché et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hidden Complexity of Yeast Adaptation under Simple Evolutionary Conditions

(2018) Yuping Li et al.   CURRENT BIOLOGY

An incoherent feedforward loop facilitates adaptive tuning of gene expression

(2018) Jungeui Hong et al.   eLife

Experimental Evolution as a High-Throughput Screen for Genetic Adaptations

(2018) Vaughn S. Cooper   mSphere

Transposable element insertions in fission yeast drive adaptation to environmental stress

(2018) Caroline Esnault et al.   GENOME RESEARCH

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

(2018) Stephanie Lauer et al.   PLOS BIOLOGY

The dynamics of adaptive genetic diversity during the early stages of clonal evolution

(2018) Jamie R. Blundell et al.   Nature Ecology & Evolution

Ribosome Biogenesis Modulates Ty1 Copy Number Control in Saccharomyces cerevisiae

(2017) Hyo Won Ahn et al.   GENETICS

The dynamics of molecular evolution over 60,000 generations

(2017) Benjamin H. Good et al.   NATURE

The frenemies within: viruses, retrotransposons and plasmids that naturally infect Saccharomyces yeasts

(2017) Paul A. Rowley   YEAST

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data

(2017) Michael G. Nelson et al.   G3-Genes Genomes Genetics

Differential paralog divergence modulates genome evolution across yeast species

(2017) Monica R. Sanchez et al.   PLoS Genetics

Ribosome Biogenesis Modulates Ty1 Copy Number Control in Saccharomyces cerevisiae

(2017) Hyo Won Ahn et al.   GENETICS

RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

(2017) Jinfeng Chen et al.   PeerJ

Transposable elements: Self-seekers of the germline, team-players of the soma

(2016) David Haig   BIOESSAYS

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast

(2016) Sandeep Venkataram et al.   CELL

Ty1 Integrase Interacts with RNA Polymerase III-specific Subcomplexes to Promote Insertion of Ty1 Elements Upstream of Polymerase (Pol) III-transcribed Genes

(2016) Stephanie Cheung et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

High-Throughput Identification of Adaptive Mutations in Experimentally Evolved Yeast Populations

(2016) Celia Payen et al.   PLoS Genetics

Effects of heat and UV radiation on the mobilization of transposon mariner-Mos1

(2015) Sinara Santos Jardim et al.   CELL STRESS & CHAPERONES

Experimental evolution of the model eukaryote Saccharomyces cerevisiae yields insight into the molecular mechanisms underlying adaptation

(2015) Karin Voordeckers et al.   CURRENT OPINION IN MICROBIOLOGY

Atrans-Dominant Form of Gag Restricts Ty1 Retrotransposition and Mediates Copy Number Control

(2015) Agniva Saha et al.   JOURNAL OF VIROLOGY

Response of transposable elements to environmental stressors

(2015) Isabelle R. Miousse et al.   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

Elucidating the molecular architecture of adaptation via evolve and resequence experiments

(2015) Anthony Long et al.   NATURE REVIEWS GENETICS

Ty1 retrovirus-like element Gag contains overlapping restriction factor and nucleic acid chaperone functions

(2015) Yuri Nishida et al.   NUCLEIC ACIDS RESEARCH

Identification of a Novel Regulatory Mechanism of Nutrient Transport Controlled by TORC1-Npr1-Amu1/Par32

(2015) Mélanie Boeckstaens et al.   PLoS Genetics

The Ty1 Retrotransposon Restriction Factor p22 Targets Gag

(2015) Jessica M. Tucker et al.   PLoS Genetics

The enduring utility of continuous culturing in experimental evolution

(2014) David Gresham et al.   GENOMICS

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

The role of microhomology in genomic structural variation

(2014) Diego Ottaviani et al.   TRENDS IN GENETICS

Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments

(2014) Jungeui Hong et al.   PLoS Genetics

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Characterization of Chromosome Stability in Diploid, Polyploid and Hybrid Yeast Cells

(2013) Rajaraman Kumaran et al.   PLoS One

Capturing the mutational landscape of the beta-lactamase TEM-1

(2013) H. Jacquier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Dynamics of Diverse Segmental Amplifications in Populations of Saccharomyces cerevisiae Adapting to Strong Selection

(2013) Celia Payen et al.   G3-Genes Genomes Genetics

Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment

(2013) Daniel J. Kvitek et al.   PLoS Genetics

The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

(2012) Benoît Chénais et al.   GENE

Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

(2012) L. Mularoni et al.   GENOME RESEARCH

Tye7 regulates yeast Ty1 retrotransposon sense and antisense transcription in response to adenylic nucleotides stress

(2012) Géraldine Servant et al.   NUCLEIC ACIDS RESEARCH

Yeasts Acquire Resistance Secondary to Antifungal Drug Treatment by Adaptive Mutagenesis

(2012) David Quinto-Alemany et al.   PLoS One

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

Hunger Artists: Yeast Adapted to Carbon Limitation Show Trade-Offs under Carbon Sufficiency

(2011) Jared W. Wenger et al.   PLoS Genetics

Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus

(2010) D. Gresham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of reactive oxygen species in the induction ofTy1retrotransposition inSaccharomyces cerevisiae

(2010) Teodora Stoycheva et al.   YEAST

The Yeast GATA Factor Gat1 Occupies a Central Position in Nitrogen Catabolite Repression-Sensitive Gene Activation

(2009) I. Georis et al.   MOLECULAR AND CELLULAR BIOLOGY

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae

(2008) Gregory I. Lang et al.   GENETICS

Remodeling Yeast Gene Transcription by Activating the Ty1 Long Terminal Repeat Retrotransposon under Severe Adenine Deficiency

(2008) G. Servant et al.   MOLECULAR AND CELLULAR BIOLOGY

A Mep2-dependent Transcriptional Profile Links Permease Function to Gene Expression during Pseudohyphal Growth in Saccharomyces cerevisiae

(2008) Julian C. Rutherford et al.   MOLECULAR BIOLOGY OF THE CELL

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

(2008) Katy C Kao et al.   NATURE GENETICS

The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast

(2008) David Gresham et al.   PLoS Genetics

Amino acid transport through the Saccharomyces cerevisiae Gap1 permease is controlled by the Ras/cAMP pathway

(2007) Jinnie M. Garrett   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY