Insights into molecular evolution from yeast genomics

Functional Divergence for Every Paralog

(2014) Patricia S. Soria et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetics of single-cell protein abundance variation in large yeast populations

(2014) Frank W. Albert et al.   NATURE

Genome-wide mapping of cellular traits using yeast

(2014) Leopold Parts   YEAST

A Super-Assembly of Whi3 Encodes Memory of Deceptive Encounters by Single Cells during Yeast Courtship

(2013) Fabrice Caudron et al.   CELL

Spatial Population Expansion Promotes the Evolution of Cooperation in an Experimental Prisoner’s Dilemma

(2013) J. David Van Dyken et al.   CURRENT BIOLOGY

The molecular basis of phenotypic variation in yeast

(2013) Justin C Fay   CURRENT OPINION IN GENETICS & DEVELOPMENT

SHIFTING FITNESS LANDSCAPES IN RESPONSE TO ALTERED ENVIRONMENTS

(2013) Ryan T. Hietpas et al.   EVOLUTION

The Evolutionary Rewiring of the Ribosomal Protein Transcription Pathway Modifies the Interaction of Transcription Factor Heteromer Ifh1-Fhl1 (Interacts with Forkhead 1-Forkhead-like 1) with the DNA-binding Specificity Element

(2013) Jaideep Mallick et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Three Independent Determinants of Protein Evolutionary Rate

(2013) Sun Shim Choi et al.   JOURNAL OF MOLECULAR EVOLUTION

GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance

(2013) Yann Lesecque et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution and functional cross-talk of protein post-translational modifications

(2013) Pedro Beltrao et al.   Molecular Systems Biology

Epigenetic epistatic interactions constrain the evolution of gene expression

(2013) S. Park et al.   Molecular Systems Biology

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds

(2013) K. L. McGary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly

(2013) C. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae

(2013) B. Oud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Following Gene Duplication, Paralog Interference Constrains Transcriptional Circuit Evolution

(2013) Christopher R. Baker et al.   SCIENCE

Saccharomyces diversity and evolution: a budding model genus

(2013) Chris Todd Hittinger   TRENDS IN 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

Improved use of a public good selects for the evolution of undifferentiated multicellularity

(2013) John H Koschwanez et al.   eLife

Protein Modularity, Cooperative Binding, and Hybrid Regulatory States Underlie Transcriptional Network Diversification

(2012) Christopher R. Baker et al.   CELL

Local Ancestry Corrects for Population Structure in Saccharomyces cerevisiae Genome-Wide Association Studies

(2012) Liyang Diao et al.   GENETICS

On the Prospects of Whole-Genome Association Mapping in Saccharomyces cerevisiae

(2012) C. F. Connelly et al.   GENETICS

Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity

(2012) H. B. Fraser et al.   GENOME RESEARCH

Evolution of a Membrane Protein Regulon in Saccharomyces

(2012) H. C. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Yeast Adapts to a Changing Stressful Environment by Evolving Cross-Protection and Anticipatory Gene Regulation

(2012) Riddhiman Dhar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Experimental evolution of multicellularity

(2012) W. C. Ratcliff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

(2012) J.-R. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteome-Wide Discovery of Evolutionary Conserved Sequences in Disordered Regions

(2012) A. N. Nguyen Ba et al.   Science Signaling

Cellular cooperation: insights from microbes

(2012) Hasan Celiker et al.   TRENDS IN CELL BIOLOGY

The Genomic Landscape and Evolutionary Resolution of Antagonistic Pleiotropy in Yeast

(2012) Wenfeng Qian et al.   Cell Reports

Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication

(2012) Karin Voordeckers et al.   PLOS BIOLOGY

Network Evolution: Rewiring and Signatures of Conservation in Signaling

(2012) Mark G. F. Sun et al.   PLoS Computational Biology

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

(2012) Wenfeng Qian et al.   PLoS Genetics

Modeling the evolution of a classic genetic switch

(2011) Christos Josephides et al.   BMC Systems Biology

The rise of yeast population genomics

(2011) Gianni Liti et al.   COMPTES RENDUS BIOLOGIES

Yeast: An Experimental Organism for 21st Century Biology

(2011) David Botstein et al.   GENETICS

Revealing the genetic structure of a trait by sequencing a population under selection

(2011) L. Parts et al.   GENOME RESEARCH

Polymorphism, Divergence, and the Role of Recombination in Saccharomyces cerevisiae Genome Evolution

(2011) A. D. Cutter et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Test of the Coordinated Expression Hypothesis for the Origin and Maintenance of the GAL Cluster in Yeast

(2011) Gregory I. Lang et al.   PLoS One

Experimental illumination of a fitness landscape

(2011) R. T. Hietpas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive DNA-binding specificity divergence of a conserved transcription regulator

(2011) C. R. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measuring the evolutionary rate of protein-protein interaction

(2011) W. Qian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

(2011) Devin R. Scannell et al.   G3-Genes Genomes Genetics

Sucrose Utilization in Budding Yeast as a Model for the Origin of Undifferentiated Multicellularity

(2011) John H. Koschwanez et al.   PLOS BIOLOGY

Evolution of Transcription Networks — Lessons from Yeasts

(2010) Hao Li et al.   CURRENT BIOLOGY

Coevolution within a transcriptional network by compensatory trans and cis mutations

(2010) D. Kuo et al.   GENOME RESEARCH

Evolution of Characterized Phosphorylation Sites in Budding Yeast

(2010) A. N. Nguyen Ba et al.   MOLECULAR BIOLOGY AND EVOLUTION

Intercalation of a new tier of transcription regulation into an ancient circuit

(2010) Lauren N. Booth et al.   NATURE

Genetic analysis of variation in transcription factor binding in yeast

(2010) Wei Zheng et al.   NATURE

Remarkably ancient balanced polymorphisms in a multi-locus gene network

(2010) Chris Todd Hittinger et al.   NATURE

Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast

(2010) K. A. Geiler-Samerotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi

(2010) J. C. Slot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for widespread adaptive evolution of gene expression in budding yeast

(2010) H. B. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polygenic and directional regulatory evolution across pathways in Saccharomyces

(2010) J. H. Bullard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Moving from transcriptional to phospho-evolution: generalizing regulatory evolution?

(2010) Alan M. Moses et al.   TRENDS IN GENETICS

Evolutionary Tinkering with Conserved Components of a Transcriptional Regulatory Network

(2010) Hugo Lavoie et al.   PLOS BIOLOGY

Dramatic changes in transcription factor binding over evolutionary time

(2010) Matthew T Weirauch et al.   GENOME BIOLOGY

From elements to modules: regulatory evolution in Ascomycota fungi

(2009) Dana J Wohlbach et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Protein Subcellular Relocalization in the Evolution of Yeast Singleton and Duplicate Genes

(2009) Wenfeng Qian et al.   Genome Biology and Evolution

Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae

(2009) Joseph Schacherer et al.   NATURE

The Beagle in a bottle

(2009) Angus Buckling et al.   NATURE

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Posttranslational regulation impacts the fate of duplicated genes

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

A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation

(2009) I. Tirosh et al.   SCIENCE

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species

(2009) Pedro Beltrao et al.   PLOS BIOLOGY

Why Is the Correlation between Gene Importance and Gene Evolutionary Rate So Weak?

(2009) Zhi Wang et al.   PLoS Genetics

FLO1 Is a Variable Green Beard Gene that Drives Biofilm-like Cooperation in Budding Yeast

(2008) Scott Smukalla et al.   CELL

A comprehensive strategy enabling high-resolution functional analysis of the yeast genome

(2008) David K Breslow et al.   NATURE METHODS

The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication

(2008) A. Presser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) David Gresham et al.   PLoS Genetics

A Catalog of Neutral and Deleterious Polymorphism in Yeast

(2008) Scott W. Doniger et al.   PLoS Genetics

Functional diversification of duplicate genes through subcellular adaptation of encoded proteins

(2008) Ana C Marques et al.   GENOME BIOLOGY