Natural gene expression variation studies in yeast

Polygenic analysis and targeted improvement of the complex trait of high acetic acid tolerance in the yeast Saccharomyces cerevisiae

(2016) Jean-Paul Meijnen et al.   Biotechnology for Biofuels

Contrasting Frequencies and Effects ofcis- andtrans-Regulatory Mutations Affecting Gene Expression

(2016) Brian P. H. Metzger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differences in environmental stress response among yeasts is consistent with species-specific lifestyles

(2016) Christian Brion et al.   MOLECULAR BIOLOGY OF THE CELL

The complex genetic and molecular basis of a model quantitative trait

(2016) Robert A. Linder et al.   MOLECULAR BIOLOGY OF THE CELL

Polygenic evolution of a sugar specialization trade-off in yeast

(2016) Jeremy I. Roop et al.   NATURE

Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets

(2016) Mina Fazlollahi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects

(2016) Florent Chuffart et al.   PLoS Genetics

Natural variation in non-coding regions underlying phenotypic diversity in budding yeast

(2016) Francisco Salinas et al.   Scientific Reports

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

(2015) Dawn Thompson et al.   Annual Review of Cell and Developmental Biology

Non-coding genetic variants in human disease: Figure 1.

(2015) Feng Zhang et al.   HUMAN MOLECULAR GENETICS

Negative feedback buffers effects of regulatory variants

(2015) D. M. Bader et al.   Molecular Systems Biology

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

Evolution of intraspecific transcriptomic landscapes in yeasts

(2015) Christian Brion et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Derepression Uncovers Cryptic Higher-Order Genetic Interactions

(2015) Matthew B. Taylor et al.   PLoS Genetics

Temporal Expression Profiling Identifies Pathways Mediating Effect of Causal Variant on Phenotype

(2015) Saumya Gupta et al.   PLoS Genetics

A genetic approach of wine yeast fermentation capacity in nitrogen-starvation reveals the key role of nitrogen signaling

(2014) Claire Brice et al.   BMC GENOMICS

Genetic Architecture of Ethanol-Responsive Transcriptome Variation in Saccharomyces cerevisiae Strains

(2014) Jeffrey A. Lewis et al.   GENETICS

Heritability and genetic basis of protein level variation in an outbred population

(2014) Leopold Parts et al.   GENOME RESEARCH

Heritable variation of mRNA decay rates in yeast

(2014) Jennifer M. Andrie et al.   GENOME RESEARCH

Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans

(2014) D. Muzzey et al.   GENOME RESEARCH

Heterochronic Meiotic Misexpression in an Interspecific Yeast Hybrid

(2014) Devjanee Swain Lenz et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Frank W. Albert et al.   NATURE

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Evolutionary dynamics of coding and non-coding transcriptomes

(2014) Anamaria Necsulea et al.   NATURE REVIEWS GENETICS

Extensivecis-Regulatory Variation Robust to Environmental Perturbation inArabidopsis

(2014) Francisco A. Cubillos et al.   PLANT CELL

Mapping Genetic Variants Underlying Differences in the Central Nitrogen Metabolism in Fermenter Yeasts

(2014) Matías Jara et al.   PLoS One

Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape

(2014) Y. Ichihashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Influences on Translation in Yeast

(2014) Frank W. Albert et al.   PLoS Genetics

Genetic interactions affecting human gene expression identified by variance association mapping

(2014) Andrew Anand Brown et al.   eLife

The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant

(2013) Bayu Tiruneh et al.   BMC BIOLOGY

Comparative transcriptomics of early dipteran development

(2013) Eva Jiménez-Guri et al.   BMC GENOMICS

High-Resolution Mapping of Complex Traits with a Four-Parent Advanced Intercross Yeast Population

(2013) Francisco A. Cubillos et al.   GENETICS

An Evaluation of High-Throughput Approaches to QTL Mapping in Saccharomyces cerevisiae

(2013) S. Wilkening et al.   GENETICS

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

(2013) S. Roy et al.   GENOME RESEARCH

Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast

(2013) C. J. McManus et al.   GENOME RESEARCH

Evolution at two levels of gene expression in yeast

(2013) C. G. Artieri et al.   GENOME RESEARCH

Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast

(2013) D. A. Skelly et al.   GENOME RESEARCH

Population Genomics and Transcriptional Consequences of Regulatory Motif Variation in Globally Diverse Saccharomyces cerevisiae Strains

(2013) Caitlin F. Connelly et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inheritance of Gene Expression Level and Selective Constraints on Trans- and Cis-Regulatory Changes in Yeast

(2013) Bernhard Schaefke et al.   MOLECULAR BIOLOGY AND EVOLUTION

Natural sequence variants of yeast environmental sensors confer cell-to-cell expression variability

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

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

Finding the sources of missing heritability in a yeast cross

(2013) Joshua S. Bloom et al.   NATURE

Expression Quantitative Trait Locus Mapping across Water Availability Environments Reveals Contrasting Associations with Genomic Features in Arabidopsis

(2013) D. B. Lowry et al.   PLANT CELL

The Molecular Mechanism of a Cis-Regulatory Adaptation in Yeast

(2013) Jessica Chang et al.   PLoS Genetics

QTL Analysis of High Thermotolerance with Superior and Downgraded Parental Yeast Strains Reveals New Minor QTLs and Converges on Novel Causative Alleles Involved in RNA Processing

(2013) Yudi Yang et al.   PLoS Genetics

Comparative Polygenic Analysis of Maximal Ethanol Accumulation Capacity and Tolerance to High Ethanol Levels of Cell Proliferation in Yeast

(2013) Thiago M. Pais et al.   PLoS Genetics

Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression

(2013) Mathilde Paris et al.   PLoS Genetics

Genotype-Environment Interactions Reveal Causal Pathways That Mediate Genetic Effects on Phenotype

(2013) Julien Gagneur et al.   PLoS Genetics

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes

(2012) Susanta K. Behura et al.   BIOLOGICAL REVIEWS

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

(2012) Christopher R. Baker et al.   CELL

Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants

(2012) Francisco A Cubillos et al.   CURRENT OPINION IN PLANT BIOLOGY

Natural genetic variation in yeast longevity

(2012) S. W. Stumpferl et al.   GENOME RESEARCH

Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity

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

Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis

(2012) S. Swinnen et al.   GENOME RESEARCH

Evolution of a Membrane Protein Regulon in Saccharomyces

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

Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS

(2012) Zia Khan et al.   Molecular Systems Biology

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks

(2012) Naomi Habib et al.   Molecular Systems Biology

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Treatment- and Population-Dependent Activity Patterns of Behavioral and Expression QTLs

(2012) Jesse D. Ziebarth et al.   PLoS One

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Genetic Architecture of Highly Complex Chemical Resistance Traits across Four Yeast Strains

(2012) Ian M. Ehrenreich et al.   PLoS Genetics

Advances in Quantitative Trait Analysis in Yeast

(2012) Gianni Liti et al.   PLoS Genetics

Regulation of cellular miRNA expression by human papillomaviruses

(2011) Zhi-Ming Zheng et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2011) L. Parts et al.   GENOME RESEARCH

Assessing the complex architecture of polygenic traits in diverged yeast populations

(2011) FRANCISCO A. CUBILLOS et al.   MOLECULAR ECOLOGY

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

(2011) C. G. de Boer et al.   NUCLEIC ACIDS RESEARCH

Extensive divergence of yeast stress responses through transitions between induced and constitutive activation

(2011) I. Tirosh 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

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

Parallel evolution of the make–accumulate–consume strategy in Saccharomyces and Dekkera yeasts

(2011) Elżbieta Rozpędowska et al.   Nature Communications

Genetic Variation Shapes Protein Networks Mainly through Non-transcriptional Mechanisms

(2011) Eric J. Foss et al.   PLOS BIOLOGY

A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand

(2010) Dan Li et al.   CELL RESEARCH

Evolution of Transcription Networks — Lessons from Yeasts

(2010) Hao Li et al.   CURRENT BIOLOGY

Natural selection on cis and trans regulation in yeasts

(2010) J. J. Emerson et al.   GENOME RESEARCH

Dissection of genetically complex traits with extremely large pools of yeast segregants

(2010) Ian M. Ehrenreich et al.   NATURE

Gene duplication and the evolution of ribosomal protein gene regulation in yeast

(2010) I. Wapinski 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

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

(2010) Robert K. Bradley et al.   PLOS BIOLOGY

Evolutionary Tinkering with Conserved Components of a Transcriptional Regulatory Network

(2010) Hugo Lavoie et al.   PLOS BIOLOGY

The Role of Nucleosome Positioning in the Evolution of Gene Regulation

(2010) Alexander M. Tsankov et al.   PLOS BIOLOGY

From elements to modules: regulatory evolution in Ascomycota fungi

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

Fungal regulatory evolution: cis and trans in the balance

(2009) Dawn Anne Thompson et al.   FEBS LETTERS

Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved

(2009) I. Yanai et al.   GENOME RESEARCH

High-resolution DNA-binding specificity analysis of yeast transcription factors

(2009) C. Zhu et al.   GENOME RESEARCH

QTL mapping of sake brewing characteristics of yeast

(2009) Taku Katou et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Genome-wide allele- and strand-specific expression profiling

(2009) Julien Gagneur et al.   Molecular Systems Biology

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

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

(2009) I. Tirosh et al.   SCIENCE

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Quantitative Genomics: Analyzing Intraspecific Variation Using Global Gene Expression Polymorphisms or eQTLs

(2008) Dan Kliebenstein   Annual Review of Plant Biology

Sequential Elimination of Major-Effect Contributors Identifies Additional Quantitative Trait Loci Conditioning High-Temperature Growth in Yeast

(2008) Himanshu Sinha et al.   GENETICS

Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation

(2008) Hervé Hogues et al.   MOLECULAR CELL

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

Gene–Environment Interaction in Yeast Gene Expression

(2008) Erin N Smith et al.   PLOS BIOLOGY

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology

Cell-to-Cell Stochastic Variation in Gene Expression Is a Complex Genetic Trait

(2008) Juliet Ansel et al.   PLoS Genetics

Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates

(2008) Daniel J. Kvitek et al.   PLoS Genetics

Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata

(2008) Gaëlle Lelandais et al.   GENOME BIOLOGY