DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories

Layers of Cryptic Genetic Variation Underlie a Yeast Complex Trait

(2019) Jonathan T. Lee et al.   GENETICS

Identification of trans-eQTLs using mediation analysis with multiple mediators

(2019) Nayang Shan et al.   BMC BIOINFORMATICS

Trans Effects on Gene Expression Can Drive Omnigenic Inheritance

(2019) Xuanyao Liu et al.   CELL

High-throughput identification of human SNPs affecting regulatory element activity

(2019) Joris van Arensbergen et al.   NATURE GENETICS

Functional testing of thousands of osteoarthritis-associated variants for regulatory activity

(2019) Jason C. Klein et al.   Nature Communications

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision

(2018) Zehua Bao et al.   NATURE BIOTECHNOLOGY

High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR–Cas9 in yeast

(2018) Xiaoge Guo et al.   NATURE BIOTECHNOLOGY

Multiplexed precision genome editing with trackable genomic barcodes in yeast

(2018) Kevin R Roy et al.   NATURE BIOTECHNOLOGY

Multiplex assessment of protein variant abundance by massively parallel sequencing

(2018) Kenneth A. Matreyek et al.   NATURE GENETICS

Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition

(2018) Kerrin S. Small et al.   NATURE GENETICS

Highly parallel genome variant engineering with CRISPR–Cas9

(2018) Meru J. Sadhu et al.   NATURE GENETICS

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk

(2018) Jian Zhou et al.   NATURE GENETICS

Genetic Analysis of Signal Generation by the Rgt2 Glucose Sensor of Saccharomyces cerevisiae

(2018) Peter Scharff-Poulsen et al.   G3-Genes Genomes Genetics

Genetics of trans-regulatory variation in gene expression

(2018) Frank Wolfgang Albert et al.   eLife

Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing

(2018) Eilon Sharon et al.   CELL

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion

(2018) David Bergenholm et al.   mSystems

A resource of variant effect predictions of single nucleotide variants in model organisms

(2018) Omar Wagih et al.   Molecular Systems Biology

Identifyingcis-mediators fortrans-eQTLs across many human tissues using genomic mediation analysis

(2017) Fan Yang et al.   GENOME RESEARCH

Lipid engineering reveals regulatory roles for membrane fluidity in yeast flocculation and oxygen-limited growth

(2017) Daniel Degreif et al.   METABOLIC ENGINEERING

Fitness Effects of Cis-Regulatory Variants in the Saccharomyces cerevisiae TDH3 Promoter

(2017) Fabien Duveau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Distant eQTLs and Non-coding Sequences Play Critical Roles in Regulating Gene Expression and Quantitative Trait Variation in Maize

(2017) Haijun Liu et al.   Molecular Plant

DNA sequencing at 40: past, present and future

(2017) Jay Shendure et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

High-resolution mapping ofcis-regulatory variation in budding yeast

(2017) Ryosuke Kita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Major sulfonate transporter Soa1 in Saccharomyces cerevisiae and considerable substrate diversity in its fungal family

(2017) Sylvester Holt et al.   Nature Communications

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

(2016) Kathleen Sprouffske et al.   BMC BIOINFORMATICS

Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness

(2016) Leeat Keren et al.   CELL

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

A Eukaryotic Sensor for Membrane Lipid Saturation

(2016) Roberto Covino et al.   MOLECULAR CELL

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering

(2016) Andrew D Garst et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Prospective functional classification of all possible missense variants in PPARG

(2016) Amit R Majithia et al.   NATURE GENETICS

Natural gene expression variation studies in yeast

(2016) Dawn A. Thompson et al.   YEAST

Quantitative Trait Loci (QTL)-Guided Metabolic Engineering of a Complex Trait

(2016) Matthew J. Maurer et al.   ACS Synthetic Biology

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

(2015) Yongwook Choi et al.   BIOINFORMATICS

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort

(2015) Christopher M. Vockley et al.   GENOME RESEARCH

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Selection on noise constrains variation in a eukaryotic promoter

(2015) Brian P. H. Metzger et al.   NATURE

The role of regulatory variation in complex traits and disease

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

New vectors for simple and streamlined CRISPR-Cas9 genome editing inSaccharomyces cerevisiae

(2015) Marian F. Laughery et al.   YEAST

Genetic interactions contribute less than additive effects to quantitative trait variation in yeast

(2015) Joshua S. Bloom et al.   Nature Communications

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Jeffrey A. Lewis et al.   GENETICS

High-Efficiency Genome Editing and Allele Replacement in Prototrophic and Wild Strains of Saccharomyces

(2014) W. G. Alexander et al.   GENETICS

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

(2014) Leopold Parts et al.   GENOME RESEARCH

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

(2014) Frank W. Albert et al.   NATURE

Saturation editing of genomic regions by multiplex homology-directed repair

(2014) Gregory M. Findlay et al.   NATURE

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Heritability and genomics of gene expression in peripheral blood

(2014) Fred A Wright et al.   NATURE GENETICS

The Reference Genome Sequence of Saccharomyces cerevisiae : Then and Now

(2014) Stacia R. Engel et al.   G3-Genes Genomes Genetics

Single Nucleotide Variants in Transcription Factors Associate More Tightly with Phenotype than with Gene Expression

(2014) Priya Sudarsanam et al.   PLoS Genetics

Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize

(2014) Jason G. Wallace et al.   PLoS Genetics

Cis and Trans Effects of Human Genomic Variants on Gene Expression

(2014) Julien Bryois et al.   PLoS Genetics

Genetic Influences on Translation in Yeast

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

Differential adaptation to multi-stressed conditions of wine fermentation revealed by variations in yeast regulatory networks

(2013) Christian Brion et al.   BMC GENOMICS

The molecular basis of phenotypic variation in yeast

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

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

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

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

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

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems

(2013) James E. DiCarlo et al.   NUCLEIC ACIDS RESEARCH

The Molecular Mechanism of a Cis-Regulatory Adaptation in Yeast

(2013) Jessica Chang et al.   PLoS Genetics

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

(2013) Julien Gagneur et al.   PLoS Genetics

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Nonlinear Fitness Consequences of Variation in Expression Level of a Eukaryotic Gene

(2012) J. S. Rest et al.   MOLECULAR BIOLOGY AND EVOLUTION

Surprisingly diverged populations ofSaccharomyces cerevisiaein natural environments remote from human activity

(2012) Qi-Ming Wang et al.   MOLECULAR ECOLOGY

Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles

(2012) Benjamin P Fairfax et al.   NATURE GENETICS

Mapping cis- and trans-regulatory effects across multiple tissues in twins

(2012) Elin Grundberg et al.   NATURE GENETICS

Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast

(2012) R. Scott McIsaac et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Natural Variation in the Yeast Glucose-Signaling Network Reveals a New Role for the Mig3p Transcription Factor

(2012) Jeffrey A. Lewis et al.   G3-Genes Genomes Genetics

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

(2011) Patricia J. Wittkopp et al.   NATURE REVIEWS GENETICS

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Genetic Variation Shapes Protein Networks Mainly through Non-transcriptional Mechanisms

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

Single-Tissue and Cross-Tissue Heritability of Gene Expression Via Identity-by-Descent in Related or Unrelated Individuals

(2011) Alkes L. Price et al.   PLoS Genetics

Natural selection on cis and trans regulation in yeasts

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

Rapid measurement of plasma free fatty acid concentration and isotopic enrichment using LC/MS

(2010) Xuan-Mai T. Persson et al.   JOURNAL OF LIPID RESEARCH

A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk

(2010) Matthias Heinig et al.   NATURE

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

Dissecting the pleiotropic consequences of a quantitative trait nucleotide

(2009) Hyun Seok Kim et al.   FEMS YEAST RESEARCH

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Modularity and interactions in the genetics of gene expression

(2009) O. Litvin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) Himanshu Sinha et al.   GENETICS

Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae

(2008) KYLE M. BROWN et al.   MOLECULAR ECOLOGY

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

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

(2008) David K Breslow et al.   NATURE METHODS

Gene–Environment Interaction in Yeast Gene Expression

(2008) Erin N Smith et al.   PLOS BIOLOGY

Effects of cis and trans Genetic Ancestry on Gene Expression in African Americans

(2008) Alkes L. Price et al.   PLoS Genetics