Evolution of Gene Regulation during Transcription and Translation

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Extensive Translational Regulation of Gene Expression in an Allopolyploid (Glycine dolichocarpa)

(2014) J. E. Coate et al.   PLANT CELL

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

Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing

(2013) J. A. Arribere et al.   GENOME RESEARCH

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

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

(2013) Paola Picotti et al.   NATURE

Intra-Specific Regulatory Variation in Drosophila pseudoobscura

(2013) Anton Suvorov et al.   PLoS One

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

The Molecular Mechanism of a Cis-Regulatory Adaptation in Yeast

(2013) Jessica Chang et al.   PLoS Genetics

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

(2013) Mallory A Freeberg et al.   GENOME BIOLOGY

Effects of cis and trans regulatory variations on the expression divergence of heat shock response genes between yeast strains

(2012) Ching-Min Li et al.   GENE

Conservation of replication timing reveals global and local regulation of replication origin activity

(2012) C. A. Muller et al.   GENOME RESEARCH

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

(2012) A. Goncalves et al.   GENOME RESEARCH

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

(2012) Zia Khan et al.   Molecular Systems Biology

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

(2012) Xiaoli Shi et al.   Nature Communications

Tempo and Mode in Evolution of Transcriptional Regulation

(2012) Kacy L. Gordon et al.   PLoS Genetics

Regulatory Variation Within and Between Species

(2011) Wei Zheng et al.   Annual Review of Genomics and Human Genetics

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Inferring regulatory mechanisms from patterns of evolutionary divergence

(2011) I. Tirosh et al.   Molecular Systems Biology

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

(2011) G. A. Brar et al.   SCIENCE

Coupled Evolution of Transcription and mRNA Degradation

(2011) Mally Dori-Bachash et al.   PLOS BIOLOGY

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

Natural selection on cis and trans regulation in yeasts

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

Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences

(2010) Itay Tirosh et al.   Molecular Systems Biology

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz 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

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

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

(2009) I. Tirosh et al.   SCIENCE

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

(2009) N. T. Ingolia et al.   SCIENCE

Two strategies for gene regulation by promoter nucleosomes

(2008) I. Tirosh et al.   GENOME RESEARCH

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?

(2008) Witold Filipowicz et al.   NATURE REVIEWS GENETICS

Revealing the architecture of gene regulation: the promise of eQTL studies

(2008) Yoav Gilad et al.   TRENDS IN GENETICS