Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data

Gene expression drives local adaptation in humans

(2013) H. B. Fraser   GENOME RESEARCH

Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence

(2013) Ilan Gronau et al.   MOLECULAR BIOLOGY AND EVOLUTION

OsLG1 regulates a closed panicle trait in domesticated rice

(2013) Takashige Ishii et al.   NATURE GENETICS

INTEGRATING FOSSILS WITH MOLECULAR PHYLOGENIES IMPROVES INFERENCE OF TRAIT EVOLUTION

(2012) Graham J. Slater et al.   EVOLUTION

IS YOUR PHYLOGENY INFORMATIVE? MEASURING THE POWER OF COMPARATIVE METHODS

(2012) Carl Boettiger et al.   EVOLUTION

Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity

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

Pervasive Antisense Transcription Is Evolutionarily Conserved in Budding Yeast

(2012) A. J. Goodman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of a Membrane Protein Regulon in Saccharomyces

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

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

Evolution of patterns on Conus shells

(2012) Z. Gong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic Analysis Using Lévy Processes: Finding Jumps in the Evolution of Continuous Traits

(2012) Michael J. Landis et al.   SYSTEMATIC BIOLOGY

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

(2012) Yoichiro Shibata et al.   PLoS Genetics

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Expression divergence measured by transcriptome sequencing of four yeast species

(2011) Michele A Busby et al.   BMC GENOMICS

A NOVEL COMPARATIVE METHOD FOR IDENTIFYING SHIFTS IN THE RATE OF CHARACTER EVOLUTION ON TREES

(2011) Jonathan M. Eastman et al.   EVOLUTION

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

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

Systematic Detection of Polygenic cis-Regulatory Evolution

(2011) Hunter B. Fraser et al.   PLoS Genetics

Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules

(2011) Bin Z. He et al.   PLoS Genetics

Evolution of Multidrug Resistance during Staphylococcus aureus Infection Involves Mutation of the Essential Two Component Regulator WalKR

(2011) Benjamin P. Howden et al.   PLoS Pathogens

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

(2010) Lauren N. Booth 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

Noncanonical transcript forms in yeast and their regulation during environmental stress

(2010) O. K. Yoon et al.   RNA

Optimization of gene expression by natural selection

(2009) T. Bedford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stepwise Modification of a Modular Enhancer Underlies Adaptation in a Drosophila Population

(2009) M. Rebeiz et al.   SCIENCE

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

(2009) Y. F. Chan et al.   SCIENCE

Evolutionary Processes Acting on Candidate cis-Regulatory Regions in Humans Inferred from Patterns of Polymorphism and Divergence

(2009) Dara G. Torgerson et al.   PLoS Genetics

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Analysis of comparative data with hierarchical autocorrelation

(2008) Cécile Ané   Annals of Applied Statistics

Evolution of Primate Gene Expression: Drift and Corrective Sweeps?

(2008) R. Chaix et al.   GENETICS

Transcriptome Divergence and the Loss of Plasticity in Bacillus subtilis after 6,000 Generations of Evolution under Relaxed Selection for Sporulation

(2008) H. Maughan et al.   JOURNAL OF BACTERIOLOGY

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

(2008) Ran Blekhman et al.   PLoS Genetics