Comparative studies of gene expression and the evolution of gene regulation

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

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

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

(2011) Antoine Molaro et al.   CELL

Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification

(2011) C. E. Cain et al.   GENETICS

Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states

(2011) D. I. K. Martin et al.   GENOME RESEARCH

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization

(2011) A. Tsankov et al.   GENOME RESEARCH

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

(2011) G. H. Perry et al.   GENOME RESEARCH

Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons

(2011) S. Gelfman et al.   GENOME RESEARCH

Evolution of Nucleosome Occupancy: Conservation of Global Properties and Divergence of Gene-Specific Patterns

(2011) K. Tsui et al.   MOLECULAR AND CELLULAR BIOLOGY

Human-specific loss of regulatory DNA and the evolution of human-specific traits

(2011) Cory Y. McLean et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

Molecular spandrels: tests of adaptation at the genetic level

(2011) Rowan D. H. Barrett et al.   NATURE REVIEWS GENETICS

Evolutionary origin of a novel gene expression pattern through co-option of the latent activities of existing regulatory sequences

(2011) M. Rebeiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry

(2011) R. D. Reed et al.   SCIENCE

The Developmental Role of Agouti in Color Pattern Evolution

(2011) M. Manceau et al.   SCIENCE

Genomic and chromatin signals underlying transcription start-site selection

(2011) Eivind Valen et al.   TRENDS IN GENETICS

Coupled Evolution of Transcription and mRNA Degradation

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

De Novo Genesis of Enhancers in Vertebrates

(2011) Michael P. Eichenlaub et al.   PLOS BIOLOGY

MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates

(2011) Mehmet Somel et al.   PLOS BIOLOGY

Consequences of Eukaryotic Enhancer Architecture for Gene Expression Dynamics, Development, and Fitness

(2011) Michael Z. Ludwig et al.   PLoS Genetics

A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila

(2011) Charless C. Fowlkes et al.   PLoS Genetics

Distinct Functional Constraints Partition Sequence Conservation in a cis-Regulatory Element

(2011) Antoine Barrière et al.   PLoS Genetics

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

(2011) Athma A. Pai et al.   PLoS Genetics

MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains

(2011) Hai Yang Hu et al.   PLoS Genetics

Sequence features that drive human promoter function and tissue specificity

(2010) J. M. Landolin et al.   GENOME RESEARCH

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

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Gene regulation and the origins of human biological uniqueness

(2010) Samuel J. Sholtis et al.   TRENDS IN GENETICS

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

(2010) Jacek Majewski et al.   TRENDS IN GENETICS

Genome-wide maps of transcription regulatory elements

(2010) Noboru J. Sakabe et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

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

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

The Role of Nucleosome Positioning in the Evolution of Gene Regulation

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

Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq

(2010) Augix Guohua Xu et al.   PLoS Computational Biology

Gene–Environment Interactions at Nucleotide Resolution

(2010) Justin Gerke et al.   PLoS Genetics

Incipient Balancing Selection through Adaptive Loss of Aquaporins in Natural Saccharomyces cerevisiae Populations

(2010) Jessica L. Will et al.   PLoS Genetics

A Humanized Version of Foxp2 Affects Cortico-Basal Ganglia Circuits in Mice

(2009) Wolfgang Enard et al.   CELL

Sex-specific and lineage-specific alternative splicing in primates

(2009) R. Blekhman et al.   GENOME RESEARCH

Constructing genomic maps of positive selection in humans: Where do we go from here?

(2009) J. M. Akey   GENOME RESEARCH

An ensemble model of competitive multi-factor binding of the genome

(2009) T. Wasson et al.   GENOME RESEARCH

Incorporating nucleosomes into thermodynamic models of transcription regulation

(2009) T. Raveh-Sadka et al.   GENOME RESEARCH

Signals of recent positive selection in a worldwide sample of human populations

(2009) J. K. Pickrell et al.   GENOME RESEARCH

Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization

(2009) Yair Field et al.   NATURE GENETICS

From DNA sequence to transcriptional behaviour: a quantitative approach

(2009) Eran Segal et al.   NATURE REVIEWS GENETICS

Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain

(2009) Katja Nowick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional neoteny in the human brain

(2009) M. Somel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Interactions Between Transcription Factors Cause Natural Variation in Yeast

(2009) J. Gerke et al.   SCIENCE

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

Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability

(2009) M. D. Vinces et al.   SCIENCE

Epistasis in a quantitative trait captured by a molecular model of transcription factor interactions

(2009) Jason Gertz et al.   THEORETICAL POPULATION BIOLOGY

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION

A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity

(2008) A. M. Smith et al.   GENOME RESEARCH

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE

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

(2008) Yoav Gilad et al.   TRENDS IN GENETICS

Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts

(2008) Justin Crocker et al.   PLOS BIOLOGY