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

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

(2012) Jacob F. Degner et al.   NATURE

Subsampling methods for genomic inference

(2011) Peter J. Bickel et al.   Annals of Applied Statistics

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

(2011) C. E. Cain et al.   GENETICS

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

(2011) Simon C. Biddie et al.   MOLECULAR CELL

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

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

ZEB1 and CtBP form a repressive complex at a distal promoter element of the BCL6 locus

(2010) Vasiliki Papadopoulou et al.   BIOCHEMICAL JOURNAL

The evolution of gene regulation, the RNA universe, and the vexed questions of artefact and noise

(2010) Miranda Robertson   BMC BIOLOGY

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain

(2010) Courtney C. Babbitt et al.   Genome Biology and Evolution

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

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

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

(2010) Robert K. Bradley 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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Sex-specific and lineage-specific alternative splicing in primates

(2009) R. Blekhman et al.   GENOME RESEARCH

Transcriptional neoteny in the human brain

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

Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome

(2009) S. C. J. Parker et al.   SCIENCE

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

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

(2008) Sean B. Carroll   CELL

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

(2008) Ran Blekhman et al.   PLoS Genetics