Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution

The ENCODE project: Missteps overshadowing a success

(2013) Sean R. Eddy   CURRENT BIOLOGY

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

Is junk DNA bunk? A critique of ENCODE

(2013) W. F. Doolittle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Can ENCODE tell us how much junk DNA we carry in our genome?

(2012) Deng-Ke Niu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The C-value paradox, junk DNA and ENCODE

(2012) Sean R. Eddy   CURRENT BIOLOGY

Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function

(2012) Noboru J. Sakabe et al.   HUMAN MOLECULAR GENETICS

Evolutionary Conservation of Histone Modifications in Mammals

(2012) Y. H. Woo et al.   MOLECULAR BIOLOGY AND EVOLUTION

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

(2012) W. W. Fisher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

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

(2011) C. E. Cain et al.   GENETICS

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

(2011) Qiye He et al.   NATURE GENETICS

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

(2011) David Martin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Switching the mechanism of mating type switching: a domesticated transposase supplants a domesticated homing endonuclease

(2010) L. N. Rusche et al.   GENES & DEVELOPMENT

Identification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages

(2010) Serena Ghisletti et al.   IMMUNITY

Genetic analysis of variation in transcription factor binding in yeast

(2010) Wei Zheng et al.   NATURE

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton 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

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

(2010) Matthew T. Weirauch et al.   TRENDS IN GENETICS

Transcription factor binding variation in the evolution of gene regulation

(2010) Robin D. Dowell   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

Dramatic changes in transcription factor binding over evolutionary time

(2010) Matthew T Weirauch et al.   GENOME BIOLOGY

Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation

(2009) Kairong Cui et al.   Cell Stem Cell

Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

(2009) Ming Yu et al.   MOLECULAR CELL

Backup in gene regulatory networks explains differences between binding and knockout results

(2009) Anthony Gitter et al.   Molecular Systems Biology

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb

(2008) S. A. Vokes et al.   GENES & DEVELOPMENT

Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation

(2008) Hervé Hogues et al.   MOLECULAR CELL

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

The Evolution of Combinatorial Gene Regulation in Fungi

(2008) Brian B Tuch et al.   PLOS BIOLOGY