De Novo Genesis of Enhancers in Vertebrates

Morphological evolution caused by many subtle-effect substitutions in regulatory DNA

(2011) Nicolás Frankel et al.   NATURE

Combining Computational Prediction of Cis-Regulatory Elements with a New Enhancer Assay to Efficiently Label Neuronal Structures in the Medaka Fish

(2011) Emmanuel Mongin et al.   PLoS One

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

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

(2010) Michael W. Perry et al.   CURRENT BIOLOGY

The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer Activity

(2010) Deborah I. Ritter et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

The mouse Gene Expression Database (GXD): 2011 update

(2010) J. H. Finger et al.   NUCLEIC ACIDS RESEARCH

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

Nomadic Enhancers: Tissue-Specific cis-Regulatory Elements of yellow Have Divergent Genomic Positions among Drosophila Species

(2010) Gizem Kalay et al.   PLoS Genetics

Recent de novo origin of human protein-coding genes

(2009) D. G. Knowles et al.   GENOME RESEARCH

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons

(2009) Xianjun Dong et al.   NUCLEIC ACIDS RESEARCH

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

A global survey identifies novel upstream components of the Ath5 neurogenic network

(2009) Marcel Souren et al.   GENOME BIOLOGY

Ultraconserved coding regions outside the homeobox of mammalian Hox genes

(2008) Zhenguo Lin et al.   BMC EVOLUTIONARY BIOLOGY

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

(2008) Sean B. Carroll   CELL

De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae

(2008) J. Cai et al.   GENETICS

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Ensembl 2009

(2008) T. J. P. Hubbard et al.   NUCLEIC ACIDS RESEARCH

A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2

(2008) S. Tumpel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Possible involvement of SINEs in mammalian-specific brain formation

(2008) T. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE