Deep conservation of cis-regulatory elements in metazoans

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

FGF signaling induces mesoderm in the hemichordate Saccoglossus kowalevskii

(2013) S. A. Green et al.   DEVELOPMENT

Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development

(2013) Remo Sanges et al.   NUCLEIC ACIDS RESEARCH

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

(2013) N. J. Sakabe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

Ancient cis-regulatory constraints and the evolution of genome architecture

(2013) Manuel Irimia et al.   TRENDS IN GENETICS

Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression

(2012) Ana Ariza-Cosano et al.   BMC GENOMICS

A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development

(2012) Sharon L. Paige et al.   CELL

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(2012) Joseph A. Wamstad et al.   CELL

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

Epigenomic Annotation of Enhancers Predicts Transcriptional Regulators of Human Neural Crest

(2012) Alvaro Rada-Iglesias et al.   Cell Stem Cell

Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo

(2012) Michal Levin et al.   DEVELOPMENTAL CELL

Characterization of Genomic Regulatory Domains Conserved across the Genus Drosophila

(2012) Virginia Sahagun et al.   Genome Biology and Evolution

An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement

(2012) I. Maeso et al.   GENOME RESEARCH

Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints

(2012) M. Irimia et al.   GENOME RESEARCH

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

(2012) O. Bogdanovic et al.   GENOME RESEARCH

ENCODE: The human encyclopaedia

(2012) Brendan Maher   NATURE

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Ancient deuterostome origins of vertebrate brain signalling centres

(2012) Ariel M. Pani et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

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

Landscapes and archipelagos: spatial organization of gene regulation in vertebrates

(2012) Thomas Montavon et al.   TRENDS IN CELL BIOLOGY

Concept of neural genoarchitecture and its genomic fundament

(2012) Luis Puelles et al.   Frontiers in Neuroanatomy

Development of the larval anterior neurogenic domains of Terebratalia transversa (Brachiopoda) provides insights into the diversification of larval apical organs and the spiralian nervous system

(2012) Scott Santagata et al.   EvoDevo

Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State

(2012) Bartek Wilczynski et al.   PLoS Computational Biology

Human Developmental Enhancers Conserved between Deuterostomes and Protostomes

(2012) Shoa L. Clarke et al.   PLoS Genetics

A Framework for the Establishment of a Cnidarian Gene Regulatory Network for “Endomesoderm” Specification: The Inputs of ß-Catenin/TCF Signaling

(2012) Eric Röttinger et al.   PLoS Genetics

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

Evolution of Gene Regulatory Networks Controlling Body Plan Development

(2011) Isabelle S. Peter et al.   CELL

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency

(2011) R David Hawkins et al.   CELL RESEARCH

Noggin and Noggin-Like Genes Control Dorsoventral Axis Regeneration in Planarians

(2011) M. Dolores Molina et al.   CURRENT BIOLOGY

A Bmp/Admp Regulatory Circuit Controls Maintenance and Regeneration of Dorsal-Ventral Polarity in Planarians

(2011) Michael A. Gaviño et al.   CURRENT BIOLOGY

Evolutionary crossroads in developmental biology: amphioxus

(2011) S. Bertrand et al.   DEVELOPMENT

Genome-wide identification of conserved regulatory function in diverged sequences

(2011) L. Taher et al.   GENOME RESEARCH

Dissecting the Transcriptional Regulatory Properties of Human Chromosome 16 Highly Conserved Non-Coding Regions

(2011) José Luis Royo et al.   PLoS One

Transphyletic conservation of developmental regulatory state in animal evolution

(2011) J. L. Royo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

(2011) Naoki Irie et al.   Nature Communications

An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation

(2011) Juan J. Tena et al.   Nature Communications

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

Ancient Vertebrate Conserved Noncoding Elements Have Been Evolving Rapidly in Teleost Fishes

(2010) A. P. Lee et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

(2010) Tomislav Domazet-Lošo et al.   NATURE

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

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

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

(2010) D. Schmidt et al.   SCIENCE

Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer

(2010) Manuel Irimia et al.   EvoDevo

Conserved noncoding elements and the evolution of animal body plans

(2009) Tanya Vavouri et al.   BIOESSAYS

Cis-regulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split

(2009) Anna Z Komisarczuk et al.   DEVELOPMENTAL BIOLOGY

A Developmental Perspective: Changes in the Position of the Blastopore during Bilaterian Evolution

(2009) Mark Q. Martindale et al.   DEVELOPMENTAL CELL

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention

(2009) A. L. Hufton et al.   GENOME RESEARCH

From the American to the European amphioxus: towards experimental Evo-Devo at the origin of chordates

(2009) Jordi Garcia-Fernandez et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish

(2009) Pavla Navratilova et al.   MOLECULAR GENETICS AND GENOMICS

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

(2009) Nathaniel D. Heintzman et al.   NATURE

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Eye evolution: common use and independent recruitment of genetic components

(2009) P. Vopalensky et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Conservation of enhancer location in divergent insects

(2009) J. Cande et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates

(2009) Gayle K. McEwen et al.   PLoS Genetics

Evolution of Otx paralogue usages in early patterning of the vertebrate head

(2008) Yoko Suda et al.   DEVELOPMENTAL BIOLOGY

Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes

(2008) Pavla Navratilova et al.   DEVELOPMENTAL BIOLOGY

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

(2008) L. Z. Holland et al.   GENOME RESEARCH

Identification of DPPA4 and other genes as putative Sox2:Oct‐3/4 target genes using a combination of in silico analysis and transcription‐based assays

(2008) Harini Chakravarthy et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Convergent Evolution of Clustering of Iroquois Homeobox Genes across Metazoans

(2008) M. Irimia et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene Expansion and Retention Leads to a Diverse Tyrosine Kinase Superfamily in Amphioxus

(2008) S. D'Aniello et al.   MOLECULAR BIOLOGY AND EVOLUTION

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

(2008) Axel Visel et al.   NATURE GENETICS

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE