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

A systematic approach to identify functional motifs within vertebrate developmental enhancers

(2009) Qiang Li et al.   DEVELOPMENTAL BIOLOGY

Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis ofcis-regulatory regions in zebrafish

(2009) José Bessa et al.   DEVELOPMENTAL DYNAMICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

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

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos

(2009) Jochen Gehrig et al.   NATURE METHODS

Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates

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

Transcriptional features of genomic regulatory blocks

(2009) Altuna Akalin et al.   GENOME BIOLOGY

cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation

(2008) J. Persampieri et al.   BIOINFORMATICS

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Functional resolution of duplicated hoxb5 genes in teleosts

(2008) O. Jarinova et al.   DEVELOPMENT

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

(2008) Pavla Navratilova et al.   DEVELOPMENTAL BIOLOGY

Large Number of Ultraconserved Elements Were Already Present in the Jawed Vertebrate Ancestor

(2008) J. Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters

(2008) Gwenael Badis et al.   MOLECULAR CELL

Subfunctionalization of Duplicated Zebrafish pax6 Genes by cis-Regulatory Divergence

(2008) Dirk A. Kleinjan et al.   PLoS 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

Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation

(2008) Emily E. Hare et al.   PLoS Genetics

Identification of Neural Crest and Glial Enhancers at the Mouse Sox10 Locus through Transgenesis in Zebrafish

(2008) Anthony Antonellis et al.   PLoS Genetics

Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes

(2008) Pär G Engström et al.   GENOME BIOLOGY

Conserved non-coding sequences and transcriptional regulation

(2007) Uwe Strähle et al.   BRAIN RESEARCH BULLETIN

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b

(2007) D. M. McGaughey et al.   GENOME RESEARCH

Large-Scale Appearance of Ultraconserved Elements in Tetrapod Genomes and Slowdown of the Molecular Clock

(2007) S. Stephen et al.   MOLECULAR BIOLOGY AND EVOLUTION