Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression

HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature

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GENCODE: The reference human genome annotation for The ENCODE Project

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

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Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome

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Analysis of variation at transcription factor binding sites in Drosophila and humans

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Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

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Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer

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The evolution of gene expression levels in mammalian organs

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

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The evolution of gene expression and the transcriptome–phenotype relationship

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Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq

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A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila

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Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

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Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

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The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

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Gene expression divergence recapitulates the developmental hourglass model

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Genetic analysis of variation in transcription factor binding in yeast

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

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Variation in Transcription Factor Binding Among Humans

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

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Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

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

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Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

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

(2008) Sean B. Carroll   CELL

Evolution of Primate Gene Expression: Drift and Corrective Sweeps?

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Polytene Chromosomal Maps of 11 Drosophila Species: The Order of Genomic Scaffolds Inferred From Genetic and Physical Maps

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

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On the relation between promoter divergence and gene expression evolution

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Structure and function of a transcriptional network activated by the MAPK Hog1

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Extant mammal body masses suggest punctuated equilibrium

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Species-Specific Transcription in Mice Carrying Human Chromosome 21

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Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts

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Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

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Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes

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

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Model-based Analysis of ChIP-Seq (MACS)

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