Abstract Changes in the patterns of gene expression are widely believed to underlie many of
the phenotypic differences within and between species. Although much emphasis has been …

Coordinated regulation of gene expression relies on transcription factors (TFs) binding to
specific DNA sites. Our large-scale information–theoretical analysis of> 950 TF-binding …

By the onset of morphogenesis, Drosophila embryos consist of about 6000 cells that express
distinct gene combinations. Here, we used single-cell sequencing of precisely staged …

In higher eukaryotes, transcriptional enhancers play critical roles in the integration of cellular
signaling information, but apart from a few well‐studied model enhancers, we lack a general …

We have sequenced the genome of a second Drosophila species, Drosophila
pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a …

A central problem in the bioinformatics of gene regulation is to find the binding sites for
regulatory proteins. One of the most promising approaches toward identifying these short …

Non-coding DNA comprises∼ 80% of the euchromatic portion of the Drosophila
melanogaster genome. Non-coding sequences are known to contain functionally important …

The segmentation gene network of Drosophila consists of maternal and zygotic factors that
generate, by transcriptional (cross-) regulation, expression patterns of increasing complexity …

Background The identification of sequences that control transcription in metazoans is a
major goal of genome analysis. In a previous study, we demonstrated that searching for …

Background Cis-regulatory modules are combinations of regulatory elements occurring in
close proximity to each other that control the spatial and temporal expression of genes. The …