There is an increasing interest in detecting genes, or genomic regions, that have been
targeted by natural selection. The interest stems from a basic desire to learn more about …

Identifying genomic locations of transcription-factor binding sites, particularly in higher
eukaryotic genomes, has been an enormous challenge. Various experimental and …

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the
chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to …

Despite the central importance of noncoding DNA to gene regulation and evolution,
understanding of the extent of selection on plant noncoding DNA remains limited compared …

Genomic array analysis of endogenous mammalian ribonucleoproteins has recently
revealed three novel findings:(1) mRNA binding proteins are associated with unique …

Targeted transcript profiling studies can identify sets of co-expressed genes; however,
identification of the underlying functional mechanism (s) is a significant challenge …

Computational analysis of polymerase II (Pol II) promoters may contribute to improved gene
identification and to prediction of the expression context of genes. Before assessing the state …

With the continuing accomplishments of the human genome project, high-throughput
strategies to identify DNA sequences that are important in mammalian gene regulation are …

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of
orthologous regulatory regions from multiple species. It does so by identifying the best …

Identifying transcriptional regulatory elements represents a significant challenge in
annotating the genomes of higher vertebrates. We have developed a computational tool …