The compilation of multiple metazoan genome sequences and the deluge of large-scale
expression data have combined to motivate the maturation of bioinformatics methods for the …

Proteins, such as many transcription factors, that bind to specific DNA sequences are
essential for the proper regulation of gene expression. Identifying the specific sequences …

Although the proteins that read the gene regulatory code, transcription factors (TFs), have
been largely identified, it is not well known which sequences TFs can recognize. We have …

Abstract JASPAR (http://jaspar. genereg. net) is the largest open-access database of matrix-
based nucleotide profiles describing the binding preference of transcription factors from …

Sequence preferences of DNA binding proteins are a primary mechanism by which cells
interpret the genome. Despite the central importance of these proteins in physiology …

Most homeodomains are unique within a genome, yet many are highly conserved across
vast evolutionary distances, implying strong selection on their precise DNA-binding …

A major goal of systems biology is to predict the function of biological networks. Although
network topologies have been successfully determined in many cases, the quantitative …

Transcription factors recognize specific genomic sequences to regulate complex gene-
expression programs. Although it is well-established that transcription factors bind to specific …

The genetic code—the binding specificity of all transfer-RNAs—defines how protein primary
structure is determined by DNA sequence. DNA also dictates when and where proteins are …

Metastases are the main cause of cancer deaths, but the mechanisms underlying metastatic
progression remain poorly understood. We isolated pure populations of cancer cells from …