The purpose of this article is to provide a brief history of the development and application of
computer algorithms for the analysis and prediction of DNA binding sites. This problem can …

Background Unraveling the mechanisms that regulate gene expression is a major challenge
in biology. An important task in this challenge is to identify regulatory elements, especially …

The MEME Suite is a powerful, integrated set of web-based tools for studying sequence
motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their …

Problems with multiple objectives arise in a natural fashion in most disciplines and their
solution has been a challenge to researchers for a long time. Despite the considerable …

Improving the accuracy of prediction of gene starts is one of a few remaining open problems
in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of …

The gaseous plant hormone ethylene regulates a multitude of growth and developmental
processes. How the numerous growth control pathways are coordinated by the ethylene …

Abstract Activator protein 1 (AP-1, also known as JUN) transcription factors are dimers of
JUN, FOS, MAF and activating transcription factor (ATF) family proteins characterized by …

Most human transcription factors bind a small subset of potential genomic sites and often
use different subsets in different cell types. To identify mechanisms that govern cell-type …

Quorum-sensing bacteria communicate with extracellular signal molecules called
autoinducers. This process allows community-wide synchronization of gene expression. A …

The prediction of regulatory elements is a problem where computational methods offer great
hope. Over the past few years, numerous tools have become available for this task. The …