The regulatory interactions between transcription factors and their target genes can be
conceptualised as a directed graph. At a global level, these regulatory networks display a …

The term 'transcriptional interference'(TI) is widely used but poorly defined in the literature.
There are a variety of methods by which one can interfere with the process or the product of …

A full description of a protein's function requires knowledge of all partner proteins with which
it specifically associates. From a functional perspective,'association'can mean direct physical …

Prediction of metabolic changes that result from genetic or environmental perturbations has
several important applications, including diagnosing metabolic disorders and discovering …

Metagenomics projects based on shotgun sequencing of populations of micro-organisms
yield insight into protein families. We used sequence similarity clustering to explore proteins …

Most of the published quantitative models in biology are lost for the community because they
are either not made available or they are insufficiently characterized to allow them to be …

The goal of this group project has been to coordinate and bring up-to-date information on all
genes of Escherichia coli K-12. Annotation of the genome of an organism entails …

Numerous studies have considered the emergence of metabolic pathways, but the modes of
recent evolution of metabolic networks are poorly understood. Here, we integrate …

Abstract The EcoCyc database (http://EcoCyc. org/) is a comprehensive source of
information on the biology of the prototypical model organism Escherichia coli K12. The …

A new online framework for the accurate and integrative prediction of transcription factor
binding sites (TFBSs) in prokaryotes was developed. The system consists of three …