Understanding complex systems often requires a bottom-up analysis towards a systems
biology approach. The need to investigate a system, not only as individual components but …

Abstract Systems analysis of metabolic and growth functions in microbial organisms is
rapidly developing and maturing. Such studies are enabled by reconstruction, at the …

Gene co-expression networks can be used to associate genes of unknown function with
biological processes, to prioritize candidate disease genes or to discern transcriptional …

Machine learning approaches offer the potential to systematically identify transcriptional
regulatory interactions from a compendium of microarray expression profiles. However …

Living organisms have evolved a plethora of sensing systems for the intra-and extracellular
detection of small molecules, ions or physical parameters. Several recent studies have …

We consider the problem of learning a binary classifier from a training set of positive and
unlabeled examples, both in the inductive and in the transductive setting. This problem …

Aminoglycoside antibiotics, such as gentamicin and kanamycin, directly target the ribosome,
yet the mechanisms by which these bactericidal drugs induce cell death are not fully …

Modulation of bacterial chromosomal supercoiling is a function of DNA gyrase‐catalyzed
strand breakage and rejoining. This reaction is exploited by both antibiotic and proteic …

A survey of the use of graph theoretical techniques in Biology is presented. In particular,
recent work on identifying and modelling the structure of bio-molecular networks is …

Sequence motifs are becoming increasingly important in the analysis of gene regulation.
How do we define sequence motifs, and why should we use sequence logos instead of …