Statistical models of TF/DNA interaction

Gene expression is regulated in response to metabolic necessities and environ-mental changes throughout the life of a cell. A major part of this regulation is governed at the level of transcription, deciding whether messengers to specific genes are produced or not. This decision is triggered by the action of transcrip-tion factors, proteins which interact with specific sites on DNA and thus influ-ence the rate of transcription of proximal genes. Mapping the organisation of these transcription factor binding sites sheds light on potential causal relations between genes and is the key to establishing networks of genetic interactions, which determine how the cell adapts to external changes. In this work I review briefly the basics of genetics and summarise popular ap-proaches to describe transcription factor binding sites, from the most straight forward to finally discuss a biophysically motivated representation based on the estimation of free energies of molecular interactions. Two articles on tran-scription factors are contained in this thesis, one published (Aurell, Fouquie