ABSTRACT
This Chapter surveys graphical models as used in molecular and systems biology, with an emphasis on their use for making inferences about molecular networks, that is the task of estimating molecular networks directly from data on e.g. genes or proteins. It covers the use of graphical models in genetics as well as in metagenomics. Molecules in cells, including proteins, transcripts and DNA, influence one another via diverse physical and chemical mechanisms. One kind of influence is clear from the description above, namely that the DNA sequence influences the transcript which in turn influences the protein. Graphical models are increasingly becoming a key part of the molecular and systems biology toolkit. They provide a principled statistical framework for network-related questions that arise in systems biology. The majority of graphical model applications in the literature to date have focused on one data type. However, it is increasingly common to obtain multiple complementary data types from the same set of biological samples.
