New Publication: Computational Prediction of Domain-domain Interactions: Factor-graph Based Modelling and Inference

This is very much Mudassar’s paper – a review of work he has done prior to being in my lab. Full credit (and congratulations) goes to Mudassar. That said, we very much appreciate Charlie’s editorial input that really helped improve the final version.


Iqbal, M., Hodgman, T.C. and Stekel, D.J. 2014. Computational prediction of domain-domain interactions: factor-graph based modelling and inference. Current Chemical Biology 7:234-240.


Proteins interact with each other to perform an array of cellular functions. A systems-level knowledge of protein interaction networks, as well as the underlying domain-domain interactions, constitutes a major goal in systems biology. In this mini-review, we discuss some background to the problem of inference of domain-domain interactions and briefly discuss some relevant computational and statistical approaches. Specifically, we review our earlier work in which we formulate this problem using a graphical model combined with inference of domain-interaction probabilities using powerful statistical inference methods, namely belief propagation. The inferred interactions can be used for analysing network data, and, by looking at the specificity of protein-protein interactions, they can also be used to predict novel protein interactions within and across orthologous species.