For starters, chemical environment modeling. But also cells differentiate, so in any system you need to understand the differentiation, and how those differentiated cells will change the environment of other cells, based on the environment they encounter.

That's not to say you can't glean a ton from DNA, but there are some external inputs we may simply never know enough about to incorporate into the model. Ultimately DNA IS all you need...if you have perfect environmental information.

The article I posted shows what is working better - the Olga Troyanskaya / David Kelley style models. There was another one (Kundaje group?) recently that used Hi-C data.