Graphs embedded in 3-manifolds

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Is there any work done in graph theory, where graphs are embedded in different 3-manifolds? E.g. several graph properties can have expanded meanings in this case, even cycles can be of two types: trivial (bound a disk) or non-trivial... What would be some references?

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Some keywords: "spatial graphs", "flat vertex graphs", "ribbon graphs"

An example is graphs show up as the 1-skeleton of a cellular/simplicial decomposition of a manifold.

There are invariants of embeddings of graphs, at least in $S^3$:

(Yamada doesn't mention this, but the polynomial is a renormalization of the $U_q(\mathfrak{sl}(2))$ Reshetikhin-Turaev invariant colored by the 3-d irreducible representation.)

In Dror Bar-Natan's answer for this MathOverflow question, he says that the theory of knotted graphs in $S^3$ reduces to the theory of tangles by choosing a maximal spanning tree and isotoping it to some standard form.