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I'm looking for references on embedding graphs in surfaces (motivation: I was doodling and wondered how many distinct embeddings of $K_{3,3}$ into the torus there are.)

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Lando S.K., Zvonkin A.K. — Graphs on Surfaces and Their Applications

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See the wikipedia article on topological graph theory and the book Topological graph theory by Gross and Tucker.

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J.A. Bondy and U.S.R.Murty, Graph Theory with Applications.

Jonathan Gross and Thomas Tucker, Topological Graph Theory