  We prove that the open topological string partition function on a D-brane
configuration in a Calabi-Yau manifold X takes the form of a closed topological
string partition function on a different Calabi-Yau manifold X_b. This
identification shows that the physics of D-branes in an arbitrary background X
of topological string theory can be described either by open+closed string
theory in X or by closed string theory in X_b. The physical interpretation of
the ''bubbling'' Calabi-Yau X_b is as the space obtained by letting the
D-branes in X undergo a geometric transition. This implies, in particular, that
the partition function of closed topological string theory on certain bubbling
Calabi-Yau manifolds are invariants of knots in the three-sphere.
