The following algorithm problem occurred to me while drawing a graph for something unrelated:
The paper On the one-sided crossing minimization in a bipartite graph with large degrees by Hiroshi Nagamochi mentions that the original paper on the crossing number by Garey and Johnson also proved that minimising the number of edge crossings is NP-hard for bipartite graphs. In fact, it is still NP-hard even if you are told the optimal order for one column:
Given a bipartite graph, a 2-layered drawing consists of placing nodes in the first node set V on a straight line L1 and placing nodes in the second node set W on a parallel line L2. The problem of minimizing the number of crossings between arcs in a 2-layered drawing was first introduced by Harary and Schwenk. The one-sided crossing minimization problem asks to find an ordering of nodes in V to be placed on L1 so that the number of arc crossings is minimized (while the ordering of the nodes in W on L2 is given and fixed). Applications of the problem can be found in VLSI layouts and hierarchical drawings.
However, the two-sided and one-sided problems are shown to be NP-hard by Garey and Johnson and by Eades and Wormald , respectively.