The only thing wrong with your assumption is that anyone but a non-native speaker would say "by the bus." As the others have pointed out, the construction would be "by bus" or "by train" or whatever.
Nevertheless, it is certainly possible to say
John went to the academic conference on the bus.
Here is a movie poster that illustrates what I'm talking about:
Some may object that this might seem ambiguous, that it might seem as if the conference were being held on the bus itself, but in normal informal speech it would be easily understood. More likely the sentence would be reordered in this case, such as
John went on the bus to the academic conference.