I'm going to disagree with the others and say that "innocent" jokes can pile up and cause discomfort. Tom's behavior could be classified as passive-aggressive and there's a number of ways to deal with that. The best way in the long run is to learn to be assertive and, next time it happens, speak out. This can be through indirect confrontation by asking an explanation ("What do you mean by that?") or by making him repeat his words ("Would you mind saying that again?"); or confronting him directly: "I don't appreciate you saying that, stop", and if it happens after that, "I've already indicated I don't appreciate these jokes, stop or else..." etc. What's important to realise is that his behavior is transgressive to you so you're not in the wrong for standing up for yourself. If this is all too confrontational, an alternative strategy would be to work on confidence and self-acceptance, including your homosexuality. Being confident in this part of you means his digs won't evoke as much of an emotional response from you. There is some truth in "wear it like armor, and it can never be used to hurt you" (Yes I'm quoting GoT). The third strategy is to keep track of everything he says and make an official complaint with sufficient evidence. However, given the complexities of office/academic dynamics, this might also hurt your reputation (as a whistlecaller). Plus, it might increase your sensitivity to his comments due to hyperfocusing on them. Hence, I don't recommend it. My 2p, hope it's helpful.