How can I encourage students to ask questions in class
Here are several ideas to consider. I'm not sure I necessarily recommend all of them but I've seen them being tried for better or worse results:
Make it a dialog by asking your students questions yourself. More specifically, pose questions which students are not very likely to just figure out; this will lead to almost no people raising their hands. Now pick someone you've decided in your infinite wisdom you should be hearing more from. Ask them to answer you. They may protest, or evade, but try to get them to explain what's preventing them from answering. Then "rhetorically reward" them for posing their problem in the form of the question. Repeat the question to the class, then answer it. Or rather - don't quite answer it completely, answer it partially so that you end up posing another question.
Teach slower. One of the reasons people don't ask questions is that they "lose" the teacher, who's going through things much faster for them to even formulate questions.
Don't hastily assume there are no questions. When you've finished a segment of your presentation, don't immediately rush to ask "any questions?" - make a pause first; then ask; then wait a while; like @Anonymous suggests, it should be a good number of seconds. It will seem like an eternity to you - but not to them, they're just catching their breath / trying to wrap their brains about what you just said.
Be more creative about how to ask for questions. Asking "any questions?" often comes off as you wanting to not hear any questions. A Professor at my alma mater is famous for using "so, are you 'buying' this? Yes or no?" and then saying "Well, ok, but if you're buying it, you're going to have to accept it as an assumption, and that's on you, not on me. So are you sure?"
Offer rewards for participating in class. The final grade in the course can be improved over the 'dry' results of HW assignment and exam grades based on participating in class; and when students ask a meaningful question (but this is also for comments; you can't usually only reward questions), you write down their name.
Get someone to contradict you. This is obviously much easier when you're teaching history, social studies, political science etc., but with some work it's sort-of possible also in hard sciences and math. Either by having an opponent present cases in which your claim is difficult to apply; or by you intentionally glossing over a proof of some lemma; and so on. This of course requires the participation of a TA, another lecturer, or in some cases a student who's able enough to handle it (this can be a bit problematic in terms of his/her experience in your class, but in graduate school not terribly hard).
Plant student questions yourself (v1). Before class, find one or two willing students; give them a question on a piece of paper; ask them not to reveal it to their friends (but maybe make sure their friends will try to peek and read it); and ask them to raise their hands and ask the question at some point (perhaps say when it should be asked on the paper). Now, these can sometimes be questions you actually want to answer yourself; sometimes they can be "faux questions", the relevance of which you want to get other students to challenge; or they could be questions which you want to direct back either at the person who asked them, or at other in class - asking them for help in answering.
Plant student questions yourself (v2). Add to the lecture notes several questions which are non-immediate conclusions, or lessons, which one can derive with some thought from what you're going to teach. Remind students at the beginning and the end of classes of these questions, and perhaps even state they may well appear on the exam, as stated or in variations. Perhaps have your TAs go over a part of them (not many) in their sessions, maybe once or twice at the beginning of the semester so that the students experience the nature of these questions. You are then likely to get either these questions themselves asked in class, or questions which students believe will help them resolve these questions.
Again, these different methods have pros and cons, and are rooted in different conceptions of the students-teachers relationship; take your pick according to your philosophy of teaching.
I frequently stop for questions. I find that it's helpful to stop for about seven seconds.
Seven seconds is longer than it sounds. It's nearly enough time for Usain Bolt to run 100 meters. Towards the end of it, you might start to feel a bit foolish standing in front of the class silently, smiling and looking around. I sometimes do.
But I often get a question around second five or six.
I'm teaching a very large lecture class in linguistics at the moment; I use an anonymous live-polling system that accepts answers by text, Wi-Fi, etc.
Normally I open a lecture by quickly reviewing key concepts of the previous one and asking for votes on which concepts to go over. I wait a couple of minutes for results, then revisit the top five in more detail.
Then I stop halfway through the lecture, open the poll, stand there, and say, "Okay. Ask me questions."
Making a poll anonymous always brings the risk of abuse, but removes the fear-of-judgment factor whatever its cause (shyness/introversion/low self-esteem, doubt about worthiness of question, anti-'keener' sentiment, etc.). And I keep standing there expectantly even if there are no questions for the first couple of minutes, which usually acts as a further antidote to reluctance. They might as well if no one else is asking questions!
I usually get a mix of A) useful questions ("Why doesn't English have as much inflection as Old English did?" or "Can you explain the Great Vowel Shift again?"), B) silly questions ("How many roads must a man walk down?" or "I like your shirt; where did you get it?", and C) a few profane/nonsensical questions. I answer the A)s, playfully integrate a B) or two if there's time, and ignore the C)s entirely (or be facetiously dismissive of them if I feel like trying to make the rest of the class laugh).
I thought about doing this at the end of lecture, but when one student out of 317 in attendance decides to pack up and leave, they all do that. Halfway through seems to work better for waiting around for questions.