I'm moving to BKK in January for research at Chula and will be staying until mid of May.

I've been to Thailand various times already but my scholarship is limited and I'm a little worried about where I might end accommodationwise - sois are to be avoided, I guess? But how with all the apartments being in there?

Who told you that Bangkok is such a danger place to live????????

Well, my Thai friends recommended me to pay attention on a couple of things and I would certainly feel better not walking home alone through darkish alleys. Same things I avoid here.

Fair enough but not all sois are dark alleys. Perhaps stay in a cheap hotel for a bit while you check around.

To a certain extent you can't avoid the sois but some of them are well lit and have people walking until the late hours.

Personally I would avoid the sois around Victory Monument area and try and stick to something more central.

Kasemsan soi 3 has quite a few rental places and is a very safe soi. Doesn't bother me to walk up there late at night at all. Same for Kasemsan 1

At the end of the day you need to have your wits about you at all times and have some common sense. I personally don't avoid somewhere just because it is a soi. However I would avoid it if it was not very well lit and there were few people round after dark. Also I avoid going through any slum areas on my own. There are a few dotted around Bangkok.

Any experiences with the sois off BTS Phayathai, especially Petchburi 7ish?

Petchburi is fine, as is anywhere in the city as long as you take usual precautions.