Hi--Your best bet is the south end of San Francisco, where you can jump on the freeways and get to your job. Some areas to consider are Bernal Heights, Excelsior, the Mission, and of course, those areas just outside SF such as Brisbane and Daly City.

In terms of apartment share prices, Craigslist will be your best bet. I'd actually recommend plugging in your criteria and seeing what neighborhoods pop up.

With the new UC Med Center and other organizations not only moving, but building brand new buildings in the area, Mission Bay has the potential to be fantastic. Currently, it's a trendy area with the most know neighborhood being the Dogpatch...lots of lofts, condos and some brand new stuff there as well. Also, both Hayes Valley, Mission Dolores, parts of the Mission and Bernal Heights are all wonderful places to live. Lots of places to go, eat, hang out, etc.

I'd say Daly City. But there are really quite a few. Cheapest and relatively safe huh?
How much danger will you tolerate to feel "relatively safe". You can be in the worst parts of the city and be "relatively safe".
There is a writer that is just back from a tour of duty in Iraq and is being interviewed on NPR about his book. He lives in the Tenderloin neighborhood and he says he loves it "the women are all so nice they are constantly asking him if he wants a date and there are so many young men that ask if he needs anything. It is the most friendly neighborhood he's ever lived in".
If you are an urban person you will be fine anywhere. Look to Craigslist for prices and get a map of the neighborhoods. The Bio/Phrama areas are in Mission Bay in San Francisco, Brisbane and South San Francisco on the Peninsula and Emeryville, North Oakland and South Berkeley in the East Bay. Genentech runs shuttles from Glen Park BART to the So SF campus.