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.
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.