There has been a lot of discussion on this topic, including a couple of threads this year. But,
this post of mine gives an overview of the available methods. Nothing has changed recently, so it is still correct.
I don't know if any of them are suitable for references needed for writing papers. They give you the highlighted text, any annotation you make and a vague location. The location is chapter name and a percent read. Any of the methods listed should give you something you can copy elsewhere.