Maybe not the right spot but...does anybody know about good note-taking software for PDF files?

Basically I'd like to go digital for what I've been doing old school up to this point.

I've been reading lots of scientific studies and articles and they usually come in PDF.

I used to print them, write my notes in the margins and store them in a filing cabinet, but this is getting really cumbersome (and the university is now forcing me to relocate my filing cabinets).

While reading, I'd like to be able to click on a paragraph and add a note with my thoughts, questions, etc. and also save these notes into the document somehow so they show up for others or when they are printed etc.

Does anybody have a good suggestion? Thanks