The following is a list of security references that I have found to be useful. Two of the best books on systems security engineering also happen to be freely available as PDFs. These include:

• Security Engineering by Ross Anderson (2nd edition) http://www.cl.cam.ac.uk/~rja14/book.html
• Engineering Security by Peter Gutmann https://www.cs.auckland.ac.nz/~pgut001/pubs/book.pdf