Introduction to Automata Theory, Languages, and Computation, 2nd Ed.
Which is basically all the goodness in Structure and Interpretation... and any book on compilers and interpreters. Basically, though I don't reckon that any modern courses teach from Hopcroft & Ullman, it's a major textbook in the field (unfortunately the 2nd ed is easier to find but the 1st has the works).
Another foundational text is Andrew Tennebaum's book on Operating Systems:
Operating Systems Design and Implementation
To be honest I don't how it compares with the book proposed in the article, since I haven't read that book.
Finally, two personal recommendations for anyone interested in AI (as a study of advanced CS concepts and not just as a way to make a quick buck with a shallow understanding of a few machine learning tutorials):
Artificial Intelligence: A modern approach (Russel & Norvig)
And the free pdf of AI Algorithms, Data Structures, and Idioms in Prolog, Lisp, and Java:
Which doubles as a good textbook for programming languages in general.
That's the book Linus Torvalds read. :)
 - http://www.amazon.com/dp/0131429388
At the end of the course, we had only the boot loader and a little command interpreter, aside from FAT-12 support.
Then, much later, I messed with OS by playing with the code from the Minix Book .
Last year I wrote a little emulator for a virtually unknown architecture that can run uClinux on a modern browser (i.e., Chrome).
 Operating System Design and Implemenation: http://www.amazon.com/Operating-Systems-Design-Implementatio...
Computer Systems: A Programmer's Perspective
I liked this much better than Computer Organization and Design by Patterson and Hennessy which everyone has encountered at some point. The developer-centric view was very cool.
Kernel Exploitation: Attacking the Core
Most 'hacking' books are goofy. This one is very good and doubles nicely as a hackers operating systems text.
Web Application Hackers Handbook
Very nice overview for web concerns.
Operating System Design and Implementation
I don't agree with Tanenbaum's views on micro vs. monolithic kernels but this book is a great mix of theory and implementation.
Linux Kernel Devleopment
I used this to get a feel for the monolithic implementations of topics covered by Tanenbaum.
TCP/IP Illustrated Series. More than you would ever want to know.
It is written be Andrew S Tanenbaum, the author of minix. The book contains whole of minix source code. Nothing beats learning from reading actual codes. Linus Torvalds was inspired by this book. In his autobiography "Just For Fun", Torvalds describes it as "the book that launched me to new heights".
Also, Operating Systems Design and Implementation, aka the Minix book, is an amazing resource.( http://www.amazon.com/Operating-Systems-Design-Implementatio... )
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