The answer is based on the question before the edit, when Winnie-the-Pooh was the first example. But it does hold for the new example as well. are multiple books on Winnie the Pooh:
When We Were Very Young (1924) · Winnie-the-Pooh (1926) · Now We Are Six (1927) · The House at Pooh Corner (1928) · Return to the Hundred Acre Wood (2009)
I am now in a dilemma: there is a book with that exact title, and therefore I would prefer "I read the book Winnie-the-Pooh".
If the book is of great fame, I would only say "I read Winnie-the-Pooh, as people would know that it was a book.
But the majority of people would probably not be aware that there is a book of that exact title, but know that there are multiple books on Winnie the Pooh available.
The first form would emphasize on "you know, the one and only book about Winnie the Pooh". There might be several books (or papers), but one stands out. Like talking about the SQL paper would lead me back to the original SQL proposal by Edgar Frank Codd. Or the C++ book would certainly point to Bjarne Stroustrup's "The C++ Programming Language".
Therefore, if there is a reference paper on a subject, or the book is of great fame (maybe only within the audience you are talking to), I would use the first form. Otherwise I would use the second. I even would insert something like "called" or "titled" in the second form, but that just might be me.
For your second example I would also use the second form, as it pinpoints one definitively defined paper. And the title is so long that the short term memory is under stress parsing the sentence, waiting for the subject you are talking about ;).
If the book or paper is of great fame:
I read To Kill a Mockingbird.
If it is rather unknown, part of a series, or available on several medias (book, comics, e-book):
I read the book Winnie-the-Pooh.
If it is a reference of a whole class of books or papers:
I read the C++ book.