Blood Music

Nothing is lost. Nothing is forgotten.
It was in the blood, the flesh,

And now it is forever.

—Closing lines

Blood Music is a 1985 science fiction novel by Greg Bear.

Biotechnologist Vergil Ulam creates simple biological computers based on his own lymphocytes ('noocytes'). After his employer orders him to destroy them, Vergil injects them into his own body with the intention of smuggling them out to work on them elsewhere. Inside the hostile -- but not completely lethal -- environment of his body, the noocytes multiply and evolve, quickly gaining self-awareness and building a civilization in his blood. When the civilization begins to spread to other humans and starts improving, then transforming its hosts, Hilarity Ensues.

Tropes used in Blood Music include:

Apocalypse How: Class 1, with the assimilation of North America, plus all the interesting aftereffects of the nano-civilization slightly breaking reality.
Ascend to a Higher Plane of Existence: The noocytes have to do this, since their presence is breaking reality. Everybody else too.
Assimilation Plot
Bio Augmentation: Vergil injecting the biological computers into himself. Augmentation indeed...
Body Horror: Some of the intermediate stages between Vergil injecting himself and The Singularity look to the uninformed a whole lot like a horror film.
Empty Piles of Clothing: In most cases, the spreading infection vaporizes humans almost instantly, leaving only their clothes.
Fictional Counterpart: Vergil drives into Livermore, California, and passes a Guinevere's Pizza. From the local description, this fictional pizza place is exactly where a Round Table Pizza existed at the time.
From a Single Cell: The noocytes are able to encode the squishy chemical versions of people into molecular memories based on DNA/RNA. The noocytes can rebuild and upload the original person -- or an amalgam of all who want to participate -- back into a squishy flesh body should they so wish.
Lego Genetics
Nanomachines: Technically biological in origin, but on the nano-scale the line between organism and machine is blurry anyway.
The Singularity: After assimilating most of North America, the new civilization is forced to Ascend to a Higher Plane of Existence to avoid breaking reality by overloading or freezing it solid it with the quantum Observer Effect of an ever-increasing number of nanoscale intelligences always watching and measuring the world around them.
Synthetic Plague: Oops.