Apocalypse no Toride, or "Fortress of the Apocalypse" by Kuraishi Yuu, follows 4 inmates at the Shouran Juvenile Reformatory: the falsely accused Maeda Yoshiaki, cool but dangerous Masafumi Yoshioka, the strong and silent but fair Iwakura Gou, and the smart-mouthed genius Yamanoi Mitsuru. Upon arriving at Shouran on false murder convictions, Maeda Yoshiaki would rather be anywhere on earth, but when a van full of infected zombies crashes into the prison and its passengers begin to attack the guards and inmates, Maeda and his cellmates begin a fight to the death to stay alive amongst the infected from the outside world and the anarchy that arises within the prison. Eventually forced to leave the prison's walls of safety, the boys of Cell 4 find horrors in the ravaged cities beyond what they could have ever imagined.
This manga provides examples of:
Abusive Parents: Mitsuru's mom was mentally unhinged and would lascerate his hands if he scored anything less than 100% on all of his exams. Mitsuru still cared deeply enough for her to murder a social worker who'd come to get him out of such an unsafe household.
An Arm and a Leg: Maeda thought they were going to kill him, but they were simply planning on cutting off the limb that was bitten by the Bokor.
And Then Maeda Was A Bokor: He's certainly infected, showed the increased regeneration and the ability to control the mindless zombies. The change wasn't full yet though, he still had only 1 pupil... and his genitals.
Apocalypse Anarchy: Type 2, and only because it happened fast. Uninfested shops are treated as open season for free supplies and equipment.
Bad Ass Pacifist: Played with when it comes to the cultists. They believe the zombies are divine, and have developed a special fighting style to deal with them without killing them. However, when it comes to humans who get in their way, they either shoot them on sight or toss them to the hoard.
Bad Guys Do the Dirty Work: At first. Maeda tries to hang back from the action, but eventually is forced to carry his weight in combat.
Blob Monster / The Worm That Walks: The Bokor uses a mound made of hundreds of zombies, which can form 'arms' to strike or capture targets. The mound also shift its mass around to protect him.
Cool Chair: And on top of the mound, he sits on a chair made of several zombies kneeling subserviently in the form of a throne.
Cast Full of Pretty Boys: While the "pretty" part is debatable*: While the main group of four and the juvie warden certainly aren't half bad, pretty much everyone else is either ordinary or sometimes rather ugly, the trope mostly comes from the fact that there have so far been two female characters in the entire series so far. Justified in that the main setting is a male juvenile detention center.
Chekhov's Gun: Iwakura's missile launcher was later used by Hitotsukabuto to shoot down the helicopter piloted by Hatt.
Combat Clairvoyance: Hitotsukabuto claimed that he can see 2 seconds into the future, allowing him to preemptively react to many dangers. He wasn't exaggerating.
Cult: The people pretending to be from the UN worship the Bokor as one closest to God and view the zombies as "angels".
Dwindling Party: At the end of each chapter there is a tally on the population of the academy for both inmates and guards. The initial tally was 144 survivors and, as of Chapter 29, now currently has 31 (along with additional survivors).
Even Bad Men Love Their Mamas: Yoshioka leads the boys to his mom's old arcade, which she kept open even after he left home, and sets the high score one last time.
Genre Savvy: Mitsuru is very intelligent, and figures out many central plot points simply through intuition. For instance, he manages to figure out that the Bokor's goal was to infect Maeda, and that the infection probably spreads very slowly based on how it would do things like bite of its own tongue so it could force Maeda to drink the resulting blood. When a survivor who's a biologist contact's the juvenile detention facility, he nearly hangs up on her because he's offended at how she felt the need to explain the nature of the outbreak to him using rabies as a point of reference—he'd figured out that a virus was to blame way earlier in the story.
Healing Factor: The Bokor can regenerate from having its head cut off or even its brains blown to bits. Though it takes time for it to fully regenerate.
Hive Mind: Maeda encounters a mysterious man who can exert some form of sound-based control over the zombies. They pile on top of one another to carry him, and grow in ferocity to defend him.
At first the zombies show intelligence even as they try to devour others, but become mindless very quickly. The "nimble" creatures appear to retain their intelligence and even trick the protagonists to entering a shed where they store food. They are also shown running away from the Bokor.
There's even those that "evolved" into seal-like creatures.
Power-Upgrading Deformation: First appearing in Vol. 2, the mutant zombies are roughly canine quadrupeds with human heads, hands, and feet. They completely lose the ability to speak, but run much faster than normal undead.
Reasonable Authority Figure: Arguably, Hitotsukabuto. At first he kicked the main characters out of the Academy as a form of death sentence, but when they returned with the promised weapons, he stuck true to his words of letting them stay (albeit with a little threat). During the Rikkun incident, he was willing to let the main characters go because they were attacked first. And during the Bokor's attack on the Academy, he protected Maeda from the Bokor's sound blast.
Stalker with a Crush / Stalker Without A Crush: Who knows what the deal is when it comes to the Bokor, but it's been obsessed with Maeda ever since he first harmed it and its got is to infect him and make Maeda into another Bokor.