Evidence convinced the judge to deny bail.
The 25-year-old victim was found dead in her apartment after it had been burglarized.
Harvey told police that Howard had burglarized his apartment, but lack of evidence at the time precluded his arrest.
Enhanced DNA testing technology allowed investigators to connect Howard to the murder.
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"In Mr. Howard’s case, he’s managed to go decades because he did it behind closed doors and because the science wasn't available in 1988," said prosecutor Brian Davidson.
During Thursday’s bail hearing, Detective Meredith Hopper said investigators submitted evidence for DNA testing in 2012 and got a hit in 2013.
She said tests determined Howard's DNA was found on a pair of bloody pink underwear tucked into Harvey’s waistband and on a bloody white pillowcase found two to three feet from her body.
Detectives said Harvey was wearing another pair of underwear. There was no evidence Harvey was sexually assaulted, according to investigators.
Howard's defense attorney argued the evidence and the prosecution's theories about the motive for the killing were not enough to deny his client bail, but the judge disagreed.
Howard's trial is set to begin February 22.
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