The body of 24-year-old Annie Le was found stuffed behind a Yale research lab wall in September. An autopsy determined she was strangled.
Authorities say in the warrant that a green-ink pen found under Le's body had her blood on it as well as DNA from suspect Raymond Clark III on its cap. Police have said Clark signed into the secure building with a green pen on Sept. 8, the day Le disappeared.
The warrant says DNA from both Le and Clark was on a bloody sock found hidden in a ceiling.
A message was left for Clark's public defender Friday.
Clark, 24, is charged with murder. Le vanished Sept. 8 from the Yale medical school research building where she and Clark worked, and her body was found five days later on what was to be her wedding day. She was wearing surgical gloves, according to the affidavit.
Clark has not yet entered a plea, but his attorney has said he will plead not guilty.
The warrant, which does not offer a motive, describes a bloody crime scene and Clark's efforts to scrub floors.
Clark said he knew Le for at least four months and did not socialize with her. He told police Le left the building 15 minutes before him carrying her notebook and two bags of mouse food.
Two days after Le disappeared, a graduate student showed a Yale police officer a box of "wipe alls" on a cart in a lab that had what appeared to be blood splattered on it. The officer watched Clark move the box of wipes and turn the box so that the bloody spots were no longer visible, authorities said.
"Once Clark moved the box of wipes, he then leaned up against the cart and made small talk" with the officer, the affidavit states.
Clark later came back into the room and began scrubbing the floor with SOS pads and cleaning solution even though the floor appeared clean, according to the affidavit.
Investigators uncovered "a possible medium velocity blood-like spray pattern" on the wall that tested positive for blood and apparent efforts to clean the blood off the wall.
Authorities said Clark changed his clothes at least once when the FBI was processing the scene, citing video surveillance of the building.
Authorities said they also found in the building a pair of work boots labeld "Ray-C" that had blood-like stains on them, and a hospital scrub shirt with blood-like stains that was similar to the shirt Clark wore.
Le entered her lab, known as G13, at 10:11 a.m. Sept. 8. Clark's card shows he accessed the victim's lab at about 10:40 a.m. and again at 11:04 a.m. and no other locations for 46 minutes.
Clark's key card was the only one used to access a room where blood was found after Le entered the building, according to the affidavit.
"Clark's movements after this entry are considered uncharacteristic for his normal movements throughout his work day," the affidavit states.
He used his key card to gain entry into the room where Le worked and another room 55 times from 10:40 a.m. to 3:45 p.m. the day Le disappeared, according to the affidavit.
Clark had a scratch on his face and left biceps that he said came from a cat, according to the affidavit.
A judge last week ordered portions of the court documents to be unsealed.