Maryland man arrested in alleged sexual assault on Green Line near Kenmore Square in 2004

By John R. Ellement, Globe Staff

Using DNA evidence, MBTA Transit Police have arrested a Maryland man for an alleged sexual assault on a woman on the Green Line in 2004 -- two years after he allegedly committed a similar offense on the Metro system in the Washington, D.C., area.

Timothy L. Day pleaded not guilty at his arraignment today in Suffolk Superior Court to a single count of indecent assault and battery on a 23-year-old woman from Boston on June 22, 2004.

Bail was set at $1,500 cash for the 52-year-old Day, who was a consulting economist with a Washington firm prior to his arrest. Day lives in Bethesda, Md., officials said.

Timothy L. Day (Transit police)

According to Lewis Best, deputy transit police chief, the woman boarded a crowded B Line outbound trolley on a day that the Red Sox were playing at Fenway Park.

Day allegedly boarded the same train at Copley Square station and positioned himself behind the woman as the train progressed towards Kenmore Square, Best said. During the ride, Day allegedly touched himself inappropriately and also touched the woman, Best said.

As the woman exited the train, she discovered biological material on the exterior of her purse and her pants, Best said. According to prosecutors, the woman tossed the purse in the trash and washed her stained clothes

However, transit police recovered the purse from the trash and handed it over to the Boston police department crime lab in 2004 where technicians were able to build a genetic profile of the assailant, authorities said.

In November 2004, transit police obtained an arrest warrant for “John Doe.’’

Police developed a DNA profile of the assailant and discovered that it matched the genetic profile of a man who had committed a similar offense on the Metro transit system in 2002 while a train was traveling through Arlington, Va., outside Washington.

It wasn’t until 2011 that Day was linked to the MBTA incident when the John Doe profile from 2004 matched a profile for Day that had been entered into a national DNA database by federal law enforcement, Suffolk prosecutors said. It was not immediately clear why federal authorities had entered Day’s information into that database.

Working with Suffolk District Attorney Daniel F. Conley’s office, transit police and prosecutors recently collected genetic material from Day. It matched the evidence collected in 2004, Best said.

Day was arrested in Maryland May 15 and surrendered to transit police today prior to his arraignment.

“This is a disturbing incident,’’ Best said. “The message is clear that this type of criminal behavior will not be tolerated. We will use whatever means to identify, apprehend and prosecute individuals that engage in this type of criminal behavior.’’

He added, “It may take a while … but we will eventually get a match.’’

While officials say the DNA evidence collected from the 2002 assault allegedly matches Day, Arlington County Commonwealth’s Attorney Theophani Stamos said Monday her office would not prosecute Day.

Stamos said the incident on the Metro was legally considered a misdemeanor and that under Virginia law, misdemeanors have a one-year statute of limitations.