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Joi Ito, director of MIT’s Media Lab.
Joi Ito, director of MIT’s Media Lab.Getty Images

The embattled head of the MIT Media Lab abruptly resigned Saturday afternoon, less than a day after an explosive new report in The New Yorker detailed close ties between the research center and financier Jeffrey Epstein, a convicted sex offender who died by suicide last month in a New York prison.

Joi Ito, the Media Lab’s director since 2011, resigned by e-mail hours after the Friday night publication of an article by investigative reporter Ronan Farrow that alleged Ito and Peter Cohen, the Media Lab’s former director of development and strategy, worked to keep Epstein’s donations anonymous and to omit his name when reporting gifts Epstein solicited from philanthropists on the lab’s behalf.

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Some staff members in Ito’s office called Epstein “Voldemort” or “he who must not be named” in reference to the efforts to conceal his connections to the lab, Farrow reported.

Acting as an intermediary, Epstein secured major donations for the lab, including $5.5 million from investor Leon Black, founder of one of the world’s largest private-equity firms, and $2 million from Microsoft founder Bill Gates, in addition to his own beneficence, Farrow reported.

MIT had previously disclosed only $800,000 in contributions to the university over a 20-year span from foundations Epstein controlled. On Wednesday, Ito told attendees at a meeting to address the scandal that Epstein had contributed $525,000 to the Media Lab and $1.2 million to investment funds Ito controlled, according to Farrow and the New York Times.

Ito publicly apologized last month for accepting donations from Epstein, the disgraced financier who died while facing federal charges of sex trafficking of underage girls. Since then, the director of the lab’s Center for Civic Media and a visiting scholar at the lab have announced plans to sever their ties.

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Ito, a Japanese-born entrepreneur who became the head of the Media Lab at 44, said in his apology last month that he will raise the equivalent to what Epstein gave the Media Lab and donate it to nonprofits that work with survivors of trafficking. He will also return the money Epstein invested in his funds, Ito said.

Also last month, MIT President L. Rafael Reif pledged to commit a monetary amount equal to the funds MIT received from Epstein’s foundations to a charity that benefits Epstein’s victims or other victims of sexual abuse.

The New Yorker article details several ways Ito and his staff worked to hide or downplay connections to Epstein, including listing the financier by his initials on Ito’s calendar, recording his direct contributions as anonymous gifts, and omitting his efforts when recording gifts he solicited for the Media Lab.

Screenshots of e-mail exchanges show Ito contacting Epstein to ask for $100,000 to extend a researcher’s contract, Epstein responding simply, “yes,” and Ito and Cohen then issuing instructions that the donation be logged anonymously. “Make sure this gets accounted for as anonymous,” Ito says in one message, to which Cohen responds, “Jeffrey money, needs to be anonymous. Thanks.”

When Gates donated $2 million to the Media Lab at Epstein’s request, Ito notified Cohen, who said in his response that “we will not be mentioning Jeffrey’s name as the impetus for this gift.”

Signe Swenson, a former alumni coordinator and development associate at the Media Lab, told Farrow that when the issue of accepting Epstein’s money arose, Ito told her, “We can take small gifts anonymously.”

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Jeremy C. Fox can be reached at jeremy.fox@globe.com. Follow him on Twitter @jeremycfox.