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Editor’s note: For more on The New Yorker’s report earlier Saturday, click here.

The head of the MIT Media Lab resigned Saturday following fresh allegations that he had deliberately masked the full extent of his ties to convicted sex offender and financier Jeffrey Epstein, leaving the university and its acclaimed research center in turmoil, and the scientists who work there stunned and anxious about a place that has been dubbed the “future factory.”

Joi Ito, who led the Media Lab for eight years and is credited with invigorating the center with more money, new ideas, and a diverse and ambitious crew of scientists, said he would step down immediately.

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“After giving the matter a great deal of thought over the past several days and weeks, I think that it is best that I resign as Director of the Media Lab and as a Professor and employee of the Institute, effective immediately,” Ito wrote in an e-mail Saturday afternoon to MIT administrators.

Ito also resigned from two other prominent posts.

The New York Times Co. announced that he resigned from its governing board, where he had held a seat since 2012. And he resigned as a visiting professor from Harvard University, where he taught a class on ethics and technology.

For weeks, Ito had been dogged by criticism over the money he had accepted from Epstein for the Media Lab and his own personal ventures, along with visits he made to Epstein’s homes. But an explosive report in The New Yorker, published online Friday, suggested that Ito and other employees of the Media Lab tried to obscure Epstein’s ties from MIT administrators and internal critics.

Massachusetts Institute of Technology president L. Rafael Reif said Saturday that the university will hire an outside legal firm to look into the allegations outlined in The New Yorker report by investigative reporter Ronan Farrow.

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The report contained “deeply disturbing allegations about the engagement between individuals at the Media Lab and Jeffrey Epstein,” Reif said in a message to the MIT community, adding that they “demand an immediate, thorough and independent investigation.”

MIT had designated Epstein as “disqualified” to donate, but e-mails and other documents show Ito and Peter Cohen, the lab’s former director of development and strategy, worked to keep Epstein’s donations anonymous and to omit his name when reporting donations Epstein solicited from other philanthropists on the lab’s behalf, according to The New Yorker.

Ito and other lab staff would list the financier by his initials on Ito’s calendar and recorded his direct contributions as anonymous gifts, according to The New Yorker report.

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, the report said.

Ito has said that the Media Lab took $525,000 from Epstein, and media reports suggest that he took $1.2 million from the financier for his venture funds.

But these new allegations raise serious questions about whether that was really the extent of the donations, said Amir Pasic, the dean of Indiana University Lily Family School of Philanthropy.

“For one unit not to tell and hide the nature of the gift, is a big no-no,” Pasic said. He added that the case opens up legal concerns about how the Media Lab handled large donations as well as the safeguards the university had in place to avoid employees purposefully obscuring gifts.

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“It’s hard to understand how these gifts were held secret from central administration. . . . It was almost laundered in some way,” Pasic said. “It was unclear who was managing Ito. It seems he was given free rein, maybe too much.”

Epstein was found dead in August in his jail cell at a federal detention facility in Manhattan, where he was being held on charges of sex trafficking of minors. He had been convicted as a sex offender in 2008 for soliciting a minor for prostitution and had spent a year in jail. Despite that criminal history, Ito said he met Epstein in 2013 and wooed him as a donor for the lab and his personal ventures.

The Media Lab is home to more than 30 faculty and senior researchers and 275 other students and staff. Its $80 million budget is funded primarily by corporate giants including IBM, ExxonMobil, and Google, which gain broad access to the lab’s research.

Ito, an Internet entrepreneur who was an early investor in Twitter, Flickr, and Kickstarter, had boosted its fund-raising and inspired deep loyalty within the lab. Now, some researchers are worried sponsors who joined because of Ito will leave or others may not want to be tainted by the association to Epstein.

“I’m very saddened,” said Shuguang Zhang, a molecular architect, who joined the Media Lab earlier this year, drawn by Ito’s energy and vision for the research center.

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Outside the Media Lab on Saturday, more than two dozen MIT students and others declined to comment. Alex, 20, a third-year student majoring in computer science who declined to give his last name, said that learning of Epstein’s contributions made him consider for the first time the background of MIT donors.

“While mistakes were made in the past, I think it’s really good that going forward we are taking steps to amend those mistakes by giving back the money and doing what we can . . . to make sure this doesn’t happen again,” he said, adding later that Ito’s resignation was “a very good first step toward making amends.”

Two former Media Lab directors said despite the recent controversy, the lab remains viable.

“It will survive,” Walter Bender, a founding member and former director, who left in 2006, said in an e-mail. “But it will be (should be) a bit more introspective.”

Nicholas Negroponte, who cofounded the Media Lab, has said he had encouraged Ito to take Epstein’s money and, based on the information they had at the time, would do it again. But he said he was surprised by the revelations in The New Yorker article.

Negroponte said the lab can be rebuilt.

“It means that we have to work very hard to re-construct an institution appropriate to the present, but no less edgy than it was in the past,” he said.

Ito had been fighting to retain his position since mid-August, when he first revealed he had taken money from Epstein for the Media Lab and for his own private venture funds. A prominent professor and a visiting scholar each announced soon after they would leave the lab in protest, while others came to his defense.

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But by Saturday midmorning, many backers abandoned him, including several who had previously signed a petition in support of Ito.

“I believed what he said happened was everything that happened . . . but there was a lot more that he wasn’t saying,” said Bruce Schneier, a security technologist, who withdrew his support of Ito Saturday morning. “People trusted his ethics.”


Globe correspondent Jeremy C. Fox contributed to this report. Deirdre Fernandes can be reached at deirdre.fernandes@globe.com. Follow her on Twitter @fernandesglobe.