In the letter, Malatras called persistent questions about his role in the Cuomo administration a "distraction."
"I believe deeply in an individual's ability to evolve, change and grow, but I also believe deeply in SUNY and would never want to be an impediment to its success," Malatras wrote.
With Malatras' resignation, the Cuomo scandal has now taken down a university system president, a governor, a CNN anchor, the CEO of Time's Up, the head of the Human Rights Campaign and others.
"We want to thank Dr. Jim Malatras for his extraordinary service to the entire SUNY system," the Board of Trustees said in a statement. "The past two years have been among the most trying in SUNY's history-and Jim's leadership and collaboration with our faculty and staff have allowed our institution to continue to thrive and serve our nearly 400,000 students at 64 campuses across our state safely and in person. He has been a champion for our students, for access, for equity, and for deeper public investment in this great institution. The entire board expresses our gratitude for his dedication and leadership."
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Previously, the leaders of New York's public college system were standing by Malatras, who had faced calls to resign after the release of text messages showing he mocked one of the women who later accused Cuomo of sexual harassment.
"He's acknowledged he made a mistake, taken full responsibility for it, and apologized appropriately," the Board said in a statement Friday night, following a written apology from Malatras. "He is fully focused on the critical work of keeping our facilities open and our students and faculty safe through the ongoing pandemic."
Malatras, a former top adviser to Cuomo, came under fire after Attorney General Letitia James made public transcripts and evidence from a monthslong probe of sexual harassment allegations that forced Cuomo from office. +
Cuomo has denied harassing anyone.
A text exchange involving Malatras and other Cuomo allies showed them mocking Lindsey Boylan, a former economic development official who was the first woman to publicly accuse Cuomo. Boylan, after leaving the administration, tweeted in 2019 that working in politics had been "a toxic and demoralizing experience."
She had yet to go public with her sexual harassment allegations against the governor.
"Let's release some of her cray emails," Malatras texted, using slang for crazy.
After Boylan called him out in a series of tweets, Malatras texted to the group: "Malatras to Boylan: Go (expletive) yourself."
The SUNY Student Assembly on Friday called for the trustees to remove Malatras with a vote of no confidence.
"Allowing the chancellor to remain in place damages the reputation of the system, detracting from our education and devaluing the degrees we are all working towards," the group, which represents students in SUNY governance, said.
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In a statement Friday, Malatras said he owed Boylan and the SUNY community an apology.
"Leadership in public service is a privilege and with it comes immense responsibility for upholding the values of professionalism, decency, and respect. I take that responsibility very seriously and in recent days it has been clear I have fallen short," he wrote, calling his remarks "inappropriate, disrespectful and wrong."
Boylan later tweeted that she had received no apology from Malatras.
"I'm glad he didn't apologize because, based on his email, he continues to lie," she said.
(The Associated Press contributed to this report)
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