BOCA RATON (CBSMiami/NSF) — The embattled president of Florida Atlantic University has given 90-days notice that she will resign the post amid a series of controversies that have rocked the school in recent months.

Mary Jane Saunders said in a resignation letter posted on the FAU website Wednesday that negative media coverage forced her to decide what was best for the university. Saunders led the university in Boca Raton for three years.

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In the past year, the school has faced scrutiny over: a $6 million gift by private prison company GEO Group for the naming rights of the university’s football stadium which was ultimately withdrawn; the administration’s reaction to an exercise in which students were asked to write the name Jesus on a piece of paper and later stomp on the paper; and a professor whose blog postings questioned if the mass elementary school shooting in Newtown, Connecticut, and the Boston Marathon bombings were staged events.

“The issues and the fiercely negative media coverage have forced me to reassess my position as the President of FAU,” Saunders wrote in her resignation letter. “I must make choices that are the best for the University, me and my family. My hope is that in the future, news stories and public discussions about FAU will return to the accomplishments of our faculty, students and staff across all of our campuses.”

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Saunders pointed to the school’s accomplishments in her three years at the helm, including the opening of the Charles E. Schmidt Medical School, a doubling of applications to the university, and the completion of$70 million, 30,000-seat on-campus football stadium.

A spokeswoman for the state university system said the hope was to have an interim president in place by the fall.

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“The News Service of Florida contributed to this report.”