Updated

The president of Florida Atlantic University has resigned 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.

The problems included protests over a $6 million plan to allow a for-profit prison company naming rights at the FAU football stadium, which was ultimately withdrawn.

Others issues were an instructor's lesson in which students were told stomp on papers containing the word "Jesus" and a professor's suggestions that the Newtown school killings and Boston Marathon bombings were hoaxes.

Trustees hope to hire a new president by the fall.