The Department of Buildings issued a partial stop work order at the former P.S. 64 building Tuesday.
Mayor Michael Bloomberg gave the commencement speech to Cooper Union's graduating students.
About 50 students from the Cooper Union were camped out in school president Jamshed Bharucha's office.
The school's Board of Trustees may consider charging tuition in future years.
Students at Cooper Union were protesting possible tuition charges at the traditionally free school.
Barricaded students living inside the school continue their clock tower protest.
The longtime bookshop is looking for a smaller space in the East Village.
A man scaled the Peter Cooper statue at Cooper Square in protest of the tuition for graduate programs.
People from Marcus Samuelsson to Aldon James made news in Manhattan's neighborhoods in 2011.
The St. Mark's Bookshop celebrated a rent reduction and clearance of debt on Thursday night.
The Standard took over the Cooper Square Hotel and more boutique coffee was added to the neighborhood.
Supporters of the store sang an original song pleading for the school to lower the shop's rent at the inauguration of new Cooper Union president Jamshed Bharucha Tuesday.
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