Boyd (left) and Raines had been in their jobs since 2001
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The editor of the New York Times Howell Raines has resigned following weeks of scandal over reporting standards.
Mr Raines, and another senior editor, Gerald
Boyd quit their posts on Thursday, the paper announced.
"This is a day that breaks my heart," Times publisher Arthur Sulzberger told the staff at a morning newsroom meeting.
The paper has been dogged by scandal since a young reporter, Jayson Blair, resigned in May after it was found he had stolen material from other papers and invented quotes.
Last week one of the paper's top reporters, Rick Bragg, resigned after he was accused of relying too heavily on the work of a freelance journalist.
Executive editor Mr Raines and Mr Boyd, the managing editor, had been the focus of much criticism in recent weeks, particularly over the Blair incident.
They were blamed for overlooking Mr Blair's errors
and warnings about the quality of his work by other editors.
'Arrogant'
Critics said Mr Raines, 60, had an autocratic management style.
"You view me as inaccessible and arrogant," he told staff as a meeting on 14 May, the Associated Press news agency reported.
"You believe the newsroom is too hierarchical, that my ideas get acted on and others get
ignored.
The newspaper had apologised over the Jayson Blair scandal
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"I heard that you were convinced there's a star
system that singles out my favourites for elevation."
Mr Raines took on the job just days before the 11 September 2001 attacks on New York and Washington.
The following April, the newspaper received a record seven Pulitzer Prizes - five for its coverage of the attacks and another for the war in Afghanistan.
"They have made enormous contributions during their
tenure," Mr Sulzberger said. "I appreciate all of their efforts in continuing the legacy of our great newspaper."
The newspaper has named a former executive editor Joseph Lelyveld to take on the job again for the interim.
Mr Lelyveld, 66, retired in 2001 after seven years as executive editor.
Following the recent scandals the New York Times assigned a committee to review newsroom policies, including hiring practices, the use of unidentified sources and the use of freelancers.