Jim Dao, a deputy in the paper's opinion section who oversees op-eds, is stepping off the masthead to move into a new role in the newsroom, according to the Times.
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Before joining the New York Times as an editor, Bennet was the editor-in-chief of news magazine The Atlantic. He was in the running for the top job at The New York Times.
Earlier in his career, he was a reporter with the New York Times.
His resignation comes as newsrooms across the United States examine their own track record with diversity and sensitivity to issues to people of color.
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On Saturday, the top editor of the Philadelphia Inquirer, Stan Wischnowski, resigned after employees walked out in protest over a headline "Buildings Matter, Too," on a story about the impact of civil unrest on property.