Helen, 92, died here yesterday.
She covered 10 presidents over nearly half a century, and became a legend in the industry.
She was a regular fixture at White House news conferences -- sitting front and centre late in her career -- where she frequently exasperated government spokesmen with her pointed questions.
In a condolence message, Obama said he was saddened to learn of the death of Helen.
"Helen was a true pioneer, opening doors and breaking down barriers for generations of women in journalism.
"What made Helen the 'Dean of the White House Press Corps' was not just the length of her tenure, but her fierce belief that our democracy works best when we ask tough questions and hold our leaders to account," he said.
Former President Bill Clinton and his wife, former Secretary of State Hillary Clinton, recalled Thomas' "tough- minded dedication."
"Helen was a pioneering journalist who, while adding more than her share of cracks to the glass ceiling, never failed to bring intensity and tenacity to her White House beat," the CNN quoted the Clintons as saying in a statement.
In January 2009, as President George Bush was preparing to leave office, she attacked him editorially.
Among her criticisms: that before the 9/11 terror attacks, Bush administration officials ignored "significant early warnings of an imminent strike against the US"
In a commentary, she slammed Bush for what she considered his failings, including leading the country "into a senseless war against Iraq, a calamity still under way as he leaves office almost six years after the invasion."
Her career, however, came to an end under a cloud of controversy.
Helen, the daughter of Lebanese immigrants, was blasted for comments she made regarding Jewish people.
In 2010, a YouTube video surfaced showing her saying that Israel should "get the hell out of Palestine," and that the Jewish people should go home to "Poland, Germany ... And America and everywhere else."
Helen apologised for her remarks and she announced her retirement one week later.
Meanwhile, Helen's family said she will be buried in Detroit, and a memorial service is planned in Washington in October, the CNN reported.
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