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Athenahealth, the Watertown-based electronic health records company, said Monday that it will be acquired for $17 billion by private equity firms Bain Capital and Hellman & Friedman. The deal is expected to close by the first quarter of next year.

Bob Segert, Athenahealth’s chief executive officer, is expected to stay on in that role. He called the acquisition “a significant milestone” for the company, which provides cloud-based software to health care providers that improves communication between patients and doctors, and streamlines billing and record-keeping.

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