Bhupathi and Knowles, who are number two in the ATP Doubles Race, came into their third ATP final of the season having won 14 of their last 15 matches.
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They won back-to-back titles in Memphis and Dubai without dropping a set before their 10-match winning streak ended in the quarterfinals at Indian Wells to eventual champions Jonathan Erlich and Andy Ram.
The win gave the Bryan twins their first ATP title of the season.