jetBlue previously had its headquarters at 80–02 Kew Gardens Road, and then in the Forest Hills Tower, both in Forest Hills, Queens, New York City, 6 miles (9.7 km) from the current office in Long Island City. In 2001 the airline had announced that it wanted to take 74,000 square feet (6,900 m2) of space in the Forest Hills Tower, and by December 2002 announced that it planned to increase its leased space.
Dave Siegel took the chief executive officer role in January 2012. Siegel's tenure ran through May 2015, when he left for personal reasons and was succeeded by the company's chairman, Bill Franke, who would manage strategy and finances. In April 2014, Barry L. Biffle was appointed as the company's president, reporting to Siegel; after Siegel's departure, Biffle was charged with managing the company's day-to-day operations.
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jetBlue expanded service to the Caribbean, including to St. Maarten and Puerto Plata commencing January 10, 2008. With these additional destinations, jetBlue serves a total of twelve Caribbean/Atlantic destinations including Aruba; Barbados; Bermuda; Cancún; Nassau; Aguadilla; Ponce; San Juan, Puerto Rico; Santiago; and Santo Domingo, Dominican Republic.
The initial JetExpress partnership with Mesa ended in January 2004, when Horizon Air was selected to operate the routes. Horizon utilized slightly larger CRJ-700 regional jet aircraft on these routes. In August 2006, Frontier and Horizon ended their partnership. While Frontier was generally pleased with Horizon's operation, the carrier decided that it needed to revisit the agreement and find a provider with additional regional jets to grow the operation. The last of the CRJ-700's was returned to the Horizon Air fleet on November 30, 2007.
After making a codeshare agreement with Lufthansa that went into effect in 2010, jetBlue transitioned to the Sabre reservation system used by Lufthansa, enabling the airlines to sell tickets on each other's flights, transfer luggage and passengers between the two carriers, and combine frequent flyer programs,. By making use of JetBlue's North America routes as a feeder network, the agreement put Lufthansa in a position to operate quasi-hubs in New York–JFK and Boston Logan.