Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014
Cash flows from operating activities:
Net income	$ 22,708	$ 34,254
Adjustments for non-cash operating items:
Stock-based compensation	27,450	20,842
Excess tax benefits from stock-based compensation	(13,572)
Loss on extinguishment of Convertible Notes	7,871
Amortization of debt discount and debt issuance costs	7,827	7,170
Change in fair value of contingent purchase consideration	5,013
Depreciation on property and equipment	3,085	2,193
Amortization of deferred revenue	(2,257)	(8,465)
Change in deferred income taxes	(773)
Net accretion of discount on investment securities	6
Other non-cash items	(66)
Changes in operating assets and liabilities:
Receivable from collaboration partner	(12,420)	7,272
Prepaid expenses and other current assets	(6,085)	1,768
Other non-current assets	2,689	(4,847)
Accounts payable, accrued expenses and other current liabilities	25,352	(3,647)
Interest payable	(305)
Other non-current liabilities	718	(1)
Net cash provided by operating activities	67,241	56,539
Cash flows from investing activities:
Purchases of short-term investments	(76,397)
Purchases of property and equipment	(6,478)	(4,506)
Change in restricted cash	(1,574)	(2,073)
Net cash used in investing activities	(84,449)	(6,579)
Cash flows from financing activities:
Principal repayment of Convertible Notes	(90,994)	(1)
Cash settlement of Convertible Notes conversion premium	(1,126)
Proceeds from issuance of common stock under equity incentive and stock purchase plans	14,699	11,289
Excess tax benefits from stock-based compensation	13,572
Reduction of build-to-suit lease obligation	(470)
Net cash (used in) provided by financing activities	(64,319)	11,288
Net (decrease) increase in cash and cash equivalents	(81,527)	61,248
Cash and cash equivalents at beginning of period	502,677	228,788
Cash and cash equivalents at end of period	421,150	290,036
Non-cash investing and financing activities:
Reacquisition of Convertible Note equity component upon conversion	135,988
Fair value of common stock issued for conversion of Convertible Notes	131,084
Derecognition of build-to-suit lease asset	3,241
Derecognition of build-to-suit lease obligation	3,176
Property and equipment expenditures incurred but not yet paid	1,650	3,082
Interest capitalized during construction period for build-to-suit lease transactions	1,070	450
Accrued interest payable forfeited upon conversion of Convertible Notes	292
Amounts capitalized under build-to-suit lease transactions	$ 283	$ 16,800