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Condensed Consolidated Statements of Cash Flows - USD ($)
$ in Thousands
9 Months Ended
Sep. 30, 2015
Sep. 30, 2014
Cash flows from operating activities:    
Net income $ 102,218 $ 112,247
Adjustments for non-cash operating items:    
Excess tax benefits from stock-based compensation (57,472) (362)
Stock-based compensation 40,842 32,799
Loss on extinguishment of Convertible Notes 21,087  
Change in deferred income taxes (9,037)  
Amortization of debt discount and debt issuance costs 8,548 11,007
Change in fair value of contingent purchase consideration 6,799  
Depreciation on property and equipment 4,957 3,603
Amortization of deferred revenue (2,822) (12,698)
Other non-cash items 36 1,112
Changes in operating assets and liabilities:    
Receivable from collaboration partner (92,875) (100,880)
Prepaid expenses and other current assets (4,968) 3,599
Other non-current assets 2,087 (4,289)
Accounts payable, accrued expenses and other current liabilities 84,591 28,460
Interest payable 51 1,698
Other non-current liabilities 5,917 16
Net cash provided by operating activities 109,959 76,312
Cash flows from investing activities:    
Purchases of short-term investments (90,381)  
Sales or maturities of short-term investments 90,224  
Purchases of property and equipment (13,638) (9,223)
Change in restricted cash (1,371) (2,073)
Net cash used in investing activities (15,166) (11,296)
Cash flows from financing activities:    
Principal repayment of Convertible Notes (258,742) (4)
Cash settlement of Convertible Notes conversion premium (1,126)  
Proceeds from borrowings under Revolving Credit Facility 75,000  
Excess tax benefits from stock-based compensation 57,472 362
Proceeds from issuance of common stock under equity incentive and stock purchase plans 19,548 26,891
Reduction of build-to-suit lease obligation (678)  
Net cash (used in) provided by financing activities (108,526) 27,249
Net (decrease) increase in cash and cash equivalents (13,733) 92,265
Cash and cash equivalents at beginning of period 502,677 228,788
Cash and cash equivalents at end of period 488,944 321,053
Non-cash investing and financing activities:    
Reacquisition of Convertible Notes equity component upon conversion 324,177  
Fair value of common stock issued for conversion of Convertible Notes 312,990  
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 618 355
Interest capitalized during construction period for build-to-suit lease transactions 1,541 945
Accrued interest payable forfeited upon conversion of Convertible Notes 1,686  
Amounts capitalized under build-to-suit lease transactions $ 283 $ 18,085