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CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $)
In Thousands, unless otherwise specified
12 Months Ended
Dec. 31, 2013
Dec. 31, 2012
Dec. 31, 2011
Operating activities:      
Net loss $ (60,644) $ (65,478) $ (84,801)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:      
Depreciation 6,591 7,074 6,594
Amortization of patents 1,184 1,224 1,938
Amortization of licenses 2,007 2,457 3,252
Amortization of premium on investments, net 5,572 4,193 5,410
Amortization of debt issuance costs 415 619 507
Amortization of 2 5/8 percent convertible subordinated notes discount   6,169 8,553
Amortization of 2 3/4 percent convertible senior notes discount 6,344 2,268  
Amortization of long-term financing liability for leased facility 6,567 6,503 2,872
Share-based compensation expense 11,418 8,571 9,845
Equity in net loss of Regulus Therapeutics Inc.   1,406 3,554
Gain on investment in Regulus Therapeutics Inc.   (18,356)  
Loss on early retirement of debt   4,770  
Gain on investments, net (2,378) (1,465) (4,182)
Non-cash losses related to patents, licensing and property, plant and equipment 6,306 825 1,924
Tax benefit from other unrealized gains on securities (5,914) (9,111)  
Changes in operating assets and liabilities:      
Contracts receivable (10,580) 6,399 (5,679)
Inventories (1,912) (1,982) (1,655)
Other current and long-term assets (1,091) 279 914
Accounts payable 66 1,292 875
Accrued compensation 4,290 (1,305) 2,352
Deferred rent 217 255 382
Accrued liabilities 6,691 (3,254) 6,273
Deferred contract revenue 88,344 48,523 (70,857)
Net cash provided by (used in) operating activities 63,493 1,876 (111,929)
Investing activities:      
Purchases of short-term investments (425,554) (217,877) (371,108)
Proceeds from the sale of short-term investments 172,762 242,659 488,918
Purchases of property, plant and equipment (1,552) (1,479) (10,203)
Acquisition of licenses and other assets, net (3,810) (3,691) (3,667)
Investment in Regulus Therapeutics Inc.   (3,000)  
Purchases of strategic investments   (790) (359)
Proceeds from the sale of strategic investments 2,428 2,177 4,445
Net cash (used in) provided by investing activities (255,726) 17,999 108,026
Financing activities:      
Proceeds from equity awards 62,958 9,470 3,567
Proceeds from issuance of 2 3/4 percent convertible senior notes, net of issuance costs   194,697  
Principal and premium payment on redemption of the 2 5/8 percent convertible subordinated notes   (163,718)  
Proceeds from public common stock offering 173,292    
Proceeds from equipment financing arrangement 2,513 9,100 1,625
Principal payments on debt and capital lease obligations (11,039) (10,419) (5,864)
Net cash provided by (used in) financing activities 227,724 39,130 (672)
Net increase (decrease) in cash and cash equivalents 35,491 59,005 (4,575)
Cash and cash equivalents at beginning of year 124,482 65,477 70,052
Cash and cash equivalents at end of year 159,973 124,482 65,477
Supplemental disclosures of cash flow information:      
Interest paid 6,000 5,770 4,804
Income taxes paid, net of refund received 2 2 2
Supplemental disclosures of non-cash investing and financing activities:      
Amounts accrued for capital and patent expenditures 704 647 902
Capitalized costs and financing liability associated with leased facility     $ 59,730