CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (Unaudited) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Operating activities:
Net loss	$ (112,421)	$ (16,845)
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Depreciation	5,592	5,190
Amortization of patents	1,171	1,012
Amortization of licenses	1	1,405
Amortization of premium on investments, net	5,314	5,495
Amortization of debt issuance costs	910	841
Amortization of long-term financing liability for leased facility	5,018	4,994
Stock-based compensation expense	56,950	41,907
Gain on investment in Regulus Therapeutics Inc.	0	(20,211)
Non-cash losses related to patents, licensing and property, plant and equipment	1,134	244
Changes in operating assets and liabilities:
Contracts receivable	2,812	2,077
Inventories	(2,420)	(293)
Other current and long-term assets	(27)	(13,457)
Accounts payable	(15,200)	862
Accrued compensation	(5,057)	(2,794)
Accrued liabilities and deferred rent	(4,403)	(5,946)
Deferred contract revenue	(43,258)	37,726
Net cash provided by (used in) operating activities	(86,146)	58,599
Investing activities:
Purchases of short-term investments	(234,486)	(398,076)
Proceeds from the sale of short-term investments	277,971	293,109
Purchases of property, plant and equipment	(4,313)	(5,281)
Acquisition of licenses and other assets, net	(3,374)	(3,334)
Proceeds from the sale of equity investments	0	25,566
Net cash provided by (used in) investing activities	35,798	(88,016)
Financing activities:
Proceeds from equity awards	7,254	20,275
Proceeds from borrowing on line of credit facility	4,000	0
Principal payments on debt and capital lease obligations	(5,428)	(7,263)
Net cash provided by financing activities	5,826	13,012
Net decrease in cash and cash equivalents	(44,522)	(16,405)
Cash and cash equivalents at beginning of period	128,797	142,998
Cash and cash equivalents at end of period	84,275	126,593
Supplemental disclosures of cash flow information:
Interest paid	4,295	4,233
Supplemental disclosures of non-cash investing and financing activities:
Amounts accrued for capital and patent expenditures	2,521	447
2 3/4 Percent Convertible Senior Notes [Member]
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Amortization of convertible senior notes discount	1,902	1,741
1 Percent Convertible Senior Notes [Member]
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Amortization of convertible senior notes discount	$ 15,836	$ 14,651