CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (Unaudited) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014
Operating activities:
Net loss	$ (16,845)	$ (70,037)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Depreciation	5,190	4,791
Amortization of patents	1,012	841
Amortization of licenses	1,405	1,412
Amortization of premium on investments, net	5,495	5,649
Amortization of debt issuance costs	841	412
Amortization of long-term financing liability for leased facility	4,994	4,962
Stock-based compensation expense	41,907	22,894
Gain on investment in Regulus Therapeutics Inc.	(20,211)	(535)
Gain on investments, net	(200)	(140)
Non-cash losses related to patents, licensing and property, plant and equipment	244	753
Tax benefit from other unrealized gains on securities	0	0
Changes in operating assets and liabilities:
Contracts receivable	2,077	(15,211)
Inventories	(293)	948
Other current and long-term assets	(13,257)	(1,239)
Accounts payable	862	1,414
Accrued compensation	(2,794)	(5,004)
Deferred rent	163	126
Accrued liabilities	(6,109)	7,046
Deferred contract revenue	37,726	(28,584)
Net cash provided by (used in) operating activities	58,599	(64,399)
Investing activities:
Purchases of short-term investments	(398,076)	(250,580)
Proceeds from the sale of short-term investments	293,109	222,896
Purchases of property, plant and equipment	(5,281)	(3,969)
Acquisition of licenses and other assets, net	(3,334)	(2,443)
Proceeds from the sale of Regulus	25,527	0
Proceeds from the sale of strategic investments	39	2,036
Net cash used in investing activities	(88,016)	(32,060)
Financing activities:
Proceeds from equity awards	20,275	17,709
Principal payments on debt and capital lease obligations	(7,263)	(8,003)
Net cash provided by financing activities	13,012	9,706
Net decrease in cash and cash equivalents	(16,405)	(86,753)
Cash and cash equivalents at beginning of period	142,998	159,973
Cash and cash equivalents at end of period	126,593	73,220
Supplemental disclosures of cash flow information:
Interest paid	4,233	2,977
Supplemental disclosures of non-cash investing and financing activities:
Amounts accrued for capital and patent expenditures	447	3,204
2 3/4 Percent Convertible Senior Notes [Member]
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Amortization of convertible notes discount	1,741	5,103
1 Percent Convertible Senior Notes [Member]
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Amortization of convertible notes discount	$ 14,651	$ 0