CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (Unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Operating activities:
Net income (loss)	$ 3,468	$ (62,917)
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Depreciation	1,980	1,841
Amortization of patents	393	377
Amortization of premium on investments, net	1,608	2,039
Amortization of debt issuance costs	396	298
Amortization of convertible senior notes discount	7,506	5,795
Amortization of long-term financing liability for leased facility	1,675	1,672
Stock-based compensation expense	20,912	20,103
Gain on investment in Regulus Therapeutics, Inc.	(374)	0
Non-cash losses related to patents, licensing and property, plant and equipment	93	396
Changes in operating assets and liabilities:
Contracts receivable	38,686	(5,124)
Inventories	688	379
Other current and long-term assets	(14,077)	(2,747)
Accounts payable	472	(11,417)
Accrued compensation	(15,919)	(9,728)
Accrued liabilities and deferred rent	(6,273)	(1,886)
Deferred contract revenue	81,431	(14,849)
Net cash provided by (used in) operating activities	122,665	(75,768)
Investing activities:
Purchases of short-term investments	(266,185)	(41,366)
Proceeds from the sale of short-term investments	99,223	81,805
Purchases of property, plant and equipment	(3,237)	(628)
Acquisition of licenses and other assets, net	(983)	(382)
Proceeds from the sale of Regulus Therapeutics	2,507	0
Net cash (used in) provided by investing activities	(168,675)	39,429
Financing activities:
Proceeds from equity awards	6,324	2,736
Proceeds from sale of stock to Novartis	71,640	0
Offering costs paid	(778)	0
Principal payments on debt and capital lease obligations	(1,640)	(1,857)
Net cash provided by financing activities	75,546	879
Net increase (decrease) in cash and cash equivalents	29,536	(35,460)
Cash and cash equivalents at beginning of period	84,685	128,797
Cash and cash equivalents at end of period	114,221	93,337
Supplemental disclosures of cash flow information:
Interest paid	106	31
Supplemental disclosures of non-cash investing and financing activities:
Amounts accrued for capital and patent expenditures	1,648	2,524
Unpaid deferred offering costs	$ 319	$ 0