CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Operating activities:
Net loss	$ (17,296)	$ (86,556)	$ (88,278)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Depreciation	6,708	7,481	6,984
Amortization of patents	1,641	1,552	1,381
Amortization of licenses	0	0	1,873
Amortization of premium on investments, net	6,752	6,813	7,812
Amortization of debt issuance costs	1,616	1,225	1,133
Amortization of senior convertible notes discount	30,920	23,890	22,075
Amortization of long-term financing liability for leased facility	3,659	6,693	6,665
Stock-based compensation expense	85,975	72,108	59,314
Gain on investment in Regulus Therapeutics, Inc.	(374)	0	(20,211)
Loss on extinguishment of financing liability for leased facility	7,689	0	0
Loss on early retirement of debt	0	3,983	0
Non-cash losses related to patents, licensing, property, plant and equipment and strategic investments	3,302	2,297	1,881
Changes in operating assets and liabilities:
Contracts receivable	45,088	(96,687)	(7,453)
Inventories	(2,493)	(590)	(609)
Other current and long-term assets	(58,367)	1,603	(4,394)
Long-term income tax receivable	(9,114)	0	0
Accounts payable	1,784	(10,677)	9,211
Income taxes	435	1,069	0
Accrued compensation	965	8,121	3,763
Accrued liabilities and deferred rent	28,564	4,720	(2,140)
Deferred contract revenue	36,695	(59,150)	22,118
Net cash (used in) provided by operating activities	174,149	(112,105)	21,125
Investing activities:
Purchases of short-term investments	(877,810)	(300,912)	(493,467)
Proceeds from the sale of short-term investments	557,369	364,572	419,584
Purchases of property, plant and equipment	(34,764)	(7,107)	(7,692)
Acquisition of licenses and other assets, net	(3,093)	(4,421)	(4,056)
Purchase of strategic investments	(2,500)	0	0
Proceeds from the sale of Regulus Therapeutics, Inc.	2,507	4,467	25,527
Proceeds from the sale of strategic investments	0	0	52
Net cash (used in) provided by investing activities	(358,291)	56,599	(60,052)
Financing activities:
Proceeds from equity awards	22,931	13,417	24,888
Proceeds from the issuance of common stock in Akcea Therapeutics, Inc. from its initial public offering, net of underwriters' discount	110,438	0	0
Proceeds from building mortgage debt, net of issuance costs	59,750	0	0
Proceeds from the issuance of common stock to Novartis	71,737	0	0
Proceeds from borrowing on line of credit facility	0	4,000	8,500
Proceeds from sale of Akcea Therapeutics, Inc. common stock to Novartis in a private placement	50,000	0	0
Offering costs paid	(2,037)	(818)	0
Payment to settle financing liability for leased facility	(80,133)	0	0
Excess tax benefits from stock-based compensation awards	0	1,861	396
Principal payments on debt and capital lease obligations	(3,599)	(7,066)	(9,058)
Net cash provided by financing activities	229,087	11,394	24,726
Net increase (decrease) in cash and cash equivalents	44,945	(44,112)	(14,201)
Cash and cash equivalents at beginning of year	84,685	128,797	142,998
Cash and cash equivalents at end of year	129,630	84,685	128,797
Supplemental disclosures of cash flow information:
Interest paid	8,035	7,313	6,800
Supplemental disclosures of non-cash investing and financing activities:
Amounts accrued for capital and patent expenditures	1,983	3,439	1,162
1 percent convertible senior notes principal issued related to our December 2016 debt exchange	0	185,450	0
2 3/4 percent convertible senior notes principal extinguished related to our December 2016 debt exchange	0	61,099	0
Unpaid deferred offering costs	$ 0	$ 291	$ 0