CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Operating activities:
Net income (loss)	$ 214,985	$ (10,783)	$ (60,400)
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities
Depreciation	10,706	6,708	7,481
Amortization of patents	1,822	1,641	1,552
Amortization of premium (discount) on investments, net	(1,013)	6,752	6,813
Amortization of debt issuance costs	1,810	1,616	1,225
Amortization of convertible senior notes discount	33,363	30,920	23,890
Amortization of long-term financing liability for leased facility	0	3,659	6,693
Stock-based compensation expense	131,312	85,975	72,108
Gain on investment in Regulus Therapeutics, Inc.	0	(374)	0
Loss on extinguishment of financing liability for leased facility	0	7,689	0
Loss on early retirement of debt	0	0	3,983
Deferred income taxes (including benefit from valuation allowance release)	(290,516)	0	0
Non-cash losses related to patents, licensing, property, plant and equipment and strategic investments	1,012	3,302	2,297
Changes in operating assets and liabilities:
Contracts receivable	47,595	45,088	(96,687)
Inventories	1,400	(2,493)	(590)
Other current and long-term assets	(29,348)	(58,367)	1,603
Long-term income tax receivable	(223)	(9,114)	0
Accounts payable	(655)	1,784	(10,677)
Income taxes	(710)	435	1,069
Accrued compensation	4,117	965	8,121
Accrued liabilities and deferred rent	(17,023)	28,564	4,720
Deferred contract revenue	494,254	30,182	(85,306)
Net cash provided by (used in) operating activities	602,888	174,149	(112,105)
Investing activities:
Purchases of short-term investments	(1,794,735)	(877,810)	(300,912)
Proceeds from the sale of short-term investments	882,824	557,369	364,572
Purchases of property, plant and equipment	(13,608)	(34,764)	(7,107)
Acquisition of licenses and other assets, net	(4,044)	(3,093)	(4,421)
Purchase of strategic investments	0	(2,500)	0
Proceeds from the sale of Regulus Therapeutics, Inc.	0	2,507	4,467
Net cash (used in) provided by investing activities	(929,563)	(358,291)	56,599
Financing activities:
Proceeds from equity, net	27,900	22,931	13,417
Proceeds from issuance of common stock in Akcea Therapeutics, Inc. from its initial public offering, net of underwriters' discount	0	110,438	0
Proceeds from building mortgage debt, net of issuance costs	0	59,750	0
Proceeds from borrowing on line of credit facility	0	0	4,000
Proceeds from the sale of Akcea Therapeutics, Inc. common stock to Novartis in a private placement	0	50,000	0
Offering costs paid	0	(2,037)	(818)
Payment to settle financing liability for leased facility	0	(80,133)	0
Excess tax benefits from stock-based compensation awards	0	0	1,861
Principal payments on debt and capital lease obligations	0	(3,599)	(7,066)
Net cash provided by financing activities	475,865	229,087	11,394
Net increase (decrease) in cash and cash equivalents	149,190	44,945	(44,112)
Cash and cash equivalents at beginning of year	129,630	84,685	128,797
Cash and cash equivalents at end of year	278,820	129,630	84,685
Supplemental disclosures of cash flow information:
Interest paid	9,592	8,035	7,313
Supplemental disclosures of non-cash investing and financing activities:
Amounts accrued for capital and patent expenditures	4,428	1,983	3,439
Purchases of property, plant and equipment included in long-term obligations	3,350	0	0
1 percent convertible senior notes principal issued related to our December 2016 debt exchange	0	0	185,450
2 3/4 percent convertible senior notes principal extinguished related to our December 2016 debt exchange	0	0	61,099
Unpaid deferred offering costs	0	0	291
Biogen [Member]
Financing activities:
Proceeds from the issuance of common stock	447,965	0	0
Novartis [Member]
Financing activities:
Proceeds from the issuance of common stock	$ 0	$ 71,737	$ 0