CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (Unaudited) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016
Operating activities:
Net loss	$ (7,739)	$ (119,772)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Depreciation	3,990	3,715
Amortization of patents	802	775
Amortization of premium on investments, net	3,558	3,793
Amortization of debt issuance costs	797	601
Amortization of convertible senior notes discount	15,163	11,709
Amortization of long-term financing liability for leased facility	3,352	3,345
Stock-based compensation expense	42,170	39,364
Gain on investment in Regulus Therapeutics, Inc.	(374)	0
Non-cash losses related to patents, licensing and property, plant and equipment	129	464
Changes in operating assets and liabilities:
Contracts receivable	57,428	10,610
Inventories	985	(769)
Other current and long-term assets	(39,371)	(2,576)
Accounts payable	(10,030)	(12,436)
Accrued compensation	(13,888)	(8,624)
Accrued liabilities and deferred rent	(1,149)	(9,032)
Deferred contract revenue	69,205	(30,719)
Net cash (used in) provided by operating activities	125,028	(109,552)
Investing activities:
Purchases of short-term investments	(347,916)	(81,814)
Proceeds from the sale of short-term investments	202,475	180,158
Purchases of property, plant and equipment	(9,453)	(3,263)
Acquisition of licenses and other assets, net	(1,593)	(2,195)
Proceeds from the sale of Regulus Therapeutics stock	2,507	0
Net cash (used in) provided by investing activities	(153,980)	92,886
Financing activities:
Proceeds from equity awards	9,927	4,120
Proceeds from sale of stock to Novartis	71,640	0
Offering costs paid	(1,031)	0
Principal payments on debt and capital lease obligations	(3,278)	(3,717)
Net cash provided by financing activities	77,258	403
Net increase (decrease) in cash and cash equivalents	48,306	(16,263)
Cash and cash equivalents at beginning of period	84,685	128,797
Cash and cash equivalents at end of period	132,991	112,534
Supplemental disclosures of cash flow information:
Interest paid	3,607	3,414
Supplemental disclosures of non-cash investing and financing activities:
Amounts accrued for capital and patent expenditures	1,705	1,662
Unpaid deferred offering costs	$ 473	$ 379