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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (Unaudited) - USD ($)
$ in Thousands
3 Months Ended
Mar. 31, 2018
Mar. 31, 2017
Operating activities:    
Net income (loss) $ (10,812) $ 8,964
Adjustments to reconcile net income (loss) to net cash provided by operating activities:    
Depreciation 2,363 1,980
Amortization of patents 443 393
Amortization of premium on investments, net 1,192 1,608
Amortization of debt issuance costs 441 396
Amortization of convertible senior notes discount 8,083 7,506
Amortization of long-term financing liability for leased facility 0 1,675
Stock-based compensation expense 28,451 20,912
Gain on investment in Regulus Therapeutics, Inc. 0 (374)
Non-cash losses related to patents, licensing and property, plant and equipment 175 93
Changes in operating assets and liabilities:    
Contracts receivable 26,097 38,686
Inventories 922 688
Other current and long-term assets 11,422 (14,077)
Accounts payable (13,144) 472
Accrued compensation (12,985) (15,919)
Accrued liabilities and deferred rent (1,695) (6,273)
Deferred contract revenue (27,788) 75,935
Net cash provided by operating activities 13,165 122,665
Investing activities:    
Purchases of short-term investments (91,157) (266,185)
Proceeds from the sale of short-term investments 173,724 99,223
Purchases of property, plant and equipment (2,343) (3,237)
Acquisition of licenses and other assets, net (738) (983)
Proceeds from the sale of Regulus Therapeutics stock 0 2,507
Net cash provided by (used in) investing activities 79,486 (168,675)
Financing activities:    
Proceeds from equity awards 5,675 6,324
Proceeds from the issuance of common stock to Novartis 0 71,640
Stock issuance costs paid (451) (778)
Principal payments on debt and capital lease obligations 0 (1,640)
Net cash provided by financing activities 5,224 75,546
Net increase in cash and cash equivalents 97,875 29,536
Cash and cash equivalents at beginning of period 129,630 84,685
Cash and cash equivalents at end of period 227,505 114,221
Supplemental disclosures of cash flow information:    
Interest paid 644 106
Supplemental disclosures of non-cash investing and financing activities:    
Amounts accrued for capital and patent expenditures 2,091 1,648
Unpaid deferred offering costs $ 0 $ 319