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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (Unaudited) - USD ($) $ in Thousands | 9 Months Ended
--- | ---
Sep. 30, 2018 | Sep. 30, 2017
Operating activities: |  |
Net loss | $ (87,747) | $ (1,616)
Adjustments to reconcile net loss to net cash provided by operating activities: |  |
Depreciation | 7,650 | 6,138
Amortization of patents | 1,356 | 1,216
Amortization of premium on investments, net | 791 | 5,227
Amortization of debt issuance costs | 1,343 | 1,202
Amortization of convertible senior notes discount | 24,781 | 22,963
Amortization of long-term financing liability for leased facility | 0 | 3,659
Stock-based compensation expense | 97,210 | 63,642
Gain on investment in Regulus Therapeutics, Inc. | 0 | (374)
Loss on extinguishment of financing liability for leased facility | 0 | 7,689
Non-cash losses related to patents, licensing and property, plant and equipment | 482 | (403)
Changes in operating assets and liabilities: |  |
Contracts receivable | 48,223 | 65,119
Inventories | 1,604 | (962)
Other current and long-term assets | (26,573) | (34,866)
Accounts payable | (13,606) | (1,707)
Accrued compensation | (892) | (8,999)
Accrued liabilities and deferred rent | (14,392) | (5,251)
Deferred contract revenue | 447,168 | 31,071
Net cash provided by operating activities | 487,398 | 153,748
Investing activities: |  |
Purchases of short-term investments | (1,156,335) | (589,655)
Proceeds from the sale of short-term investments | 568,517 | 313,860
Purchases of property, plant and equipment | (12,221) | (26,502)
Acquisition of licenses and other assets, net | (3,317) | (4,289)
Proceeds from the sale of Regulus Therapeutics stock | 0 | 2,507
Net cash used in investing activities | (603,356) | (304,079)
Financing activities: |  |
Proceeds from equity awards | 18,254 | 17,672
Proceeds from the issuance of common stock from Akcea Therapeutics, Inc.'s initial public offering, net of underwriters' discount | 0 | 110,438
Proceeds from building mortgage debt, net of issuance costs | 0 | 59,750
Offering costs paid | 0 | (1,057)
Proceeds from the sale of Akcea Therapeutics, Inc. common stock to Novartis in a private placement | 0 | 50,000
Payment to settle financing liability for leased facility | 0 | (80,133)
Principal payments on debt and capital lease obligations | 0 | (3,577)
Net cash provided by financing activities | 466,219 | 224,830
Net increase in cash and cash equivalents | 350,261 | 74,499
Cash and cash equivalents at beginning of period | 129,630 | 84,685
Cash and cash equivalents at end of period | 479,891 | 159,184
Supplemental disclosures of cash flow information: |  |
Interest paid | 5,434 | 4,020
Supplemental disclosures of non-cash investing and financing activities: |  |
Amounts accrued for capital and patent expenditures | 2,296 | 3,475
Purchases of property, plant and equipment included in long-term obligations | 3,596 | 0
Unpaid deferred offering costs | 0 | 638
Novartis [Member] |  |
Financing activities: |  |
Proceeds from issuance of common stock | 0 | 71,737
Biogen [Member] |  |
Financing activities: |  |
Proceeds from issuance of common stock | $ 447,965 | $ 0

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- Definition The cash inflow associated with the amount received from entity's first offering of stock to the public. + References Reference 1: http://fasb.org/us-gaap/role/ref/legacyRef -Publisher FASB -Name Accounting Standards Codification -Topic 230 -SubTopic 10 -Section 45 -Paragraph 14 -Subparagraph (a) -URI http://asc.fasb.org/extlink&oid=109223946&loc=d3e3255-108585 + Details
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- Definition The cash inflow from the additional capital contribution to the entity. + References Reference 1: http://fasb.org/us-gaap/role/ref/legacyRef -Publisher FASB -Name Accounting Standards Codification -Topic 230 -SubTopic 10 -Section 45 -Paragraph 14 -Subparagraph (a) -URI http://asc.fasb.org/extlink&oid=109223946&loc=d3e3255-108585 + Details
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- Definition The cash inflow associated with the amount received from entity's raising of capital via private rather than public placement. + References Reference 1: http://fasb.org/us-gaap/role/ref/legacyRef -Publisher FASB -Name Accounting Standards Codification -Topic 230 -SubTopic 10 -Section 45 -Paragraph 14 -Subparagraph (a) -URI http://asc.fasb.org/extlink&oid=109223946&loc=d3e3255-108585 + Details
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- Definition Amount of cash inflow from issuance of shares under share-based compensation arrangement. Issuance includes, but is not limited to, exercise of stock options and similar instruments. + References Reference 1: http://fasb.org/us-gaap/role/ref/legacyRef -Publisher FASB -Name Accounting Standards Codification -Topic 718 -SubTopic 10 -Section 50 -Paragraph 2A -Subparagraph (a) -URI http://asc.fasb.org/extlink&oid=109197908&loc=SL79508275-113901 Reference 2: http://fasb.org/us-gaap/role/ref/legacyRef -Publisher FASB -Name Accounting Standards Codification -Topic 230 -SubTopic 10 -Section 45 -Paragraph 14 -Subparagraph (a) -URI http://asc.fasb.org/extlink&oid=109223946&loc=d3e3255-108585 + Details
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- Definition Amount of cash inflow from sale, maturity, prepayment and call of investment in debt security measured at fair value with change in fair value recognized in other comprehensive income (available-for-sale). + References Reference 1: http://www.xbrl.org/2003/role/disclosureRef -Publisher FASB -Name Accounting Standards Codification -Topic 230 -SubTopic 10 -Section 45 -Paragraph 11 -URI http://asc.fasb.org/extlink&oid=109223946&loc=d3e3151-108585 Reference 2: http://www.xbrl.org/2003/role/disclosureRef -Publisher FASB -Name Accounting Standards Codification -Topic 230 -SubTopic 10 -Section 45 -Paragraph 12 -Subparagraph (a) -URI http://asc.fasb.org/extlink&oid=109223946&loc=d3e3179-108585 Reference 3: http://fasb.org/us-gaap/role/ref/legacyRef -Publisher FASB -Name Accounting Standards Codification -Topic 320 -SubTopic 10 -Section 45 -Paragraph 11 -URI http://asc.fasb.org/extlink&oid=109979856&loc=d3e26853-111562 + Details
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- Definition The cash inflow associated with the sale of equity method investments, which are investments in joint ventures and entities in which the entity has an equity ownership interest normally of 20 to 50 percent and exercises significant influence. + References Reference 1: http://fasb.org/us-gaap/role/ref/legacyRef -Publisher FASB -Name Accounting Standards Codification -Topic 230 -SubTopic 10 -Section 45 -Paragraph 12 -Subparagraph (b) -URI http://asc.fasb.org/extlink&oid=109223946&loc=d3e3179-108585 + Details
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