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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

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- Definition The fair value of notes issued in noncash investing and financing activities. + References Reference 1: http://fasb.org/us-gaap/role/ref/legacyRef -Publisher FASB -Name Accounting Standards Codification -Topic 230 -SubTopic 10 -Section 50 -Paragraph 4 -URI http://asc.fasb.org/extlink&oid=98513485&loc=d3e4313-108586 Reference 2: http://fasb.org/us-gaap/role/ref/legacyRef -Publisher FASB -Name Accounting Standards Codification -Topic 230 -SubTopic 10 -Section 50 -Paragraph 5 -URI http://asc.fasb.org/extlink&oid=98513485&loc=d3e4332-108586 Reference 3: http://fasb.org/us-gaap/role/ref/legacyRef -Publisher FASB -Name Accounting Standards Codification -Topic 230 -SubTopic 10 -Section 50 -Paragraph 3 -URI http://asc.fasb.org/extlink&oid=98513485&loc=d3e4304-108586 + Details
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