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Other comprehensive (loss) income, net of tax of $0, $0 and $106

$ (169,737)

$ (268,542)

$ (244,760)

^[1]

(111)

(267)

238

Comprehensive loss

$ (169,848)

$ (268,809)

$ (244,522)

[1]	Other comprehensive (loss) income consisted solely of unrealized losses or gains, net on available for sale securities arising during the periods presented. There were no reclassification adjustments to net loss resulting from realized losses or gains on the sale of securities.

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

Balance, shares at Dec. 31, 2012

Consolidated Statements of Comprehensive Loss (Parenthetical) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Statement of Comprehensive Income [Abstract]
Other comprehensive income (loss), tax	$ 0	$ 0	$ 106

Consolidated Statements of Stockholders' Equity (Deficit) - USD ($)
$ in Thousands

Total

Common Stock [Member]

Additional Paid-In Capital [Member]

Accumulated Other Comprehensive (Loss) Income [Member]

Accumulated Deficit [Member]

183,697,213

Balance at Dec. 31, 2012

$ 296,434

$ 183

$ 1,550,345

$ (92)

$ (1,254,002)

Increase (Decrease) in Stockholders' Equity [Roll Forward]

Other comprehensive (loss) income

(244,760)

238

^[1]

238

Issuance of common stock under stock plans, net, shares

836,438

Issuance of common stock under stock plans

2,295

$ 1

2,294

Stock-based compensation expense

12,031

Balance, shares at Dec. 31, 2013

184,533,651

Balance at Dec. 31, 2013

66,238

$ 184

1,564,670

146

(1,498,762)

Increase (Decrease) in Stockholders' Equity [Roll Forward]

Other comprehensive (loss) income

(268,542)

(267)

^[1]

(267)

Issuance of common stock under stock plans, net, shares

1,362,118

Issuance of common stock under stock plans

2,093

$ 2

2,091

Sale of shares of common stock, shares

10,000,000

Sale of shares of common stock, net

75,643

$ 10

75,633

Stock-based compensation expense

$ 10,006

10,006

Balance, shares at Dec. 31, 2014

195,895,769

Balance at Dec. 31, 2014

$ (114,829)

$ 196

1,652,400

(121)

(1,767,304)

Increase (Decrease) in Stockholders' Equity [Roll Forward]

Other comprehensive (loss) income

(169,737)

(111)

^[1]

(111)

Warrants transferred from other long-term liabilities

1,470

Issuance of common stock under stock plans, net, shares

3,315,174

Issuance of common stock under stock plans

11,277

$ 3

11,274

Sale of shares of common stock, shares

28,750,000

Sale of shares of common stock, net

145,649

$ 29

145,620

Stock-based compensation expense

$ 21,977

21,977

Balance, shares at Dec. 31, 2015

227,960,943

Balance at Dec. 31, 2015

$ (104,304)

$ 228

$ 1,832,741

$ (232)

$ (1,937,041)

[1]	Other comprehensive (loss) income consisted solely of unrealized losses or gains, net on available for sale securities arising during the periods presented. There were no reclassification adjustments to net loss resulting from realized losses or gains on the sale of securities.

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Cash flows from operating activities:
Net (loss) income	$ (169,737)	$ (268,542)	$ (244,760)
Adjustments to reconcile net (loss) income to net cash used in operating activities:
Depreciation and amortization	1,406	2,391	3,147
Stock-based compensation expense	21,977	10,006	12,031
Accretion of debt discount	25,034	29,534	26,290
Accrual of interest paid in kind	3,817	0	0
Gain on sale of businesses	(112)	(838)	0
Changes in the fair value of warrants	548	(1,840)	0
Other	1,327	4,161	6,787
Changes in assets and liabilities:
Trade and other receivables	(646)	(941)	(1,190)
Inventory	(235)	509	(2,890)
Prepaid expenses and other current assets	(325)	1,526	1,034
Other long-term assets	1,340	(2,149)	0
Accounts payable and other accrued liabilities	(1,276)	(13,945)	8,691
Clinical trial liability	(23,474)	6,587	14,398
Accrued collaboration liability	10,206	732	0
Restructuring liability	(7,180)	(2,302)	(5,750)
Deferred revenue	(2,582)	1,133	(14,871)
Other long-term liabilities	(1,673)	(1,427)	(1,690)
Net cash used in operating activities	(141,585)	(235,405)	(198,773)
Cash flows from investing activities:
Purchases of property and equipment	(447)	(474)	(2,171)
Proceeds from sale of property and equipment	1,346	392	143
Proceeds from sale of business and other equity investment	95	838	0
Proceeds from maturities of restricted cash and investments	19,789	20,354	17,268
Purchase of restricted cash and investments	(5,650)	(8,143)	(6,085)
Proceeds from maturities of investments	178,936	252,891	325,171
Purchases of investments	(143,992)	(119,528)	(189,975)
Net cash provided by investing activities	50,077	146,330	144,351
Cash flows from financing activities:
Proceeds from issuance of common stock, net	145,649	75,643	0
Proceeds from exercise of stock options and warrants	10,911	120	72
Proceeds from employee stock purchase plan	568	1,438	1,429
Principal payments on debt	(4,381)	(11,709)	(13,170)
Net cash provided by (used in) financing activities	152,747	65,492	(11,669)
Net increase (decrease) in cash and cash equivalents	61,239	(23,583)	(66,091)
Cash and cash equivalents at beginning of year	80,395	103,978	170,069
Cash and cash equivalents at end of year	141,634	80,395	103,978
Supplemental cash flow disclosure:
Cash paid for interest	19,822	19,109	19,160
Cash paid for taxes	192	60	0
Non-cash financing activity:
Issuance of warrants in connection with amendment to convertible notes	$ 0	$ 2,762	$ 0

Organization and Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2015

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Organization and Summary of Significant Accounting Policies

ORGANIZATION AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

Organization

Exelixis, Inc. (“Exelixis,” “we,” “our” or “us”) is a biopharmaceutical company that discovers, develops and commercializes small molecule therapies for the treatment of cancer. Our business focuses predominantly on the development and commercialization of cabozantinib, an internally-discovered inhibitor of multiple receptor tyrosine kinases, in various tumor indications. Cabozantinib is currently approved in the United States and European Union for the treatment of progressive, metastatic medullary thyroid cancer (“MTC”), and is marketed under the brand name COMETRIQ^®.

Basis of Consolidation

The consolidated financial statements include the accounts of Exelixis and those of our wholly-owned subsidiaries. These entities’ functional currency is the U.S. dollar. All intercompany balances and transactions have been eliminated.

Basis of Presentation

Exelixis has adopted a 52- or 53-week fiscal year that generally ends on the Friday closest to December 31st. Fiscal year 2013, a 52-week year, ended on December 27, 2013, fiscal year 2014, a 53-week year, ended on January 2, 2015, fiscal year 2015, a 52-week year, ended on January 1, 2016, and fiscal year 2016 will end on December 30, 2016. For convenience, references in this report as of and for the fiscal years ended December 27, 2013, January 2, 2015 and January 1, 2016, are indicated on a calendar year basis, ended December 31, 2013, 2014 and 2015, respectively. The quarter ended January 2, 2015 is a 14-week fiscal quarter; all other interim periods presented are 13-week fiscal quarters.

Segment Information

We operate as a single reportable segment.

Use of Estimates

The preparation of our consolidated financial statements is in conformity with accounting principles generally accepted in the United States which requires management to make judgments. The preparation of our consolidated financial statements is in conformity with accounting principles generally accepted in the United States which requires management to make judgments, estimates and assumptions that affect the reported amounts of assets, liabilities, revenue and expenses, and related disclosures. On an ongoing basis, management evaluates its estimates including, but not limited to, those related to revenue recognition, including for deductions from revenues (such as rebates, chargebacks, sales returns and sales allowances), recoverability of inventory, certain accrued liabilities including clinical trial accruals and restructuring liabilities, share-based compensation and valuation of warrants. We base our estimates on historical experience and on various other market-specific and other relevant assumptions that we believe to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results could differ materially from those estimates.

Reclassifications

Certain prior period amounts in the consolidated balance sheet have been reclassified to conform to current period presentation. We reclassified $0.7 million of Other accrued liabilities as of December 31, 2014 to Accrued collaboration liability in the accompanying consolidated balance sheets.

Limited Sources of Revenues and the Need to Raise Additional Capital

We have incurred net losses since inception through December 31, 2015, with the exception of the 2011 fiscal year. We anticipate net losses and negative operating cash flow for the foreseeable future. For the year ended December 31, 2015, we incurred a net loss of $169.7 million and as of December 31, 2015, we had an accumulated deficit of $1.9 billion. We expect to continue to incur substantial operating expenses and, consequently, we will need to generate significant additional revenues to achieve future profitability.

We commercially launched COMETRIQ for the treatment of progressive, metastatic MTC in the United States in late January 2013, and from the commercial launch through December 31, 2015, we have generated $74.3 million in net revenues from the sale of COMETRIQ. Other than revenues from COMETRIQ, we have derived substantially all of our revenues since inception from collaborative research and development agreements, which depend on research funding, the achievement of milestones, and royalties we earn from any future products developed from the collaborative research.

The amount of our net losses will depend, in part, on: the rate of growth, if any, in our sales of COMETRIQ; the level of sales of cabozantinib in the United States for the treatment of advanced RCC, if approved by the FDA for such indication; receipt of the upfront payment, achievement of clinical, regulatory and commercial milestones and the amount of royalties from sales of cabozantinib for the treatment of advanced RCC in the European Union and elsewhere, if approved for such indication under our collaboration with Ipsen; our share of the net profits and losses for the commercialization of COTELLIC in the U.S.; the amount of royalties from COTELLIC sales outside the U.S.; other license and contract revenues; and, the level of expenses primarily with respect to expanded commercialization activities for cabozantinib.

As of December 31, 2015, we had $253.3 million in cash and investments, which included $169.0 million available for operations, $81.6 million of compensating balance investments that we are required to maintain on deposit with Silicon Valley Bank, and $2.7 million of long-term restricted investments. We anticipate that our current cash and cash equivalents, and short-term investments available for operations, and product revenues, will enable us to maintain our operations for a period of at least 12 months following the filing date of this report. Our capital requirements will depend on many factors, and we may need to use available capital resources and raise additional capital significantly earlier than we currently anticipate.

Cash and Investments

We consider all highly liquid investments purchased with an original maturity of three months or less to be cash equivalents. Cash equivalents include investments in high-grade, short-term money market funds, commercial paper and municipal securities, which are subject to minimal credit and market risk.

We have designated all investments as available-for-sale and therefore, such investments are reported at fair value, with unrealized gains and losses recorded in accumulated other comprehensive loss. For securities sold prior to maturity, the cost of securities sold is based on the specific identification method. Realized gains and losses on the sale of investments are recorded in interest and other income, net.

We classify those investments we do not require for use in current operations that mature in more than 12 months as Long-term investments on our Consolidated Balance Sheets. Additionally, those investments that collateralize loan balances with terms that extend 12 months or longer were classified as long-term investments even if the investment’s remaining term to maturity was one year or less; they are not restricted to withdrawal.

All of our investments are subject to a quarterly impairment review. We recognize an impairment charge when a decline in the fair value of an investment below its cost basis is judged to be other-than-temporary. Factors considered in determining whether a loss is temporary included the length of time and extent to which the investments fair value has been less than the cost basis, the financial condition and near-term prospects of the investee, extent of the loss related to credit of the issuer, the expected cash flows from the security, our intent to sell the security and whether or not we will be required to sell the security before the recovery of its amortized cost. During the years ended December 31, 2015, 2014, and 2013, we did not record any other-than-temporary impairment charges on our available-for-sale securities.

Fair Value Measurements

Fair value reflects the amounts that would be received upon sale of an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date (exit price). We disclose the fair value of financial instruments for assets and liabilities for which the value is practicable to estimate. For those financial instruments measured and recorded at fair value on a recurring basis, we also provide fair value hierarchy information in these Notes to Consolidated Financial Statements. The fair value hierarchy has the following three levels:

Level 1 – quoted prices (unadjusted) in active markets for identical assets and liabilities that the reporting entity can access at the measurement date.

Level 2 – observable inputs, other than quoted prices in active markets for identical assets and liabilities that are observable either directly or indirectly. These inputs include using prices from independent pricing services based on quoted prices in active markets for similar instruments or on industry models using data inputs, such as interest rates and prices that can be directly observed or corroborated in active markets.

Level 3 – unobservable inputs.

A review of the fair value hierarchy classification is conducted on a quarterly basis. Changes in the observability of valuation inputs may result in a reclassification of levels for certain investments within the fair value hierarchy. During the years ended December 31, 2015, 2014, and 2013, there were no such reclassifications.

Inventory

Inventory is valued at the lower of cost or net realizable value. We determine the cost of inventory using the standard-cost method, which approximates actual cost based on a first-in, first-out method. We analyze our inventory levels quarterly and write down inventory subject to expiry in excess of expected requirements, or that has a cost basis in excess of its expected net realizable value. The related costs are recognized as cost of goods sold in the Consolidated Statements of Operations.

We analyze our estimated production levels for the following twelve month period , which is our normal operating cycle, quarterly and reclassify inventory we do not expect to use within the next twelve months into Other long-term assets in the Consolidated Balance Sheets.

We consider regulatory approval of product candidates to be uncertain and product manufactured prior to regulatory approval may not be sold unless regulatory approval is obtained. As such, the manufacturing costs for product candidates incurred prior to regulatory approval were not capitalized as inventory but were expensed as research and development costs. When regulatory approval is obtained, we begin capitalization of inventory related costs.

Property and Equipment

Property and equipment are recorded at cost and depreciated using the straight-line method over the following estimated useful lives:



Equipment and furniture	5 years
Computer equipment and software	3 years
Leasehold improvements	Shorter of lease life or 7 years

Capitalized software includes certain internal use computer software costs.

Repairs and maintenance costs are charged to expense as incurred.

Goodwill

Goodwill amounts have been recorded as the excess purchase price over tangible assets, liabilities and intangible assets acquired based on their estimated fair value. Goodwill is not subject to amortization. We evaluate goodwill for impairment on an annual basis and on an interim basis if events or changes in circumstances between annual impairment tests indicate that the asset might be impaired. We continue to operate in one segment, which is also considered to be our sole reporting unit and therefore, goodwill was tested for impairment at the enterprise level as of December 31, 2015 and 2014.

Long-Lived Assets

Long-lived assets include property and equipment. The carrying value of our long-lived assets is reviewed for impairment whenever events or changes in circumstances indicate that the asset may not be recoverable. An impairment loss would be recognized when estimated future cash flows expected to result from the use of the asset and its eventual disposition is less than its carrying amount.

Revenue Recognition

We recognize revenue from product sales and from license fees, milestones, contingent payments and royalties earned on research and collaboration arrangements.

Net Product Revenues

We recognize revenue when it is both realized or realizable and earned, meaning persuasive evidence of an arrangement exists, delivery has occurred, title has transferred, the price is fixed or determinable, there are no remaining customer acceptance requirements, and collectability of the resulting receivable is reasonably assured. For product sales in the United States, this generally occurs upon delivery of the product to the specialty pharmacy. For product sales in Europe, this generally occurs when our European distribution partner has accepted the product, at which time they are no longer able to return the product.

We sell our product, COMETRIQ, in the United States to a specialty pharmacy that benefits from customer incentives and has a right of return. Prior to 2015, COMETRIQ had limited sales history and we could not reliably estimate expected future returns, discounts and rebates of the product at the time the product was sold to the specialty pharmacy, therefore we recognized revenue when the specialty pharmacy provided the product to a patient based on the fulfillment of a prescription, frequently referred to as the “sell-through” revenue recognition model. Recently we have established sufficient historical experience and data to reasonably estimate expected future returns of the product and the discounts and rebates due to payors at the time of shipment to the specialty pharmacy. Accordingly, beginning in January 2015 we began to recognize revenue upon delivery to our U.S. specialty pharmacy. This approach is frequently referred to as the “sell-in” revenue recognition model. In connection with the change in the timing of recognition of U.S. COMETRIQ sales, we recorded a one-time adjustment to recognize revenue and related costs that had previously been deferred at December 31, 2014, resulting in additional gross product revenues of $2.6 million and a nominal amount of cost of goods sold for the year ended December 31, 2015; there were no such adjustments recorded during 2014 and 2013.

We also utilize the “sell-in” revenue recognition model for sales to our European distribution partner for all periods presented. Once the European distributer has accepted the product, the product is no longer subject to return; therefore, we record revenue at the time our European distribution partner has accepted the product.

Product Sales Discounts and Allowances

We calculate gross product revenues based on the price that we charge our United States specialty pharmacy and our European distribution partner. We estimate our domestic net product revenues by deducting from our gross product revenues (a) trade allowances, such as discounts for prompt payment, (b) estimated government rebates and chargebacks, (c) estimated costs of patient assistance programs, and (d) certain other fees paid to the U.S specialty pharmacy. Discounts and allowances for foreign sales for the years ended December 31, 2015 and 2014 included portions of a one-time $2.4 million project management fee payable to our European distribution partner upon its achievement of a cumulative revenue goal. During 2014, we determined that the achievement of the revenue goal was probable and therefore we recorded $2.3 million of the $2.4 million project management fee, of which $0.7 million would have been recorded in 2013 had the cumulative revenue goal been determined to be probable in that period. During 2015 we recorded an additional $0.1 million of the project management fee.

We initially record estimates for these deductions at the time we recognize the gross revenue. We update our estimates on a recurring basis as new information becomes available.

Customer Credits: The United States specialty pharmacy receives a discount of 2% for prompt payment. We expect this specialty pharmacy will earn 100% of its prompt payment discounts and, therefore, we deduct the full amount of these discounts from total product sales when revenues are recognized.

Mandated Rebates: Allowances for rebates include mandated discounts under the Medicaid Drug Rebate Program and other government programs. Rebate amounts owed after the final dispensing of the product to a benefit plan participant are based upon contractual agreements or legal requirements with public sector benefit providers, such as Medicaid. The allowance for rebates is based on statutory discount rates and expected utilization. Our estimates for the expected utilization of rebates are based on customer and payer data received from the United States specialty pharmacy and historical utilization rates. Rebates are generally invoiced by the payer and paid in arrears, such that the accrual balance consists of an estimate of the amount expected to be incurred for the current quarter’s shipments to patients, plus an accrual balance for known prior quarter’s unpaid rebates. If actual future rebates vary from estimates, we may need to adjust our accruals, which would affect net revenue in the period of adjustment.

Chargebacks: Chargebacks are discounts that occur when contracted customers purchase directly from a specialty pharmacy. Contracted customers, which currently consist primarily of Public Health Service institutions, non-profit clinics, and Federal government entities purchasing via the Federal Supply Schedule, generally purchase the product at a discounted price. The United States specialty pharmacy, in turn, charges back to us the difference between the price initially paid by the specialty pharmacy and the discounted price paid to the specialty pharmacy by the customer. The allowance for chargebacks is based on an estimate of sales to contracted customers.

Medicare Part D Coverage Gap: In the United States, the Medicare Part D prescription drug benefit mandates manufacturers to fund 50% of the Medicare Part D insurance coverage gap for prescription drugs sold to eligible patients. Our estimates for expected Medicare Part D coverage gap are based in part on third party market research data and on customer and payer data received from the United States specialty pharmacy. Funding of the coverage gap is invoiced and paid in arrears so that the accrual balance consists of an estimate of the amount expected to be incurred for the current quarter's shipments to patients, plus an accrual balance for prior sales. If actual future funding varies from estimates, we may need to adjust our accruals, which would affect net revenue in the period of adjustment.

Co-payment Assistance: Patients who have commercial insurance and meet certain eligibility requirements may receive co-payment assistance. We accrue a liability for co-payment assistance based on actual program participation and estimates of program redemption using customer data provided by our United States specialty pharmacy.

Our European distribution partner is entitled to receive a project management fee based upon the achievement of a pre-specified revenue goal which, when deemed probable, is ratably accrued as a reduction to gross revenue.

License and Contract Revenues

Under the terms of our collaboration agreement with Genentech, Inc. (a member of the Roche Group) (“Genentech”) for cobimetinib, we are entitled to a share of U.S. profits and losses for cobimetinib. We are entitled to low double-digit royalties on ex-U.S. net sales. See “Note 2 - Research and Collaboration Agreements” for additional information about our collaboration agreement with Genentech. We record our share of profits and royalties under the collaboration agreement when reported to us by our collaboration partner; losses under the collaboration agreement are recorded in the period incurred based on our estimate of those losses. Profits and royalties are classified as license revenues in our Consolidated Statements of Operations. As of December 31, 2015, we have not recognized any profits from the commercialization of cobimetinib in the U.S. Until we have recognized such a profit under the agreement, losses are recognized as Selling, General and Administrative expenses in our Consolidated Statements of Operations. We have determined that we are an agent under the agreement and therefore revenues are recorded net of costs incurred.

License, research commitment and other non-refundable payments received in connection with research collaboration agreements are deferred and recognized on a straight-line basis over the period of continuing involvement, generally the research term specified in the agreement. Contract research revenues are recognized as services are performed pursuant to the terms of the agreements. Any amounts received in advance of performance are recorded as deferred revenue. Payments are not refundable if research is not successful. License fees are classified as license revenues in our Consolidated Statements of Operations.

We enter into corporate collaborations under which we may obtain upfront license fees, research funding, contingent, milestone and royalty payments. Our deliverables under these arrangements typically consist of intellectual property rights and research and development services. We evaluate whether the delivered elements under these arrangements have value to our collaboration partner on a stand-alone basis and whether objective and reliable evidence of fair value of the undelivered item exists. If we determine that multiple deliverables exist, the consideration is allocated to one or more units of accounting based upon the best estimate of the selling price of each deliverable. The selling price used for each deliverable will be based on vendor-specific objective evidence, if available, third-party evidence if vendor-specific objective evidence is not available, or estimated selling price if neither vendor-specific or third-party evidence is available. A delivered item or items that do not qualify as a separate unit of accounting within the arrangement shall be combined with the other applicable undelivered items within the arrangement. The allocation of arrangement consideration and the recognition of revenue then shall be determined for those combined deliverables as a single unit of accounting. A delivered item or items that do not have stand-alone value to our collaboration partner shall be combined with the other applicable undelivered items within the arrangement. The allocation of arrangement consideration and the recognition of revenue then shall be determined for those combined deliverables as a single unit of accounting. For a combined unit of accounting, non-refundable upfront fees and milestones are recognized in a manner consistent with the final deliverable, which has generally been ratably over the period of the research and development obligation.

Contingency payments (received upon the achievement of certain events by our collaborators) and milestone payments (received upon the achievement of certain events by us) are non-refundable and recognized as revenues over the period of the research arrangement. This typically results in a portion of the payments being recognized at the date the contingency or milestone is achieved, which portion is equal to the applicable percentage of the research term that has elapsed at the date of achievement, and the balance being recognized over the remaining research term of the agreement. In certain situations, we may receive contingent payments after the end of our period of continued involvement. In such circumstances, we would recognize 100% of the contingent revenues when the contingency is achieved. Contingency and milestones payments, when recognized as revenue, are classified as contract revenues in our Consolidated Statements of Operations.

Patient Assistance Program

We provide COMETRIQ at no cost to eligible patients who have no insurance and meet certain financial and clinical criteria through our Patient Assistance Program (“PAP”). We record the cost of the product as a selling, general and administrative expense at the time the product is shipped to the specialty pharmacy for PAP use.

Cost of Goods Sold

Cost of goods sold is related to our product revenues and consists primarily of a 3% royalty on net sales of any product incorporating cabozantinib payable to GlaxoSmithKline, indirect labor costs, the cost of manufacturing, write-downs related to expiring and excess inventory, and other third party logistics costs of our product. A portion of the manufacturing costs for product sales were incurred prior to regulatory approval of COMETRIQ for the treatment of progressive, metastatic MTC and, therefore, were expensed as research and development costs when those costs were incurred, rather than capitalized as inventory.

In accordance with our product development and commercialization agreement with GlaxoSmithKline, we are required to pay GlaxoSmithKline a 3% royalty on the Net Sales of any product incorporating cabozantinib, including COMETRIQ. Net Sales is defined in the product development and commercialization agreement as the gross invoiced sales price less customer credits, rebates, chargebacks, shipping costs, customs duties, and sales tax and other similar tax payments we are required to make.

Research and Development Expenses

Research and development costs are expensed as incurred and include costs associated with research performed pursuant to collaborative agreements. Research and development costs consist of direct and indirect internal costs related to specific projects as well as fees paid to other entities that conduct certain research activities on our behalf.

Substantial portions of our preclinical studies and all of our clinical trials have been executed with support from third-party contract research organizations (“CROs”) and other vendors. We accrue expenses for preclinical studies performed by our vendors based on certain estimates over the term of the service period and adjust our estimates as required. We accrue expenses for clinical trial activities performed by CROs based upon the estimated amount of work completed on each trial. For clinical trial expenses, the significant factors used in estimating accruals include the number of patients enrolled, the number of active clinical sites, and the duration for which the patients will be enrolled in the trial. We monitor patient enrollment levels and related activities to the extent possible through internal reviews, correspondence with CROs and review of contractual terms. We base our estimates on the best information available at the time. However, additional information may become available to us which may allow us to make a more accurate estimate in future periods. In this event, we may be required to record adjustments to research and development expenses in future periods when the actual level of activity becomes more certain. Such increases or decreases in cost are generally considered to be changes in estimates and will be reflected in research and development expenses in the period first known.

Net Loss Per Share

Basic net loss per share is computed by dividing the net loss for the period by the weighted average number of shares of common stock outstanding during the period. Diluted net loss per share gives effect to potential incremental common shares issuable upon the exercise of stock options and warrants, and shares issuable pursuant to restricted stock units (“RSUs”) (calculated based on the treasury stock method), and upon conversion of our convertible debt (calculated using an as-if-converted method) as long as such shares are not anti-dilutive. The calculation of diluted loss per share requires that, to the extent the average market price of the underlying shares for the reporting period exceeds the exercise price of the warrants and the presumed exercise of such securities are dilutive to loss per share for the period, adjustments to net loss used in the calculation are required to remove the change in fair value of the warrants for the period. Likewise, adjustments to the denominator are required to reflect the related dilutive shares.

Foreign Currency Translation and Remeasurement

Monetary assets and liabilities denominated in currencies other than the functional currency are remeasured using exchange rates in effect at the end of the period and related gains or losses are recorded in interest income and other, net. Gains and losses on the remeasurement of monetary assets and liabilities were not material for any of the years presented. We do not have any nonmonetary assets or liabilities denominated in currencies other than the U.S. dollar.

Stock-Based Compensation

Stock-based compensation expense for all stock-based compensation awards is based on the grant date fair value estimated using the Black-Scholes Merton option pricing model. Because there is a market for options on our common stock, we have considered implied volatilities as well as our historical realized volatilities when developing an estimate of expected volatility. We estimate the term using historical data. We recognize compensation expense on a straight-line basis over the requisite service period. Compensation expense relating to awards subject to performance conditions is recognized if it is probable that the performance goals will be achieved. The probability of achievement is assessed on a quarterly basis. The total number of awards expected to vest is adjusted for estimated forfeitures. We have elected to use the simplified method to calculate the beginning pool of excess tax benefits.

Recently Adopted Accounting Pronouncements

In November 2015, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update No. 2015-17 Income Taxes (Topic 740): Balance Sheet Classification of Deferred Taxes, or ASU 2015-17. ASU 2015-17 simplifies the presentation of deferred income taxes by eliminating the separate classification of deferred income tax liabilities and assets into current and noncurrent amounts in the consolidated balance sheet statement of financial position. The amendments in the update require that all deferred tax liabilities and assets be classified as noncurrent in the consolidated balance sheet. The amendments in this update are effective for annual periods beginning after December 15, 2016, and interim periods therein and may be applied either prospectively or retrospectively to all periods presented. Early adoption is permitted. We have early adopted this standard in the fourth quarter of 2015 on a prospective basis. Prior periods have not been adjusted.

In April 2015, the FASB issued Accounting Standards Update 2015-03 Simplifying the Presentation of Debt Issuance Costs which Changes the Presentation of Debt Issuance Costs in Financial Statements (“ASU 2015-03”), which requires that debt issuance costs related to a recognized debt liability be presented in the balance sheet as a direct deduction from the carrying amount of that debt liability, consistent with debt discounts. The Company early adopted ASU 2015-03 as of December 31, 2015, as permitted. There is no impact of early adoption of ASU 2015-03 on the consolidated statements of operations and comprehensive loss. The impact of early adoption on the consolidated balance sheets as of the dates presented is noted in the table below (in thousands):



	December 31, 2015				December 31, 2014
	Prior to Adoption of ASU 2015-03	ASU 2015-03 Adjustment		As Adopted	Prior to Adoption of ASU 2015-03 (as previously reported)	ASU 2015-03 Adjustment		As Adopted
Other long-term assets	5,579	(3,270	)	2,309	8,340	(4,691	)	3,649
Total assets	335,612	(3,270	)	332,342	327,960	(4,691	)	323,269

Current portion of convertible notes	—	—		—	98,880	(1,431	)	97,449
Current liabilities	52,251	—		52,251	171,860	(1,431	)	170,429

Long-term portion of convertible notes	304,705	(3,270	)	301,435	182,395	(3,260	)	179,135
Total liabilities	439,916	(3,270	)	436,646	442,789	(4,691	)	438,098

Recently Issued Accounting Pronouncements

In May 2014, the FASB issued Accounting Standards Update 2014-09, Revenue from Contracts with Customers, (“ASU 2014-09”). ASU 2014-09 supersedes the revenue recognition requirements of FASB Accounting Standards Codification (“ASC”) Topic 605, Revenue Recognition and most industry-specific guidance throughout the ASC, resulting in the creation of FASB ASC Topic 606, Revenue from Contracts with Customers. ASU 2014-09 requires entities to recognize revenue in a way that depicts the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled to in exchange for those goods or services. In August 2015, the FASB deferred the effective date by one year for public entities for annual and interim reporting periods beginning after December 15, 2017. Early adoption is permitted for periods after December 15, 2016. We are currently evaluating the impact of adopting ASU 2014-09, inclusive of available transitional methods on our consolidated financial statements and related disclosures.

In August 2014, the FASB issued Accounting Standards Update No. 2014-15, Disclosure of Uncertainties about an Entity’s Ability to Continue as a Going Concern, (“ASU 2014-15”). ASU 2014-15 explicitly requires management to evaluate, at each annual or interim reporting period, whether there are conditions or events that exist that raise substantial doubt about an entity’s ability to continue as a going concern within one year after the date the financial statements are issued and to provide related disclosures. ASU 2014-15 is effective for annual periods ending after December 15, 2016 and earlier application is permitted. The adoption of this guidance will not have any impact on the Company’s financial position and results of operations and, at this time, we do not expect any impact on its disclosures.

In February 2016, the FASB issued Accounting Standards Update No. 2016-02, Leases, (“ASU 2016-02”). ASU 2016-02 is aimed at making leasing activities more transparent and comparable, and requires substantially all leases be recognized by lessees on their balance sheet as a right-of-use asset and corresponding lease liability, including leases currently accounted for as operating leases. ASU 2016-02 is effective for all interim and annual reporting periods beginning after December 15, 2018. Early adoption is permitted. We are currently evaluating the impact that the adoption of ASU 2016-02 will have on our consolidated financial statements and related disclosures.

Research and Collaboration Agreements	12 Months Ended
Research and Collaboration Agreements	Dec. 31, 2015
Research And Collaboration Agreements [Abstract]
Research and Collaboration Agreements	RESEARCH AND COLLABORATION AGREEMENTS Ipsen Collaboration On February 29, 2016, we entered into a collaboration and license agreement with Ipsen Pharma SAS, (“Ipsen”) pursuant to which Ipsen has exclusive commercialization rights for current and potential future cabozantinib indications outside of the United States, Canada and Japan. The companies have agreed to collaborate on the development of cabozantinib for current and potential future indications. See “Note 15 - Subsequent Events” for more information regarding our Ipsen collaboration. Genentech Collaboration In December 2006, we out-licensed the development and commercialization of cobimetinib to Genentech pursuant to a worldwide collaboration agreement. Exelixis discovered cobimetinib internally and advanced the compound to investigational new drug (“IND”), status. Genentech paid upfront and milestone payments of $25.0 million in December 2006 and $15.0 million in January 2007 upon signing of the collaboration agreement and with the submission of the IND application for cobimetinib. Under the terms of the agreement, we were responsible for developing cobimetinib through the determination of the maximum-tolerated dose in a phase 1 clinical trial, and Genentech had the option to co-develop cobimetinib, which Genentech could exercise after receipt of certain phase 1 data from us. In March 2008, Genentech exercised its option to co-develop cobimetinib. In March 2009, we granted to Genentech an exclusive worldwide revenue-bearing license to cobimetinib, at which point Genentech became responsible for completing the phase 1 clinical trial and subsequent clinical development. The U.S. Food and Drug Administration approved cobimetinib in the United States under the brand name COTELLIC^TM on November 10, 2015. It is indicated in combination with vemurafenib as a treatment for patients with BRAF V600E or V600K mutation-positive advanced melanoma. COTELLIC in combination with vemurafenib has also been approved in Switzerland, the European Union and Canada for use in the same indication. Under the terms of our collaboration agreement with Genentech for cobimetinib, we are entitled to a share of U.S. profits and losses for cobimetinib. The profit and loss share has multiple tiers: we are entitled to 50% of profits and losses from the first $200 million of U.S. actual sales, decreasing to 30% of profits and losses from U.S. actual sales in excess of $400 million. We are entitled to low double-digit royalties on ex-U.S. net sales. In November 2013, we exercised an option under the collaboration agreement to co-promote in the United States, if commercialized. Following the approval of COTELLIC in the United States in November 2015, we began fielding 25% of the sales force promoting COTELLIC in combination with vemurafenib as a treatment for patients with BRAF V600E or V600K mutation-positive advanced melanoma. We recorded net losses of $16.6 million, $2.9 million and $0.7 million under the collaboration agreement during the years ended December 31, 2015, 2014 and 2013, respectively; those costs are included in Selling, General and Administrative expenses on the accompanying Consolidated Statement of Operations. A portion of the liability for those costs, identified as Accrued collaboration liability on the accompanying Consolidated Balance Sheets, includes commercialization expenses that Genentech has allocated to the collaboration but remain under discussion between us and Genentech. We also recognized license revenues of $14 thousand for royalties on ex-U.S. net sales of COTELLIC during the year ended December 31, 2015. We recognized no such royalties during the years ended December 31, 2014 and 2013. Other Collaborations We have established collaborations with other leading pharmaceutical and biotechnology companies, including GlaxoSmithKline, Bristol-Myers Squibb Company (“Bristol-Myers Squibb”), Sanofi, Merck (known as MSD outside of the United States and Canada) and Daiichi Sankyo Company Limited (“Daiichi Sankyo”), for various compounds and programs in our portfolio. With the exception of collaboration with Ipsen, we have fully out-licensed compounds or programs to a partner for further development and commercialization under these collaborations and have no further development cost obligations under our collaborations. Under each of our collaborations, we are entitled to receive milestones and royalties, or in the case of cobimetinib, a share of profits (or losses) from commercialization. With respect to our partnered compounds, other than cabozantinib and cobimetinib, we are eligible to receive potential contingent payments totaling approximately $2.3 billion in the aggregate on a non-risk adjusted basis, of which 10% are related to clinical development milestones, 42% are related to regulatory milestones and 48% are related to commercial milestones, all to be achieved by the various licensees, which may not be paid, if at all, until certain conditions are met. Bristol-Myers Squibb ROR Collaboration Agreement In October 2010, we entered into a worldwide collaboration with Bristol-Myers Squibb pursuant to which each party granted to the other certain intellectual property licenses to enable the parties to discover, optimize and characterize ROR antagonists that may subsequently be developed and commercialized by Bristol-Myers Squibb. Since the collaborative research period ended in July 2013, Bristol-Myers Squibb has and will continue to have sole responsibility for any further research, development, manufacture and commercialization of products developed under the collaboration and will bear all costs and expenses associated with those activities. For each product developed by Bristol-Myers Squibb under the collaboration, we will be eligible to receive payments upon the achievement by Bristol-Myers Squibb of development and regulatory milestones of up to $252.5 million in the aggregate and commercialization milestones of up to $150.0 million in the aggregate, as well as royalties on commercial sales of any such products. We recognized contract revenues of $1.5 million during the year ended December 31, 2013 under our ROR collaboration agreement with Bristol-Myers Squibb. We recognized no such revenue during the years ended December 31, 2015 and 2014. LXR Collaboration Agreement In December 2005, we entered into a collaboration agreement with Bristol-Myers Squibb for the discovery, development and commercialization of novel therapies targeted against LXR, a nuclear hormone receptor implicated in a variety of cardiovascular and metabolic disorders. This agreement became effective in January 2006, at which time we granted Bristol-Myers Squibb an exclusive worldwide license with respect to certain intellectual property primarily relating to compounds that modulate LXR. The research term expired in January 2010 and we transferred the technology to Bristol-Myers Squibb in 2011 to enable it to continue the LXR program. We have been advised that BMS is continuing additional preclinical research on the program. Under the collaboration agreement, Bristol-Myers Squibb is required to pay us contingent amounts associated with development and regulatory milestones of up to $138.0 million per product for up to two products from the collaboration. In addition, we are also entitled to receive payments associated with sales milestones of up to $225.0 million and royalties on sales of any products commercialized under the collaboration. We did not any recognize any revenue under our LXR collaboration agreement with Bristol-Myers Squibb during the three years ended December 31, 2015. Terminated Agreements During 2013, additional license and collaboration agreements with Bristol-Myers Squibb were terminated or concluded. We recognized license and contract revenues of $14.8 million during the year ended December 31, 2013 under these terminated agreements with Bristol-Myers Squibb. Sanofi In May 2009, we entered into a global license agreement with Sanofi for SAR245408 (XL147) and SAR245409 (XL765), leading inhibitors of phosphoinositide-3 kinase (“PI3K”), and a broad collaboration for the discovery of inhibitors of PI3K for the treatment of cancer. The license agreement and collaboration agreement became effective on July 7, 2009. We will be eligible to receive contingent payments associated with development, regulatory and commercial milestones under the license agreement of $745.0 million in the aggregate, as well as royalties on sales of any products commercialized under the license. We did not recognize any revenue under our collaboration agreement with Sanofi during the three years ended December 31, 2015. Merck In December 2011, we entered into an agreement with Merck pursuant to which we granted Merck an exclusive worldwide license to our PI3K-delta (“PI3K-d”) program, including XL499 and other related compounds. Pursuant to the terms of the agreement, Merck has sole responsibility to research, develop, and commercialize compounds from our PI3K-d program. The agreement became effective in December 2011. We will be eligible to receive payments associated with the successful achievement of potential development and regulatory milestones for multiple indications of up to $236.0 million. We will also be eligible to receive payments for combined sales performance milestones of up to $375.0 million and royalties on net-sales of products emerging from the agreement. Contingent payments associated with milestones achieved by Merck and royalties are payable on compounds emerging from our PI3K-d program or from certain compounds that arise from Merck’s internal discovery efforts targeting PI3K-d during a certain period. We recognized contract revenues of $3.0 million from a milestone payment during the year ended December 31, 2015 under our collaboration agreement with Merck. We did not any recognize any such revenue during the years ended December 31, 2014 and 2013. Daiichi Sankyo In March 2006, we entered into a collaboration agreement with Daiichi Sankyo for the discovery, development and commercialization of novel therapies targeted against the mineralocorticoid receptor (“MR”), a nuclear hormone receptor implicated in a variety of cardiovascular and metabolic diseases. Under the terms of the agreement, we granted to Daiichi Sankyo an exclusive, worldwide license to certain intellectual property primarily relating to compounds that modulate MR, including CS-3150 (an isomer of XL550). Daiichi Sankyo is responsible for all further preclinical and clinical development, regulatory, manufacturing and commercialization activities for the compounds and we do not have rights to reacquire such compounds, except as described below. We are eligible to receive additional development, regulatory and commercialization milestone payments of up to $145.0 million. In addition, we are also entitled to receive royalties on any sales of certain products commercialized under the collaboration. We did not recognize any revenue under our collaboration agreement with Daiichi Sankyo during the three years ended December 31, 2015. GlaxoSmithKline In October 2002, we established a collaboration with GlaxoSmithKline to discover and develop novel therapeutics in the areas of vascular biology, inflammatory disease and oncology. Under the terms of the product development and commercialization agreement, GlaxoSmithKline had the right to choose cabozantinib for further development and commercialization, but notified us in October 2008 that it had waived its right to select the compound for such activities. As a result, we retained the rights to develop, commercialize, and/or license cabozantinib, subject to payment to GlaxoSmithKline of a 3% royalty on net sales of any product incorporating cabozantinib. The product development and commercialization agreement has terminated during 2014, although GlaxoSmithKline will continue to be entitled to a 3% royalty on net sales of any product incorporating cabozantinib, including COMETRIQ. In connection with the sales of COMETRIQ, during the years ended December 31, 2015, 2014 and 2013 we recorded $1.0 million, $0.7 million and $0.4 million, respectively in royalty expense to GlaxoSmithKline; the royalty expense is included in Cost of goods sold in the accompanying Consolidated Statements of Operations.

Restructurings

12 Months Ended

Dec. 31, 2015

Restructuring Charges [Abstract]

Restructurings

RESTRUCTURINGS

2014 Restructuring

On September 2, 2014, as a consequence of the failure of COMET-1, one of our two phase 3 pivotal trials of cabozantinib in metastatic castration-resistant prostate cancer, we initiated a restructuring, which we refer to as the 2014 Restructuring, to reduce our workforce. The aggregate reduction in headcount from the 2014 Restructuring was 143 employees. The principal objective of the 2014 Restructuring was to enable us to focus our financial resources on the phase 3 pivotal trials of cabozantinib in advanced renal cell carcinoma and advanced hepatocellular carcinoma.

For the years ended December 31, 2015 and 2014, we recorded restructuring charges of $0.3 million and $6.1 million, respectively, for the 2014 Restructuring. The restructuring charge for the year ended December 31, 2015 included $1.6 million in additional charges due to the partial termination of one of our building leases and additional facility-related charges related to the decommissioning and exit of certain buildings. The restructuring charge for the year ended December 31, 2015 was partially offset by $1.0 million in recoveries recorded in connection with the sale of excess equipment and other assets that had previously been fully depreciated. The restructuring charge for the year ended December 31, 2014 includes $5.8 million of employee severance and other benefits that are recognized ratably during the period from the implementation date of the 2014 Restructuring through the employees’ termination dates. In addition, we recorded charges of $0.3 million for property and equipment write-downs and other charges, which were partially offset by recoveries recorded in connection with the sale of excess equipment and other assets that were previously fully impaired and the reversal of severance charges recorded in 2014 for employees that were recalled in 2015.

The restructuring liability related to the 2014 Restructuring is included in the current and long-term portion of restructuring liability on the accompanying Consolidated Balance Sheets. The components of and changes to these liabilities during the year ended December 31, 2015 are summarized in the following table (in thousands):



	Employee Severance and Other Benefits			Facility Charges			Asset Impairment and Sales			Legal and Other Fees			Total
Restructuring charge	$	5,775		$	65		$	188		$	59		$	6,087
Proceeds from sale of assets	—			—			100			—			100
Cash payments, net	(4,507		)	(65		)	—			(12		)	(4,584		)
Other items	22			—			(288		)	—			(266		)
Restructuring liability as of December 31, 2014	1,290			—			—			47			1,337
Restructuring charge (recovery)	(269		)	1,582			(981		)	(47		)	285
Proceeds from sale of assets	—			—			1,325			—			1,325
Cash payments, net	(1,021		)	(1,357		)	—			—			(2,378		)
Other items	—			278			(344		)	—			(66		)
Restructuring liability as of December 31, 2015	$	—		$	503		$	—		$	—		$	503

2010 Restructurings

Between March 2010 and May 2013, we implemented five restructurings (referred to collectively as the “2010 Restructurings”) to manage costs and as a consequence of our decision in 2010 to focus our proprietary resources and development efforts on the development and commercialization of cabozantinib. The aggregate reduction in headcount from the 2010 Restructurings was 429 employees. Charges and credits related to the 2010 Restructurings were recorded in periods other than those in which the 2010 Restructurings were implemented as a result of sublease activities for certain of our buildings in South San Francisco, California, changes in assumptions regarding anticipated sublease activities, the effect of the passage of time on our discounted cash flow computations, previously planned employee terminations, and sales of excess equipment and other assets.

For the years ended December 31, 2015, 2014 and 2013, we recorded restructuring charges of $0.8 million, $1.5 million and $1.2 million, respectively, for the 2010 Restructurings. The charges for the periods presented were related to the effect of the passage of time on our discounted cash flow computations for the exit, in prior periods, of certain of our South San Francisco buildings and changes in estimates regarding future subleases. During the year ended December 31, 2014, those charges were partially offset by $0.1 million in recoveries recorded in connection with the sale of excess equipment and other assets.

The total outstanding restructuring liability related to the 2010 Restructurings is included in the current and long-term portion of restructuring liability on the accompanying Consolidated Balance Sheets. The changes of these liabilities, all of which related to facility charges during the year ended December 31, 2015, are summarized in the following table (in thousands):



	Facility Charges			Other			Total
Restructuring liability as of December 31, 2012	$	19,202		$	20		$	19,222
Restructuring charge	662			569			1,231
Proceeds from sale of assets	—			95			95
Cash payments, net	(6,331		)	(434		)	(6,765		)
Other items	(73		)	(238		)	(311		)
Restructuring liability as of December 31, 2013	13,460			12			13,472
Restructuring charge (recovery)	1,626			(117		)	1,509
Proceeds from sale of assets	—			199			199
Cash payments, net	(5,644		)	(8		)	(5,652		)
Other items	12			(86		)	(74		)
Restructuring liability as of December 31, 2014	9,454			—			9,454
Restructuring charge	757			—			757
Cash payments, net	(6,449		)	—			(6,449		)
Other items	325			—			325
Restructuring liability as of December 31, 2015	$	4,087		$	—		$	4,087

We expect to pay the combined accrued facility charges for both the 2014 Restructuring and the 2010 Restructurings of $4.6 million, net of $6.1 million to be received from our subtenants, through the end of our lease terms of the buildings, the last of which ends in 2017. We expect to incur additional restructuring charges for both restructuring plans of approximately $0.3 million relating to the effect of the passage of time on our discounted cash flow computations used to determine the accrued facilities charges through the end of the building lease terms.

Cash and Investments

12 Months Ended

Dec. 31, 2015

Investments, Debt and Equity Securities [Abstract]

Cash and Investments

CASH AND INVESTMENTS

The following table summarizes cash and cash equivalents, investments, and restricted cash and investments by balance sheet line item as of December 31, 2015 and 2014 (in thousands):



	December 31, 2015
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Cash and cash equivalents	$	141,634	$	—	$	—		$	141,634
Short-term investments	25,484		5		(63		)	25,426
Long-term investments	83,665		2		(67		)	83,600
Long-term restricted cash and investments	2,650		—		—			2,650
Total cash and investments	$	253,433	$	7	$	(130	)	$	253,310



	December 31, 2014
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Cash and cash equivalents	$	80,395	$	—	$	—		$	80,395
Short-term investments	63,988		37		(135		)	63,890
Short-term restricted cash and investments	12,105		107		—			12,212
Long-term investments	81,600		1		(22		)	81,579
Long-term restricted cash and investments	4,684		—		—			4,684
Total cash and investments	$	242,772	$	145	$	(157	)	$	242,760

Under our loan and security agreement with Silicon Valley Bank, we are required to maintain compensating balances on deposit in one or more investment accounts with Silicon Valley Bank or one of its affiliates. The total collateral balances as of December 31, 2015 and 2014 were $81.6 million and $82.0 million, respectively and are reflected in our Consolidated Balance Sheets in Long-term investments. See “Note 7 - Debt” for more information regarding the collateral balance requirements under our Silicon Valley Bank loan and security agreement.

All of our cash equivalents and investments are classified as available-for-sale. The following table summarizes our cash equivalents and investments by security type as of December 31, 2015 and 2014. The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	December 31, 2015
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	72,000	$	—	$	—		$	72,000
Commercial paper	78,155		—		—			78,155
Corporate bonds	72,205		4		(118		)	72,091
U.S. Treasury and government sponsored enterprises	28,434		1		(12		)	28,423
Marketable equity securities	16		2		—			18
Total investments	$	250,810	$	7	$	(130	)	$	250,687



	December 31, 2014
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	23,376	$	—	$	—		$	23,376
Commercial paper	56,714		—		—			56,714
Corporate bonds	143,444		35		(157		)	143,322
U.S. Treasury and government sponsored enterprises	12,105		107		—			12,212
Municipal bonds	2,659		3		—			2,662
Total investments	$	238,298	$	145	$	(157	)	$	238,286

There were no gains or losses on the sales of investments during the years ended December 31, 2015, 2014 and 2013.

All of our investments are subject to a quarterly impairment review. During the years ended December 31, 2015, 2014, and 2013 we did not record any other-than-temporary impairment charges on our available-for-sale securities. As of December 31, 2015, there were 62 investments in an unrealized loss position with gross unrealized losses of $130 thousand and an aggregate fair value $109.5 million. We had a single investment with a gross unrealized loss of $3 thousand and an aggregate fair value of $1.4 million that has been in an unrealized loss position for more than one year. Investments in an unrealized loss position are primarily comprised of corporate bonds. The unrealized losses were not attributed to credit risk, but rather associated with the changes in interest rates. Based on the scheduled maturities of our investments, we concluded that the unrealized losses in our investment securities are not other-than-temporary, as it is more likely than not that we will hold these investments for a period of time sufficient for a recovery of our cost basis.

The following summarizes the fair value of securities classified as available-for-sale by contractual maturity as of December 31, 2015 (in thousands):



	Mature within One Year		After One Year through Two Years		Fair Value
Money market funds	$	72,000	$	—	$	72,000
Commercial paper	78,155		—		78,155
Corporate bonds	49,483		22,608		72,091
U.S. Treasury and government sponsored enterprises	22,427		5,996		28,423
Total	$	222,065	$	28,604	$	250,669

Cash and marketable equity securities are excluded from the table above. The classification of certain compensating balances and restricted investments are dependent upon the term of the underlying restriction on the asset and not the maturity date of the investment. Therefore, certain long-term investments and long-term restricted cash and investments have contractual maturities within one year.

Inventory

12 Months Ended

Dec. 31, 2015

Inventory Disclosure [Abstract]

Inventory

INVENTORY

Inventory consists of the following (in thousands):



	December 31,
	2015			2014
Raw materials	$	1,037		$	1,118
Work in process	2,251			2,845
Finished goods	583			559
Total	3,871			4,522
Less: non-current portion included in Other long-term assets	(1,255		)	(2,141		)
Inventory	$	2,616		$	2,381

We generally relieve inventory on a first-expiry, first-out basis. Write-downs related to expiring and excess inventory are charged to cost of goods sold. Such write-downs were $1.2 million and $0.2 million for the years ended December 31, 2015 and 2014, respectively. The non-current portion of inventory is recorded within Other long-term assets on the accompanying Consolidated Balance Sheets and is comprised of a portion of the active pharmaceutical ingredient that is included in raw materials and work in process inventories. There were no other write-downs for obsolete inventory.

Property and Equipment

12 Months Ended

Dec. 31, 2015

Property, Plant and Equipment [Abstract]

Property and Equipment

PROPERTY AND EQUIPMENT

Property and equipment consisted of the following (in thousands):



	December 31,
	2015			2014
Laboratory equipment	$	4,749		$	13,677
Computer equipment and software	11,890			14,840
Furniture and fixtures	2,253			3,701
Leasehold improvements	6,395			16,364
Construction-in-progress	456			120
	25,743			48,702
Less: accumulated depreciation and amortization	(24,309		)	(46,270		)
Property and equipment, net	$	1,434		$	2,432

For the years ended December 31, 2015, 2014 and 2013, we recorded depreciation expense of $1.4 million, $2.4 million and $3.1 million, respectively.

In 2014 and 2013, we recorded gross asset impairment charges in the amounts of $0.7 million and $0.1 million, respectively, in connection with the Restructurings. There were no such charges in 2015. The amount recorded as a restructuring charge for asset impairment, as presented in “Note 3 - Restructurings,” was net of the gain on the sale of such assets. In 2015 and 2014, the gain on the sale of excess equipment was $1.0 million and $0.6 million, respectively. There were no such gains in 2013. Cash proceeds on those sales were $1.3 million, $0.3 million and $0.1 million during 2015, 2014 and 2013, respectively.

Debt

12 Months Ended

Dec. 31, 2015

Debt Disclosure [Abstract]

Debt

DEBT

The amortized carrying amount of our debt consists of the following (in thousands):



	December 31,
	2015		2014
Convertible Senior Subordinated Notes due 2019	$	198,708	$	179,135
Secured Convertible Notes due 2018	102,727		97,449
Silicon Valley Bank term loan	80,000		80,000
Silicon Valley Bank line of credit	—		381
Total debt	381,435		356,965
Less: current portion	—		(97,830		)
Long-term debt	$	381,435	$	259,135

Convertible Senior Subordinated Notes due 2019

In August 2012, we issued and sold $287.5 million aggregate principal amount of the 4.25% Convertible Senior Subordinated Notes due 2019, (the “2019 Notes”), for net proceeds of $277.7 million. The 2019 Notes mature on August 15, 2019, unless earlier converted, redeemed or repurchased, and bear interest at a rate of 4.25% per annum, payable semi-annually in arrears on February 15 and August 15 of each year, beginning February 15, 2013. Subject to certain terms and conditions, at any time on or after August 15, 2016, we may redeem for cash all or a portion of the 2019 Notes. The redemption price will equal 100% of the principal amount of the 2019 Notes to be redeemed plus accrued and unpaid interest, if any, to, but excluding, the redemption date. Upon the occurrence of certain circumstances, holders may convert their 2019 Notes prior to the close of business on the business day immediately preceding May 15, 2019. On or after May 15, 2019, until the close of business on the second trading day immediately preceding August 15, 2019, holders may surrender their 2019 Notes for conversion at any time. Upon conversion, we will pay or deliver, as the case may be, cash, shares of our common stock or a combination of cash and shares of our common stock, at our election. The initial conversion rate of 188.2353 shares of common stock per $1,000 principal amount of the 2019 Notes is equivalent to a conversion price of approximately $5.31 per share of common stock and is subject to adjustment in connection with certain events. If a Fundamental Change, as defined in the indenture governing the 2019 Notes, occurs, holders of the 2019 Notes may require us to purchase for cash all or any portion of their 2019 Notes at a purchase price equal to 100% of the principal amount of the Notes to be purchased plus accrued and unpaid interest, if any, to, but excluding, the Fundamental Change purchase date. In addition, if certain specified bankruptcy and insolvency-related events of default occur, the principal of, and accrued and unpaid interest on, all of the then outstanding notes will automatically become due and payable. If an event of default other than certain specified bankruptcy and insolvency-related events of default occurs and is continuing, the Trustee of the 2019 Notes by notice to us or the holders of at least 25% in principal amount of the outstanding 2019 Notes by notice to us and the Trustee, may declare the principal of, and accrued and unpaid interest on, all of the then outstanding 2019 Notes to be due and payable.

In connection with the offering of the 2019 Notes, $36.5 million of the proceeds were deposited into an escrow account which contained an amount of permitted securities sufficient to fund, when due, the total aggregate amount of the first six scheduled semi-annual interest payments on the 2019 Notes. As of December 31, 2015, we have used all of the remaining amount held in the escrow account to pay the required semi-annual interest payments and therefore future semi-annual interest payments will be made from unrestricted cash and investments.

The debt discount and debt issuance costs will be amortized as interest expense through August 2019. The following is a summary of interest expense for the 2019 Notes (in thousands):



	Year Ended December 31,
	2015		2014		2013
Stated coupon interest	$	12,218	$	12,253	$	12,219
Amortization of debt discount and debt issuance costs	19,573		17,804		16,201
Total interest expense	$	31,791	$	30,057	$	28,420

The balance of unamortized debt costs was $2.6 million and $3.3 million as of December 31, 2015 and December 31, 2014, respectively, which, pursuant to the early adoption of ASU 2015-03, is recorded as a reduction of the carrying amount of the 2019 Notes on the accompanying Consolidated Balance Sheets. See “Note 1 - Organization and Summary of Significant Accounting Policies” for more information regarding the early adoption ASU 2015-03.

Secured Convertible Notes due June 2018

In June 2010, we entered into a note purchase agreement with Deerfield Private Design Fund, L.P. and Deerfield Private Design International, L.P., (the “Original Deerfield Purchasers”), pursuant to which, on July 1, 2010, we sold to the Original Deerfield Purchasers an aggregate of $124.0 million principal amount of our Secured Convertible Notes due July 1, 2015, which we refer to as the Original Deerfield Notes, for an aggregate purchase price of $80.0 million, less closing fees and expenses of approximately $2.0 million. On January 22, 2014, the note purchase agreement was amended to provide us with an option to extend the maturity date of our indebtedness under the note purchase agreement to July 1, 2018. On July 1, 2015, we made a $4.0 million principal payment and then extended the maturity date of the Original Deerfield Notes from July 1, 2015 to July 1, 2018. In connection with the extension, Deerfield Partners, L.P. and Deerfield International Master Fund, L.P. (the “New Deerfield Purchasers”) acquired the $100.0 million principal amount of the Original Deerfield Notes and we entered into the Restated Deerfield Notes with each of the New Deerfield Purchasers, representing the $100.0 million principal amount. We refer to the Original Deerfield Purchasers and the New Deerfield Purchasers collectively as Deerfield, and to the Original Deerfield Notes and Restated Deerfield Notes, collectively as the Deerfield Notes.

As of December 31, 2015 and 2014, the outstanding principal balance on the Deerfield Notes was $103.8 million and $104.0 million, respectively, which, subject to certain limitations, is payable in cash or in stock at our discretion. Beginning on July 2, 2015, the outstanding principal amount of the Deerfield Notes bears interest at the rate of 7.5% per annum to be paid in cash, quarterly in arrears, and 7.5% per annum to be paid in kind, quarterly in arrears, for a total interest rate of 15% per annum. Through July 1, 2015, the outstanding principal amount of the Deerfield Notes bore interest in the annual amount of $6.0 million, payable quarterly in arrears.

On August 6, 2012, the parties amended the note purchase agreement to permit the issuance of the 2019 Notes and modify certain optional prepayment rights. The amendment became effective upon the issuance of the 2019 Notes and the payment to the Original Deerfield Purchasers of a $1.5 million consent fee. On August 1, 2013, the parties further amended the note purchase agreement to clarify certain of our other rights under the note purchase agreement. On January 22, 2014, the note purchase agreement was amended to provide us with an option to extend the maturity date of our indebtedness under the note purchase agreement to July 1, 2018, which extension was completed on July 1, 2015. On July 10, 2014, the parties further amended the note purchase agreement to clarify certain provisions of the note purchase agreement.

The following is a summary of interest expense for the Deerfield Notes (in thousands):



	Year Ended December 31,
	2015		2014		2013
Stated coupon interest	$	6,792	$	6,000	$	6,000
Amortization of debt discount, debt issuance costs and interest paid in kind	9,278		11,731		10,089
Total interest expense	$	16,070	$	17,731	$	16,089

The balance of unamortized debt issuance costs was $0.7 million and $1.4 million as of December 31, 2015 and December 31, 2014, respectively, which, pursuant to the early adoption of ASU 2015-03, is recorded as a reduction of the carrying amount of the 2019 Notes on the accompanying Consolidated Balance Sheets. See “Note 1 - Organization and Summary of Significant Accounting Policies” for more information regarding the early adoption ASU 2015-03. Prior to our exercise of the option to extend the maturity date to July 1, 2018, the unamortized discount, fees and costs were amortized into interest expense as a yield adjustment through July 1, 2015. Effective March 4, 2015, upon notification of our election to require the New Deerfield Purchasers to acquire the Deerfield Notes and extend the maturity date to July 1, 2018, we began to amortize the remaining unamortized discount, fees and costs through July 1, 2018 using the effective interest method and an effective interest rate of 15.26%.

In each of January 2014 and 2013, we made mandatory prepayments of $10.0 million on the Deerfield Notes. We were required to make an additional mandatory prepayment on the Deerfield Notes in January 2015 equal to 15% of certain revenues from collaborative arrangements, which we refer to as Development/Commercialization Revenue, received during the prior fiscal year, subject to a maximum prepayment amount of $27.5 million. We received no such revenues during the fiscal year ended December 31, 2014 and therefore made no minimum prepayment in January 2015. As a result of the extension of the maturity date of the Deerfield Notes to July 1, 2018, our obligation to make annual mandatory prepayments equal to 15% of Development/Commercialization Revenue received by us during the prior fiscal year will continue to apply in each of 2016, 2017 and 2018. However, we will only be obligated to make any such annual mandatory prepayment if the New Deerfield Purchasers provide notice to us of their election to receive the prepayment. Pursuant to this requirement, we notified Deerfield that they were entitled to a mandatory prepayment of $450,000 as a result of to the $3.0 million milestone payment received from Merck during 2015; the New Deerfield Purchasers elected not to receive a mandatory prepayment in January 2016. Mandatory prepayments relating to Development/Commercialization Revenue will continue to be subject to a maximum annual prepayment amount of $27.5 million. The definition of “Development/Commercialization Revenue” expressly excludes any sale or distribution of drug or pharmaceutical products in the ordinary course of our business, and any proceeds from any Intellectual Property Sales (as further described below), but would include our share of the net profits from the commercialization of cobimetinib in the U.S. and the receipt of royalties from cobimetinib sales outside the U.S., if any.

Under the note purchase agreement, we may at our sole discretion, prepay all of the principal amount of the Deerfield Notes at a prepayment price equal to 105% of the outstanding principal amount of the Deerfield Notes, plus all accrued and unpaid interest through the date of such prepayment, plus, if prior to July 1, 2017, all interest that would have accrued on the principal amount of the Deerfield Notes between the date of such prepayment and July 1, 2017, if the outstanding principal amount of the Deerfield Notes as of such prepayment date had remained outstanding through July 1, 2017, plus all other accrued and unpaid obligations, collectively referred to as the Prepayment Price.

In lieu of making any portion of the Prepayment Price or mandatory prepayment in cash, subject to certain limitations (including a cap on the number of shares issuable under the note purchase agreement), we have the right to convert all or a portion of the principal amount of the Deerfield Notes into, or satisfy all or any portion of the Prepayment Price amounts or mandatory prepayment amounts with shares of our common stock. Additionally, in lieu of making any payment of accrued and unpaid interest in respect of the Deerfield Notes in cash, subject to certain limitations, we may elect to satisfy any such payment with shares of our common stock. The number of shares of our common stock issuable upon conversion or in settlement of principal and interest obligations will be based upon the discounted trading price of our common stock over a specified trading period. Upon certain changes of control of Exelixis, a sale or transfer of assets in one transaction or a series of related transactions for a purchase price of more than (i) $400 million or (ii) 50% of our market capitalization, Deerfield may require us to prepay the Deerfield Notes at the Prepayment Price. Upon an event of default, as defined in the Deerfield Notes, Deerfield may declare all or a portion of the Prepayment Price to be immediately due and payable.

We are required to notify the applicable Deerfield entities of certain sales, assignments, grants of exclusive licenses or other transfers of our intellectual property pursuant to which we transfer all or substantially all of our legal or economic interests, defined as an Intellectual Property Sale, and the Deerfield entities may elect to require us to prepay the principal amount of the Deerfield Notes in an amount equal to (i) 100% of the cash proceeds of any Intellectual Property Sale relating to cabozantinib and (ii) 50% of the cash proceeds of any other Intellectual Property Sale.

In connection with the January 2014 amendment to the note purchase agreement, on January 22, 2014, we issued to the New Deerfield Purchasers two-year warrants, which we refer to as the 2014 Warrants, to purchase an aggregate of 1,000,000 shares of our common stock at an exercise price of $9.70 per share. Subsequent to our election to extend the maturity date of the Deerfield Notes, the exercise price of the 2014 Warrants was reset to $3.445 per share and the term was extended by two years to January 22, 2018. See “Note 8 - Common Stock and Warrants” for more information on the valuation of the 2014 Warrants.

In connection with the note purchase agreement, we also entered into a security agreement in favor of Deerfield which provides that our obligations under the Deerfield Notes will be secured by substantially all of our assets except intellectual property. On August 1, 2013, the security agreement was amended to limit the extent to which voting equity interests in any of our foreign subsidiaries shall be secured assets.

The note purchase agreement as amended and the security agreement include customary representations and warranties and covenants made by us, including restrictions on the incurrence of additional indebtedness.

Silicon Valley Bank Loan and Security Agreement

On May 22, 2002, we entered into a loan and security agreement with Silicon Valley Bank for an equipment line of credit. On December 21, 2004, December 21, 2006 and December 21, 2007, we amended the loan and security agreement to provide for additional equipment lines of credit and on June 2, 2010, we further amended the loan and security agreement to provide for a new seven-year term loan in the amount of $80.0 million. As of both December 31, 2015 and 2014, the outstanding principal balance due under the term loan was $80.0 million. As of December 31, 2015 and 2014, the outstanding principal balance under the lines of credit was $0 and $0.4 million, respectively. The principal amount outstanding under the term loan accrues interest at 1.0% per annum, which interest is due and payable monthly. We are required to repay the term loan in one balloon principal payment, representing 100% of the principal balance and accrued and unpaid interest, on May 31, 2017. We have the option to prepay all, but not less than all, of the amounts advanced under the term loan, provided that we pay all unpaid accrued interest thereon that is due through the date of such prepayment and the interest on the entire principal balance of the term loan that would otherwise have been paid after such prepayment date until the maturity date of the term loan. In accordance with the terms of the loan and security agreement, we are required to maintain an amount equal to at least 100%, but not to exceed 107%, of the outstanding principal balance of the term loan and all equipment lines of credit under the loan and security agreement on deposit in one or more investment accounts with Silicon Valley Bank or one of its affiliates as support for our obligations under the loan and security agreement (although we are entitled to retain income earned or the amounts maintained in such accounts). Any amounts outstanding under the term loan during the continuance of an event of default under the loan and security agreement will, at the election of Silicon Valley Bank, bear interest at a per annum rate equal to 6.0%. If one or more events of default under the loan and security agreement occurs and continues beyond any applicable cure period, Silicon Valley Bank may declare all or part of the obligations under the loan and security agreement to be immediately due and payable and stop advancing money or extending credit to us under the loan and security agreement.

The total collateral balance as of December 31, 2015 and 2014 was $81.6 million and $82.0 million, respectively, and is reflected in our Consolidated Balance Sheet in Long-term Investments as the amounts are not restricted as to withdrawal. However, withdrawal of some or all of this amount such that the collateral balance falls below the required level could result in Silicon Valley Bank declaring the obligation immediately due and payable.

Future Principal Payments

Aggregate contractual future principal payments of our debt were as follows as of December 31, 2015 (in thousands):



Year Ending December 31, (1)
2016	$	—
2017	80,000
2018	124,972
2019	287,500
Thereafter	—

____________________


(1)	The actual timing of payments made may differ materially.

Common Stock And Warrants	12 Months Ended
Common Stock And Warrants	Dec. 31, 2015
Warrants and Rights Note Disclosure [Abstract]
Common Stock And Warrants	COMMON STOCK AND WARRANTS Sale of Shares of Common Stock In July 2015, we completed a registered underwritten public offering of 28,750,000 shares of our common stock, including 3,750,000 shares issued under the underwriters’ 30-day option to buy shares, at a price of $5.40 per share pursuant to a shelf registration statement previously filed with the Securities and Exchange Commission (“SEC”), which was filed and automatically became effective on July 1, 2015. We received $145.6 million in net proceeds from the offering after deducting the underwriting discount and other estimated expenses. The shares of common stock were listed on The NASDAQ Global Select Market. All of the shares in the offering were sold by the Company. The Underwriting Agreement contains customary representations, warranties and agreements by the Company, indemnification obligations of the Company and the Underwriter, including for liabilities under the Securities Act of 1933, as amended, other obligations of the parties and termination provisions. The representations, warranties and covenants contained in the Underwriting Agreement were made only for purposes of such agreement and as of specific dates, were solely for the benefit of the parties to such agreement and may be subject to limitations agreed upon by the contracting parties. In January 2014, we completed a registered underwritten public offering of 10,000,000 shares of our common stock at a price of $8.00 per share pursuant to a shelf registration statement previously filed with the SEC, which the SEC declared effective on June 8, 2012. We received $75.6 million in net proceeds from the offering after deducting the underwriting discount and related offering expenses. Conversion of Debt into Common Stock The 2019 Notes and the Deerfield Notes are, under certain circumstances, convertible into shares of our common stock. See “Note 7 - Debt” for more information regarding the conversion features of these instruments. 2014 Warrants In connection with an amendment to the note purchase agreement for the Original Deerfield Notes, in January 2014 we issued to the New Deerfield Purchasers two-year warrants to purchase an aggregate of 1,000,000 shares of our common stock at an exercise price of $9.70 per share. Subsequent to our March 2015 notification of our election to extend the maturity date of the Deerfield Notes, the exercise price of the 2014 Warrants was reset to $3.445 per share and the term was extended by two years to January 22, 2018. The 2014 Warrants contain certain limitations that prevent the holder from acquiring shares upon exercise that would result in the number of shares beneficially owned by the holder to exceed 9.98% of the total number of shares of our common stock then issued and outstanding. In addition, upon certain changes in control of Exelixis, to the extent the 2014 Warrants are not assumed by the acquiring entity, or upon certain defaults under the 2014 Warrants, the holder has the right to net exercise the 2014 Warrants for shares of common stock, or be paid an amount in cash in certain circumstances where the current holders of our common stock would also receive cash, equal to the Black-Scholes Merton value of the 2014 Warrants. In connection with the issuance of the 2014 Warrants, we entered into a registration rights agreement with Deerfield, pursuant to which we filed a registration statement with the SEC covering the resale of the shares of common stock issuable upon exercise of the 2014 Warrants. Due to the potential increase in term and decrease of the exercise price, the 2014 Warrants were included in Other long-term liabilities at their current estimated fair value, which was $1.5 million and $0.9 million as of March 18, 2015 and December 31, 2014, respectively. We recorded an unrealized loss of $0.5 million and an unrealized gain of $1.8 million on the 2014 Warrants during the years ended December 31, 2015 and 2014, respectively, which is included in Interest income and other, net. Subsequent to our March 2015 notification of our election to extend the maturity date of the Deerfield Notes, the terms of the 2014 Warrants became fixed as of March 18, 2015 and the 2014 Warrants were transferred to Additional paid-in capital as of that date at their then estimated fair value of $1.5 million. See “Note 9 - Fair Value Measurements” for more information on the valuation of the 2014 Warrants. The warrants are participating securities. The warrant holders do not have a contractual obligation to share in our losses.

Fair Value Measurements

12 Months Ended

Dec. 31, 2015

Fair Value Disclosures [Abstract]

Fair Value Measurements

FAIR VALUE MEASUREMENTS

The following table sets forth the fair value of our financial assets and liabilities that were measured and recorded on a recurring basis as of December 31, 2015 and 2014. We did not have any financial liabilities that were measured and recorded on a recurring basis or Level 3 investments as of December 31, 2015. The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	December 31, 2015
	Level 1		Level 2		Total
Money market funds	$	72,000	$	—	$	72,000
Commercial paper	—		78,155		78,155
Corporate bonds	—		72,091		72,091
U.S. Treasury and government sponsored enterprises	—		28,423		28,423
Marketable equity securities	18		—		18
Total financial assets	$	72,018	$	178,669	$	250,687



	December 31, 2014
	Level 1		Level 2		Level 3		Total
Financial assets:
Money market funds	$	23,376	$	—	$	—	$	23,376
Commercial paper	—		56,714		—		56,714
Corporate bonds	—		143,322		—		143,322
U.S. Treasury and government sponsored enterprises	—		12,212		—		12,212
Municipal bonds	—		2,662		—		2,662
Total financial assets	$	23,376	$	214,910	$	—	$	238,286
Financial liabilities:
Warrants	$	—	$	—	$	921	$	921

The following is a reconciliation of changes in the fair value of warrants which are classified as Level 3 in the fair value hierarchy (in thousands):



Balance at December 31, 2014	$	921
Unrealized loss at final re-measurement of warrants on March 18, 2015, included in Interest income and other, net	549
Transfer of warrants from Other long-term liabilities to Additional paid-in capital at their estimated fair value upon warrant repricing on March 18, 2015	(1,470		)
Balance at December 31, 2015	$	—

The estimated fair value of our financial instruments that are carried at amortized cost for which it is practicable to determine a fair value was as follows (in thousands):



	December 31, 2015				December 31, 2014
	Carrying Amount		Fair Value		Carrying Amount		Fair Value
2019 Notes	$	198,708	$	336,260	$	179,135	$	156,889
Silicon Valley Bank Term Loan	$	80,000	$	79,815	$	80,000	$	79,943
Silicon Valley Bank Line of Credit	$	—	$	—	$	381	$	381

As of December 31, 2015, the carrying value and estimated fair value of our Deerfield Notes was $102.7 million and $101.1 million, respectively. As of December 31, 2014, we had determined that it was not practicable to determine the fair value of the Deerfield Notes due to the unique structure of the instrument, including the Extension Option, which was exercised in March 2015, and was financed by entities affiliated with Deerfield.

The carrying amounts of cash, trade and other receivables, accounts payable, accrued clinical trial liabilities, accrued compensation and benefits, and other accrued liabilities approximate their fair values and are excluded from the tables above.

The following methods and assumptions were used to estimate the fair value of each class of financial instrument for which it is practicable to estimate a value:


•	When available, we value investments based on quoted prices for those financial instruments, which is a Level 1 input. Our remaining investments are valued using third-party pricing sources, which use observable market prices, interest rates and yield curves observable at commonly quoted intervals of similar assets as observable inputs for pricing, which is a Level 2 input.


•	The 2019 Notes are valued using a third-party pricing model that is based in part on average trading prices, which is a Level 2 input. The 2019 Notes are not marked-to-market and are shown at their initial fair value less the unamortized discount; the portion of the value allocated to the conversion option is included in Stockholders’ deficit on the accompanying Consolidated Balance Sheets.

•

We estimate the fair value of our other debt instruments, where possible, using the net present value of the payments. For the Silicon Valley Bank term loan and line of credit, we use an interest rate that is consistent with money-market rates that would have been earned on our non-interest-bearing compensating balances as our discount rate, which is a Level 2 input. For the Deerfield Notes, we used a discount rate of 17%, which we estimate as our current borrowing rate for similar debt as of December 31, 2015, which is a Level 3 input.

•

The 2014 Warrants were valued using a Monte Carlo simulation model until December 31, 2014 and the Black-Scholes Merton option pricing model on March 18, 2015. The expected life was based on the contractual terms of the 2014 Warrants, and in certain simulations, assumed the two year extension that would result from our exercise of the Extension Option; as of and subsequent to September 30, 2014, we estimated that it was probable that we would exercise this two-year extension. We considered implied volatility as well as our historical volatility in developing our estimate of expected volatility. The fair value of the 2014 Warrants was estimated using the following assumptions, which, except for risk-free interest rate, are Level 3 inputs (dollars in thousands):



	March 18, 2015		December 31, 2014
Risk-free interest rate	0.87	%	1.07	%
Dividend yield	—	%	—	%
Volatility	95	%	96	%
Average expected life	2.8 years		3.1 years

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Employee Benefit Plans

12 Months Ended

Dec. 31, 2015

Employee Benefit Plans

EMPLOYEE BENEFIT PLANS

Equity Incentive Plans

We have several equity incentive plans under which we have granted incentive stock options, non-qualified stock options and RSUs to employees, directors and consultants. The Board of Directors or a designated Committee of the Board is responsible for administration of our employee equity incentive plans and determines the term, exercise price and vesting terms of each option. Prior to May 2011, options issued to our employees had a four-year vesting term, an exercise price equal to the fair market value on the date of grant, and a ten year life from the date of grant (6.2 years for options issued in exchange for options cancelled under our 2009 option exchange program). Stock options issued after May 2011 have a four-year vesting term, an exercise price equal to the fair market value on the date of grant, and a seven year life from the date of grant. RSUs granted to our employees vest over a four year term; RSUs issued after September 29, 2011 vest annually; the remaining unvested portion of RSUs issued prior to September 29, 2011 vested quarterly.

In December 2005, our Board of Directors adopted a Change in Control and Severance Benefit Plan for executives and certain non-executives. Eligible Change in Control and Severance Benefit Plan participants include our employees with the title of vice president and above. If a participant’s employment is terminated without cause during a period commencing one month before and ending thirteen months following a change in control, as defined in the plan document, then the Change in Control and Severance Benefit Plan participant is entitled to have the vesting of all of such participant’s stock options accelerated with the exercise period being extended to no more than one year.

Employee Stock Purchase Plan

In January 2000, we adopted the 2000 Employee Stock Purchase Plan (the “ESPP”). The ESPP allows for qualified employees (as defined in the ESPP) to purchase shares of our common stock at a price equal to the lower of 85% of the closing price at the beginning of the offering period or 85% of the closing price at the end of each six month purchase period. Compensation expense related to our ESPP was $0.4 million, $0.8 million, and $0.6 million for the years ended December 31, 2015, 2014 and 2013, respectively. As of December 31, 2015, we had 1,046,959 shares available for issuance under our ESPP. We issued 324,315 shares, 669,565 shares, and 345,828 shares of common stock during the years ended December 31, 2015, 2014 and 2013, respectively, pursuant to the ESPP at an average price per share of $1.75, $2.14 and $4.13, respectively.

Stock-Based Compensation

We recorded and allocated employee stock-based compensation expense for our equity incentive plans and our ESPP as follows (in thousands):



	Year Ended December 31,
	2015		2014			2013
Research and development expense	$	11,691	$	3,245		$	6,021
Selling, general and administrative	10,286		6,783			5,948
Restructuring-related stock compensation expense (recovery)	—		(22		)	49
Total employee stock-based compensation expense	$	21,977	$	10,006		$	12,018

We use the Black-Scholes Merton option pricing model to value our stock options. The weighted average grant-date fair value of our stock options and ESPP purchases was as follows:



	2015		2014		2013
Stock options	$	2.55	$	1.46	$	2.97
ESPP	$	1.20	$	1.28	$	1.64

The fair value of employee stock option awards and ESPP purchases was estimated using the following assumptions:



	Stock Options
	2015		2014		2013
Risk-free interest rate	1.22	%	1.80	%	1.51	%
Dividend yield	—	%	—	%	—	%
Volatility	93	%	85	%	61	%
Expected life	4.5 years		5.5 years		5.6 years



	ESPP
	2015		2014		2013
Risk-free interest rate	0.15	%	0.06	%	0.11	%
Dividend yield	—	%	—	%	—	%
Volatility	98	%	69	%	66	%
Expected life	6 months		6 months		6 months

The expected life computation is based on historical exercise patterns and post-vesting termination behavior. We considered implied volatility as well as our historical volatility in developing our estimate of expected volatility.

A summary of all option activity was as follows for the periods presented (dollars in thousands, except per share amounts):



	Shares		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Options outstanding at December 31, 2014	27,811,992		$	5.00
Granted	8,894,800		$	3.78
Exercised	(2,340,963	)	$	4.66
Forfeited	(924,890	)	$	3.67
Expired	(6,015,085	)	$	7.12
Options outstanding at December 31, 2015	27,425,854		$	4.22	5.09 years	$	51,501
Exercisable at December 31, 2015	15,666,177		$	4.68	4.38 years	$	25,532

At December 31, 2015, a total of 8,041,842 shares were available for grant under our stock option plans.

The aggregate intrinsic value in the table above represents the total intrinsic value (the difference between our closing stock price on the last trading day of fiscal 2015 and the exercise prices, multiplied by the number of in-the-money options) that would have been received by the option holders had all option holders exercised their options on December 31, 2015. The total intrinsic value of options exercised was $2.9 million during the year ended December 31, 2015 and nominal in 2014 and 2013. The total estimated fair value of employee options vested and recorded as expense in 2015, 2014 and 2013 was $18.9 million, $8.6 million and $7.4 million, respectively.

On July 20, 2015, as a result of positive top-line results from the primary analysis of METEOR, the Compensation Committee of the Board of Directors of Exelixis convened to determine we had met certain performance objectives for performance-based stock options granted to employees in 2013, 2014 and 2015. As a result of this determination, 6,982,613 performance-based stock options vested on July 20, 2015. Previously, we had not considered achievement of those performance objectives to be probable and therefore, we recorded $9.9 million in employee stock-based compensation expense during 2015 related to those options.

We have an additional 5,934,052 outstanding unvested stock options as of December 31, 2015 which were granted to employees in 2014 and 2015 and are subject to performance objectives tied to the achievement of regulatory goals set by the Compensation Committee of our Board of Directors and will vest in part based on achievement of such goals. As of December 31, 2015, we expect that achievement of the performance objectives tied to 2,967,026 performance-based stock options with a fair value of $3.7 million is probable and have, therefore, recorded $3.3 million of stock-based compensation expense in connection with such awards; the remainder of the expense for these awards will be recognized on a straight-line basis through the anticipated achievement date of the performance objectives. We have not included any stock-based compensation expense for the remaining 2,967,026 stock options with performance objectives for which the achievement of the performance goals is not considered probable; the grant date fair value of such awards outstanding was $3.7 million.

The following table summarizes information about stock options outstanding and exercisable at December 31, 2015:



	Options Outstanding					Options Outstanding and Exercisable
Exercise Price Range	Number	Weighted Average Remaining Contractual Life		Weighted Average Exercise Price		Number Exercisable	Weighted Average Exercise Price
$1.46 - $1.87	7,997,474	5.78 years		$	1.70	3,857,469	$	1.70
$1.90	3,738,000	6.07 years		$	1.90	1,826,502	$	1.90
$2.57 - $4.88	2,772,796	5.27 years		$	3.80	1,681,199	$	3.98
$5.01 - $5.51	4,043,479	4.02 years	3,186,063	$	5.44	3,186,063	$	5.44
$5.55 - $6.02	2,600,943	4.70 years		$	5.73	1,890,661	$	5.70
$6.21	2,822,900	6.69 years		$	6.21	—
$6.25 - $11.66	3,450,262	2.53 years		$	8.71	3,224,283	$	8.82
	27,425,854	5.09 years		$	4.22	15,666,177	$	4.68

As of December 31, 2015, $19.5 million of total unrecognized compensation expense related to stock options is expected to be recognized over a weighted-average period of 2.56 years.

Cash received from option exercises and purchases under the ESPP in 2015, 2014 and 2013 was $11.5 million, $1.6 million and $1.5 million, respectively.

A summary of all RSU activity was as follows for all periods presented (dollars in thousands, except per share amounts):



	Shares		Weighted Average Grant Date Fair Value		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Awards outstanding at December 31, 2014	961,469		$	3.82
Awarded	838,535		$	5.01
Vested and released	(672,951	)	$	5.62
Forfeited	(124,865	)	$	5.32
Awards outstanding at December 31, 2015	1,002,188		$	5.16	2.50 years	$	5,652

As of December 31, 2015, $3.4 million of total unrecognized compensation expense related to employee RSUs was expected to be recognized over a weighted-average period of 2.50 years.

401(k) Retirement Plan

We sponsor a 401(k) Retirement Plan (the “401(k) Plan”) whereby eligible employees may elect to contribute up to the lesser of 50% of their annual compensation or the statutorily prescribed annual limit allowable under Internal Revenue Service regulations. The 401(k) Plan permits us to make matching contributions on behalf of all participants. We matched 100% of the first 3% of participant contributions into the 401(k) Plan in the form of our common stock. We recorded expense of $0.4 million, $1.1 million, and $0.8 million related to the stock match for the years ended December 31, 2015, 2014 and 2013, respectively. As of December 31, 2015, we had 450,042 shares available for issuance under our 401(k) Plan.

Income Taxes

12 Months Ended

Dec. 31, 2015

Income Tax Disclosure [Abstract]

Income Taxes

INCOME TAXES

The income tax (benefit) provision is based on the following loss before income taxes (in thousands):



	Year Ended December 31,
	2015			2014			2013
Domestic	$	(158,839	)	$	(237,780	)	$	(236,076	)
Foreign	(10,843		)	(30,944		)	(8,780		)
Total	$	(169,682	)	$	(268,724	)	$	(244,856	)

Income tax expense (benefit) consists of the following for the periods shown below (in thousands):



	Year Ended December 31,
	2015		2014			2013
Current:
Federal	$	—	$	—		$	—
State	55		(182		)	12
Total current tax expense	55		(182		)	12
Deferred:
Federal	—		—			(106		)
State	—		—			(2		)
Total deferred tax expense	—		—			(108		)
Income tax provision (benefit)	$	55	$	(182	)	$	(96	)

The 2015 income tax provision of $0.1 million relates to state minimum and franchise tax expenses as well as true ups related to prior year tax entries. The 2014 income tax benefit of $0.2 million resulted from the lapse of the applicable statute of limitations in California for the 2009 tax year, offset by current year state income tax expense. The 2013 income tax benefit of $0.1 million resulted from the exception to the general intra-period allocation rules required by ASC 740-20-45-7, and is related to the income tax effect of unrealized gains on available-for-sale investments included in other comprehensive income.

During 2013, Exelixis International (Bermuda) Ltd. (“Exelixis Bermuda”) acquired the existing and future intellectual property rights to exploit cabozantinib in jurisdictions outside of the United States. The transfer of the existing rights created a taxable gain in the U.S. and state jurisdictions. For tax purposes, that gain is primarily offset by current fiscal year losses and the remainder through the utilization of an insignificant amount of net operating loss carry-forwards for which there is a corresponding reduction to our valuation allowance. Because this was an intercompany transaction, ASC 740-10-25-3(e) applies, however, there was no impact to tax expense due to the full valuation allowance and therefore no deferred prepaid charge was recorded to the balance sheet.

A reconciliation of income taxes at the statutory federal income tax rate to our income tax (benefit) provision included in the Consolidated Statements of Operations is as follows (in thousands):



	Year Ended December 31,
	2015			2014			2013
U.S. federal income tax benefit at statutory rate	$	(57,692	)	$	(91,366	)	$	(83,251	)
Unutilized net operating losses	54,139			87,448			(3,438		)
Non-deductible interest	3,308			3,598			3,380
Stock-based compensation	195			255			393
State tax expense	55			(182		)	10
Available-for-sale investments	—			—			(106		)
Impact of intellectual property rights transfer	—			—			82,858
Other	50			65			58
Income tax (benefit) provision	$	55		$	(182	)	$	(96	)

Deferred tax assets and liabilities reflect the net tax effects of net operating loss and tax credit carry-forwards and temporary differences between the carrying amounts of assets and liabilities for financial reporting and the amounts used for income tax purposes.

Our deferred tax assets and liabilities consist of the following (in thousands):



	December 31,
	2015			2014
Deferred tax assets:
Net operating loss carry-forwards	$	464,504		$	446,343
Tax credit and charitable contribution carry-forwards	64,350			64,368
Amortization of deferred stock compensation – non-qualified	14,615			27,500
Accruals and reserves not currently deductible	7,775			6,521
Book over tax depreciation and amortization	1,752			5,118
Deferred revenue	—			988
Total deferred tax assets	552,996			550,838
Valuation allowance	(523,574		)	(511,171		)
Net deferred tax assets	29,422			39,667
Deferred tax liabilities:
Unrealized gain on derivatives	(497		)	(704		)
Convertible debt	(28,925		)	(38,963		)
Total deferred tax liabilities	(29,422		)	(39,667		)
Net deferred taxes	$	—		$	—

Realization of deferred tax assets is dependent upon future earnings, if any, the timing and amount of which are uncertain. Accordingly, the net deferred tax assets have been fully offset by a valuation allowance. The valuation allowance increased by $12.4 million, increased by $89.7 million and decreased by $16.8 million during 2015, 2014 and 2013, respectively.

At December 31, 2015, we had federal net operating loss carry-forwards of approximately $1,323 million which expire in the years 2019 through 2035, and federal business tax credits of approximately $75 million which expire in the years 2020 through 2029. We also had state net operating loss carry-forwards of approximately $692 million, which expire in the years 2016 through 2035, California research and development tax credits of approximately $25 million which have no expiration. Included in the federal and state carry-forwards is $18 million related to deductions from the exercise of stock options and the related tax benefit that will result in an increase in additional paid-in capital if and when realized through a reduction of taxes paid in cash.

Under the Internal Revenue Code and similar state provisions, certain substantial changes in our ownership could result in an annual limitation on the amount of net operating loss and credit carry-forwards that can be utilized in future years to offset future taxable income. The annual limitation may result in the expiration of net operating losses and credit carry-forwards before utilization. We completed a Section 382 study through December 31, 2015, and concluded that an ownership change, as defined under Section 382, had not occurred.

ASC Topic 740-10 clarifies the accounting for uncertainty in income taxes by prescribing the recognition threshold a tax position is required to meet before being recognized in the financial statements. It also provides guidance on derecognition, classification, interest and penalties, accounting in interim periods, disclosure and transition. The following table summarizes the activity related to our unrecognized tax benefits (in thousands):



	Year Ended December 31,
	2015		2014			2013
Beginning balance	$	58,215	$	55,077		$	47,298
Increase (decrease) relating to prior year provision	21,696		719			(112		)
Increase relating to current year provision	8,727		2,706			7,891
Reductions based on the lapse of the applicable statutes of limitations	—		(287		)	—
Ending balance	$	88,638	$	58,215		$	55,077

Included in the balance of unrecognized tax benefits as of December 31, 2013 was $0.1 million of tax benefits that if recognized would affect the effective tax rate. There were no such unrecognized benefits as of December 31, 2015 or 2014. All of our deferred tax assets are subject to a valuation allowance. As of December 31, 2013 we had an accrued interest balance of $20 thousand related to tax contingencies. Interest expense related to those tax contingencies was $4 thousand during the year ended December 31, 2013. There were no such interest accruals or expenses during the years ended December 31, 2015 and 2014. There were no penalties recognized or accrued during any of the periods presented. Any tax-related interest and penalties are included in income tax (benefit) provision in the Consolidated Statements of Operations. We do not anticipate that the amount of unrecognized tax benefits existing as of December 31, 2015, will significantly decrease over the next 12 months.

We file U.S. and state income tax returns in jurisdictions with varying statues of limitations during which such tax returns may be audited and adjusted by the relevant tax authorities. The 1998 through 2014 years generally remain subject to examination by federal and most state tax authorities to the extent of net operating losses and credits generated during these periods and are being utilized in the open tax periods.

It is our intention to reinvest the earnings of our non-U.S. subsidiaries in those operations. As of December 31, 2015, there were no undistributed foreign earnings of our only non-U.S. subsidiary, Exelixis Bermuda.

Net Loss Per Share

12 Months Ended

Dec. 31, 2015

Earnings Per Share [Abstract]

Net Loss Per Share

NET LOSS PER SHARE

The following table sets forth a reconciliation of basic and diluted net loss per share (in thousands, except per share amounts):



	Year Ended December 31,
	2015			2014			2013
Numerator:
Net loss	$	(169,737	)	$	(268,542	)	$	(244,760	)
Denominator:
Shares used in computing basic and diluted net loss per share	209,227			194,299			184,062
Net loss per share, basic and diluted	$	(0.81	)	$	(1.38	)	$	(1.33	)

The following table sets forth outstanding potential shares of common stock outstanding as of dates presented that are not included in the computation of diluted net loss per share because to do so would be anti-dilutive (in thousands):



	December 31,
	2015	2014	2013
Convertible debt	88,008	75,734	54,123
Outstanding stock options, unvested RSUs and ESPP contributions	28,470	28,930	21,401
Warrants	1,000	1,000	1,441
Total potentially dilutive shares	117,478	105,664	76,965

Commitments

12 Months Ended

Dec. 31, 2015

Commitments and Contingencies Disclosure [Abstract]

Commitments

COMMITMENTS

Leases

We lease office and research space under operating leases that expire at various dates through the year 2018. Certain operating leases contain renewal provisions and require us to pay other expenses. As a result of the Restructurings, we exited certain facilities in South San Francisco. Aggregate future minimum lease payments under our operating leases are as follows (in thousands):



Year Ending December 31,	Operating Leases (1)
2016	$	14,236
2017	8,474
2018	3,007
	$	25,717

____________________


(1)	Minimum payments have not been reduced by minimum sublease rentals of $6.1 million due in the future under noncancelable subleases.

The following is a summary of aggregate future minimum lease payments under operating leases at December 31, 2015, by operating lease agreements (in thousands):



	Original Term (Expiration)	Renewal Options	Future Minimum Lease Payments
Building Lease #1 and 2	May 2017	2 additional periods of 5 years	$	12,732
Building Lease #3	July 2018	1 additional period of 5 years	12,985
Total			$	25,717

Rent expense under operating leases was $8.7 million, $10.3 million, and $9.1 million for the years ended December 31, 2015, 2014 and 2013, respectively. Rent expense was recorded net of sublease rental incomes of $5.2 million, $4.9 million and $4.1 million for the years ended December 31, 2015, 2014 and 2013, respectively.

Letters of Credit and Restricted Cash

We entered into a standby letter of credit with a bank in July 2004, which is related to a building lease, with a credit limit of $0.5 million at both December 31, 2015 and 2014. We entered into two standby letters of credit with a bank in May 2007, which is related to our workers compensation insurance policy, for a combined credit limit of $0.6 million and $0.7 million at December 31, 2015 and 2014, respectively. All three letters of credit are fully collateralized by long-term restricted cash and investments. As of December 31, 2015, the full amount of our three letters of credit was still available.

As part of a purchasing card program with a bank we initiated during 2007, we were required to provide collateral in the form of a non-interest bearing certificate of deposit. The collateral at December 31, 2015 and 2014 was $1.5 million and $3.5 million, respectively. We recorded these amounts in the Consolidated Balance Sheet as Long-term restricted cash and investments as the certificates of deposit were restricted as to withdrawal.

Indemnification Agreements

In connection with the sale of our plant trait business, we agreed to indemnify the purchaser and its affiliates up to a specified amount if they incur damages due to any infringement or alleged infringement of certain patents. We have certain collaboration licensing agreements that contain standard indemnification clauses. Such clauses typically indemnify the customer or vendor for an adverse judgment in a lawsuit in the event of our misuse or negligence. We consider the likelihood of an adverse judgment related to any of our indemnification agreements to be remote. Furthermore, in the event of an adverse judgment, any losses under such an adverse judgment may be substantially offset by applicable corporate insurance.

Concentrations of Credit Risk

12 Months Ended

Dec. 31, 2015

Risks and Uncertainties [Abstract]

Concentrations of Credit Risk

CONCENTRATIONS OF CREDIT RISK

Financial instruments that potentially subject us to concentrations of credit risk are primarily trade and other receivables and investments. Investments consist of money market funds, taxable commercial paper, corporate bonds with high credit quality, U.S. Treasury and government sponsored enterprises, and municipal bonds. All investments are maintained with financial institutions that management believes are creditworthy.

Trade and other receivables are unsecured and are concentrated in the pharmaceutical and biotechnology industries. Accordingly, we may be exposed to credit risk generally associated with pharmaceutical and biotechnology companies. We have incurred no bad debt expense since inception. As of December 31, 2015, 95% of our trade and other receivables are with the specialty pharmacy that sells COMETRIQ in the United States and 5% are with our European distribution partner. Both of these customers pay promptly and within their respective payment terms. All of our long-lived assets are located in the United States.

We have operations primarily in the United States, while some of our collaboration partners have headquarters outside of the United States and some of our clinical trials for cabozantinib are also conducted outside of the United States. During the second quarter of 2013, we initiated a Named Patient Use program through our distribution partner, Swedish Orphan Biovitrum (“Sobi”), to support the distribution and commercialization of COMETRIQ for metastatic MTC primarily in the European Union and potentially other countries. In March 2014, the European Commission approved cabozantinib for the treatment of adult patients with progressive, unresectable locally advanced or metastatic MTC, also under the brand name COMETRIQ. In June 2014, we began selling COMETRIQ to Sobi in preparation for commercial sales in certain countries in the European Union. The following table shows the percentage of revenues earned in the United States and European Union.



	Year Ended December 31,
	2015		2014		2013
Percentage of revenues earned in the United States	91	%	99	%	97	%
Percentage of revenues earned in the European Union ⁽¹⁾	9	%	1	%	3	%

____________________

(1) Net product revenues in the European Union for the year ended December 31, 2015 and 2014 included a $0.1 million and $2.3 million reduction, respectively, to revenue for a project management fee payable to our European distributor upon their achievement of a cumulative revenue goal.

We recorded a $0.1 million and $0.5 million gain relating to foreign exchange fluctuations for the year ended December 31, 2015 and 2014, respectively. Such gains were nominal in 2013.

The following table sets forth the percentage of revenues recognized under our collaboration agreements and product sales to the specialty pharmacy that represent 10% or more of total revenues:



	Year Ended December 31,
	2015		2014		2013
Product sales:
Diplomat Specialty Pharmacy	83	%	99	%	45	%
Collaboration agreement:
Bristol-Myers Squibb	—	%	—	%	52	%

Subsequent Event	12 Months Ended
Subsequent Event	Dec. 31, 2015
Subsequent Events [Abstract]
Subsequent Event	SUBSEQUENT EVENT On February 29, 2016, we entered into a collaboration and license agreement with Ipsen for the commercialization and further development of cabozantinib. Pursuant to the terms of this agreement, Ipsen will have exclusive commercialization rights for current and potential future cabozantinib indications outside of the United States, Canada and Japan. The companies have agreed to collaborate on the development of cabozantinib for current and potential future indications. In consideration for the exclusive license and other rights contained in the agreement, Ipsen will pay us an upfront payment of $200.0 million. We will be eligible to receive regulatory milestones, including a $60.0 million milestone payment upon approval of cabozantinib by the EMA in second-line RCC and milestone payments of $10.0 million upon the filing and $40.0 million upon the approval of cabozantinib in second-line HCC, as well as additional regulatory milestone payments for potential further indications. The agreement also provides that we will be eligible to receive payments of up to $545.0 million associated with potential commercial milestone payments, including two $10.0 million milestone payments upon the launch of the product in the first two of the following countries: Germany, France, Italy, Spain and the United Kingdom. Exelixis will also receive royalties on net sales of cabozantinib outside of the United States, Canada and Japan. We will receive a 2% royalty on the initial $50 million of net sales, and 12% royalty on the next $100 million of net sales. After this initial period, Exelixis will receive a tiered royalty of 22% to 26% on annual net sales. These tiers will reset each calendar year. Exelixis is responsible for funding cabozantinib related development costs for existing trials; development costs for potential future trials will be shared between the parties, with Ipsen to reimburse us for 35% of such costs. Pursuant to the terms of the agreement, we will remain responsible for the manufacture and supply of cabozantinib for all development and commercialization activities under the collaboration. As part of the collaboration, we entered into a supply agreement which provides that through the end of the second quarter of 2018, we will supply finished, labeled product to Ipsen for distribution in the territories outside of the United States, Canada and Japan, and from the end of the second quarter of 2018 forward, we will supply primary packaged bulk tablets to Ipsen. In connection with the establishment of our collaboration with Ipsen, we intend to provide Sobi with notice of termination and following a transition period, Ipsen will become responsible for the continued distribution and commercialization of COMETRIQ for the approved MTC indication in territories currently supported by Sobi.

Quarterly Financial Data (Unaudited)

12 Months Ended

Dec. 31, 2015

Quarterly Financial Information Disclosure [Abstract]

Quarterly Financial Data (Unaudited)

QUARTERLY FINANCIAL DATA (UNAUDITED)

The following tables summarize the unaudited quarterly financial data for the last two fiscal years (in thousands, except per share data):



	Quarter Ended
	December 31,			September 30,			June 30,			March 31,
2015:
Revenues	$	9,938		$	9,854		$	7,992		$	9,388
Gross profit	$	8,915		$	8,434		$	7,306		$	8,622
Loss from operations	$	(31,600	)	$	(35,781	)	$	(31,280	)	$	(22,760	)
Net loss	$	(43,641	)	$	(47,564	)	$	(43,362	)	$	(35,170	)
Net loss per share, basic and diluted	$	(0.19	)	$	(0.22	)	$	(0.22	)	$	(0.18	)
2014:
Revenues	$	7,353		$	6,291		$	6,562		$	4,905
Gross profit	$	6,669		$	5,718		$	6,085		$	4,596
Loss from operations	$	(46,208	)	$	(51,574	)	$	(61,688	)	$	(64,988	)
Net loss	$	(57,953	)	$	(62,560	)	$	(73,410	)	$	(74,619	)
Net loss per share, basic and diluted	$	(0.30	)	$	(0.32	)	$	(0.38	)	$	(0.39	)

On September 2, 2014, as a consequence of the failure of COMET-1, we initiated the 2014 Restructuring to reduce our workforce. The aggregate reduction in headcount from the 2014 Restructuring was 143 employees. The 2014 Restructuring, along with associated reductions in clinical trial costs related to COMET-1 and COMET-2, resulted in a decrease in operating expenses and a corresponding decrease the loss from operations and net loss. See “Note 2 - Restructurings” for more information on the 2014 Restructuring.

Organization and Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2015

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Organization

Basis of Consolidation

Basis of Presentation

Segment Information

We operate as a single reportable segment.

Use of Estimates

Reclassifications

Certain prior period amounts in the consolidated balance sheet have been reclassified to conform to current period presentation.

Cash

Cash and Investments

Investments

Fair Value Measurements

Level 1 – quoted prices (unadjusted) in active markets for identical assets and liabilities that the reporting entity can access at the measurement date.

Level 3 – unobservable inputs.

Inventory

Property and Equipment

Property and equipment are recorded at cost and depreciated using the straight-line method over the following estimated useful lives:



Equipment and furniture	5 years
Computer equipment and software	3 years
Leasehold improvements	Shorter of lease life or 7 years

Capitalized software includes certain internal use computer software costs.

Repairs and maintenance costs are charged to expense as incurred.

Goodwill

Long-Lived Assets

Revenue Recognition

We recognize revenue from product sales and from license fees, milestones, contingent payments and royalties earned on research and collaboration arrangements.

Net Product Revenues

Product Sales Discounts and Allowances

We initially record estimates for these deductions at the time we recognize the gross revenue. We update our estimates on a recurring basis as new information becomes available.

License and Contract Revenues

Patient Assistance Program

Cost of Goods Sold

Research and Development Expenses

Net Loss Per Share

Foreign Currency Translation and Remeasurement

Stock-Based Compensation

Recently Issued and Recently Adopted Accounting Pronouncements

Recently Issued Accounting Pronouncements

Organization and Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2015

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Estimated useful lives of Property and Equipment

Property and equipment are recorded at cost and depreciated using the straight-line method over the following estimated useful lives:



Equipment and furniture	5 years
Computer equipment and software	3 years
Leasehold improvements	Shorter of lease life or 7 years

New Accounting Pronouncement, Early Adoption



	December 31, 2015				December 31, 2014
	Prior to Adoption of ASU 2015-03	ASU 2015-03 Adjustment		As Adopted	Prior to Adoption of ASU 2015-03 (as previously reported)	ASU 2015-03 Adjustment		As Adopted
Other long-term assets	5,579	(3,270	)	2,309	8,340	(4,691	)	3,649
Total assets	335,612	(3,270	)	332,342	327,960	(4,691	)	323,269

Current portion of convertible notes	—	—		—	98,880	(1,431	)	97,449
Current liabilities	52,251	—		52,251	171,860	(1,431	)	170,429

Long-term portion of convertible notes	304,705	(3,270	)	301,435	182,395	(3,260	)	179,135
Total liabilities	439,916	(3,270	)	436,646	442,789	(4,691	)	438,098

Restructurings (Tables)

12 Months Ended

Dec. 31, 2015

Restructuring Charges [Abstract]

Schedule of outstanding restructuring liability

The changes of these liabilities, all of which related to facility charges during the year ended December 31, 2015, are summarized in the following table (in thousands):



	Facility Charges			Other			Total
Restructuring liability as of December 31, 2012	$	19,202		$	20		$	19,222
Restructuring charge	662			569			1,231
Proceeds from sale of assets	—			95			95
Cash payments, net	(6,331		)	(434		)	(6,765		)
Other items	(73		)	(238		)	(311		)
Restructuring liability as of December 31, 2013	13,460			12			13,472
Restructuring charge (recovery)	1,626			(117		)	1,509
Proceeds from sale of assets	—			199			199
Cash payments, net	(5,644		)	(8		)	(5,652		)
Other items	12			(86		)	(74		)
Restructuring liability as of December 31, 2014	9,454			—			9,454
Restructuring charge	757			—			757
Cash payments, net	(6,449		)	—			(6,449		)
Other items	325			—			325
Restructuring liability as of December 31, 2015	$	4,087		$	—		$	4,087

The components of and changes to these liabilities during the year ended December 31, 2015 are summarized in the following table (in thousands):



	Employee Severance and Other Benefits			Facility Charges			Asset Impairment and Sales			Legal and Other Fees			Total
Restructuring charge	$	5,775		$	65		$	188		$	59		$	6,087
Proceeds from sale of assets	—			—			100			—			100
Cash payments, net	(4,507		)	(65		)	—			(12		)	(4,584		)
Other items	22			—			(288		)	—			(266		)
Restructuring liability as of December 31, 2014	1,290			—			—			47			1,337
Restructuring charge (recovery)	(269		)	1,582			(981		)	(47		)	285
Proceeds from sale of assets	—			—			1,325			—			1,325
Cash payments, net	(1,021		)	(1,357		)	—			—			(2,378		)
Other items	—			278			(344		)	—			(66		)
Restructuring liability as of December 31, 2015	$	—		$	503		$	—		$	—		$	503

Cash and Investments (Tables)

12 Months Ended

Dec. 31, 2015

Investments, Debt and Equity Securities [Abstract]

Schedule of Available-for-Sale Securities

The following table summarizes cash and cash equivalents, investments, and restricted cash and investments by balance sheet line item as of December 31, 2015 and 2014 (in thousands):



	December 31, 2015
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Cash and cash equivalents	$	141,634	$	—	$	—		$	141,634
Short-term investments	25,484		5		(63		)	25,426
Long-term investments	83,665		2		(67		)	83,600
Long-term restricted cash and investments	2,650		—		—			2,650
Total cash and investments	$	253,433	$	7	$	(130	)	$	253,310



	December 31, 2014
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Cash and cash equivalents	$	80,395	$	—	$	—		$	80,395
Short-term investments	63,988		37		(135		)	63,890
Short-term restricted cash and investments	12,105		107		—			12,212
Long-term investments	81,600		1		(22		)	81,579
Long-term restricted cash and investments	4,684		—		—			4,684
Total cash and investments	$	242,772	$	145	$	(157	)	$	242,760

Summary of Cash Equivalents and Investments by Security Type

The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	December 31, 2015
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	72,000	$	—	$	—		$	72,000
Commercial paper	78,155		—		—			78,155
Corporate bonds	72,205		4		(118		)	72,091
U.S. Treasury and government sponsored enterprises	28,434		1		(12		)	28,423
Marketable equity securities	16		2		—			18
Total investments	$	250,810	$	7	$	(130	)	$	250,687



	December 31, 2014
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	23,376	$	—	$	—		$	23,376
Commercial paper	56,714		—		—			56,714
Corporate bonds	143,444		35		(157		)	143,322
U.S. Treasury and government sponsored enterprises	12,105		107		—			12,212
Municipal bonds	2,659		3		—			2,662
Total investments	$	238,298	$	145	$	(157	)	$	238,286

Summary of Available-for-Sale Securities by Contractual Maturity

The following summarizes the fair value of securities classified as available-for-sale by contractual maturity as of December 31, 2015 (in thousands):



	Mature within One Year		After One Year through Two Years		Fair Value
Money market funds	$	72,000	$	—	$	72,000
Commercial paper	78,155		—		78,155
Corporate bonds	49,483		22,608		72,091
U.S. Treasury and government sponsored enterprises	22,427		5,996		28,423
Total	$	222,065	$	28,604	$	250,669

Inventory (Tables)

12 Months Ended

Dec. 31, 2015

Inventory Disclosure [Abstract]

Schedule of Inventory

Inventory consists of the following (in thousands):



	December 31,
	2015			2014
Raw materials	$	1,037		$	1,118
Work in process	2,251			2,845
Finished goods	583			559
Total	3,871			4,522
Less: non-current portion included in Other long-term assets	(1,255		)	(2,141		)
Inventory	$	2,616		$	2,381

Property and Equipment (Tables)

12 Months Ended

Dec. 31, 2015

Property, Plant and Equipment [Abstract]

Schedule Of Property And Equipment

Property and equipment consisted of the following (in thousands):



	December 31,
	2015			2014
Laboratory equipment	$	4,749		$	13,677
Computer equipment and software	11,890			14,840
Furniture and fixtures	2,253			3,701
Leasehold improvements	6,395			16,364
Construction-in-progress	456			120
	25,743			48,702
Less: accumulated depreciation and amortization	(24,309		)	(46,270		)
Property and equipment, net	$	1,434		$	2,432

Debt (Tables)

12 Months Ended

Dec. 31, 2015

Debt Disclosure [Abstract]

Schedule Of Debt

The amortized carrying amount of our debt consists of the following (in thousands):



	December 31,
	2015		2014
Convertible Senior Subordinated Notes due 2019	$	198,708	$	179,135
Secured Convertible Notes due 2018	102,727		97,449
Silicon Valley Bank term loan	80,000		80,000
Silicon Valley Bank line of credit	—		381
Total debt	381,435		356,965
Less: current portion	—		(97,830		)
Long-term debt	$	381,435	$	259,135

Summary Of The Liability Component Of The 2019 Notes

The debt discount and debt issuance costs will be amortized as interest expense through August 2019. The following is a summary of interest expense for the 2019 Notes (in thousands):



	Year Ended December 31,
	2015		2014		2013
Stated coupon interest	$	12,218	$	12,253	$	12,219
Amortization of debt discount and debt issuance costs	19,573		17,804		16,201
Total interest expense	$	31,791	$	30,057	$	28,420

The following is a summary of interest expense for the Deerfield Notes (in thousands):



	Year Ended December 31,
	2015		2014		2013
Stated coupon interest	$	6,792	$	6,000	$	6,000
Amortization of debt discount, debt issuance costs and interest paid in kind	9,278		11,731		10,089
Total interest expense	$	16,070	$	17,731	$	16,089

Schedule Of Future Principal Payments Of Total Long-Term Debt

Aggregate contractual future principal payments of our debt were as follows as of December 31, 2015 (in thousands):



Year Ending December 31, (1)
2016	$	—
2017	80,000
2018	124,972
2019	287,500
Thereafter	—

____________________


(1)	The actual timing of payments made may differ materially.

Schedule Of Fair Value Of Financial Assets Measured On A Recurring Basis

Tabular disclosure of long-debt instruments or arrangements, including identification, terms, features, collateral requirements and other information necessary to a fair presentation. These are debt arrangements that originally required repayment more than twelve months after issuance or greater than the normal operating cycle of the entity, if longer.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02.22)
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21475-112644

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 470
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6479336&loc=d3e64711-112823

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08.(e),(f))
-URI http://asc.fasb.org/extlink&oid=26873400&loc=d3e23780-122690

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 835
-SubTopic 30
-Section 55
-Paragraph 8
-URI http://asc.fasb.org/extlink&oid=34725769&loc=d3e28878-108400

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 8
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21538-112644

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21506-112644

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 835
-SubTopic 30
-Section 45
-Paragraph 1A
-URI http://asc.fasb.org/extlink&oid=6451184&loc=d3e28541-108399

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 835
-SubTopic 30
-Section 45
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6451184&loc=d3e28551-108399

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 7
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21521-112644

+ Details

Fair Value Measurements (Tables)

12 Months Ended

Dec. 31, 2015

Fair Value Disclosures [Abstract]



	December 31, 2015
	Level 1		Level 2		Total
Money market funds	$	72,000	$	—	$	72,000
Commercial paper	—		78,155		78,155
Corporate bonds	—		72,091		72,091
U.S. Treasury and government sponsored enterprises	—		28,423		28,423
Marketable equity securities	18		—		18
Total financial assets	$	72,018	$	178,669	$	250,687



	December 31, 2014
	Level 1		Level 2		Level 3		Total
Financial assets:
Money market funds	$	23,376	$	—	$	—	$	23,376
Commercial paper	—		56,714		—		56,714
Corporate bonds	—		143,322		—		143,322
U.S. Treasury and government sponsored enterprises	—		12,212		—		12,212
Municipal bonds	—		2,662		—		2,662
Total financial assets	$	23,376	$	214,910	$	—	$	238,286
Financial liabilities:
Warrants	$	—	$	—	$	921	$	921

Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation

The following is a reconciliation of changes in the fair value of warrants which are classified as Level 3 in the fair value hierarchy (in thousands):



Balance at December 31, 2014	$	921
Unrealized loss at final re-measurement of warrants on March 18, 2015, included in Interest income and other, net	549
Transfer of warrants from Other long-term liabilities to Additional paid-in capital at their estimated fair value upon warrant repricing on March 18, 2015	(1,470		)
Balance at December 31, 2015	$	—

Schedule Of Estimated Fair Value Of Outstanding Debt

The estimated fair value of our financial instruments that are carried at amortized cost for which it is practicable to determine a fair value was as follows (in thousands):



	December 31, 2015				December 31, 2014
	Carrying Amount		Fair Value		Carrying Amount		Fair Value
2019 Notes	$	198,708	$	336,260	$	179,135	$	156,889
Silicon Valley Bank Term Loan	$	80,000	$	79,815	$	80,000	$	79,943
Silicon Valley Bank Line of Credit	$	—	$	—	$	381	$	381

Schedule Of Assumptions Used

The fair value of the 2014 Warrants was estimated using the following assumptions, which, except for risk-free interest rate, are Level 3 inputs (dollars in thousands):



	March 18, 2015		December 31, 2014
Risk-free interest rate	0.87	%	1.07	%
Dividend yield	—	%	—	%
Volatility	95	%	96	%
Average expected life	2.8 years		3.1 years

Employee Benefit Plans (Tables)

12 Months Ended

Dec. 31, 2015

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Schedule Of Allocated Employee Stock-Based Compensation Expense

We recorded and allocated employee stock-based compensation expense for our equity incentive plans and our ESPP as follows (in thousands):



	Year Ended December 31,
	2015		2014			2013
Research and development expense	$	11,691	$	3,245		$	6,021
Selling, general and administrative	10,286		6,783			5,948
Restructuring-related stock compensation expense (recovery)	—		(22		)	49
Total employee stock-based compensation expense	$	21,977	$	10,006		$	12,018

Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Weighted Average Grant Date Fair Value

The weighted average grant-date fair value of our stock options and ESPP purchases was as follows:



	2015		2014		2013
Stock options	$	2.55	$	1.46	$	2.97
ESPP	$	1.20	$	1.28	$	1.64

Schedule Of Fair Value Of Employee Share-Based Payments Awards Stock Option Assumptions And Weighted Average Fair Values

The fair value of employee stock option awards and ESPP purchases was estimated using the following assumptions:



	Stock Options
	2015		2014		2013
Risk-free interest rate	1.22	%	1.80	%	1.51	%
Dividend yield	—	%	—	%	—	%
Volatility	93	%	85	%	61	%
Expected life	4.5 years		5.5 years		5.6 years

Schedule Of Fair Value Of Employee Share-Based Payments Awards ESPP Assumptions And Weighted Average Fair Values



	ESPP
	2015		2014		2013
Risk-free interest rate	0.15	%	0.06	%	0.11	%
Dividend yield	—	%	—	%	—	%
Volatility	98	%	69	%	66	%
Expected life	6 months		6 months		6 months

Summary Of All Stock Option Activity

A summary of all option activity was as follows for the periods presented (dollars in thousands, except per share amounts):



	Shares		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Options outstanding at December 31, 2014	27,811,992		$	5.00
Granted	8,894,800		$	3.78
Exercised	(2,340,963	)	$	4.66
Forfeited	(924,890	)	$	3.67
Expired	(6,015,085	)	$	7.12
Options outstanding at December 31, 2015	27,425,854		$	4.22	5.09 years	$	51,501
Exercisable at December 31, 2015	15,666,177		$	4.68	4.38 years	$	25,532

Summary Of Information About Stock Options Outstanding

The following table summarizes information about stock options outstanding and exercisable at December 31, 2015:



	Options Outstanding					Options Outstanding and Exercisable
Exercise Price Range	Number	Weighted Average Remaining Contractual Life		Weighted Average Exercise Price		Number Exercisable	Weighted Average Exercise Price
$1.46 - $1.87	7,997,474	5.78 years		$	1.70	3,857,469	$	1.70
$1.90	3,738,000	6.07 years		$	1.90	1,826,502	$	1.90
$2.57 - $4.88	2,772,796	5.27 years		$	3.80	1,681,199	$	3.98
$5.01 - $5.51	4,043,479	4.02 years	3,186,063	$	5.44	3,186,063	$	5.44
$5.55 - $6.02	2,600,943	4.70 years		$	5.73	1,890,661	$	5.70
$6.21	2,822,900	6.69 years		$	6.21	—
$6.25 - $11.66	3,450,262	2.53 years		$	8.71	3,224,283	$	8.82
	27,425,854	5.09 years		$	4.22	15,666,177	$	4.68

Summary Of All RSU Activity

A summary of all RSU activity was as follows for all periods presented (dollars in thousands, except per share amounts):



	Shares		Weighted Average Grant Date Fair Value		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Awards outstanding at December 31, 2014	961,469		$	3.82
Awarded	838,535		$	5.01
Vested and released	(672,951	)	$	5.62
Forfeited	(124,865	)	$	5.32
Awards outstanding at December 31, 2015	1,002,188		$	5.16	2.50 years	$	5,652

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2015

Income Tax Disclosure [Abstract]

Schedule Of Consolidated Net Income (Loss)

The income tax (benefit) provision is based on the following loss before income taxes (in thousands):



	Year Ended December 31,
	2015			2014			2013
Domestic	$	(158,839	)	$	(237,780	)	$	(236,076	)
Foreign	(10,843		)	(30,944		)	(8,780		)
Total	$	(169,682	)	$	(268,724	)	$	(244,856	)

Schedule of Components of Income Tax Expense (Benefit)

Income tax expense (benefit) consists of the following for the periods shown below (in thousands):



	Year Ended December 31,
	2015		2014			2013
Current:
Federal	$	—	$	—		$	—
State	55		(182		)	12
Total current tax expense	55		(182		)	12
Deferred:
Federal	—		—			(106		)
State	—		—			(2		)
Total deferred tax expense	—		—			(108		)
Income tax provision (benefit)	$	55	$	(182	)	$	(96	)

Schedule Of Reconciliation Of Income Taxes At The Statutory Federal Income Tax Rate To Net Income Taxes

A reconciliation of income taxes at the statutory federal income tax rate to our income tax (benefit) provision included in the Consolidated Statements of Operations is as follows (in thousands):



	Year Ended December 31,
	2015			2014			2013
U.S. federal income tax benefit at statutory rate	$	(57,692	)	$	(91,366	)	$	(83,251	)
Unutilized net operating losses	54,139			87,448			(3,438		)
Non-deductible interest	3,308			3,598			3,380
Stock-based compensation	195			255			393
State tax expense	55			(182		)	10
Available-for-sale investments	—			—			(106		)
Impact of intellectual property rights transfer	—			—			82,858
Other	50			65			58
Income tax (benefit) provision	$	55		$	(182	)	$	(96	)

Schedule Of Deferred Assets And Liabilities

Our deferred tax assets and liabilities consist of the following (in thousands):



	December 31,
	2015			2014
Deferred tax assets:
Net operating loss carry-forwards	$	464,504		$	446,343
Tax credit and charitable contribution carry-forwards	64,350			64,368
Amortization of deferred stock compensation – non-qualified	14,615			27,500
Accruals and reserves not currently deductible	7,775			6,521
Book over tax depreciation and amortization	1,752			5,118
Deferred revenue	—			988
Total deferred tax assets	552,996			550,838
Valuation allowance	(523,574		)	(511,171		)
Net deferred tax assets	29,422			39,667
Deferred tax liabilities:
Unrealized gain on derivatives	(497		)	(704		)
Convertible debt	(28,925		)	(38,963		)
Total deferred tax liabilities	(29,422		)	(39,667		)
Net deferred taxes	$	—		$	—

Schedule Of Unrecognized Tax Benefits

The following table summarizes the activity related to our unrecognized tax benefits (in thousands):



	Year Ended December 31,
	2015		2014			2013
Beginning balance	$	58,215	$	55,077		$	47,298
Increase (decrease) relating to prior year provision	21,696		719			(112		)
Increase relating to current year provision	8,727		2,706			7,891
Reductions based on the lapse of the applicable statutes of limitations	—		(287		)	—
Ending balance	$	88,638	$	58,215		$	55,077

Net Loss Per Share (Tables)

12 Months Ended

Dec. 31, 2015

Earnings Per Share [Abstract]

Schedule Of Reconciliation Of Basic And Diluted Net Income (Loss) Per Share

The following table sets forth a reconciliation of basic and diluted net loss per share (in thousands, except per share amounts):



	Year Ended December 31,
	2015			2014			2013
Numerator:
Net loss	$	(169,737	)	$	(268,542	)	$	(244,760	)
Denominator:
Shares used in computing basic and diluted net loss per share	209,227			194,299			184,062
Net loss per share, basic and diluted	$	(0.81	)	$	(1.38	)	$	(1.33	)

Schedule Of Potential Shares Of Common Stock Not Included In Computation Of Diluted Net Loss Per Share



	December 31,
	2015	2014	2013
Convertible debt	88,008	75,734	54,123
Outstanding stock options, unvested RSUs and ESPP contributions	28,470	28,930	21,401
Warrants	1,000	1,000	1,441
Total potentially dilutive shares	117,478	105,664	76,965

Commitments (Tables)

12 Months Ended

Dec. 31, 2015

Commitments and Contingencies Disclosure [Abstract]

Schedule Of Aggregate Future Minimum Lease Payments Under Operating Leases

Aggregate future minimum lease payments under our operating leases are as follows (in thousands):



Year Ending December 31,	Operating Leases (1)
2016	$	14,236
2017	8,474
2018	3,007
	$	25,717

____________________


(1)	Minimum payments have not been reduced by minimum sublease rentals of $6.1 million due in the future under noncancelable subleases.

Schedule Of Aggregate Future Minimum Lease Payments Under Operating Leases By Material Lease Agreements

The following is a summary of aggregate future minimum lease payments under operating leases at December 31, 2015, by operating lease agreements (in thousands):



	Original Term (Expiration)	Renewal Options	Future Minimum Lease Payments
Building Lease #1 and 2	May 2017	2 additional periods of 5 years	$	12,732
Building Lease #3	July 2018	1 additional period of 5 years	12,985
Total			$	25,717

Concentrations of Credit Risk (Tables)

12 Months Ended

Dec. 31, 2015

Risks and Uncertainties [Abstract]

Schedules of collaborators that represent 10% or more of total revenues

The following table shows the percentage of revenues earned in the United States and European Union.



	Year Ended December 31,
	2015		2014		2013
Percentage of revenues earned in the United States	91	%	99	%	97	%
Percentage of revenues earned in the European Union ⁽¹⁾	9	%	1	%	3	%

____________________

The following table sets forth the percentage of revenues recognized under our collaboration agreements and product sales to the specialty pharmacy that represent 10% or more of total revenues:



	Year Ended December 31,
	2015		2014		2013
Product sales:
Diplomat Specialty Pharmacy	83	%	99	%	45	%
Collaboration agreement:
Bristol-Myers Squibb	—	%	—	%	52	%

Quarterly Financial Data (Unaudited) (Tables)

12 Months Ended

Dec. 31, 2015

Quarterly Financial Information Disclosure [Abstract]

Schedule Of Quarterly Financial Data

The following tables summarize the unaudited quarterly financial data for the last two fiscal years (in thousands, except per share data):



	Quarter Ended
	December 31,			September 30,			June 30,			March 31,
2015:
Revenues	$	9,938		$	9,854		$	7,992		$	9,388
Gross profit	$	8,915		$	8,434		$	7,306		$	8,622
Loss from operations	$	(31,600	)	$	(35,781	)	$	(31,280	)	$	(22,760	)
Net loss	$	(43,641	)	$	(47,564	)	$	(43,362	)	$	(35,170	)
Net loss per share, basic and diluted	$	(0.19	)	$	(0.22	)	$	(0.22	)	$	(0.18	)
2014:
Revenues	$	7,353		$	6,291		$	6,562		$	4,905
Gross profit	$	6,669		$	5,718		$	6,085		$	4,596
Loss from operations	$	(46,208	)	$	(51,574	)	$	(61,688	)	$	(64,988	)
Net loss	$	(57,953	)	$	(62,560	)	$	(73,410	)	$	(74,619	)
Net loss per share, basic and diluted	$	(0.30	)	$	(0.32	)	$	(0.38	)	$	(0.39	)

Organization and Summary of Significant Accounting Policies (Narrative) (Details) $ in Thousands	3 Months Ended									12 Months Ended			24 Months Ended	36 Months Ended
	Dec. 31, 2015 USD ($)	Sep. 30, 2015 USD ($)	Jun. 30, 2015 USD ($)	Mar. 31, 2015 USD ($)	Dec. 31, 2014 USD ($)	Sep. 30, 2014 USD ($)	Jun. 30, 2014 USD ($)	Mar. 31, 2014 USD ($)	Dec. 31, 2013	Dec. 31, 2015 USD ($) segment	Dec. 31, 2014 USD ($)	Dec. 31, 2013 USD ($)	Dec. 31, 2015 USD ($)	Dec. 31, 2015 USD ($)
Organization And Summary Of Significant Policies [Line Items]
Annual operating cycle										364 days	371 days	364 days
Fiscal period duration	98 days				91 days				91 days
Number of operating segments \| segment										1
Accrued collaboration liability	$ 10,938				$ 732					$ 10,938	$ 732		$ 10,938	$ 10,938
Net (loss) income	(43,641)	$ (47,564)	$ (43,362)	$ (35,170)	(57,953)	$ (62,560)	$ (73,410)	$ (74,619)		(169,737)	(268,542)	$ (244,760)
Retained earnings (accumulated deficit)	(1,937,041)				(1,767,304)					(1,937,041)	(1,767,304)		(1,937,041)	(1,937,041)
Net product revenues										34,158	25,111	15,017		74,300
Cash and investments	253,310				242,760					253,310	242,760		253,310	253,310
Cash available for operations	169,000									169,000			169,000	169,000
Compensating balance investments	81,600									81,600			81,600	81,600
Long-term restricted cash and investments	$ 2,650				$ 4,684					$ 2,650	4,684		2,650	$ 2,650
Percent discount for prompt payment										2.00%
Discount expected to be earned (as a percent)										100.00%
Sobi [Member]
Organization And Summary Of Significant Policies [Line Items]
Reduction to net product revenues										$ 100	$ 2,300		$ 2,400
Amount of reduction relating to prior periods												$ 700
GlaxoSmithKline [Member]
Organization And Summary Of Significant Policies [Line Items]
Percent of royalty on net sale										3.00%
Minimum [Member]
Organization And Summary Of Significant Policies [Line Items]
Annual operating cycle										364 days
Maximum [Member]
Organization And Summary Of Significant Policies [Line Items]
Annual operating cycle										371 days
“Sell-In” Revenue Recognition Model [Member]
Organization And Summary Of Significant Policies [Line Items]
Net product revenues										$ 2,600

Organization and Summary of Significant Accounting Policies (Estimated Useful Lives Of Property Plant And Equipment) (Details)	12 Months Ended
	Dec. 31, 2015
Equipment And Furniture [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives, years	5 years
Computer Equipment And Software [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives, years	3 years
Maximum [Member] \| Leasehold Improvements [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives, years	7 years

Organization and Summary of Significant Accounting Policies (Adoption of New Accounting Pronouncements) (Details) - USD ($) $ in Thousands	Dec. 31, 2015	Dec. 31, 2014
New Accounting Pronouncement, Early Adoption [Line Items]
Other long-term assets	$ 2,309	$ 3,649
Total assets	332,342	323,269
Current portion of convertible notes	0	97,449
Current liabilities	52,251	170,429
Long-term portion of convertible notes	301,435	179,135
Total liabilities	436,646	438,098
Prior to Adoption of ASU 2015-03 [Member]
New Accounting Pronouncement, Early Adoption [Line Items]
Other long-term assets	5,579	8,340
Total assets	335,612	327,960
Current portion of convertible notes	0	98,880
Current liabilities	52,251	171,860
Long-term portion of convertible notes	304,705	182,395
Total liabilities	439,916	442,789
ASU 2015-03 Adjustment [Member]
New Accounting Pronouncement, Early Adoption [Line Items]
Other long-term assets	(3,270)	(4,691)
Total assets	(3,270)	(4,691)
Current portion of convertible notes	0	(1,431)
Current liabilities	0	(1,431)
Long-term portion of convertible notes	(3,270)	(3,260)
Total liabilities	$ (3,270)	$ (4,691)

Research and Collaboration Agreements (Genentech Collaboration To Bristol-Meyers Squibb) (Details) - USD ($)	1 Months Ended			12 Months Ended
	Nov. 30, 2015	Jan. 31, 2007	Dec. 31, 2006	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum Potential Milestone Payments				$ 2,300,000,000
Percentage of Maximum Potential Milestone Payments - Clinical Development				10.00%
Percentage of Maximum Potential Milestone Payments - Regulatory				42.00%
Percentage of Maximum Potential Milestone Payments - Commercial				48.00%
Genentech [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront and milestone payments		$ 15,000,000.0	$ 25,000,000.0
Optional percent of total sales	25.00%
License and contract revenues				$ 14,000	$ 0	$ 0
Genentech [Member] \| Profit Sharing Tier One [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of profits				50.00%
Profit threshold				$ 200,000,000
Genentech [Member] \| Profit Sharing Tier Two [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of profits				30.00%
Profit threshold				$ 400,000,000
Bristol-Myers Squibb [Member] \| ROR Collaboration Agreement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
License and contract revenues				0	0	1,500,000
Maximum amount eligible for development and regulatory milestones				252,500,000.0
Maximum amount eligible for commercial milestones under collaborations agreement				150,000,000.0
Bristol-Myers Squibb [Member] \| LXR Collaboration [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
License and contract revenues				0	0	0
Maximum amount eligible for development and regulatory milestones				138,000,000.0
Maximum amount eligible for royalties on sales under collaborations agreement				225,000,000.0
Bristol-Myers Squibb [Member] \| Terminated Collaborations [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
License and contract revenues						14,800,000
Selling, general and administrative expense [Member] \| Genentech [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Net losses under collaboration agreement				$ 16,600,000	$ 2,900,000	$ 700,000

Research and Collaboration Agreements (Sanofi To GlaxoSmithKline) (Details) - USD ($)	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Sanofi [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum amount eligible for development and regulatory milestones	$ 745,000,000.0
License and contract revenues	0	$ 0	$ 0
Merck [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum amount eligible for development and regulatory milestones	236,000,000
Maximum amount eligible for royalties on sales under collaborations agreement	375,000,000
License and contract revenues	3,000,000	0	0
Daiichi Sankyo [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum amount eligible for development and regulatory milestones	145,000,000.0
License and contract revenues	0	0	0
GlaxoSmithKline [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Royalty expense	$ 1,000,000	$ 700,000	$ 400,000
GlaxoSmithKline [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sales	3.00%

Restructurings (Narrative) (Details) $ in Thousands	12 Months Ended			39 Months Ended
Restructurings (Narrative) (Details) $ in Thousands	Dec. 31, 2015 USD ($) employee	Dec. 31, 2014 USD ($)	Dec. 31, 2013 USD ($)	May 31, 2013 restructuring
Restructuring Cost and Reserve [Line Items]
Restructuring charges	$ 1,042	$ 7,596	$ 1,231
Future minimum rental under noncancelable subleases	6,100
Facility Charges [Member]
Restructuring Cost and Reserve [Line Items]
Combined accrued facility charges expected to be paid	$ 4,600
2014 Restructuring [Member]
Restructuring Cost and Reserve [Line Items]
Aggregate reduction in headcount (in employees) \| employee	143
Restructuring charges	$ 285	6,087
Recoveries recorded in connection with the sale of excess equipment	(66)	(266)
2014 Restructuring [Member] \| Facility Charges [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charges	1,582	65
Recoveries recorded in connection with the sale of excess equipment	278	0
2014 Restructuring [Member] \| Asset Impairment And Sales [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charges	(981)	188
Recoveries recorded in connection with the sale of excess equipment	(344)	(288)
2014 Restructuring [Member] \| Employee Severance And Other Benefits [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charges	(269)	5,775
Recoveries recorded in connection with the sale of excess equipment	$ 0	22
2010 Restructurings [Member]
Restructuring Cost and Reserve [Line Items]
Aggregate reduction in headcount (in employees) \| employee	429
Restructuring charges	$ 757	1,509	1,231
Number of restructurings implemented \| restructuring				5
Recoveries recorded in connection with the sale of excess equipment	325	(74)	(311)
Expected additional payment for restructuring	300
2010 Restructurings [Member] \| Facility Charges [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charges	757	1,626	662
Recoveries recorded in connection with the sale of excess equipment	$ 325	12	$ (73)
2010 Restructurings [Member] \| Recoveries From Sale Assets, Net Of Impairments [Member]
Restructuring Cost and Reserve [Line Items]
Recoveries recorded in connection with the sale of excess equipment		$ 100

Restructurings (Schedule Of Outstanding Restructuring Liability) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Restructuring Reserve [Roll Forward]
Restructuring charge (recovery)	$ 1,042	$ 7,596	$ 1,231
2014 Restructuring [Member]
Restructuring Reserve [Roll Forward]
Restructuring liability at beginning of period	1,337
Restructuring charge (recovery)	285	6,087
Proceeds from sale of assets	1,325	100
Cash payments	(2,378)	(4,584)
Other items	(66)	(266)
Restructuring liability at end of period	503	1,337
2014 Restructuring [Member] \| Employee Severance And Other Benefits [Member]
Restructuring Reserve [Roll Forward]
Restructuring liability at beginning of period	1,290
Restructuring charge (recovery)	(269)	5,775
Proceeds from sale of assets	0	0
Cash payments	(1,021)	(4,507)
Other items	0	22
Restructuring liability at end of period	0	1,290
2014 Restructuring [Member] \| Facility Charges [Member]
Restructuring Reserve [Roll Forward]
Restructuring liability at beginning of period	0
Restructuring charge (recovery)	1,582	65
Proceeds from sale of assets	0	0
Cash payments	(1,357)	(65)
Other items	278	0
Restructuring liability at end of period	503	0
2014 Restructuring [Member] \| Asset Impairment And Sales [Member]
Restructuring Reserve [Roll Forward]
Restructuring liability at beginning of period	0
Restructuring charge (recovery)	(981)	188
Proceeds from sale of assets	1,325	100
Cash payments	0	0
Other items	(344)	(288)
Restructuring liability at end of period	0	0
2014 Restructuring [Member] \| Other [Member]
Restructuring Reserve [Roll Forward]
Restructuring liability at beginning of period	47
Restructuring charge (recovery)	(47)	59
Proceeds from sale of assets	0	0
Cash payments	0	(12)
Other items	0	0
Restructuring liability at end of period	0	47
2010 Restructurings [Member]
Restructuring Reserve [Roll Forward]
Restructuring liability at beginning of period	9,454	13,472	19,222
Restructuring charge (recovery)	757	1,509	1,231
Proceeds from sale of assets		199	95
Cash payments	(6,449)	(5,652)	(6,765)
Other items	325	(74)	(311)
Restructuring liability at end of period	4,087	9,454	13,472
2010 Restructurings [Member] \| Facility Charges [Member]
Restructuring Reserve [Roll Forward]
Restructuring liability at beginning of period	9,454	13,460	19,202
Restructuring charge (recovery)	757	1,626	662
Proceeds from sale of assets		0	0
Cash payments	(6,449)	(5,644)	(6,331)
Other items	325	12	(73)
Restructuring liability at end of period	4,087	9,454	13,460
2010 Restructurings [Member] \| Other [Member]
Restructuring Reserve [Roll Forward]
Restructuring liability at beginning of period	0	12	20
Restructuring charge (recovery)	0	(117)	569
Proceeds from sale of assets		199	95
Cash payments	0	(8)	(434)
Other items	0	(86)	(238)
Restructuring liability at end of period	$ 0	$ 0	$ 12

Cash and Investments (Details)	12 Months Ended
Cash and Investments (Details)	Dec. 31, 2015 USD ($) account investment affiliate	Dec. 31, 2014 USD ($)	Dec. 31, 2013 USD ($)
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 253,433,000	$ 242,772,000
Gross Unrealized Gains	7,000	145,000
Gross Unrealized Losses	(130,000)	(157,000)
Fair Value	$ 253,310,000	242,760,000
Number of required investment accounts \| account	1
Number of affiliate banks \| affiliate	1
Amortized Cost	$ 250,810,000	238,298,000
Gross Unrealized Gains	7,000	145,000
Gross Unrealized Losses	(130,000)	(157,000)
Fair Value	250,687,000	238,286,000
Gain (loss) on sale of investments	$ 0	0	$ 0
Number of investments in unrealized loss position \| investment	62
Unrealized loss position, aggregate fair value	$ 109,500,000
Number of investments in unrealized loss position for longer than one year \| investment	1
Investments in unrealized loss position for more than one year, gross unrealized losses	$ 3,000
Investments in unrealized loss position for more than one year, aggregate fair value	1,400,000
Silicon Valley Bank Term Loan and Line of Credit [Member]
Schedule of Available-for-sale Securities [Line Items]
Collateral balance	81,600,000	82,000,000
Money Market Funds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	72,000,000	23,376,000
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	72,000,000	23,376,000
Mature within One Year	72,000,000
After One Year through Two Years	0
Commercial paper [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	78,155,000	56,714,000
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	78,155,000	56,714,000
Mature within One Year	78,155,000
After One Year through Two Years	0
Corporate bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	72,205,000	143,444,000
Gross Unrealized Gains	4,000	35,000
Gross Unrealized Losses	(118,000)	(157,000)
Fair Value	72,091,000	143,322,000
Mature within One Year	49,483,000
After One Year through Two Years	22,608,000
U.S. Treasury and government sponsored enterprises [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	28,434,000	12,105,000
Gross Unrealized Gains	1,000	107,000
Gross Unrealized Losses	(12,000)	0
Fair Value	28,423,000	12,212,000
Mature within One Year	22,427,000
After One Year through Two Years	5,996,000
Marketable equity securities [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	16,000
Gross Unrealized Gains	2,000
Gross Unrealized Losses	0
Fair Value	18,000
Municipal bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost		2,659,000
Gross Unrealized Gains		3,000
Gross Unrealized Losses		0
Fair Value		2,662,000
Cash Equivalents [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	141,634,000	80,395,000
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	141,634,000	80,395,000
Short-term investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	25,484,000	63,988,000
Gross Unrealized Gains	5,000	37,000
Gross Unrealized Losses	(63,000)	(135,000)
Fair Value	25,426,000	63,890,000
Short-term restricted cash and investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost		12,105,000
Gross Unrealized Gains		107,000
Gross Unrealized Losses		0
Fair Value		12,212,000
Long-term investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	83,665,000	81,600,000
Gross Unrealized Gains	2,000	1,000
Gross Unrealized Losses	(67,000)	(22,000)
Fair Value	83,600,000	81,579,000
Long-term restricted cash and investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	2,650,000	4,684,000
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	2,650,000	$ 4,684,000
Investments, excluding cash [Member]
Schedule of Available-for-sale Securities [Line Items]
Fair Value	250,669,000
Mature within One Year	222,065,000
After One Year through Two Years	$ 28,604,000

Inventory (Details) - USD ($) $ in Thousands	12 Months Ended
Inventory (Details) - USD ($) $ in Thousands	Dec. 31, 2015	Dec. 31, 2014
Inventory Disclosure [Abstract]
Raw materials	$ 1,037	$ 1,118
Work in process	2,251	2,845
Finished goods	583	559
Total	3,871	4,522
Less: non-current portion included in Other long-term assets	(1,255)	(2,141)
Inventory	2,616	2,381
Inventory write-down	$ 1,200	$ 200

Property and Equipment (Schedule of Property and Equipment) (Details) - USD ($) $ in Thousands	Dec. 31, 2015	Dec. 31, 2014
Property, Plant and Equipment [Abstract]
Laboratory equipment	$ 4,749	$ 13,677
Computer equipment and software	11,890	14,840
Furniture and fixtures	2,253	3,701
Leasehold improvements	6,395	16,364
Construction-in-progress	456	120
Property and equipment, gross	25,743	48,702
Less: accumulated depreciation and amortization	(24,309)	(46,270)
Property and equipment, net	$ 1,434	$ 2,432

Property and Equipment (Narrative) (Details) - USD ($)	12 Months Ended
Property and Equipment (Narrative) (Details) - USD ($)	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Property, Plant and Equipment [Line Items]
Depreciation	$ 1,400,000	$ 2,400,000	$ 3,100,000
Impairment charges	0	700,000	100,000
Gain on sale of assets	1,000,000	600,000	0
Proceeds from sale of property and equipment	1,346,000	392,000	143,000
Facility Charges [Member]
Property, Plant and Equipment [Line Items]
Proceeds from sale of property and equipment	$ 1,300,000	$ 300,000	$ 100,000

Debt (Schedule Of Debt) (Details) - USD ($) $ in Thousands	Dec. 31, 2015	Dec. 31, 2014
Debt Instrument [Line Items]
Total debt	$ 381,435	$ 356,965
Less: current portion	0	(97,830)
Long-term debt	381,435	259,135
Senior Subordinated Notes [Member] \| Convertible Senior Subordinated Notes due 2019 [Member]
Debt Instrument [Line Items]
Convertible Debt	198,708	179,135
Secured Debt [Member] \| Secured Convertible Notes due 2018 [Member]
Debt Instrument [Line Items]
Convertible Debt	102,727	97,449
Term Loan [Member] \| Silicon Valley Bank Term Loan and Line of Credit [Member]
Debt Instrument [Line Items]
Silicon Valley Bank term loan	80,000	80,000
Total debt	80,000
Line of Credit [Member] \| Silicon Valley Bank Term Loan and Line of Credit [Member]
Debt Instrument [Line Items]
Silicon Valley Bank Line of Credit	$ 0	$ 381

Debt (Narrative) (Details)					1 Months Ended					12 Months Ended
Debt (Narrative) (Details)	Jul. 01, 2015 USD ($)	Mar. 18, 2015	Jan. 22, 2014 $ / shares shares	Jun. 02, 2010 payment	Jan. 31, 2015 USD ($)	Jan. 31, 2014 USD ($)	Jan. 31, 2013 USD ($)	Aug. 31, 2012 USD ($) payment $ / shares	Jun. 30, 2010 USD ($)	Dec. 31, 2015 USD ($)	Mar. 04, 2015 $ / shares	Dec. 31, 2014 USD ($)	Aug. 06, 2012 USD ($)
Debt Instrument [Line Items]
Proceeds from convertible debt								$ 277,700,000
Book value of debt outstanding										$ 381,435,000		$ 356,965,000
Warrants Issued On January 22, 2014 [Member]
Debt Instrument [Line Items]
Warrant period		2 years	2 years							2 years
Warrants outstanding (in shares) \| shares			1,000,000
Exercise Price per Share (in dollars per share) \| $ / shares			$ 9.7								$ 3.445
Debt Payment [Member]
Debt Instrument [Line Items]
Restricted cash and investments								36,500,000
Silicon Valley Bank Term Loan and Line of Credit [Member]
Debt Instrument [Line Items]
Debt, interest rate (as a percent)				1.00%						6.00%
Collateral balance										$ 81,600,000		82,000,000
Senior Subordinated Notes [Member] \| Convertible Senior Subordinated Notes due August 15, 2019, 4.25% [Member]
Debt Instrument [Line Items]
Debt, principal amount								$ 287,500,000
Debt, interest rate (as a percent)								4.25%
Redemption price (as a percent)								100.00%
Convertible debt, conversion ratio								188.2353
Convertible debt, conversion ratio, principal amount								$ 1,000
Convertible debt, conversion price (dollars per share) \| $ / shares								$ 5.31
Debt holders, threshold principal amount held (as a percent)								25.00%
Periodic payment, number of payments secured in escrow \| payment								6
Balance of unamortized closing fees and expenses										2,600,000		3,300,000
Convertible debt										198,708,000		179,135,000
Secured Convertible Notes Due June 2018 [Member] \| Deerfield Financing [Member]
Debt Instrument [Line Items]
Debt, principal amount									$ 124,000,000.0
Balance of unamortized closing fees and expenses										700,000		1,400,000
Debt instruments, purchase price									80,000,000
Debt issuance costs									$ 2,000,000
Periodic payment, principal	$ 4,000,000
Principal eligible for extension option	100,000,000
Convertible debt										$ 103,800,000		104,000,000
Interest rate after extension option election (as a percent)										15.00%
Annual interest	$ 6,000,000
Amendment, consent fee													$ 1,500,000
Effective interest rate (as a percent)										15.26%
Mandatory prepayments of notes						$ 10,000,000	$ 10,000,000
Percentage of revenues payable under collaborative arrangements in 2013, 2014 and 2015 (as a percent)					15.00%
Maximum prepayment amount under collaborative arrangements in 2013 and 2014					$ 27,500,000					$ 27,500,000
Mandatory prepayment elected										450,000
Development milestone payment										$ 3,000,000
Prepayment price (as a percent)										105.00%
Debt instrument, minimum purchase amount for prepayment condition										$ 400,000,000
Percentage of assets minimum for prepayment condition										50.00%
Mandatory payments upon sale of intellectual property (as a percent of sales)										100.00%
Mandatory payments upon sale of other intellectual property (as a percent of sales)										50.00%
Term Loan [Member] \| Silicon Valley Bank Term Loan and Line of Credit [Member]
Debt Instrument [Line Items]
Debt instrument, term				7 years
Silicon Valley Bank term loan										$ 80,000,000		80,000,000
Book value of debt outstanding										80,000,000
Number of balloon payments \| payment				1
Principal balance payable in balloon payment				100.00%
Percentage of security deposit on outstanding obligations				100.00%
Maximum percentage required for collateral balance				107.00%
Line of Credit [Member] \| Silicon Valley Bank Term Loan and Line of Credit [Member]
Debt Instrument [Line Items]
Outstanding principal balance under line of credit										$ 0		$ 400,000
Coupon Interest [Member] \| Secured Convertible Notes Due June 2018 [Member] \| Deerfield Financing [Member]
Debt Instrument [Line Items]
Interest rate after extension option election (as a percent)										7.50%
Payment-in-Kind Interest [Member] \| Secured Convertible Notes Due June 2018 [Member] \| Deerfield Financing [Member]
Debt Instrument [Line Items]
Interest rate after extension option election (as a percent)										7.50%

Debt (Schedule of 2019 and 2010 Notes) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Senior Subordinated Notes [Member] \| Convertible Senior Subordinated Notes due August 15, 2019, 4.25% [Member]
Debt Instrument [Line Items]
Stated coupon interest	$ 12,218	$ 12,253	$ 12,219
Amortization of debt discount and debt issuance costs	19,573	17,804	16,201
Total interest expense	31,791	30,057	28,420
Secured Convertible Notes Due June 2018 [Member] \| Deerfield Financing [Member]
Debt Instrument [Line Items]
Stated coupon interest	6,792	6,000	6,000
Amortization of debt discount and debt issuance costs	9,278	11,731	10,089
Total interest expense	$ 16,070	$ 17,731	$ 16,089

Debt (Schedule Of Future Principal Payments Of Total Long-Term Debt) (Details) $ in Thousands	Dec. 31, 2015 USD ($)
Debt Disclosure [Abstract]
2016	$ 0
2017	80,000
2018	124,972
2019	287,500
Thereafter	$ 0

Common Stock And Warrants (Narrative) (Details) - USD ($) $ / shares in Units, $ in Thousands			1 Months Ended		12 Months Ended
	Mar. 18, 2015	Jan. 22, 2014	Jul. 31, 2015	Jan. 31, 2014	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013	Mar. 04, 2015
Class of Warrant or Right [Line Items]
Public offering of common stock (in shares)			28,750,000	10,000,000
Share price (dollars per share)			$ 5.40	$ 8
Net proceeds from public offering			$ 145,600	$ 75,600	$ 145,649	$ 75,643	$ 0
Warrants Issued On January 22, 2014 [Member]
Class of Warrant or Right [Line Items]
Warrant period	2 years	2 years			2 years
Warrants outstanding (in shares)		1,000,000
Exercise price per share (in dollars per share)		$ 9.7						$ 3.445
Maximum shares outstanding single holder may beneficially own (as a percent)					9.98%
Fair Value of warrants	$ 1,500					900
Unrealized gain (loss) on derivatives					$ (500)	$ 1,800
Over-Allotment Option [Member]
Class of Warrant or Right [Line Items]
Public offering of common stock (in shares)			3,750,000
Sale of stock, underwriter over allotment option period			30 days

Fair Value Measurements (Schedule Of Fair Value Of Financial Assets Measured On A Recurring Basis) (Details) - USD ($) $ in Thousands	Dec. 31, 2015	Dec. 31, 2014
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	$ 250,687	$ 238,286
Warrants		921
Money market funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	72,000	23,376
Commercial paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	78,155	56,714
Corporate bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	72,091	143,322
U.S. Treasury and government sponsored enterprises [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	28,423	12,212
Marketable equity securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	18
Municipal bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets		2,662
Level 1 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	72,018	23,376
Warrants		0
Level 1 [Member] \| Money market funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	72,000	23,376
Level 1 [Member] \| Commercial paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	0	0
Level 1 [Member] \| Corporate bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	0	0
Level 1 [Member] \| U.S. Treasury and government sponsored enterprises [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	0	0
Level 1 [Member] \| Marketable equity securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	18
Level 1 [Member] \| Municipal bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets		0
Level 2 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	178,669	214,910
Warrants		0
Level 2 [Member] \| Money market funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	0	0
Level 2 [Member] \| Commercial paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	78,155	56,714
Level 2 [Member] \| Corporate bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	72,091	143,322
Level 2 [Member] \| U.S. Treasury and government sponsored enterprises [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	28,423	12,212
Level 2 [Member] \| Marketable equity securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets	0
Level 2 [Member] \| Municipal bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets		2,662
Level 3 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets		0
Warrants	$ 0	921
Level 3 [Member] \| Money market funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets		0
Level 3 [Member] \| Commercial paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets		0
Level 3 [Member] \| Corporate bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets		0
Level 3 [Member] \| U.S. Treasury and government sponsored enterprises [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets		0
Level 3 [Member] \| Municipal bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total financial assets		$ 0

Fair Value Measurements (Fair Value Schedule of Level 3 Changes) (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2015 USD ($)
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Beginning balance	$ 921
Level 3 [Member]
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Beginning balance	921
Unrealized loss at final re-measurement of warrants on March 18, 2015, included in Interest income and other, net	549
Transfer of warrants from Other long-term liabilities to Additional paid-in capital at their estimated fair value upon warrant repricing on March 18, 2015	(1,470)
Ending balance	$ 0

Fair Value Measurements (Schedule of Estimated Fair Value of Outstanding Debt) (Details) - USD ($) $ in Thousands	Dec. 31, 2015	Dec. 31, 2014
Carrying Amount [Member] \| Senior Subordinated Notes [Member] \| Convertible Senior Subordinated Notes due August 15, 2019, 4.25% [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Debt instrument	$ 198,708	$ 179,135
Carrying Amount [Member] \| Term Loan [Member] \| Silicon Valley Bank Loan And Security Agreement [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Debt instrument	80,000	80,000
Carrying Amount [Member] \| Line of Credit [Member] \| Silicon Valley Bank Loan And Security Agreement [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Debt instrument	0	381
Carrying Amount [Member] \| Secured Convertible Notes Due June 2018 [Member] \| Deerfield Financing [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Debt instrument	102,700
Fair Value [Member] \| Senior Subordinated Notes [Member] \| Convertible Senior Subordinated Notes due August 15, 2019, 4.25% [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Debt instrument	336,260	156,889
Fair Value [Member] \| Term Loan [Member] \| Silicon Valley Bank Loan And Security Agreement [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Debt instrument	79,815	79,943
Fair Value [Member] \| Line of Credit [Member] \| Silicon Valley Bank Loan And Security Agreement [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Debt instrument	0	$ 381
Fair Value [Member] \| Secured Convertible Notes Due June 2018 [Member] \| Deerfield Financing [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Debt instrument	$ 101,100

Fair Value Measurements (Schedule of Assumptions) (Details) - Warrants Issued On January 22, 2014 [Member]				12 Months Ended
	Mar. 18, 2015	Dec. 31, 2014	Jan. 22, 2014	Dec. 31, 2015
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Line Items]
Warrant period	2 years		2 years	2 years
Warrant Liability [Member]
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Line Items]
Fair value inputs, discount rate				17.00%
Risk-free interest rate	0.87%	1.07%
Dividend yield	0.00%	0.00%
Volatility	95.00%	96.00%
Average expected life	2 years 9 months 18 days	3 years 1 month 6 days

Employee Benefit Plans (Narrative) (Details) - USD ($) $ / shares in Units, $ in Thousands		1 Months Ended	12 Months Ended
	Jul. 20, 2015	Dec. 31, 2005	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation expense			$ 21,977	$ 10,006	$ 12,018
Fair value of employee options vested and expensed			18,900	8,600	7,400
Cash received from option exercises and purchases under the ESPP			$ 11,500	1,600	1,500
Retirement Plan, employee contribution (as a percent)			50.00%
Employer matching contributions for first 3% of participant contributions (as a percent)			100.00%
Percentage of participant contributions into the 401(k) Retirement Plan (as a percent)			3.00%
Expenses relating to stock match			$ 400	1,100	$ 800
Shares available for issuance under 401 (k) Retirement Plan			450,042
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options, vesting period			4 years
Life of stock options granted			7 years		10 years
Number of shares available for grant			8,041,842
Intrinsic value of options exercised			$ 2,900
Total unrecognized compensation expense			$ 19,500
Unrecognized compensation expense weighted-average period for recognition			2 years 6 months 21 days
2009 Option Exchange Program [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Life of stock options granted			6 years 2 months 12 days
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Discount rate from market value on purchase date (as a percent)			85.00%
Discount rate from market value on offering date (as a percent)			85.00%
Stock-based compensation expense			$ 400	$ 800	$ 600
Number of shares available for grant			1,046,959
Common stock issued (shares)			324,315	669,565	345,828
Average price per share (in dollars per share)			$ 1.75	$ 2.14	$ 4.13
Performance Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation expense	$ 9,900		$ 3,300
Number of options in vested (in shares)	6,982,613
Additional unvested stock options outstanding (in shares)			5,934,052
Performance-based stock options expected to achieve performance objectives (in shares)			2,967,026
Performance-based stock options expected to achieve performance objectives, fair value			$ 3,700
Performance grants not probable, grant date fair value			$ 3,700
Restricted Stock Units (RSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options, vesting period			4 years
Total unrecognized compensation expense			$ 3,400
Unrecognized compensation expense weighted-average period for recognition			2 years 6 months
Change in Control and Severance Benefit Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Termination period prior to change in control		1 month
Termination period subsequent to change in control		13 months

Employee Benefit Plans (Schedule Of Allocated Employee Stock-Based Compensation Expense) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total employee stock-based compensation expense	$ 21,977	$ 10,006	$ 12,018
Research and development expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total employee stock-based compensation expense	11,691	3,245	6,021
Selling, general and administrative expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total employee stock-based compensation expense	10,286	6,783	5,948
Restructuring-related stock compensation expense (recovery) [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total employee stock-based compensation expense	$ 0	$ (22)	$ 49

Employee Benefit Plans (Weighted Average Grant Date Fair Value) (Details) - $ / shares	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant-date fair value (in dollars per share)	$ 2.55	$ 1.46	$ 2.97
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant-date fair value (in dollars per share)	$ 1.20	$ 1.28	$ 1.64

Employee Benefit Plans (Schedule Of Fair Value Of Employee Share-Based Payments Awards ESPP Assumptions And Weighted Average Fair Values) (Details)	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate	1.22%	1.80%	1.51%
Dividend yield	0.00%	0.00%	0.00%
Volatility	93.00%	85.00%	61.00%
Expected life	4 years 6 months	5 years 6 months	5 years 7 months 6 days
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate	0.15%	0.06%	0.11%
Dividend yield	0.00%	0.00%	0.00%
Volatility	98.00%	69.00%	66.00%
Expected life	6 months	6 months	6 months

Employee Benefit Plans (Summary Of All Stock Option Activity) (Details) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2015 USD ($) $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
Options outstanding at beginning of the year, Shares \| shares	27,811,992
Granted, Shares \| shares	8,894,800
Exercised, Shares \| shares	(2,340,963)
Forfeited, Shares \| shares	(924,890)
Expired, Shares \| shares	(6,015,085)
Options outstanding at ending of the year, Shares \| shares	27,425,854
Exercisable at December 31, 2015, Shares \| shares	15,666,177
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price [Abstract]
Options outstanding at beginning of the year, Weighted Average Exercise Price (dollars per share) \| $ / shares	$ 5.00
Granted, Weighted Average Exercise Price (dollars per share) \| $ / shares	3.78
Exercised, Weighted Average Exercise Price (dollars per share) \| $ / shares	4.66
Forfeited, Weighted Average Exercise Price (dollars per share) \| $ / shares	3.67
Expired, Weighted Average Exercise Price (dollars per share) \| $ / shares	7.12
Options outstanding at ending of the year, Weighted Average Exercise Price (dollars per share) \| $ / shares	4.22
Exercisable at December 31, 2015, Weighted Average Exercise Price (dollars per share) \| $ / shares	$ 4.68
Options outstanding, Weighted Average Remaining Contractual Term	5 years 1 month 2 days
Exercisable at December 31, 2015, Weighted Average Remaining Contractual Term	4 years 4 months 17 days
Options outstanding, Aggregate Intrinsic Value \| $	$ 51,501
Exercisable at December 31, 2015, Aggregate Intrinsic Value \| $	$ 25,532

Employee Benefit Plans (Summary Of Information About Stock Options Outstanding) (Details)	12 Months Ended
	Dec. 31, 2015 $ / shares shares
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Options Outstanding, Number (shares) \| shares	27,425,854
Options Outstanding, Weighted Average Remaining Contractual Life	5 years 1 month 2 days
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 4.22
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	15,666,177
Options Outstanding and Exercisable, Weighted Average Exercise Price (dollars per share)	$ 4.68
$1.46 - $1.87 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower (dollars per share)	1.46
Exercise Price Range, upper (dollars per share)	$ 1.87
Options Outstanding, Number (shares) \| shares	7,997,474
Options Outstanding, Weighted Average Remaining Contractual Life	5 years 9 months 10 days
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 1.70
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	3,857,469
Options Outstanding and Exercisable, Weighted Average Exercise Price (dollars per share)	$ 1.70
$1.90 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower (dollars per share)	1.90
Exercise Price Range, upper (dollars per share)	$ 1.90
Options Outstanding, Number (shares) \| shares	3,738,000
Options Outstanding, Weighted Average Remaining Contractual Life	6 years 25 days
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 1.90
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	1,826,502
Options Outstanding and Exercisable, Weighted Average Exercise Price (dollars per share)	$ 1.90
$2.57 - $4.88 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower (dollars per share)	2.57
Exercise Price Range, upper (dollars per share)	$ 4.88
Options Outstanding, Number (shares) \| shares	2,772,796
Options Outstanding, Weighted Average Remaining Contractual Life	5 years 3 months 7 days
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 3.80
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	1,681,199
Options Outstanding and Exercisable, Weighted Average Exercise Price (dollars per share)	$ 3.98
$5.01 - $5.51 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower (dollars per share)	5.01
Exercise Price Range, upper (dollars per share)	$ 5.51
Options Outstanding, Number (shares) \| shares	4,043,479
Options Outstanding, Weighted Average Remaining Contractual Life	4 years 7 days
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 5.44
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	3,186,063
Options Outstanding and Exercisable, Weighted Average Exercise Price (dollars per share)	$ 5.44
$5.55 - $6.02 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower (dollars per share)	5.55
Exercise Price Range, upper (dollars per share)	$ 6.02
Options Outstanding, Number (shares) \| shares	2,600,943
Options Outstanding, Weighted Average Remaining Contractual Life	4 years 8 months 12 days
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 5.73
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	1,890,661
Options Outstanding and Exercisable, Weighted Average Exercise Price (dollars per share)	$ 5.70
$6.21 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower (dollars per share)	6.21
Exercise Price Range, upper (dollars per share)	$ 6.21
Options Outstanding, Number (shares) \| shares	2,822,900
Options Outstanding, Weighted Average Remaining Contractual Life	6 years 8 months 8 days
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 6.21
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	0
$6.25 - $11.66 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower (dollars per share)	$ 6.25
Exercise Price Range, upper (dollars per share)	$ 11.66
Options Outstanding, Number (shares) \| shares	3,450,262
Options Outstanding, Weighted Average Remaining Contractual Life	2 years 6 months 10 days
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 8.71
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	3,224,283
Options Outstanding and Exercisable, Weighted Average Exercise Price (dollars per share)	$ 8.82

Employee Benefit Plans (Summary Of All RSU Activity) (Details) - Restricted Stock Units (RSUs) [Member] $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2015 USD ($) $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]
Awards outstanding at beginning of period, Shares \| shares	961,469
Awarded, Shares \| shares	838,535
Released, Shares \| shares	(672,951)
Forfeited, Shares \| shares	(124,865)
Awards outstanding at end of period, Shares \| shares	1,002,188
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Abstract]
Awards outstanding at beginning of period, Weighted Average Grant Date Fair Value (dollars per share) \| $ / shares	$ 3.82
Awarded, Weighted Average Grant Date Fair Value (dollars per share) \| $ / shares	5.01
Released, Weighted Average Grant Date Fair Value (dollars per share) \| $ / shares	5.62
Forfeited, Weighted Average Grant Date Fair Value (dollars per share) \| $ / shares	5.32
Awards outstanding at end of period, Weighted Average Grant Date Fair Value (dollars per share) \| $ / shares	$ 5.16
Awards outstanding, Weighted Average Remaining Contractual Term	2 years 6 months
Awards outstanding, Aggregate Intrinsic Value \| $	$ 5,652

Income Taxes (Narrative) (Details) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Narrative) (Details) - USD ($) $ in Thousands	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Income Tax Examination [Line Items]
Income tax provision (benefit)	$ 55	$ (182)	$ (96)
Valuation allowance increased (decreased)	12,400	$ 89,700	(16,800)
Tax benefit of stock option	18,000
Unrecognized tax benefit would affect the effective tax rate			100
Unrecognized Tax Benefits, Interest on Income Taxes Accrued			20
Unrecognized Tax Benefits, Interest on Income Taxes Expense			$ 4
Internal Revenue Service (IRS) [Member]
Income Tax Examination [Line Items]
Net operating loss carryforwards	1,323,000
Research and development tax credits	75,000
State and Local Jurisdiction [Member]
Income Tax Examination [Line Items]
Net operating loss carryforwards	$ 692,000
Minimum [Member] \| Internal Revenue Service (IRS) [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards, expiration dates	Dec. 31, 2019
Minimum [Member] \| Research And Development Expense [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards federal business credit expiration date	Dec. 31, 2020
Minimum [Member] \| State and Local Jurisdiction [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards, expiration dates	Dec. 31, 2016
Maximum [Member] \| Internal Revenue Service (IRS) [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards, expiration dates	Dec. 31, 2035
Maximum [Member] \| Research And Development Expense [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards federal business credit expiration date	Dec. 31, 2029
Maximum [Member] \| State and Local Jurisdiction [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards, expiration dates	Dec. 31, 2035
Research Tax Credit Carryforward [Member] \| State and Local Jurisdiction [Member]
Income Tax Examination [Line Items]
Research and development tax credits	$ 25,000

Income Taxes (Schedule Of Consolidated Net Income (Loss)) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Income Tax Disclosure [Abstract]
Domestic	$ (158,839)	$ (237,780)	$ (236,076)
Foreign	(10,843)	(30,944)	(8,780)
Loss before income taxes	$ (169,682)	$ (268,724)	$ (244,856)

Income Taxes (Components of Income Tax Expense (Benefit)) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Current:
Federal	$ 0	$ 0	$ 0
State	55	(182)	12
Total current tax expense	55	(182)	12
Deferred:
Federal	0	0	(106)
State	0	0	(2)
Total deferred tax expense	0	0	(108)
Income tax (benefit) provision	$ 55	$ (182)	$ (96)

Income Taxes (Schedule Of Reconciliation Of Income Taxes At The Statutory Federal Income Tax Rate To Net Income Taxes) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Income Tax Disclosure [Abstract]
U.S. federal income tax benefit at statutory rate	$ (57,692)	$ (91,366)	$ (83,251)
Unutilized net operating losses	54,139	87,448	(3,438)
Non-deductible interest	3,308	3,598	3,380
Stock-based compensation	195	255	393
State tax expense	55	(182)	10
Available-for-sale investments	0	0	(106)
Impact of intellectual property rights transfer	0	0	82,858
Other	50	65	58
Income tax (benefit) provision	$ 55	$ (182)	$ (96)

Income Taxes (Schedule Of Deferred Assets And Liabilities) (Details) - USD ($) $ in Thousands	Dec. 31, 2015	Dec. 31, 2014
Deferred tax assets:
Net operating loss carry-forwards	$ 464,504	$ 446,343
Tax credit and charitable contribution carry-forwards	64,350	64,368
Amortization of deferred stock compensation – non-qualified	14,615	27,500
Accruals and reserves not currently deductible	7,775	6,521
Book over tax depreciation and amortization	1,752	5,118
Deferred revenue	0	988
Total deferred tax assets	552,996	550,838
Valuation allowance	(523,574)	(511,171)
Net deferred tax assets	29,422	39,667
Deferred tax liabilities:
Unrealized gain on derivatives	(497)	(704)
Convertible debt	(28,925)	(38,963)
Total deferred tax liabilities	(29,422)	(39,667)
Net deferred taxes	$ 0	$ 0

Income Taxes (Schedule Of Unrecognized Tax Benefits) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Reconciliation of Unrecognized Tax Benefits, Excluding Amounts Pertaining to Examined Tax Returns [Roll Forward]
Beginning balance	$ 58,215	$ 55,077	$ 47,298
Increase (decrease) relating to prior year provision	21,696	719	(112)
Increase relating to current year provision	8,727	2,706	7,891
Reductions based on the lapse of the applicable statutes of limitations	0	(287)	0
Ending balance	$ 88,638	$ 58,215	$ 55,077

Net Loss Per Share (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2014	Sep. 30, 2014	Jun. 30, 2014	Mar. 31, 2014	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Earnings Per Share [Abstract]
Net loss	$ (43,641)	$ (47,564)	$ (43,362)	$ (35,170)	$ (57,953)	$ (62,560)	$ (73,410)	$ (74,619)	$ (169,737)	$ (268,542)	$ (244,760)
Shares used in computing basic and diluted net loss per share									209,227	194,299	184,062
Net loss per share, basic and diluted (in dollars per share)	$ (0.19)	$ (0.22)	$ (0.22)	$ (0.18)	$ (0.30)	$ (0.32)	$ (0.38)	$ (0.39)	$ (0.81)	$ (1.38)	$ (1.33)
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares									117,478	105,664	76,965
Convertible debt [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares									88,008	75,734	54,123
Outstanding stock options, unvested RSUs and ESPP contributions [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares									28,470	28,930	21,401
Warrants [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares									1,000	1,000	1,441

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

Commitments (Schedule Of Aggregate Future Minimum Lease Payments Under Operating Leases) (Details) $ in Thousands	Dec. 31, 2015 USD ($)
Commitments and Contingencies Disclosure [Abstract]
2016	$ 14,236
2017	8,474
2018	3,007
Total	25,717
Future minimum rental under noncancelable subleases	$ 6,100

Commitments (Schedule Of Aggregate Future Minimum Lease Payments Under Operating Leases By Material Lease Agreements) (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2015 USD ($) renewal
Operating Leased Assets [Line Items]
Future Minimum Lease Payment	$ 25,717
Building Lease #1&2 [Member]
Operating Leased Assets [Line Items]
Original Term (Expiration)	May 01, 2017
Number of Renewal Options \| renewal	2
Period of Renewal Option	5 years
Future Minimum Lease Payment	$ 12,732
Building Lease #3 [Member]
Operating Leased Assets [Line Items]
Original Term (Expiration)	Jul. 01, 2018
Number of Renewal Options \| renewal	1
Period of Renewal Option	5 years
Future Minimum Lease Payment	$ 12,985

Commitments (Narrative) (Details) $ in Millions	1 Months Ended	12 Months Ended
Commitments (Narrative) (Details) $ in Millions	May 31, 2007 debt_instrument	Dec. 31, 2015 USD ($) debt_instrument	Dec. 31, 2014 USD ($)	Dec. 31, 2013 USD ($)
Operating Leased Assets [Line Items]
Rent expenses under operating leases		$ 8.7	$ 10.3	$ 9.1
Net of sublease rentals under operating leases		$ 5.2	4.9	$ 4.1
Number of letters of credit entered into (in debt instruments) \| debt_instrument	2	3
Collateral provided for purchasing card program		$ 1.5	3.5
Building Lease [Member]
Operating Leased Assets [Line Items]
Standby letter of credit, amount		0.5	0.5
Workers Compensation Insurance Policy [Member]
Operating Leased Assets [Line Items]
Standby letter of credit, amount		$ 0.6	$ 0.7

Concentrations of Credit Risk (Details) - USD ($) $ in Millions	12 Months Ended			24 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2015
Concentration Risk [Line Items]
Foreign exchange fluctuations gain (loss)	$ 0.1	$ 0.5
Diplomat Specialty Pharmacy [Member] \| Accounts Receivable [Member] \| Customer Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration risk ( as a percentage)	95.00%
Diplomat Specialty Pharmacy [Member] \| Sales [Member] \| Customer Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration risk ( as a percentage)	83.00%	99.00%	45.00%
Swedish Orphan Biovitrum [Member] \| Accounts Receivable [Member] \| Customer Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration risk ( as a percentage)	5.00%
Bristol-Myers Squibb [Member] \| Collaboration agreement [Member] \| Customer Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration risk ( as a percentage)	0.00%	0.00%	52.00%
Sobi [Member]
Concentration Risk [Line Items]
Reduction to net product revenues	$ 0.1	$ 2.3		$ 2.4
United States [Member] \| Sales [Member] \| Geographic Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration risk ( as a percentage)	91.00%	99.00%	97.00%
European Union [Member] \| Sales [Member] \| Geographic Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration risk ( as a percentage)	9.00%	1.00%	3.00%

Subsequent Event (Narrative) (Details) - Ipsen [Member] - Subsequent Event [Member]	Feb. 29, 2016 USD ($) payment country
Subsequent Event [Line Items]
Upfront and milestone payments	$ 200,000,000.0
Maximum amount eligible for commercial milestones under collaborations agreement	$ 545,000,000.0
R&D cost reimbursement (as a percent)	35.00%
RCC [Member]
Subsequent Event [Line Items]
Milestone payment upon approval by EMA in second-line RCC	$ 60,000,000.0
HCC [Member]
Subsequent Event [Line Items]
Milestone payment upon approval by EMA in second-line RCC	10,000,000.0
HCC Acceptance [Member]
Subsequent Event [Line Items]
Milestone payment upon approval by EMA in second-line RCC	40,000,000
EU Country Launch [Member]
Subsequent Event [Line Items]
Maximum amount eligible for commercial milestones under collaborations agreement	$ 10,000,000.0
Number of payments to be received upon milestone achievement \| payment	2
Number of countries in which entity launches product \| country	2
Initial [Member]
Subsequent Event [Line Items]
Percent of royalty on net sale	2.00%
Royalty Tier	$ 50,000,000
Second [Member]
Subsequent Event [Line Items]
Percent of royalty on net sale	12.00%
Royalty Tier	$ 100,000,000
Minimum [Member]
Subsequent Event [Line Items]
Percent of royalty on net sale	22.00%
Maximum [Member]
Subsequent Event [Line Items]
Percent of royalty on net sale	26.00%

Quarterly Financial Data (Unaudited) (Schedule Of Quarterly Financial Data) (Details) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2015 USD ($) employee $ / shares	Sep. 30, 2015 USD ($) $ / shares	Jun. 30, 2015 USD ($) $ / shares	Mar. 31, 2015 USD ($) $ / shares	Dec. 31, 2014 USD ($) $ / shares	Sep. 30, 2014 USD ($) $ / shares	Jun. 30, 2014 USD ($) $ / shares	Mar. 31, 2014 USD ($) $ / shares	Dec. 31, 2015 USD ($) employee $ / shares	Dec. 31, 2014 USD ($) $ / shares	Dec. 31, 2013 USD ($) $ / shares
Quarterly Financial Information Disclosure [Abstract]
Revenues	$ 9,938	$ 9,854	$ 7,992	$ 9,388	$ 7,353	$ 6,291	$ 6,562	$ 4,905	$ 37,172	$ 25,111	$ 31,338
Gross profit	8,915	8,434	7,306	8,622	6,669	5,718	6,085	4,596
Loss from operations	(31,600)	(35,781)	(31,280)	(22,760)	(46,208)	(51,574)	(61,688)	(64,988)	(121,421)	(224,458)	(200,732)
Net loss	$ (43,641)	$ (47,564)	$ (43,362)	$ (35,170)	$ (57,953)	$ (62,560)	$ (73,410)	$ (74,619)	$ (169,737)	$ (268,542)	$ (244,760)
Net loss per share, basic and diluted (in dollars per share) \| $ / shares	$ (0.19)	$ (0.22)	$ (0.22)	$ (0.18)	$ (0.30)	$ (0.32)	$ (0.38)	$ (0.39)	$ (0.81)	$ (1.38)	$ (1.33)
2014 Restructuring [Member]
Restructuring Cost and Reserve [Line Items]
Aggregate reduction in headcount (in employees) \| employee	143								143

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.