View Filing Data

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

$ (244,760)

$ (147,645)

$ 75,697

^[1]

238

(150)

Comprehensive (loss) income

$ (244,522)

$ (147,599)

$ 75,547

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

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

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Net Income
-URI http://asc.fasb.org/extlink&oid=6518256

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 230
-SubTopic 10
-Section 45
-Paragraph 28
-URI http://asc.fasb.org/extlink&oid=31042434&loc=d3e3602-108585

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 944
-SubTopic 225
-Section S99
-Paragraph 1
-Subparagraph (SX 210.7-04.19)
-URI http://asc.fasb.org/extlink&oid=6879464&loc=d3e573970-122913

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6371337&loc=d3e3550-109257

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 225
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SX 210.5-03.18)
-URI http://asc.fasb.org/extlink&oid=26872669&loc=d3e20235-122688

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 944
-SubTopic 225
-Section S99
-Paragraph 1
-Subparagraph (SX 210.7-04.22)
-URI http://asc.fasb.org/extlink&oid=6879464&loc=d3e573970-122913

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Other Comprehensive Income
-URI http://asc.fasb.org/extlink&oid=6519514

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=28358780&loc=d3e565-108580

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 03
-Paragraph 19
-Article 5

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Paragraph 20
-Article 9

Balance, shares at Dec. 31, 2010

Consolidated Statements of Other Comprehensive (Loss) Income (Parenthetical) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Statement of Comprehensive Income [Abstract]
Other comprehensive income (loss), tax	$ 106	$ 0	$ 0

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]

109,287,160

Balance at Dec. 31, 2010

$ (228,325)

$ 109

$ 953,608

$ 12

$ (1,182,054)

Other comprehensive (loss) income

75,697

(150)

^[1]

(150)

Issuance of common stock under stock plans, shares

3,488,669

Issuance of common stock under stock plans

15,041

$ 3

15,038

Sale of shares of common stock, shares

17,250,000

Sale of shares of common stock

179,375

$ 17

179,358

Issuance of common stock for settlement of convertible loan, shares

5,537,906

Issuance of common stock for settlement of convertible loan

36,895

$ 6

36,889

Stock-based compensation expense

12,099

Balance, shares at Dec. 31, 2011

135,563,735

Balance at Dec. 31, 2011

90,632

$ 135

1,196,992

(138)

(1,106,357)

Other comprehensive (loss) income

(147,645)

^[1]

Issuance of common stock under stock plans, shares

983,478

Issuance of common stock under stock plans

2,822

$ 1

2,821

Sale of shares of common stock, shares

47,150,000

Sale of shares of common stock

203,961

$ 47

203,914

Equity component of convertible debt issued, net

137,785

Stock-based compensation expense

$ 8,833

8,833

Balance, shares at Dec. 31, 2012

183,697,213

Balance at Dec. 31, 2012

$ 296,434

$ 183

1,550,345

(92)

(1,254,002)

Other comprehensive (loss) income

(244,760)

238

^[1]

238

Issuance of common stock under stock plans, shares

836,438

Issuance of common stock under stock plans

2,295

$ 1

2,294

Stock-based compensation expense

$ 12,031

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)

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

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Cash flows from operating activities:
Net (loss) income	$ (244,760)	$ (147,645)	$ 75,697
Adjustments to reconcile net (loss) income to net cash used in operating activities:
Depreciation and amortization	3,147	5,717	6,822
Stock-based compensation expense	12,031	8,833	12,099
Restructuring (credit) charge for property and equipment	0	(204)	497
Accretion of debt discount	26,290	14,752	7,989
Gain on sale of property and equipment	0	(950)	0
Gain on sale of businesses	0	0	(2,254)
Other	6,787	4,989	4,801
Changes in assets and liabilities:
Other receivables	(1,190)	27,038	(24,294)
Inventory	(2,890)	0	0
Prepaid expenses and other current assets	1,034	(1,764)	10,553
Other assets	0	(1,966)	405
Accounts payable and other accrued liabilities	8,691	5,149	(14,801)
Clinical trial liability	14,398	1,169	9,246
Increase (Decrease) in Restructuring Reserve	(5,750)	5,244	(303)
Other long-term liabilities	(1,690)	(1,588)	(1,162)
Deferred revenue	(14,871)	(41,920)	(244,528)
Net cash used in operating activities	(198,773)	(123,146)	(159,233)
Cash flows from investing activities:
Purchases of property and equipment	(2,171)	(2,717)	(991)
Proceeds from sale of property and equipment	143	1,943	1,526
Proceeds from sale of businesses	0	0	3,010
Proceeds from maturities of restricted cash and investments	17,268	5,499	8,099
Purchase of restricted cash and investments	(6,085)	(41,485)	(5,899)
Proceeds from sale of investments	0	0	55,205
Proceeds from maturities of investments	325,171	310,765	124,800
Purchases of investments	(189,975)	(533,475)	(237,213)
Net cash provided by (used in) investing activities	144,351	(259,470)	(51,463)
Cash flows from financing activities:
Proceeds from issuance of common stock, net	0	203,479	179,375
Proceeds from exercise of stock options and warrants	72	929	12,436
Proceeds from employee stock purchase plan	1,429	1,217	1,734
Proceeds from debt issuance, net	0	277,673	2,589
Principal payments on debt	(13,170)	(4,870)	(8,621)
Net cash (used in) provided by financing activities	(11,669)	478,428	187,513
Net increase (decrease) in cash and cash equivalents	(66,091)	95,812	(23,183)
Cash and cash equivalents at beginning of year	170,069	74,257	97,440
Cash and cash equivalents at end of year	103,978	170,069	74,257
Supplemental cash flow disclosure:
Cash paid for interest	19,160	6,982	6,835
Cash paid for taxes	0	1,118	0
Non-cash financing activity:
Issuance of common stock for settlement of convertible loan, including accrued interest	$ 0	$ 0	$ 36,895

Organization And Summary Of Significant Accounting Policies

12 Months Ended

Dec. 31, 2013

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 biotechnology company committed to developing small molecule therapies for the treatment of cancer. Our two most advanced assets, COMETRIQ® (cabozantinib), our wholly-owned inhibitor of multiple receptor tyrosine kinases, and cobimetinib (GDC-0973/XL518), a potent, highly selective inhibitor of MEK, which we out-licensed to Genentech, Inc. (a wholly-owned member of the Roche Group) (“Genentech”) are currently the subject of six ongoing phase 3 pivotal trials. Top-line results from four of these pivotal trials are expected in 2014.

We are focusing our proprietary resources and development and commercialization efforts primarily on COMETRIQ® (cabozantinib), which was approved on November 29, 2012, by the U.S. Food and Drug Administration for the treatment of progressive, metastatic medullary thyroid cancer (“MTC”) in the United States, where it became commercially available in late January 2013. In December 2013, the European Committee for Medicinal Products for Human Use (“CHMP”) issued a positive opinion on the Marketing Authorization Application submitted to the European Medicines Agency for COMETRIQ for the proposed indication of progressive, unresectable, locally advanced, or metastatic MTC. The CHMP’s positive opinion will be reviewed by the European Commission, which has the authority to approve medicines for the European Union.

Cabozantinib is being evaluated in a broad development program, including two ongoing phase 3 pivotal trials in metastatic castration-resistant prostate cancer (“CRPC”) an ongoing phase 3 pivotal trial in metastatic renal cell cancer and an ongoing phase 3 pivotal trial in advanced hepatocellular cancer. We believe cabozantinib has the potential to be a high-quality, broadly-active and differentiated anti-cancer agent that can make a meaningful difference in the lives of patients. Our objective is to develop cabozantinib into a major oncology franchise, and we believe that the approval of COMETRIQ (cabozantinib) for the treatment of progressive, metastatic MTC provides us with the opportunity to establish a commercial presence in furtherance of this objective. We currently expect top-line data from our two phase 3 pivotal trials of cabozantinib in CRPC and the overall survival analysis of our phase 3 pivotal trial of cabozantinib in progressive, metastatic MTC in 2014.

Cobimetinib is also being evaluated in a broad development program, including a multicenter, randomized, double-blind, placebo-controlled phase 3 clinical trial evaluating the combination of cobimetinib with vemurafenib versus vemurafenib in previously untreated BRAFV600 mutation positive patients with unresectable locally advanced or metastatic melanoma that was initiated on November 1, 2012. Roche and Genentech have provided guidance that they expect top-line data from this trial in 2014.

Basis of Consolidation

The consolidated financial statements include the accounts of Exelixis and those of our wholly-owned subsidiaries, including Exelixis International (Bermuda) Ltd. (“Exelixis Bermuda”). Effective July 2013, Exelixis engaged in intercompany transactions whereby Exelixis Bermuda acquired the existing and future intellectual property rights to exploit cabozantinib in jurisdictions outside of the United States. Exelixis Bermuda’s 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 2011, a 52-week year, ended on December 30, 2011, fiscal year 2012, a 52-week year, ended on December 28, 2012, fiscal year 2013, a 52-week year, ended on December 27, 2013, and fiscal year 2014, a 53-week year, will end on January 2, 2015. For convenience, references in this report as of and for the fiscal years ended December 30, 2011, December 28, 2012 and December 27, 2013, are indicated on a calendar year basis, ended December 31, 2011, 2012 and 2013, respectively.

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, 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 inventory, revenue recognition, valuation of long-lived assets, certain accrued liabilities including clinical trial accruals and restructuring liability, share-based compensation and the valuation of the debt and equity components of our convertible debt at issuance. 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. Our senior management has discussed the development, selection and disclosure of these estimates with the Audit Committee of our Board of Directors. Actual results could differ materially from those estimates.

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 income. 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 its investments below the 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, 2013, 2012, and 2011, we did not record any significant 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.

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 that has become obsolete, or has a cost basis in excess of its expected net realizable value and inventory quantities in excess of expected requirements. Expired inventory is disposed of and the related costs are recognized as cost of goods sold in the Consolidated Statements of Operations.

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. We received regulatory approval for our first product, COMETRIQ, on November 29, 2012.

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 development 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, by applying the purchase method. 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. When evaluating goodwill for impairment we must determine the reporting units that exist within Exelixis. We have determined that we have one reporting unit consistent with our single business segment as of December 31, 2013 and 2012.

Long-Lived Assets

Long-lived assets include property and equipment and identified intangible assets. 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.

See “Note 4 - Restructurings” for further information on write-downs of property and equipment resulting from our Restructurings.

Revenue Recognition

We recognize revenue from the sale of COMETRIQ and from license fees, milestones and contingent payments earned on research and collaboration arrangements.

License, Contract and Collaboration Reimbursement Revenues

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. Deliverables that do not meet these criteria are not evaluated separately for the purpose of revenue recognition. 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.

Collaborative agreement reimbursement revenues or collaboration cost-sharing expenses are recorded as earned or owed based on the performance requirements by both parties under the respective contracts. For arrangements in which we and our collaborative partner are active participants in the agreement and for which both parties are exposed to significant risks and rewards depending on the commercial success of the activity, we present payments between the parties on a net basis. On an annual basis, to the extent that net research and development funding payments are received, we will record the net cash inflow as revenue. In annual periods when the net research and development funding payments result in a payable, these amounts are presented as collaboration cost-sharing expense. Agreement reimbursements are classified as either contract revenues or collaboration reimbursement in our Consolidated Statements of Operations, depending on the terms of the agreement.

Revenues and expenses from collaborations that are not co-development agreements are recorded as contract revenues or research and development expenses in the period incurred.

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 shipment of the product to the patient by our distributor. For product sales in Europe, this occurs when our European distribution partner has accepted 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. We have a limited sales history and cannot reliably estimate expected returns of the product nor the discounts and rebates due to payors at the time of shipment to the specialty pharmacy. Accordingly, upon shipment to the specialty pharmacy, we record deferred revenue on our Consolidated Balance Sheets. We recognize revenue when the specialty pharmacy provides the product to a patient based on the fulfillment of a prescription. We record revenue using an analysis of prescription data from our specialty pharmacy to ascertain the date of shipment and the payor mix. This approach is frequently referred to as the “sell-through” revenue recognition model. Once the prescription has been provided to the patient, it is not subject to return unless the product is damaged.

Product sales to our European distribution partner are not subject to customer incentives, rights of return or discounts and allowances. We record revenue at the time our European distribution partner has accepted the product, a method also known as the “sell-in” revenue recognition model.

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 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, and (c) estimated costs of patient assistance programs. 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. These discounts and allowances apply only to gross product revenues earned in the United States.

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 payor data received from the United States specialty pharmacy. Rebates are generally invoiced by the payor 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 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 payor 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.

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 designated as PAP inventory.

Cost of Goods Sold

Cost of goods sold is related to our product revenues and in 2013 consisted primarily of 3% royalty we are required to pay GlaxoSmithKline and indirect labor costs, and to a lesser extent, the cost of manufacturing and other third party logistics costs of our product. A significant portion of the manufacturing costs for 2013 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 2002 collaboration 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 collaboration agreement generally 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 by 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. For example, during the years ended December 31, 2013, 2012 and 2011, we recorded a reduction related to prior periods of approximately $0.8 million, $2.7 million, and $1.6 million, respectively, to our accrued clinical trial liabilities and research and development expenses primarily related to our phase 2 and phase 3 clinical trials for cabozantinib.

Net (Loss) Income Per Share

Basic net (loss) income per share is computed by dividing the net (loss) income for the period by the weighted average number of shares of common stock outstanding during the period. Diluted net (loss) income 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.

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 and peer 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.

Need to Raise Additional Capital

We have incurred annual net losses since inception through the year ended December 31, 2013, with the exception of the fiscal year ended December 31, 2011. In 2011, we had net income primarily as a result of the acceleration of revenue recognized under our 2008 collaboration agreement with Bristol-Myers Squibb Company (“Bristol-Myers Squibb”) that terminated in October 2011 and under our 2009 discovery collaboration agreement with Sanofi that terminated in December 2011. We anticipate net losses and negative operating cash flow for the foreseeable future. For the year ended December 31, 2013, we had a net loss of $244.8 million; as of December 31, 2013, we had an accumulated deficit of $1.5 billion. We commercially launched COMETRIQ for the treatment of progressive, metastatic MTC in the United States in late January 2013. From the commercial launch through December 31, 2013, we have generated $15.0 million in net revenues from the sale of COMETRIQ. We have derived substantially all of our revenues since inception from collaborative research and development agreements. Revenues from research and development collaborations depend on research funding, the achievement of milestones, and royalties we earn from any future products developed from the collaborative research. If we are unable to successfully achieve milestones or our collaborators fail to develop successful products, we will not earn the revenues contemplated under such collaborative agreements. The amount of our net losses will depend, in part, on the rate of growth, if any, in our sales of COMETRIQ for progressive, metastatic MTC, license and contract revenues and on the level of our expenses. These losses have had and will continue to have an adverse effect on our stockholders’ equity and working capital. Our research and development expenditures and general and administrative expenses have exceeded our revenues for each year other than 2011, and we expect to spend significant additional amounts to fund the continued development of cabozantinib. As a result, we expect to continue to incur substantial operating expenses, and, consequently, we will need to generate significant additional revenues to achieve future profitability. Because of the numerous risks and uncertainties associated with developing drugs, we are unable to predict the extent of any future losses or when we will become profitable, if at all.

Recently Adopted Accounting Pronouncements

In July 2012, Accounting Standards Codification (“ASC”) Topic 350, Testing Indefinite-Lived Intangible Assets for Impairment was amended to permit a reporting entity to first assess qualitative factors to determine whether it is necessary to perform the annual quantitative impairment test for indefinite-lived intangible assets. This guidance was effective January 1, 2013. The adoption of this amendment did not affect our financial position or results of operations.

In February 2013, ASC Topic 220, Comprehensive Income was amended to require additional information about amounts reclassified out of accumulated other comprehensive income. We adopted this guidance beginning January 1, 2013, and will provide the additional information when such reclassifications occur. The adoption of this amendment did not affect our financial position or results of operations.

Research And Collaboration Agreements

12 Months Ended

Dec. 31, 2013

Research And Collaboration Agreements [Abstract]

Research And Collaboration Agreements

RESEARCH AND COLLABORATION AGREEMENTS

Cobimetinib Collaboration

In December 2006, we entered into a worldwide co-development agreement with Genentech for the development and commercialization of cobimetinib. Cobimetinib is a potent, highly selective inhibitor of MEK, a serine/threonine kinase that is a component of the RAS/RAF/MEK/ERK pathway. This pathway mediates signaling downstream of growth factor receptors, and is prominently activated in a wide variety of human tumors. In preclinical studies, oral dosing of cobimetinib resulted in potent and sustained inhibition of MEK in RAS- or BRAF-mutant tumor models. 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 co-development agreement and with the submission of the IND for cobimetinib. Under the terms of the agreement, we were responsible for developing cobimetinib through the end of 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, triggering a payment to us of $3.0 million, which we received in April 2008. We were responsible for the phase 1 clinical trial until the point that a maximum tolerated dose (“MTD”) was determined. After MTD was determined, we granted to Genentech an exclusive worldwide revenue-bearing license to cobimetinib in March 2009, at which point Genentech became responsible for completing the phase 1 clinical trial and subsequent clinical development. We received an additional $7.0 million payment in March 2010.

Preliminary results from BRIM7, an ongoing phase 1b dose escalation study conducted by Roche and Genentech of the BRAF inhibitor vemurafenib in combination with cobimetinib in patients with locally advanced/unresectable or metastatic melanoma carrying a BRAFV600 mutation were presented at the 2012 European Society of Medical Oncologists Annual Meeting. Updated data from BRIM7 reported at the European Cancer Congress 2013 suggest that the preliminary safety profile and activity of the investigational combination of cobimetinib and vemurafenib are encouraging in BRAF inhibitor-naïve patients. Although the phase 1b dose escalation study was designed to evaluate the safety and tolerability of cobimetinib in combination with vemurafenib, objective responses (comprising complete or partial responses) were observed in 85% of the patients who had not been previously treated with a BRAF inhibitor.

As disclosed on ClinicalTrials.gov (NCT01689519), a multicenter, randomized, double-blind, placebo-controlled phase 3 clinical trial evaluating the combination of vemurafenib with cobimetinib versus vemurafenib in previously untreated BRAFV600 mutation positive patients with unresectable locally advanced or metastatic melanoma was initiated on November 1, 2012. On January 14, 2013, we received notice from Genentech that the first patient was dosed in this phase 3 pivotal trial. Roche and Genentech have provided guidance that they expect top-line data from this trial in 2014.

In addition, as disclosed on ClinicalTrials.gov, on the basis of strong scientific rationale and encouraging preclinical data, Genentech is initiating the following new clinical trials of cobimetinib in combination with other agents under the agreement:


•	A Phase 1b, Open-Label, Dose-Escalation Study of the Safety, Tolerability, and Pharmacokinetics of MEHD7945A and Cobimetinib in Patients with Locally Advanced or Metastatic Solid Tumors with Mutant KRAS (NCT01986166);


•	A Phase 1b, Open-Label Study Evaluating the Safety, Tolerability, and Pharmacokinetics of Onartuzumab in Combination with Vemurafenib and/or Cobimetinib in Patients with Advanced Solid Malignancies (NCT01974258); and


•	A Phase 1b Study of the Safety and Pharmacology of MPDL3280A Administered with Cobimetinib in Patients with Locally Advanced or Metastatic Solid Tumors (NCT01988896).

Under the terms of our agreement with Genentech, we are entitled to an initial equal share of U.S. profits and losses for cobimetinib, which will decrease as sales increase, and will share equally in the U.S. marketing and commercialization costs. The profit share has multiple tiers--we are entitled to 50% of profits from the first $200 million of U.S. actual sales, decreasing to 30% of profits 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 our option to co-promote in the U.S. We will provide up to 25% of the total sales force for cobimetinib in the U.S. if commercialized, and will call on customers and otherwise engage in promotional activities using that sales force, consistent with the terms of the co-development agreement and a co-promotion agreement to be entered into by the parties. If Genentech terminates the co-development agreement without cause, all licenses that were granted to Genentech under the agreement terminate and revert to us. Additionally, we would receive, subject to certain conditions, licenses from Genentech to research, develop and commercialize reverted product candidates.

We did not any recognize any revenue under our current agreement with Genentech during the three years ended December 31, 2013.

Other Collaborations

We have established collaborations with other leading pharmaceutical and biotechnology companies, including GlaxoSmithKline, 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. Pursuant to these collaborations, we have out-licensed compounds or programs to a partner for further development and commercialization, have no further development cost obligations related to such compounds or programs and may be entitled to receive contingent payments and royalties or a share of profits from commercialization. Several of these out-licensed compounds are in multiple phase 2 studies. These partnered compounds could potentially be of significant value to us if their development progresses successfully.

With respect to these partnered compounds, we are eligible to receive potential contingent payments under our collaborations totaling approximately $2.4 billion in the aggregate on a non-risk adjusted basis, of which approximately 10% are related to clinical development milestones, approximately 41% are related to regulatory milestones and approximately 49% are related to commercial milestones, all to be achieved by the various licensees.

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. The collaboration involved three agreements: (1) a product development and commercialization agreement, (2) a stock purchase and stock issuance agreement and (3) a loan and security agreement. During the term of the collaboration, we received $65.0 million in upfront and milestone payments, $85.0 million in research and development funding and loans in the principal amount of $85.0 million. In connection with the collaboration, GlaxoSmithKline purchased a total of three million shares of our common stock.

In October 2008, the development term under the collaboration concluded as scheduled. Under the terms of the collaboration, GlaxoSmithKline had the right to select up to two of the compounds in the collaboration for further development and commercialization. GlaxoSmithKline selected foretinib (XL880), an inhibitor of MET and VEGFR2, and had the right to choose one additional compound from a pool of compounds, which consisted of cabozantinib, XL281, XL228, XL820 and XL844 as of the end of the development term.

In July 2008, we achieved proof-of-concept for cabozantinib and submitted the corresponding data report to GlaxoSmithKline. In October 2008, GlaxoSmithKline notified us in writing that it decided not to select cabozantinib for further development and commercialization and that it waived its right to select XL281, XL228, XL820 and XL844 for further development and commercialization. As a result, we retained the rights to develop, commercialize, and/or license all of the compounds, subject to payment to GlaxoSmithKline of a 3% royalty on net sales of any product incorporating cabozantinib. We have discontinued development of XL820, XL228 and XL844.

GlaxoSmithKline continues to develop foretinib (XL880), and as disclosed on ClinicalTrials.gov, is currently recruiting patients into phase 1/2 trials studying the activity of foretinib in metastatic breast cancer both as a single agent

(NCT01147484) and in combination with lapatinib (NCT01138384), and in NSCLC as a single agent and in combination with erlotinib (NCT02034097).

In connection with the sales of COMETRIQ, during the year ended December 31, 2013 we recorded $0.4 million in royalty expense, which is included in Cost of Goods Sold on our Consolidated Statements of Operations. We did not recognize any revenue under our agreement with GlaxoSmithKline during the three years ended December 31, 2013.

The $85.0 million loan we received from GlaxoSmithKline was repayable in three annual installments. We paid the final installment of principal and accrued interest under the loan in shares of our common stock on October 27, 2011 and GlaxoSmithKline subsequently released its related security interest in certain of our patents.

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. In November 2010 we received a nonrefundable upfront cash payment of $5.0 million from Bristol-Myers Squibb. Additionally, 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 $255.0 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. The collaboration agreement was amended and restated in April 2011 in connection with an assignment of patents to a wholly-owned subsidiary.

Under the terms of the collaboration agreement, we were responsible for activities related to the discovery, optimization and characterization of the ROR antagonists during the collaborative research period. In July 2011, we earned a $2.5 million milestone payment for achieving certain lead optimization criteria. The collaborative research period began on October 8, 2010 and ended on July 8, 2013. Since the end of the collaborative research period, 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.

Bristol-Myers Squibb may, at any time, terminate the collaboration agreement upon certain prior notice to us on a product-by-product and country-by-country basis. In addition, either party may terminate the agreement for the other party’s uncured material breach. In the event of termination by Bristol-Myers Squibb at will or by us for Bristol-Myers Squibb’s uncured material breach, the license granted to Bristol-Myers Squibb would terminate, the right to such product would revert to us and we would receive a royalty-bearing license for late-stage reverted compounds and a royalty-free license for early-stage reverted compounds from Bristol-Myers Squibb to develop and commercialize such product in the related country. In the event of termination by Bristol-Myers Squibb for our uncured material breach, Bristol-Myers Squibb would retain the right to such product, subject to continued payment of milestones and royalties.

We recognized license and contract revenues of $1.5 million, $2.9 million and $2.8 million during the years ended December 31, 2013, 2012 and 2011, respectively, under our ROR collaboration agreement with Bristol-Myers Squibb.

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, including BMS-852927 (XL041). During the research term, we jointly identified drug candidates with Bristol-Myers Squibb that were ready for IND-enabling studies. After the selection of a drug candidate for further clinical development by Bristol-Myers Squibb, Bristol-Myers Squibb agreed to be solely responsible for further preclinical development as well as clinical development, regulatory, manufacturing and sales/marketing activities for the selected drug candidate. We do not have rights to reacquire the drug candidates selected by Bristol-Myers Squibb. 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. BMS has terminated development of XL041 and we have been advised that BMS is continuing additional preclinical research on the program. The collaboration agreement was amended and restated in April 2011 in connection with an assignment of patents to a wholly-owned subsidiary.

Under the collaboration agreement, Bristol-Myers Squibb paid us a nonrefundable upfront cash payment in the amount of $17.5 million and was obligated to provide research and development funding of $10.0 million per year for an initial research period of two years. In September 2007, the collaboration was extended at Bristol-Myers Squibb’s request through January 12, 2009, and in November 2008, the collaboration was further extended at Bristol-Myers Squibb’s request through January 12, 2010. 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. In connection with the extension of the collaboration through January 2009 and subsequently through January 2010, Bristol-Myers Squibb paid us additional research funding of approximately $7.7 million and approximately $5.8 million, respectively. In December 2007, we received $5.0 million in connection with the achievement by Bristol-Myers Squibb, of a development milestone with respect to BMS-852927 (XL041).

We did not any recognize any revenue under our LXR collaboration agreement with Bristol-Myers Squibb during the three years ended December 31, 2013.

Terminated Agreements

During 2013 and 2011, a number of additional license and collaboration agreements with Bristol-Myers Squibb were terminated or concluded, including a October 2010 license agreement for our small-molecule TGR5 agonist program, a December 2008 collaboration to develop and commercialize cabozantinib and XL281 (BMS-908662), a RAF inhibitor, and a January 2007 agreement to discover, develop and commercialize novel targeted therapies for the treatment of cancer. As a result of the termination, Bristol-Myers Squibb’s license relating to cabozantinib terminated and its rights to cabozantinib reverted to us, and we received, subject to certain terms and conditions, licenses from Bristol-Myers Squibb to research, develop and commercialize cabozantinib. We have no continuing obligations under these terminated agreements.

We recognized license and contract revenues of $14.8 million, $28.4 million and $168.9 million during the years ended December 31, 2013, 2012 and 2011, respectively, 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. In connection with the effectiveness of the license and collaboration, on July 20, 2009, we received upfront payments of $140.0 million ($120.0 million for the license and $20.0 million for the collaboration), less applicable withholding taxes of $7.0 million, for a net receipt of $133.0 million. We received a refund payment in December 2011 with respect to the withholding taxes previously withheld.

Under the license agreement, Sanofi received a worldwide exclusive license to SAR245408 (XL147) and SAR245409 (XL765), which are in phase 1, phase 1b/2 and phase 2 clinical trials, and has sole responsibility for all subsequent clinical, regulatory, commercial and manufacturing activities. Sanofi is responsible for funding all development activities with respect to SAR245408 (XL147) and SAR245409 (XL765), including our activities. Following the effectiveness of the license agreement, we conducted the majority of the clinical trials for SAR245408 (XL147) and SAR245409 (XL765) at the expense of Sanofi. As provided for under the license agreement, however, the parties transitioned all development activities for these compounds to Sanofi in 2011. As disclosed on ClinicalTrials.gov, SAR245408 (XL147) is currently being studied in a clinical trial evaluating pharmacokinetics of a tablet formulation in patients with solid tumors or lymphoma (NCT01943838). As disclosed on ClinicalTrials.gov, SAR245409 (XL765) is currently being studied in clinical trials in patients with lymphoma either as a single agent (NCT01403636) or in combination with bendamustine and/or rituximab (NCT01410513). In addition SAR245409 (XL765) is being studied in combination with a MEK inhibitor in patients with locally advanced or metastatic solid tumors (NCT01390818).

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.

Sanofi may, upon certain prior notice to us, terminate the license as to products containing SAR245408 (XL147) and SAR245409 (XL765). In the event of such termination election, Sanofi’s license relating to such product would terminate and revert to us, and we would receive, subject to certain terms, conditions and potential payment obligations, licenses from Sanofi to research, develop and commercialize such products.

In December 2011, we and Sanofi entered into an agreement pursuant to which the parties terminated the discovery collaboration agreement and released each other from any potential liabilities arising under the collaboration agreement prior to effectiveness of the termination in December 2011. Each party retains ownership of the intellectual property that it generated under the collaboration agreement, and we granted Sanofi covenants not-to-enforce with respect to certain of our intellectual property rights. The termination agreement also provided that Sanofi would make a payment to us of $15.3 million, which we received in January 2012. If either party or its affiliate or licensee develops and commercializes a therapeutic product containing an isoform-selective PI3K inhibitor that arose from such party’s work (or was derived from such work) under the collaboration agreement, then such party will be obligated to pay royalties to the other party based upon the net sales of such products. The termination agreement provides that Sanofi will make a one-time payment to us upon the first receipt by Sanofi or its affiliate or licensee of marketing approval for the first therapeutic product containing an isoform-selective PI3K inhibitor that arose from Sanofi’s work (or was derived from such work) under the collaboration agreement.

We recognized license, contract and collaboration reimbursement revenues of $113.9 million during the year ended December 31, 2011 under our collaboration agreement with Sanofi. We did not any recognize any revenue during the years ended December 31, 2013 or 2012.

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.

Merck paid us an upfront cash payment of $12.0 million in January 2012 in connection with the agreement. We will be eligible to receive payments associated with the successful achievement of potential development and regulatory milestones for multiple indications of up to $239.0 million. We will also be eligible to receive payments for combined sales performance milestones 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.

Merck may at any time, upon specified prior notice to us, terminate the license. In addition, either party may terminate the agreement for the other party’s uncured material breach. In the event of termination by Merck at will or by us for Merck’s uncured material breach, the license granted to Merck would terminate. In the event of a termination by us for Merck’s uncured material breach, we would receive a royalty-free license from Merck to develop and commercialize certain joint products. In the event of termination by Merck for our uncured material breach, Merck would retain the licenses from us, and we would receive reduced royalties from Merck on commercial sales of products.

We recognized license revenues of $10.7 million and $1.3 million during the years ended December 31, 2012 and 2011, respectively, under our collaboration agreement with Merck. We did not any recognize any revenue during the year ended December 31, 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 (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.

Daiichi Sankyo paid us a nonrefundable upfront payment in the amount of $20.0 million and was obligated to provide research and development funding of $3.8 million over a 15-month research term. In June 2007, our collaboration agreement with Daiichi Sankyo was amended to extend the research term by six months over which Daiichi Sankyo was required to provide $1.5 million in research and development funding. In November 2007, the parties decided not to further extend the research term. For each product from the collaboration, we are also entitled to receive payments upon attainment of pre-specified development, regulatory and commercialization milestones. In December 2010, we received a milestone payment of $5.0 million in connection with an IND filing made by Daiichi Sankyo for CS-3150 (XL550) and, in August 2012, we received a milestone of $5.5 million in connection with the initiation of a phase 2 clinical trial for CS-3150 (XL550). We are eligible to receive additional development, regulatory and commercialization milestones 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. Daiichi Sankyo may terminate the agreement upon 90 days’ written notice in which case Daiichi Sankyo’s payment obligations would cease, its license relating to compounds that modulate MR would terminate and revert to us and we would receive, subject to certain terms and conditions, licenses from Daiichi Sankyo to research, develop and commercialize compounds that were discovered under the collaboration.

We recognized contract revenues of $5.5 million during the year ended December 31, 2012 under our collaboration agreement with Daiichi Sankyo. We did not any recognize any revenue during the years ended December 31, 2013 or 2011.

Disposition of Artemis Pharmaceuticals	12 Months Ended
Disposition of Artemis Pharmaceuticals	Dec. 31, 2013
Discontinued Operations and Disposal Groups [Abstract]
Disposition of Artemis Pharmaceuticals	DISPOSITION OF ARTEMIS PHARMACEUTICALS In November 2007 we entered into a share sale and transfer agreement with Taconic Farms, Inc., (“Taconic”), pursuant to which Taconic acquired from us, for $19.8 million in cash, 80.1% of the outstanding share capital in our wholly-owned subsidiary, Artemis Pharmaceuticals GmbH (“Artemis”), located in Cologne, Germany. Subsequent to the transaction, Artemis was renamed TaconicArtemis GmbH. In September 2011 we exercised our right to sell our remaining 19.9% interest in Artemis to Taconic. We received $3.0 million in consideration of our remaining 19.9% interest in December 2011, and we recognized a gain of $2.3 million after consideration of the impact of foreign currency exchange rates and the write off of the carrying value of our investment in Artemis.

The entire disclosure for the facts and circumstances leading to the completed or expected disposal, manner and timing of disposal, the gain (loss) recognized in the income statement and the income statement caption that includes that gain (loss), amounts of revenues and pretax profit or loss reported in discontinued operations, the segment in which the disposal group was reported, and the classification (whether sold or classified as held for sale) and carrying value of the assets and liabilities comprising the disposal group. Includes all disposal groups, including those classified as components of the entity (discontinued operations).

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Reference 3: http://www.xbrl.org/2003/role/presentationRef
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Reference 6: http://www.xbrl.org/2003/role/presentationRef
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Investments, Debt and Equity Securities [Abstract]

Restructurings

12 Months Ended

Dec. 31, 2013

Restructuring Charges [Abstract]

Restructurings

RESTRUCTURINGS

Between March 2010 and May 2013, we implemented five restructurings, which we refer to collectively as the Restructurings, as a consequence of our decision to focus our proprietary resources and development efforts on the development and commercialization of cabozantinib and strategy to manage costs. The aggregate reduction in headcount from the Restructurings was 429 employees. We recorded charges and credits related to the Restructurings in periods other than those in which the Restructurings were implemented as a result of sublease activities for 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.

We have recorded aggregate restructuring charges of $53.3 million from inception through December 31, 2013 in connection with the Restructurings, of which $29.2 million related to facility charges, $21.7 million related to termination benefits, $2.3 million related to the impairment of excess equipment and other assets, and an additional minor amount related to legal and other fees. Asset impairment charges, net were partially offset by cash proceeds of $2.7 million from the sale of such assets.

For the years ended December 31, 2013, 2012, and 2011 we recorded restructuring charges of $1.2 million, $9.2 million, and $10.1 million, respectively, which related primarily to termination benefits and facility charges in connection with the exit of portions of certain of our buildings in South San Francisco.

The total outstanding restructuring liability related to the Restructurings is included in current and long-term portion of restructuring on our Consolidated Balance Sheets. The components and changes of these liabilities during the annual periods from inception of the restructuring activities through December 31, 2013 are summarized in the following table (in thousands):



	Employee Severance And Other Benefits			Facility Charges			Asset Impairment			Legal and Other Fees			Total
Restructuring charge	$	17,677		$	11,814		$	3,173		$	80		$	32,744
Cash payments	(10,528		)	(3,739		)	—			(10		)	(14,277		)
Adjustments or non-cash credits including stock compensation expense	(1,626		)	613			(3,341		)	—			(4,354		)
Proceeds from sale of assets	—			—			168			—			168
Ending accrual balance as of December 31, 2010	5,523			8,688			—			70			14,281
Restructuring charge	2,566			8,480			(907		)	(3		)	10,136
Cash payments	(7,366		)	(3,469		)	—			(16		)	(10,851		)
Adjustments or non-cash credits including stock compensation expense	(717		)	222			(619		)	—			(1,114		)
Proceeds from sale of assets	—			—			1,526			—			1,526
Ending accrual balance as of December 31, 2011	6			13,921			—			51			13,978
Restructuring charge	970			8,276			(47		)	(28		)	9,171
Cash payments	(965		)	(5,299		)	—			(3		)	(6,267		)
Adjustments or non-cash credits including stock compensation expense	(11		)	2,304			(891		)	—			1,402
Proceeds from sale of assets	—			—			938			—			938
Restructuring liability as of December 31, 2012	—			19,202			—			20			19,222
Restructuring charge (credit)	496			662			88			(15		)	1,231
Cash payments	(434		)	(6,331		)	—			—			(6,765		)
Adjustments or non-cash credits including stock compensation expense	(55		)	(73		)	(183		)	—			(311		)
Proceeds from sale of assets	—			—			95			—			95
Restructuring liability as of December 31, 2013	$	7		$	13,460		$	—		$	5		$	13,472

We expect to pay accrued facility charges of $13.5 million, net of cash received from our subtenants, through the end of our lease terms of the buildings, the last of which ends in 2017. With respect to our Restructurings, we expect to incur additional restructuring charges of approximately $0.9 million which relate to the exit, in prior periods, of certain of our South San Francisco buildings. These charges will be recorded through the end of the building lease terms, the last of which ends in 2017.

The Restructurings have resulted in aggregate cash expenditures of $35.4 million, net of $10.2 million in cash received from subtenants and $2.7 million in cash received in connection with the sale of excess equipment and other assets. Net cash expenditures for the Restructurings were $6.7 million, $5.3 million and $9.3 million for the years ended December 31, 2013, 2012, and 2011, respectively.

The restructuring charges that we expect to incur in connection with the Restructurings are subject to a number of assumptions, and actual results may materially differ. We may also incur other material charges not currently contemplated due to events that may occur as a result of, or associated with, the Restructurings.

Cash and Investments

12 Months Ended

Dec. 31, 2013

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, 2013 and 2012 (in thousands):



	December 31, 2013
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
As reported:
Cash and cash equivalents	$	103,978	$	—	$	—		$	103,978
Short-term investments	138,403		94		(22		)	138,475
Short-term restricted cash and investments	12,173		40		—			12,213
Long-term investments	144,226		106		(33		)	144,299
Long-term restricted cash and investments	16,837		60		—			16,897
Total cash and investments	$	415,617	$	300	$	(55	)	$	415,862



	December 31, 2012
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
As reported:
Cash and cash equivalents	$	170,070	$	—	$	(1	)	$	170,069
Short-term investments	241,391		46		(66		)	241,371
Short-term restricted cash and investments	12,242		4		—			12,246
Long-term investments	182,407		28		(124		)	182,311
Long-term restricted cash and investments	27,943		21		—			27,964
Total cash and investments	$	634,053	$	99	$	(191	)	$	633,961

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, 2013 and 2012 were $83.7 million and $87.0 million, respectively and are reflected in our Consolidated Balance Sheets in Short- and Long-term investments. See “Note 8 - 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, 2013 and 2012. The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	December 31, 2013
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	24,813	$	—	$	—		$	24,813
Commercial paper	94,682		—		—			94,682
Corporate bonds	239,937		190		(55		)	240,072
U.S. Treasury and government sponsored enterprises	44,284		102		—			44,386
Municipal bonds	6,005		8					6,013
Total investments	$	409,721	$	300	$	(55	)	$	409,966



	December 31, 2012
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	76,048	$	—	$	—		$	76,048
Commercial paper	167,223		10		—			167,233
Corporate bonds	222,106		30		(187		)	221,949
U.S. Treasury and government sponsored enterprises	132,933		59		(1		)	132,991
Municipal bonds	30,047		—		(3		)	30,044
Total investments	$	628,357	$	99	$	(191	)	$	628,265

There were no gains or losses on the sales of investments during the years ended December 31, 2013, 2012 and 2011.

All of our investments are subject to a quarterly impairment review. During the year ended December 31, 2013 and 2012, we did not record any other-than-temporary impairment charges on our available-for-sale securities. As of December 31, 2013, there were 38 investments in an unrealized loss position with an aggregate fair value $65.3 million. All of investments in an unrealized loss position are corporate bonds. All investments in an unrealized loss position have been so for less than one year and 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, 2013 (in thousands):



	Mature within One Year		After One Year through Two Years		Fair Value
Money market funds	$	24,813	$	—	$	24,813
Commercial paper	94,682		—		94,682
Corporate bonds	155,290		84,782		240,072
U.S. Treasury and government sponsored enterprises	32,216		12,170		44,386
Municipal bonds	—		6,013		6,013
Total	$	307,001	$	102,965	$	409,966

Cash is 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, 2013

Inventory Disclosure [Abstract]

Inventory

INVENTORY

Inventory consists of the following (in thousands):



	December 31,
	2013
Raw materials	$	529
Work in process	2,280
Finished goods	81
Total	$	2,890

We received regulatory approval for our first product, COMETRIQ, on November 29, 2012. As of December 31, 2012, our recorded inventory balance was $0 as we did not incur any costs that would be recorded as inventory subsequent to the receipt of regulatory approval and prior to year end.

Property And Equipment

12 Months Ended

Dec. 31, 2013

Property, Plant and Equipment [Abstract]

Property And Equipment

PROPERTY AND EQUIPMENT

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



	December 31,
	2013			2012
Laboratory equipment	$	15,453		$	19,504
Computer equipment and software	14,462			11,897
Furniture and fixtures	3,691			3,230
Leasehold improvements	17,031			16,572
Construction-in-progress	68			1,409
	50,705			52,612
Less: accumulated depreciation and amortization	(45,795		)	(46,553		)
Property and equipment, net	$	4,910		$	6,059

For the years ended December 31, 2013, 2012 and 2011, we recorded depreciation expense of $3.1 million, $4.8 million and $6.8 million, respectively.

In 2013, 2012 and 2011, we recorded gross asset impairment charges in the amounts of approximately $0.1 million, $0.3 million and $0.5 million, respectively, in connection with the Restructurings. The amount recorded as a restructuring charge for asset impairment, as presented in “Note 4 - Restructurings,” was net of the gain on the sale of such assets. In 2012 and 2011, the gain on the sale of such assets was $0.3 million and $1.4 million, respectively. There were no such gains in 2013. Cash proceeds on those sales were $0.1 million, $0.9 million and $1.5 million during 2013, 2012 and 2011, respectively.

Debt

12 Months Ended

Dec. 31, 2013

Debt Disclosure [Abstract]

Debt

DEBT

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



	December 31,
	2013			2012
Convertible Senior Subordinated Notes due 2019	$	165,296		$	149,800
Secured Convertible Notes due 2015	99,851			100,676
Silicon Valley Bank term loan	80,000			80,000
Silicon Valley Bank line of credit	2,090			5,260
Total debt	347,237			335,736
Less: current portion	(11,762		)	(13,170		)
Long-term debt	$	335,475		$	322,566

Convertible Senior Subordinated Notes due 2019 and Related Concurrent Offering of Our Common Stock

On August 14, 2012, we issued and sold $287.5 million aggregate principal amount of 4.25% convertible senior subordinated notes due 2019 (the “2019 Notes”). On that date we completed concurrent registered underwritten public offerings in which we sold the 2019 Notes and 34.5 million shares of common stock at a price of $4.25 per share, generating aggregate net proceeds of $416.1 million. The convertible debt offering resulted in net proceeds of $277.7 million after deducting the underwriting discount and offering expenses of $9.3 million and $0.5 million, respectively. The equity offering resulted in net proceeds of $138.4 million after deducting the underwriting discount of $7.7 million and other expenses of $0.5 million.

The 2019 Notes were issued pursuant to an indenture, as supplemented by a supplemental indenture with Wells Fargo Bank, National Association, as trustee (the “Trustee”), and mature on August 15, 2019, unless earlier converted, redeemed or repurchased. The 2019 Notes bear interest at the 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 2019 Notes is equivalent to a conversion price of approximately $5.31 per share of common stock. The conversion rate is subject to adjustment upon the occurrence of 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 connection with the offering of the 2019 Notes, $36.5 million of the proceeds were deposited into an escrow account which contains 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, 2013, we have used $12.3 million of the amounts held in the escrow account to pay the required semi-annual interest payments. The short- and long-term amounts held in the escrow account as of December 31, 2013 were $12.2 million and $16.9 million, respectively, and are included in short- and long-term restricted cash and investments. We have pledged our interest in the escrow account to the Trustee as security for our obligations under the 2019 Notes.

The 2019 Notes are accounted for in accordance with ASC Subtopic 470-20, Debt with Conversion and Other Options. Under ASC Subtopic 470-20, issuers of certain convertible debt instruments that have a net settlement feature and may be settled in cash upon conversion, including partial cash settlement, are required to separately account for the liability (debt) and equity (conversion option) components of the instrument. The carrying amount of the liability component of any outstanding debt instrument is computed by estimating the fair value of a similar liability without the conversion option. The amount of the equity component is then calculated by deducting the fair value of the liability component from the principal amount of the convertible debt instrument. The effective interest rate used in determining the liability component of the 2019 Notes was 10.09%. This resulted in the recognition of $144.3 million as the liability component and the residual $143.2 million as the debt discount with a corresponding increase to paid-in capital, the equity component, for the 2019 Notes. The underwriting discount of $9.3 million and offering expenses of $0.5 million were allocated between debt issuance costs and equity issuance costs in proportion to the allocation of the proceeds. Debt issuance costs of $4.9 million are included in Other long term assets on our Consolidated Balance Sheets as of the issuance date. Equity issuance costs of $4.9 million related to the convertible debt offering were recorded as an offset to additional paid-in capital.

The following is a summary of the liability component of the 2019 Notes as of December 31, 2013 and 2012 (in thousands):



	December 31,
	2013		2012
Net carrying amount of the liability component	$	165,296	$	149,800
Unamortized discount of the liability component	122,204		137,700
Principal amount of the 2019 Notes	$	287,500	$	287,500

The debt discount and debt issuance costs will be amortized as interest expense through August 15, 2019. During the years ended December 31, 2013 and 2012 total interest expense for the 2019 Notes was $28.4 million, and $10.3 million, respectively, including stated coupon interest of $12.2 million and $4.6 million, respectively, and the amortization of the debt discount and debt issuance costs of $16.2 million and $5.7 million, respectively. The balance of unamortized fees and costs was $4.0 million and $4.7 million as of December 31, 2013 and 2012, respectively, which is recorded in the accompanying Consolidated Balance Sheet as Other assets.

Secured Convertible Notes due June 2015

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 initial principal amount our Secured Convertible Notes due July 1, 2015 (the “Deerfield Notes”) for an aggregate purchase price of $80.0 million, less closing fees and expenses of approximately $2.0 million. As of December 31, 2013 and 2012, the remaining outstanding principal balance on the Deerfield Notes was $114.0 million and $124.0 million, respectively. We refer to the Original Deerfield Purchasers and the New Deerfield Purchasers (identified below) collectively as Deerfield.

The outstanding principal amount of the Deerfield Notes bears interest in the annual amount of $6.0 million, payable quarterly in arrears. During the years ended December 31, 2013, 2012, and 2011, total interest expense for the Deerfield Notes was $16.1 million, $15.9 million, and $14.3 million, respectively, including the stated coupon rate and the amortization of the debt discount and debt issuance costs. The non-cash expense relating to the amortization of the debt discount and debt issuance costs were $10.1 million, $9.9 million, and $8.3 million, respectively, during those periods. The balance of unamortized fees and costs was $1.4 million and $2.3 million as of December 31, 2013 and 2012, respectively, which is recorded in the Consolidated Balance Sheet as Other assets.

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 further amended to provide us with an option to extend the maturity date of our indebtedness under the note purchase agreement to July 1, 2018. Under the terms of the extension option, we have the right to require Deerfield Partners, L.P. and Deerfield International Master Fund, L.P., (the “New Deerfield Purchasers”), to acquire $100 million principal amount of the Deerfield Notes and extend the maturity date thereof to July 1, 2018. We are under no obligation to exercise the extension option. To exercise the extension option, we must provide a notice of exercise to Deerfield prior to March 31, 2015. If we exercise the extension option, the Deerfield Notes would mature on July 1, 2018 and bear interest on and after July 2, 2015 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.

In each of January 2014 and 2013, we made mandatory prepayments of $10.0 million on the Deerfield Notes. We will be required to make an additional mandatory prepayment on the Deerfield Notes in 2015 equal to 15% of certain revenues from collaborative arrangements (“Development/Commercialization Revenue”) received during the prior fiscal year, subject to a maximum prepayment amount of $27.5 million. There is no minimum prepayment due in 2015. Our obligation to make annual mandatory prepayments equal to 15% of Development/Commercialization Revenue received by us during the prior fiscal year will apply in each of 2016, 2017 and 2018 if we exercise the extension option. However, we will only be obligated to make any such annual mandatory prepayment after exercise of the extension option if the New Deerfield Purchasers provide notice to us of their election to receive the prepayment. 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).

As a result of the January 2014 amendment, 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. Under the note purchase agreement as amended, we may voluntarily prepay the principal amount of the Deerfield Notes as follows (the amount at which we repay in each case below is referred to as the Prepayment Price):

•

Prior to July 1, 2015: we may prepay all of the principal amount of the Deerfield Notes at any time at a prepayment price equal to the outstanding principal amount, plus accrued and unpaid interest through the date of such prepayment, plus all interest that would have accrued on the principal amount of the Deerfield Notes between the date of such prepayment and the applicable maturity date of the Deerfield Notes if the outstanding principal amount of the Deerfield Notes as of such prepayment date had remained outstanding through the applicable maturity date, plus all other accrued and unpaid obligations; and

•

If we exercise the extension option: we may 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 our company, 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, Deerfield may declare all or a portion of the Prepayment Price to be immediately due and payable.

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 (the “2014 Deerfield Warrants”) to purchase an aggregate of 1,000,000 shares of our common stock at an exercise price of $9.70 per share. If we exercise the extension option, the exercise price will be reset to the lower of (x) the existing exercise price and (y) 120% of the volume weighted average price of our common stock for the ten trading days immediately following the date of such extension election. The 2014 Deerfield Warrants are exercisable for a term of two years, subject to a two year extension if we exercise the extension option, and contain certain limitations that prevent the holder of the 2014 Deerfield Warrants from acquiring shares upon exercise of a Warrant 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. The number of shares for which the 2014 Deerfield Warrants are exercisable and the associated exercise prices are subject to certain adjustments as set forth in the 2014 Deerfield Warrants. In addition, upon certain changes in control of our company, to the extent the 2014 Deerfield Warrants are not assumed by the acquiring entity, or upon certain defaults under the 2014 Deerfield Warrants, the holder has the right to net exercise the 2014 Deerfield 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 Deerfield Warrants.

In connection with the issuance of the 2014 Deerfield Warrants, we entered into a registration rights agreement with Deerfield, pursuant to which we agreed to file, no later than February 21, 2014, a registration statement with the Securities and Exchange Commission (“SEC”) covering the resale of the shares of common stock issuable upon exercise of the 2014 Deerfield 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

The outstanding principal obligation under the Silicon Valley Bank Loan and Security Agreement, as amended, was $82.1 million and $85.3 million as of December 31, 2013 and 2012, respectively.

Silicon Valley Bank Line of Credit

In December 2007, we entered into a loan modification agreement to a loan and security agreement originally entered into in May 2002 with Silicon Valley Bank. The terms associated with the original line of credit under the May 2002 agreement and the subsequent loan modifications were not modified. The December 2007 loan modification agreement provides for an additional equipment line of credit in the amount of up to $30.0 million with a draw down period of approximately two years (the “Line of Credit”). Each advance must be repaid in 48 equal, monthly installments of principal, plus accrued interest, at an annual rate of 0.75% fixed. In December 2009, we amended the agreement and extended the draw down period on the Line-of-Credit for an additional 18 months through June 2011 and increased the available principal amount under the line of credit from $30.0 million to $33.6 million. Pursuant to the terms of the amendment, we were required to make minimum draws of $2.5 million every 6 months through June 2011, for total additional draws of $7.5 million. The loan facility requires security for the Line of Credit in the form of a non-interest bearing certificate of deposit account with the bank, in an amount equal to at least 100% of the outstanding obligations under the line of credit. In June 2008, we drew down $13.6 million under this agreement, in December 2009, we drew down $5.0 million, and we drew down an additional $2.5 million in each of June 2010, December 2010 and June 2011 in accordance with the terms of the modified agreement. In accordance with the amended loan terms, the Line of Credit has expired and we have no further draw down obligations under the line of credit. The outstanding principal obligation under the Silicon Valley Bank Line of Credit was $2.1 million and $5.3 million as of December 31, 2013 and 2012, respectively.

Silicon Valley Bank Term Loan

In June 2010, we amended our loan and security agreement with Silicon Valley Bank to provide for a new seven-year term loan in the amount of $80.0 million. 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. We are required to maintain at all times on deposit in one or more non-interest bearing demand deposit accounts with Silicon Valley Bank or one of its affiliates a compensating balance, constituting support for the obligations under the term loan, with a principal balance in value equal to at least 100% of the outstanding principal balance of the term loan.

In August 2011, we amended our term loan agreement to allow for the compensating balance to be maintained on deposit in one or more investment accounts with Silicon Valley Bank or one of its affiliates. This compensating balance is to have a value equal to at least 100%, but not to exceed 107%, of the outstanding principal balance of the term loan and all lines of credit associated with Silicon Valley Bank. We are entitled to retain income earned on the amounts maintained in such investment account(s). 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, 2013 and 2011 was $83.7 million and $87.0 million, respectively, and is reflected in our Consolidated Balance Sheet in Short- and 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 expected future principal payments of our debt were as follows as of December 31, 2013 (in thousands):



Year Ending December 31, (1)
2014	$	11,762
2015	104,328
2016	—
2017	80,000
2018	—
Thereafter	287,500

____________________

(1)

Amounts include principal payments associated with the accretion of discounts and debt issuance costs. For the Deerfield Notes, this table is presented based the actual minimum mandatory prepayment we made in January 2014 as required by the note purchase agreement and assuming we do not make the election to extend the maturity of those notes and the remaining principal balance will be paid at the current July 2015 maturity date. The actual timing of payments made may differ materially.

Common Stock And Warrants

12 Months Ended

Dec. 31, 2013

Warrants and Rights Note Disclosure [Abstract]

Common Stock And Warrants

COMMON STOCK AND WARRANTS

Sale of Shares of Common Stock

In March 2011, we completed a registered public offering of 17.3 million shares of our common stock at a price of $11.00 per share pursuant to a shelf registration statement previously filed with the SEC, which the SEC declared effective on May 8, 2009. We received approximately $179.4 million in net proceeds from the offering after deducting the underwriting discount and related offering expenses.

In February 2012, we completed a registered public offering of 12.7 million shares of our common stock at a price of $5.17 per share pursuant to a shelf registration statement previously filed with the SEC, which the SEC declared effective on May 8, 2009. We received $65.0 million in net proceeds from the offering after deducting the underwriting discount and related offering expenses.

In August 2012, we completed a registered underwritten public offering of 34.5 million shares of our common stock at a price of $4.25 per share pursuant to a shelf registration statement previously filed with the SEC, which the SEC declared effective on June 8, 2012. We received $138.4 million in net proceeds after deducting the underwriting discount of $7.7 million and related offering expenses of $0.5 million. Concurrent with the issuance of the common stock, we sold $287.5 million aggregate principal amount of the Convertible Senior Subordinated Notes due 2019 pursuant to the same registered public offering. See “Note 8 - Debt” for more information regarding the 2019 Notes.

In January 2014, subsequent to date of these financial statements, we completed a registered underwritten public offering of 10.0 million 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 approximately $75.6 million in net proceeds from the offering after deducting the underwriting discount and related offering expenses. We also granted the underwriter a 30-day option to purchase up to an additional 1,500,000 shares of common stock in connection with the offering which will expire on February 22, 2014.

Conversion of Debt into Common Stock

In October 2011, we elected to repay the third and final installment of an outstanding loan in shares of our common stock. The shares issued in connection with this repayment were valued at $6.66 per share, resulting in the issuance of 5,537,906 shares of our common stock as satisfaction in full of our remaining $36.9 million repayment obligation, including $8.0 million in accrued interest.

The 2019 Notes and the Deerfield Notes are, under certain circumstances, convertible into shares of our common stock. See “Note 8 - Debt” for more information regarding the conversion features of these instruments.

Warrants

At December 31, 2013, the following warrants to purchase common stock were outstanding and exercisable:



Date Issued	Exercise Price per Share		Expiration Date	Number of Shares
June 4, 2008	$	7.40	June 4, 2014	1,000,000
June 10, 2009	$	6.05	June 10, 2014	441,215
				1,441,215

The warrants issued in June 2008 were granted to Deerfield pursuant to a facility agreement that expired in 2009.

The warrants issued in June 2009 were granted to Symphony Evolution Holdings LLC, the parent company of Symphony Evolution, Inc., in connection with a financing transaction that terminated in June 2009. The rights to those warrants were subsequently transferred to other parties.

On January 22, 2014 we issued Deerfield 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 in connection with an amendment the note purchase agreement for the Deerfield Notes. The term and possibly the exercise price of the warrants will be change if we elect to exercise the extension option under the amendment. See “Note 8 - Debt” for further information on the warrants, possible changes to the warrant terms and the related amendments to the Deerfield Notes.

The warrants granted to Deerfield are Participating Securities, as defined in the glossary to the ASC. The warrant holders do not have a contractual obligation to share in our losses.

Fair Value Measurements

12 Months Ended

Dec. 31, 2013

Fair Value Disclosures [Abstract]

Fair Value Measurements

FAIR VALUE MEASUREMENTS

The following table sets forth the fair value of our financial assets that were measured and recorded on a recurring basis as of December 31, 2013 and 2012. We did not have any Level 3 investments during the periods presented. The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	December 31, 2013
	Level 1		Level 2		Total
Money market funds	$	24,813	$	—	$	24,813
Commercial paper	—		94,682		94,682
Corporate bonds	—		240,072		240,072
U.S. Treasury and government sponsored enterprises	—		44,386		44,386
Municipal bonds	—		6,013		6,013
Total	$	24,813	$	385,153	$	409,966



	December 31, 2012
	Level 1		Level 2		Total
Money market funds	$	76,050	$	—	$	76,050
Commercial paper	—		167,231		167,231
Corporate bonds	—		221,949		221,949
U.S. Treasury and government sponsored enterprises	—		132,991		132,991
Municipal bonds	—		30,044		30,044
Total	$	76,050	$	552,215	$	628,265

There were no transfers between any of the fair value hierarchies, as determined at the end of each reporting period.

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, 2013				December 31, 2012
	Carrying Amount		Fair Value		Carrying Amount		Fair Value
2019 Notes	$	165,296	$	339,883	$	149,800	$	280,111
Silicon Valley Bank Term Loan	$	80,000	$	79,946	$	80,000	$	79,542
Silicon Valley Bank Line of Credit	$	2,090	$	2,090	$	5,260	$	5,253

There is no practicable method to determine the fair value of the Deerfield Notes due to the unique structure of the instrument that was financed by entities affiliated with Deerfield and the current non-liquid market in structured notes. The carrying amounts of cash, other receivables, accounts payable and accrued clinical trial 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 that 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 fair value of the 2019 Notes is based on the average trading prices, which is a Level 2 input. The 2019 Notes are not carried at fair value and are shown at their initial fair value less unamortized discount; the portion of the value allocated to the conversion option is included in stockholders’ equity in the Consolidated Balance Sheets. See “Note 8 - Debt” for further information regarding the 2019 Notes.


•	We have estimated the fair value of our other debt instruments, where possible, using the net present value of the payments discounted at an interest rate that is consistent with money-market rates that would have been earned on our non-interest-bearing compensating balances, which is a Level 2 input.

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

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.

+ References + Details

Employee Benefit Plans

12 Months Ended

Dec. 31, 2013

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 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). On May 18, 2011, at the annual meeting of stockholders, the Exelixis, Inc. 2011 Equity Incentive Plan (the “2011 Plan”) was approved and adopted as the successor plan to the certain other equity incentive plans. Stock options issued under the 2011 Plan 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. Of the stock options outstanding as of December 31, 2013, 3,720,752 were granted subject to performance objectives tied to the achievement of clinical goals set by the Compensation Committee of our Board of Directors and will vest in full or part based on achievement of such goals. As of December 31, 2013, we expect that achievement of some of those performance objectives is probable and have, therefore, included stock-based compensation for such awards. We have not included any stock-based compensation expense for stock options with performance objectives where the performance goals cannot be reasonably assured of achievement. RSUs vest over a four year term; RSUs issued after September 29, 2011 vest annually and the remaining portion of unvested RSUs issued prior to September 29, 2011 vest 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 higher. 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, 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 $0.6 million, $0.4 million, and $0.7 million for the years ended December 31, 2013, 2012 and 2011, respectively. As of December 31, 2013, we had 2,040,839 shares available for grant under our ESPP. We issued 345,828 shares, 298,533 shares, and 375,305 shares of common stock during the years ended December 31, 2013, 2012 and 2011, respectively, pursuant to the ESPP at an average price per share of $4.13, $4.08 and $4.62, 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,
	2013		2012		2011
Research and development expense	$	6,021	$	4,536	$	5,935
General and administrative expense	5,948		4,245		5,459
Restructuring-related stock compensation expense	49		—		625
Total employee stock-based compensation expense	$	12,018	$	8,781	$	12,019

In addition, we recognized stock-based compensation expense of $0.1 million relating to non-employees in each of the years ended December 31, 2012 and 2011. Such expense was nominal for the year ended December 31, 2013.

We use the Black-Scholes Merton option pricing model to value our stock options. 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. The fair value of employee stock option awards and ESPP purchases was estimated using the following assumptions and weighted average fair values:



	Stock Options
	2013			2012			2011
Weighted average grant-date fair value	$	2.97		$	3.24		$	3.50
Risk-free interest rate	1.51		%	0.81		%	1.07		%
Dividend yield	—		%	—		%	—		%
Volatility	61		%	69		%	70		%
Expected life	5.6 years			5.6 years			5.5 years



	ESPP
	2013			2012			2011
Weighted average grant-date fair value	$	1.64		$	2.07		$	2.85
Risk-free interest rate	0.11		%	0.10		%	0.11		%
Dividend yield	—		%	—		%	—		%
Volatility	66		%	68		%	68		%
Expected life	6 months			6 months			6 months

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, 2010	19,630,030		$	7.52
Granted	2,545,625		$	5.86
Exercised	(2,161,804	)	$	5.75
Forfeited	(1,021,323	)	$	6.22
Expired	(1,556,150	)	$	12.13
Options outstanding at December 31, 2011	17,436,378		$	7.16
Granted	3,442,696		$	5.45
Exercised	(181,979	)	$	5.09
Forfeited	(358,360	)	$	5.88
Expired	(1,890,185	)	$	7.54
Options outstanding at December 31, 2012	18,448,550		$	6.85
Granted	6,694,174		$	5.44
Exercised	(13,311	)	$	5.06
Forfeited	(79,942	)	$	5.27
Expired	(1,066,196	)	$	6.45
Options outstanding at December 31, 2013	23,983,275		$	6.48	4.63 years	$	8,079
Exercisable at December 31, 2013	13,818,615		$	7.21	3.44 years	$	3,458

At December 31, 2013, a total of 1,709,233 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 2013 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, 2013. Total intrinsic value of options exercised was $4,000, $0.1 million, and $7.0 million during 2013, 2012 and 2011, respectively. Total fair value of employee options vested and expensed in 2013, 2012 and 2011 was $7.4 million, $5.6 million and $8.4 million, respectively.

The following table summarizes information about stock options outstanding and exercisable at December 31, 2013:



	Options Outstanding				Options Outstanding and Exercisable
Exercise Price Range	Number	Weighted Average Remaining Contractual Life	Weighted Average Exercise Price		Number of Exercisable	Weighted Average Exercise Price
$3.05 - $5.50	4,735,373	5.18 years	$	5.07	2,841,746	$	5.04
$5.51 - $5.63	10,369,851	5.25 years	$	5.55	3,004,560	$	5.62
$5.65 - $8.86	3,877,697	5.06 years	$	6.97	2,971,955	$	7.32
$8.88 - $12.10	5,000,354	2.50 years	$	9.34	5,000,354	$	9.34
	23,983,275	4.63 years	$	6.48	13,818,615	$	7.21

As of December 31, 2013, $17.1 million of total unrecognized compensation expense related to stock options is expected to be recognized over a weighted-average period of 2.62 years.

Cash received from option exercises and purchases under the ESPP in 2013 and 2012 was $1.5 million and $2.1 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, 2010	2,172,431		$	7.31
Awarded	356,498		$	6.17
Released	(648,437	)	$	7.43
Forfeited	(488,801	)	$	7.45
Awards outstanding at December 31, 2011	1,391,691		$	6.92
Awarded	733,958		$	5.50
Released	(596,397	)	$	7.15
Forfeited	(234,631	)	$	6.62
Awards outstanding at December 31, 2012	1,294,621		$	6.07
Awarded	1,119,733		$	5.45
Released	(517,874	)	$	6.60
Forfeited	(85,959	)	$	5.49
Awards outstanding at December 31, 2013	1,810,521		$	5.56	2.05 years	$	10,736

As of December 31, 2013, $7.3 million of total unrecognized compensation expense related to employee RSUs was expected to be recognized over a weighted-average period of 3.28 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. Beginning in 2002 through 2010, we matched 50% of the first 4% of participant contributions into the 401(k) Plan in the form of our common stock. Beginning in January 2011, 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 $0.8 million, $0.6 million, and $0.8 million related to the stock match for the years ended December 31, 2013, 2012 and 2011, respectively.

Income Taxes

12 Months Ended

Dec. 31, 2013

Income Tax Disclosure [Abstract]

Income Taxes

INCOME TAXES

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



	Year Ended December 31,
	2013			2012			2011
Domestic	$	(236,076	)	$	(147,538	)	$	76,992
Foreign	(8,780		)	—			—
Total	$	(244,856	)	$	(147,538	)	$	76,992

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



	Year Ended December 31,
	2013			2012		2011
Current:
Federal	$	—		$	32	$	636
State	12			75		659
Total current tax expense	12			107		1,295
Deferred:
Federal	(106		)	—		—
State	(2		)	—		—
Total deferred tax expense	(108		)	—		—
Income tax (benefit) provision	$	(96	)	$	107	$	1,295

The $0.1 million income tax benefit in 2013 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. $0.1 million and $0.6 million of the 2012 and 2011 income tax provision, respectively, related to an adjustment resulting from a further evaluation of qualified expenses for refunds received in 2009 and 2010 as a result of the enactment of the Housing and Economy Recovery Act of 2008 and the American Recovery and Reinvestment Tax Act of 2009. The remaining $0.7 million of the 2011 provision related to a tax deferred revenue adjustment that resulted in a state tax liability due to state net operating loss carryover limitations.

During 2013, 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,
	2013			2012			2011
U.S. federal income tax (benefit) provision at statutory rate	$	(83,251	)	$	(50,163	)	$	26,177
Unutilized net operating losses	(3,438		)	46,324			(29,650		)
Non-deductible interest	3,380			3,297			2,809
Stock-based compensation	393			504			627
State tax expense	10			74			660
Refundable tax credit	—			32			636
Available-for-sale investments	(106		)	—			—
Impact of intellectual property rights transfer	82,858			—			—
Other	58			39			36
Income tax (benefit) provision	$	(96	)	$	107		$	1,295

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,
	2013			2012
Deferred tax assets:
Net operating loss carry-forwards	$	358,372		$	374,200
Tax credit carry-forwards	64,635			65,232
Amortization of deferred stock compensation – non-qualified	24,279			26,469
Accruals and reserves not currently deductible	10,107			13,732
Deferred revenue	502			6,501
Book over tax depreciation and amortization	4,499			5,140
Total deferred tax assets	462,394			491,274
Valuation allowance	(421,426		)	(438,266		)
Net deferred tax assets	40,968			53,008
Deferred tax liabilities:
Convertible debt	(40,968		)	(53,008		)
Total deferred tax liabilities	(40,968		)	(53,008		)
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 decreased by $16.8 million, increased by $6.8 million, and decreased by $49.7 million during 2013, 2012 and 2011, respectively.

At December 31, 2013, we had federal net operating loss carry-forwards of approximately $988 million which expire in the years 2018 through 2032, 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 $918 million, which expire in the years 2014 through 2033, California research and development tax credits of approximately $25 million which have no expiration, and California Manufacturing Investment Credits of approximately $1 million that expire in 2014. Included in the federal and state carry-forwards is $15.7 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, 2013, 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 for the years ended December 31, 2013, 2012 and 2011 (in thousands):



	Year Ended December 31,
	2013			2012		2011
Beginning balance	$	47,298		$	39,310	$	46,381
(Decrease) increase relating to prior year provision	(112		)	5,894		(9,782		)
Increase relating to current year provision	7,891			2,094		2,711
Ending balance	$	55,077		$	47,298	$	39,310

Included in the balance of unrecognized tax benefits as of December 31, 2013, 2012 and 2011 are $0.1 million, $0.1 million and $0.1 million, respectively, of tax benefits that if recognized would affect the effective tax rate. All of our deferred tax assets are subject to a valuation allowance. As of December 31, 2013, 2012 and 2011, we had an accrued interest balance of $20,000, $15,000 and $9,000, respectively, related to tax contingencies. Interest expense related to those tax contingencies was $4,000, $6,000 and $9,000 during the years ended December 31, 2013, 2012 and 2011, respectively. 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, 2013 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 2012 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, 2013, there were no undistributed foreign earnings of our only non-U.S. subsidiary, Exelixis Bermuda.

Net (Loss) Income Per Share

12 Months Ended

Dec. 31, 2013

Earnings Per Share [Abstract]

Net (Loss) Income Per Share

NET (LOSS) INCOME PER SHARE

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



	Year Ended December 31,
	2013			2012			2011
Numerator:
Net (loss) income	$	(244,760	)	$	(147,645	)	$	75,697
Denominator:
Shares used in computing basic (loss) income per share amounts	184,062			160,138			126,018
Add effect of dilutive securities:
Shares issuable upon exercise of outstanding stock options	—			—			2,064
Shares issuable upon exercise of warrants	—			—			1,858
Shares issuable upon vesting of RSUs	—			—			515
Shares issuable upon purchase from ESPP contributions	—			—			24
Total dilutive securities	—			—			4,461
Shares used in computing diluted (loss) income per share amounts	184,062			160,138			130,479
Net (loss) income per share, basic	$	(1.33	)	$	(0.92	)	$	0.60
Net (loss) income per share, diluted	$	(1.33	)	$	(0.92	)	$	0.58

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,
	2013	2012	2011
2019 Notes	54,123	54,123	—
Outstanding stock options, unvested RSUs and ESPP contributions	21,401	16,568	9,085
Warrants	1,441	1,441	—
Total potentially dilutive shares	76,965	72,132	9,085

Commitments

12 Months Ended

Dec. 31, 2013

Commitments and Contingencies Disclosure [Abstract]

Commitments

COMMITMENTS

Leases

We lease office and research space and certain equipment 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)
2014	$	19,896
2015	20,152
2016	16,431
2017	9,104
2018	2,806
Thereafter	—
	$	68,389

____________________


(1)	Minimum payments have not been reduced by minimum sublease rentals of $16.1 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, 2013 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	$	38,483
Building Lease #3	July 2018	1 additional period of 5 years	21,070
Building Lease #4	December 2015	1 additional period of 3 years	8,692
Other			144
Total			$	68,389

Rent expense under operating leases was $9.1 million, $17.8 million, and $21.3 million for the years ended December 31, 2013, 2012 and 2011, respectively. Rent expense was net of sublease rentals of $4.1 million, $3.8 million and $1.9 million for the years ended December 31, 2013, 2012 and 2011, 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, 2013 and 2012. 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 $0.7 million and $0.6 million at December 31, 2013 and 2012, respectively. All three letters of credit are fully collateralized by long-term restricted cash and investments. As of December 31, 2013, 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, 2013 and 2012 was $3.5 million and $2.5 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 corporate insurance.

Concentrations of Credit Risk

12 Months Ended

Dec. 31, 2013

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. government agency obligations and U.S. government sponsored enterprises. 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, 2013, 87% of our trade receivables are with the specialty pharmacy that sells COMETRIQ in the United States. This customer pays promptly and within their respective payment terms.

We have operations primarily in the United States, while some of our collaboration partners have headquarters outside of the United States and certain of our clinical trials for cabozantinib are conducted outside of the United States. During the years ended December 31, 2012 and 2011, 100% of our revenues were earned in the United States. During the 2013, we initiated a Named Patient Use (“NPU”) program through our distribution partner, Swedish Orphan Biovitrum, to support the distribution and commercialization of COMETRIQ for metastatic MTC primarily in the European Union and potentially other countries. During the year ended December 31, 2013, 97% of our revenues were earned in the United States; the remainder of our revenues were earned in the European Union under this NPU program. All of our long-lived assets are located in the United States.

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 during the years ending December 31, 2013, 2012 and 2011:



Collaborator	2013		2012		2011
Bristol-Myers Squibb	52	%	66	%	59	%
Diplomat Specialty Pharmacy	45	%	—	%	—	%
Merck	—	%	22	%	—	%
Daiichi Sankyo	—	%	12	%	—	%
Sanofi	—	%	—	%	39	%

Subsequent Events Subsequent Events	12 Months Ended
Subsequent Events Subsequent Events	Dec. 31, 2013
Subsequent Events [Abstract]
Subsequent Events	SUBSEQUENT EVENTS Amendment to Deerfield Note Purchase Agreement and Issuance of 2014 Deerfield Warrants On January 22, 2014, we and Deerfield amended the note purchase agreement for the Deerfield Notes to provide us with an option to extend the maturity date of our indebtedness under the note purchase agreement to July 1, 2018. Under the terms of the extension option, we have the right to require the New Deerfield Purchasers to acquire $100 million principal amount of the Deerfield Notes and extend the maturity date thereof to July 1, 2018. We are under no obligation to exercise the extension option. In connection with the January 2014 amendment to the note purchase agreement, on January 22, 2014 we issued Deerfield 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. See “Note 8 - Debt” for further information on amended the note purchase agreement the related 2014 Deerfield Warrants. Issuance of Common Stock In January 2014, we completed a registered underwritten public offering of 10.0 million 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 approximately $75.6 million in net proceeds from the offering after deducting the underwriting discount and related offering expenses. We also granted the underwriter a 30-day option to purchase up to an additional 1,500,000 shares of common stock in connection with the offering which will expire on February 22, 2014.

Quarterly Financial Data (Unaudited)

12 Months Ended

Dec. 31, 2013

Quarterly Financial Information Disclosure [Abstract]

Quarterly Financial Data

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,
2013:
Revenues	$	4,347		$	5,466		$	11,856		$	9,669
Gross profit	$	4,084		$	5,176		$	11,571		$	9,389
Loss from operations	$	(59,514	)	$	(55,913	)	$	(51,295	)	$	(34,010	)
Net loss	$	(70,746	)	$	(67,124	)	$	(62,161	)	$	(44,729	)
Net loss per share, basic and diluted	$	(0.38	)	$	(0.36	)	$	(0.34	)	$	(0.24	)
2012:
Revenues	$	7,814		$	13,313		$	7,813		$	18,510
Loss from operations	$	(41,974	)	$	(25,443	)	$	(32,723	)	$	(22,296	)
Net loss	$	(52,193	)	$	(32,814	)	$	(36,487	)	$	(26,151	)
Net loss per share, basic and diluted	$	(0.28	)	$	(0.20	)	$	(0.25	)	$	(0.18	)

Organization And Summary Of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2013

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

Use of Estimates

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

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 development costs.

Repairs and maintenance costs are charged to expense as incurred.

Goodwill

Long-Lived Assets

Revenue Recognition

We recognize revenue from the sale of COMETRIQ and from license fees, milestones and contingent payments earned on research and collaboration arrangements.

License, Contract and Collaboration Reimbursement Revenues

Revenues and expenses from collaborations that are not co-development agreements are recorded as contract revenues or research and development expenses in the period incurred.

Net Product Revenues

Product Sales Discounts and Allowances

Patient Assistance Program

Cost of Goods Sold

Research And Development Expenses

Research and Development Expenses

Net (Loss) Income Per Share

Foreign Currency Translation And Remeasurement

Foreign Currency Translation and Remeasurement

Stock-Based Compensation

Recently Adopted Accounting Pronouncements

Organization And Summary Of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2013

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

Restructurings (Tables)

12 Months Ended

Dec. 31, 2013

Restructuring Charges [Abstract]

Schedule of outstanding restructuring liability

The components and changes of these liabilities during the annual periods from inception of the restructuring activities through December 31, 2013 are summarized in the following table (in thousands):



	Employee Severance And Other Benefits			Facility Charges			Asset Impairment			Legal and Other Fees			Total
Restructuring charge	$	17,677		$	11,814		$	3,173		$	80		$	32,744
Cash payments	(10,528		)	(3,739		)	—			(10		)	(14,277		)
Adjustments or non-cash credits including stock compensation expense	(1,626		)	613			(3,341		)	—			(4,354		)
Proceeds from sale of assets	—			—			168			—			168
Ending accrual balance as of December 31, 2010	5,523			8,688			—			70			14,281
Restructuring charge	2,566			8,480			(907		)	(3		)	10,136
Cash payments	(7,366		)	(3,469		)	—			(16		)	(10,851		)
Adjustments or non-cash credits including stock compensation expense	(717		)	222			(619		)	—			(1,114		)
Proceeds from sale of assets	—			—			1,526			—			1,526
Ending accrual balance as of December 31, 2011	6			13,921			—			51			13,978
Restructuring charge	970			8,276			(47		)	(28		)	9,171
Cash payments	(965		)	(5,299		)	—			(3		)	(6,267		)
Adjustments or non-cash credits including stock compensation expense	(11		)	2,304			(891		)	—			1,402
Proceeds from sale of assets	—			—			938			—			938
Restructuring liability as of December 31, 2012	—			19,202			—			20			19,222
Restructuring charge (credit)	496			662			88			(15		)	1,231
Cash payments	(434		)	(6,331		)	—			—			(6,765		)
Adjustments or non-cash credits including stock compensation expense	(55		)	(73		)	(183		)	—			(311		)
Proceeds from sale of assets	—			—			95			—			95
Restructuring liability as of December 31, 2013	$	7		$	13,460		$	—		$	5		$	13,472

Cash and Investments Cash and Investments (Tables)

12 Months Ended

Dec. 31, 2013

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, 2013 and 2012 (in thousands):



	December 31, 2013
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
As reported:
Cash and cash equivalents	$	103,978	$	—	$	—		$	103,978
Short-term investments	138,403		94		(22		)	138,475
Short-term restricted cash and investments	12,173		40		—			12,213
Long-term investments	144,226		106		(33		)	144,299
Long-term restricted cash and investments	16,837		60		—			16,897
Total cash and investments	$	415,617	$	300	$	(55	)	$	415,862



	December 31, 2012
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
As reported:
Cash and cash equivalents	$	170,070	$	—	$	(1	)	$	170,069
Short-term investments	241,391		46		(66		)	241,371
Short-term restricted cash and investments	12,242		4		—			12,246
Long-term investments	182,407		28		(124		)	182,311
Long-term restricted cash and investments	27,943		21		—			27,964
Total cash and investments	$	634,053	$	99	$	(191	)	$	633,961

Summary of Cash Equivalents and Investments by Security Type



	December 31, 2013
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	24,813	$	—	$	—		$	24,813
Commercial paper	94,682		—		—			94,682
Corporate bonds	239,937		190		(55		)	240,072
U.S. Treasury and government sponsored enterprises	44,284		102		—			44,386
Municipal bonds	6,005		8					6,013
Total investments	$	409,721	$	300	$	(55	)	$	409,966



	December 31, 2012
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	76,048	$	—	$	—		$	76,048
Commercial paper	167,223		10		—			167,233
Corporate bonds	222,106		30		(187		)	221,949
U.S. Treasury and government sponsored enterprises	132,933		59		(1		)	132,991
Municipal bonds	30,047		—		(3		)	30,044
Total investments	$	628,357	$	99	$	(191	)	$	628,265

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, 2013 (in thousands):



	Mature within One Year		After One Year through Two Years		Fair Value
Money market funds	$	24,813	$	—	$	24,813
Commercial paper	94,682		—		94,682
Corporate bonds	155,290		84,782		240,072
U.S. Treasury and government sponsored enterprises	32,216		12,170		44,386
Municipal bonds	—		6,013		6,013
Total	$	307,001	$	102,965	$	409,966

Inventory (Tables)

12 Months Ended

Dec. 31, 2013

Inventory Disclosure [Abstract]

Schedule of Inventory

Inventory consists of the following (in thousands):



	December 31,
	2013
Raw materials	$	529
Work in process	2,280
Finished goods	81
Total	$	2,890

Property And Equipment (Tables)

12 Months Ended

Dec. 31, 2013

Property, Plant and Equipment [Abstract]

Schedule Of Property And Equipment

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



	December 31,
	2013			2012
Laboratory equipment	$	15,453		$	19,504
Computer equipment and software	14,462			11,897
Furniture and fixtures	3,691			3,230
Leasehold improvements	17,031			16,572
Construction-in-progress	68			1,409
	50,705			52,612
Less: accumulated depreciation and amortization	(45,795		)	(46,553		)
Property and equipment, net	$	4,910		$	6,059

Debt (Tables)

12 Months Ended

Dec. 31, 2013

Debt Disclosure [Abstract]

Schedule Of Debt

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



	December 31,
	2013			2012
Convertible Senior Subordinated Notes due 2019	$	165,296		$	149,800
Secured Convertible Notes due 2015	99,851			100,676
Silicon Valley Bank term loan	80,000			80,000
Silicon Valley Bank line of credit	2,090			5,260
Total debt	347,237			335,736
Less: current portion	(11,762		)	(13,170		)
Long-term debt	$	335,475		$	322,566

Summary Of The Liability Component Of The 2019 Notes

The following is a summary of the liability component of the 2019 Notes as of December 31, 2013 and 2012 (in thousands):



	December 31,
	2013		2012
Net carrying amount of the liability component	$	165,296	$	149,800
Unamortized discount of the liability component	122,204		137,700
Principal amount of the 2019 Notes	$	287,500	$	287,500

Schedule Of Future Principal Payments Of Total Long-Term Debt

Aggregate expected future principal payments of our debt were as follows as of December 31, 2013 (in thousands):



Year Ending December 31, (1)
2014	$	11,762
2015	104,328
2016	—
2017	80,000
2018	—
Thereafter	287,500

____________________

(1)

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.

Reference 1: http://www.xbrl.org/2003/role/presentationRef
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-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
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-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=6584090&loc=d3e28878-108400

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

Reference 8: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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-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
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-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
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-Paragraph 7
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21521-112644

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 02
-Paragraph 22
-Article 5

Warrants and Rights Note Disclosure [Abstract]

Common Stock And Warrants (Tables)

12 Months Ended

Dec. 31, 2013

Schedule Of Warrants To Purchase Common Stock Outstanding And Exercisable

At December 31, 2013, the following warrants to purchase common stock were outstanding and exercisable:



Date Issued	Exercise Price per Share		Expiration Date	Number of Shares
June 4, 2008	$	7.40	June 4, 2014	1,000,000
June 10, 2009	$	6.05	June 10, 2014	441,215
				1,441,215

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

Tabular disclosure of warrants or rights issued. Warrants and rights outstanding are derivative securities that give the holder the right to purchase securities (usually equity) from the issuer at a specific price within a certain time frame. Warrants are often included in a new debt issue to entice investors by a higher return potential. The main difference between warrants and call options is that warrants are issued and guaranteed by the company, whereas options are exchange instruments and are not issued by the company. Also, the lifetime of a warrant is often measured in years, while the lifetime of a typical option is measured in months. Disclose the title of issue of securities called for by warrants and rights outstanding, the aggregate amount of securities called for by warrants and rights outstanding, the date from which the warrants or rights are exercisable, and the price at which the warrant or right is exercisable.

+ References + Details

Fair Value Measurements Fair Value Measurements (Tables)

12 Months Ended

Dec. 31, 2013

Fair Value Disclosures [Abstract]



	December 31, 2013
	Level 1		Level 2		Total
Money market funds	$	24,813	$	—	$	24,813
Commercial paper	—		94,682		94,682
Corporate bonds	—		240,072		240,072
U.S. Treasury and government sponsored enterprises	—		44,386		44,386
Municipal bonds	—		6,013		6,013
Total	$	24,813	$	385,153	$	409,966



	December 31, 2012
	Level 1		Level 2		Total
Money market funds	$	76,050	$	—	$	76,050
Commercial paper	—		167,231		167,231
Corporate bonds	—		221,949		221,949
U.S. Treasury and government sponsored enterprises	—		132,991		132,991
Municipal bonds	—		30,044		30,044
Total	$	76,050	$	552,215	$	628,265

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, 2013				December 31, 2012
	Carrying Amount		Fair Value		Carrying Amount		Fair Value
2019 Notes	$	165,296	$	339,883	$	149,800	$	280,111
Silicon Valley Bank Term Loan	$	80,000	$	79,946	$	80,000	$	79,542
Silicon Valley Bank Line of Credit	$	2,090	$	2,090	$	5,260	$	5,253

Employee Benefit Plans (Tables)

12 Months Ended

Dec. 31, 2013

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

Schedule Of Allocated Employee Stock-Based Compensation Expense



	Year Ended December 31,
	2013		2012		2011
Research and development expense	$	6,021	$	4,536	$	5,935
General and administrative expense	5,948		4,245		5,459
Restructuring-related stock compensation expense	49		—		625
Total employee stock-based compensation expense	$	12,018	$	8,781	$	12,019

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



	Stock Options
	2013			2012			2011
Weighted average grant-date fair value	$	2.97		$	3.24		$	3.50
Risk-free interest rate	1.51		%	0.81		%	1.07		%
Dividend yield	—		%	—		%	—		%
Volatility	61		%	69		%	70		%
Expected life	5.6 years			5.6 years			5.5 years

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



	ESPP
	2013			2012			2011
Weighted average grant-date fair value	$	1.64		$	2.07		$	2.85
Risk-free interest rate	0.11		%	0.10		%	0.11		%
Dividend yield	—		%	—		%	—		%
Volatility	66		%	68		%	68		%
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, 2010	19,630,030		$	7.52
Granted	2,545,625		$	5.86
Exercised	(2,161,804	)	$	5.75
Forfeited	(1,021,323	)	$	6.22
Expired	(1,556,150	)	$	12.13
Options outstanding at December 31, 2011	17,436,378		$	7.16
Granted	3,442,696		$	5.45
Exercised	(181,979	)	$	5.09
Forfeited	(358,360	)	$	5.88
Expired	(1,890,185	)	$	7.54
Options outstanding at December 31, 2012	18,448,550		$	6.85
Granted	6,694,174		$	5.44
Exercised	(13,311	)	$	5.06
Forfeited	(79,942	)	$	5.27
Expired	(1,066,196	)	$	6.45
Options outstanding at December 31, 2013	23,983,275		$	6.48	4.63 years	$	8,079
Exercisable at December 31, 2013	13,818,615		$	7.21	3.44 years	$	3,458

Summary Of Information About Stock Options Outstanding

The following table summarizes information about stock options outstanding and exercisable at December 31, 2013:



	Options Outstanding				Options Outstanding and Exercisable
Exercise Price Range	Number	Weighted Average Remaining Contractual Life	Weighted Average Exercise Price		Number of Exercisable	Weighted Average Exercise Price
$3.05 - $5.50	4,735,373	5.18 years	$	5.07	2,841,746	$	5.04
$5.51 - $5.63	10,369,851	5.25 years	$	5.55	3,004,560	$	5.62
$5.65 - $8.86	3,877,697	5.06 years	$	6.97	2,971,955	$	7.32
$8.88 - $12.10	5,000,354	2.50 years	$	9.34	5,000,354	$	9.34
	23,983,275	4.63 years	$	6.48	13,818,615	$	7.21

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, 2010	2,172,431		$	7.31
Awarded	356,498		$	6.17
Released	(648,437	)	$	7.43
Forfeited	(488,801	)	$	7.45
Awards outstanding at December 31, 2011	1,391,691		$	6.92
Awarded	733,958		$	5.50
Released	(596,397	)	$	7.15
Forfeited	(234,631	)	$	6.62
Awards outstanding at December 31, 2012	1,294,621		$	6.07
Awarded	1,119,733		$	5.45
Released	(517,874	)	$	6.60
Forfeited	(85,959	)	$	5.49
Awards outstanding at December 31, 2013	1,810,521		$	5.56	2.05 years	$	10,736

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2013

Income Tax Disclosure [Abstract]

Schedule Of Consolidated Net Income (Loss)

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



	Year Ended December 31,
	2013			2012			2011
Domestic	$	(236,076	)	$	(147,538	)	$	76,992
Foreign	(8,780		)	—			—
Total	$	(244,856	)	$	(147,538	)	$	76,992

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,
	2013			2012		2011
Current:
Federal	$	—		$	32	$	636
State	12			75		659
Total current tax expense	12			107		1,295
Deferred:
Federal	(106		)	—		—
State	(2		)	—		—
Total deferred tax expense	(108		)	—		—
Income tax (benefit) provision	$	(96	)	$	107	$	1,295

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,
	2013			2012			2011
U.S. federal income tax (benefit) provision at statutory rate	$	(83,251	)	$	(50,163	)	$	26,177
Unutilized net operating losses	(3,438		)	46,324			(29,650		)
Non-deductible interest	3,380			3,297			2,809
Stock-based compensation	393			504			627
State tax expense	10			74			660
Refundable tax credit	—			32			636
Available-for-sale investments	(106		)	—			—
Impact of intellectual property rights transfer	82,858			—			—
Other	58			39			36
Income tax (benefit) provision	$	(96	)	$	107		$	1,295

Schedule Of Deferred Assets And Liabilities

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



	December 31,
	2013			2012
Deferred tax assets:
Net operating loss carry-forwards	$	358,372		$	374,200
Tax credit carry-forwards	64,635			65,232
Amortization of deferred stock compensation – non-qualified	24,279			26,469
Accruals and reserves not currently deductible	10,107			13,732
Deferred revenue	502			6,501
Book over tax depreciation and amortization	4,499			5,140
Total deferred tax assets	462,394			491,274
Valuation allowance	(421,426		)	(438,266		)
Net deferred tax assets	40,968			53,008
Deferred tax liabilities:
Convertible debt	(40,968		)	(53,008		)
Total deferred tax liabilities	(40,968		)	(53,008		)
Net deferred taxes	$	—		$	—

Schedule Of Unrecognized Tax Benefits

The following table summarizes the activity related to our unrecognized tax benefits for the years ended December 31, 2013, 2012 and 2011 (in thousands):



	Year Ended December 31,
	2013			2012		2011
Beginning balance	$	47,298		$	39,310	$	46,381
(Decrease) increase relating to prior year provision	(112		)	5,894		(9,782		)
Increase relating to current year provision	7,891			2,094		2,711
Ending balance	$	55,077		$	47,298	$	39,310

Net (Loss) Income Per Share (Tables)

12 Months Ended

Dec. 31, 2013

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 income (loss) per share (in thousands, except per share amounts):



	Year Ended December 31,
	2013			2012			2011
Numerator:
Net (loss) income	$	(244,760	)	$	(147,645	)	$	75,697
Denominator:
Shares used in computing basic (loss) income per share amounts	184,062			160,138			126,018
Add effect of dilutive securities:
Shares issuable upon exercise of outstanding stock options	—			—			2,064
Shares issuable upon exercise of warrants	—			—			1,858
Shares issuable upon vesting of RSUs	—			—			515
Shares issuable upon purchase from ESPP contributions	—			—			24
Total dilutive securities	—			—			4,461
Shares used in computing diluted (loss) income per share amounts	184,062			160,138			130,479
Net (loss) income per share, basic	$	(1.33	)	$	(0.92	)	$	0.60
Net (loss) income per share, diluted	$	(1.33	)	$	(0.92	)	$	0.58

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



	December 31,
	2013	2012	2011
2019 Notes	54,123	54,123	—
Outstanding stock options, unvested RSUs and ESPP contributions	21,401	16,568	9,085
Warrants	1,441	1,441	—
Total potentially dilutive shares	76,965	72,132	9,085

Commitments (Tables)

12 Months Ended

Dec. 31, 2013

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)
2014	$	19,896
2015	20,152
2016	16,431
2017	9,104
2018	2,806
Thereafter	—
	$	68,389

____________________


(1)	Minimum payments have not been reduced by minimum sublease rentals of $16.1 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, 2013 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	$	38,483
Building Lease #3	July 2018	1 additional period of 5 years	21,070
Building Lease #4	December 2015	1 additional period of 3 years	8,692
Other			144
Total			$	68,389

Concentrations of Credit Risk (Tables)

12 Months Ended

Dec. 31, 2013

Risks and Uncertainties [Abstract]

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

10% or more of total revenues during the years ending December 31, 2013, 2012 and 2011:



Collaborator	2013		2012		2011
Bristol-Myers Squibb	52	%	66	%	59	%
Diplomat Specialty Pharmacy	45	%	—	%	—	%
Merck	—	%	22	%	—	%
Daiichi Sankyo	—	%	12	%	—	%
Sanofi	—	%	—	%	39	%

Quarterly Financial Data (Unaudited) (Tables)

12 Months Ended

Dec. 31, 2013

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,
2013:
Revenues	$	4,347		$	5,466		$	11,856		$	9,669
Gross profit	$	4,084		$	5,176		$	11,571		$	9,389
Loss from operations	$	(59,514	)	$	(55,913	)	$	(51,295	)	$	(34,010	)
Net loss	$	(70,746	)	$	(67,124	)	$	(62,161	)	$	(44,729	)
Net loss per share, basic and diluted	$	(0.38	)	$	(0.36	)	$	(0.34	)	$	(0.24	)
2012:
Revenues	$	7,814		$	13,313		$	7,813		$	18,510
Loss from operations	$	(41,974	)	$	(25,443	)	$	(32,723	)	$	(22,296	)
Net loss	$	(52,193	)	$	(32,814	)	$	(36,487	)	$	(26,151	)
Net loss per share, basic and diluted	$	(0.28	)	$	(0.20	)	$	(0.25	)	$	(0.18	)

Organization And Summary Of Significant Accounting Policies (Narrative) (Details)	3 Months Ended								12 Months Ended
	Dec. 31, 2013 USD ($) phase	Sep. 30, 2013 USD ($)	Jun. 30, 2013 USD ($)	Mar. 31, 2013 USD ($)	Dec. 31, 2012 USD ($)	Sep. 30, 2012 USD ($)	Jun. 30, 2012 USD ($)	Mar. 31, 2012 USD ($)	Dec. 31, 2014	Dec. 31, 2013 USD ($) phase segment	Dec. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)
Organization And Summary Of Significant Policies [Line Items]
Net (loss) income	$ (70,746,000)	$ (67,124,000)	$ (62,161,000)	$ (44,729,000)	$ (52,193,000)	$ (32,814,000)	$ (36,487,000)	$ (26,151,000)		$ (244,760,000)	$ (147,645,000)	$ 75,697,000
Accumulated deficit	$ (1,498,762,000)				(1,254,002,000)					$ (1,498,762,000)	$ (1,254,002,000)
Number of phases in process \| phase	2									2
Annual operating cycle										364 days	364 days	364 days
Number of Operating Segments \| segment										1
Foreign currency forward contract, notional amount	$ 0				$ 0					$ 0	$ 0
Percent discount for prompt payment										2.00%
Amount of reduction relating to prior periods										$ 800,000	2,700,000	$ 1,600,000
Net product revenues										$ 15,017,000	$ 0	$ 0
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
Glaxo SmithKline [Member]
Organization And Summary Of Significant Policies [Line Items]
Percent of royalty on net sale										3.00%
Subsequent Event [Member]
Organization And Summary Of Significant Policies [Line Items]
Annual operating cycle									371 days

Organization And Summary Of Significant Accounting Policies (Estimated Useful Lives Of Property Plant And Equipment) (Details)	12 Months Ended
	Dec. 31, 2013
Equipment And Furniture [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives, years	P5Y
Computer Equipment And Software [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives, years	P3Y
Maximum [Member] \| Leasehold Improvements [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives, years	P7Y

Research And Collaboration Agreements (Cobimetinib Collaboration To Bristol-Meyers Squibb) (Details)	1 Months Ended											12 Months Ended
	Jul. 31, 2011 USD ($)	Nov. 30, 2010 USD ($)	Mar. 31, 2010 USD ($)	Jan. 31, 2010 USD ($)	Jan. 31, 2009 USD ($)	Mar. 31, 2008 USD ($)	Dec. 31, 2007 USD ($)	Jan. 31, 2007 USD ($)	Dec. 31, 2006 USD ($)	Dec. 31, 2005 USD ($)	Oct. 31, 2002 USD ($) shares	Dec. 31, 2013 USD ($) product shares	Dec. 31, 2012 USD ($) shares	Dec. 31, 2011 USD ($)	Oct. 31, 2011 shares
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum Potential Milestone Payments												$ 2,400,000,000
Percentage of Maximum Potential Milestone Payments - Clinical Development												10.00%
Percentage of Maximum Potential Milestone Payments - Regulatory												41.00%
Percentage of Maximum Potential Milestone Payments - Commercial												49.00%
Common stock, shares issued \| shares												184,533,651	183,697,213
License, contract and collaboration reimbursement revenues												$ 16,321,000	$ 47,450,000	$ 289,636,000
Glaxo SmithKline [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale												3.00%
Genentech [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront and milestone payments								$ 15,000,000.0	$ 25,000,000.0
Payment to use exercise of option related to co-development agreement						$ 3,000,000.0
Milestone payment			$ 7,000,000.0
Optional percent of total sales												25.00%
License, contract and collaboration reimbursement revenues												$ 0	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
Glaxo SmithKline [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront and milestone payments											$ 65,000,000.0
Research and development funding and loan											$ 85,000,000.0
Common stock, shares issued \| shares											3,000,000				5,537,906
Royalty Expense												400,000
License, contract and collaboration reimbursement revenues												0	0	0
Bristol-Myers Squibb [Member] \| ROR Collaboration Agreement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment		$ 5,000,000
Maximum amount eligible for development and regulatory milestones		255,000,000
Income from development milestone	$ 2,500,000.0
License, contract and collaboration reimbursement revenues												1,500,000	2,900,000	2,800,000
Bristol-Myers Squibb [Member] \| TGR5 License Agreement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum amount eligible for commercial milestones under collaborations agreement		$ 150,000,000
Bristol-Myers Squibb [Member] \| LXR Collaboration [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment										$ 17,500,000.0
Number of years for initial research										2 years
Maximum amount eligible for development and regulatory milestones												$ 138,000,000
Number of products \| product												2
Maximum amount eligible for royalties on sales under collaborations agreement												$ 225,000,000.0
Income from development milestone							$ 5,000,000.0
Additional research fund					$ 7,700,000
Research and development fund				$ 5,800,000						$ 10,000,000.0
Bristol-Myers Squibb [Member] \| Terminated Collaborations [Member] [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
License, contract and collaboration reimbursement revenues												$ 14,800,000	$ 28,400,000	$ 168,900,000

Research And Collaboration Agreements (Sanofi To Daiichi Sankyo) (Details) - USD ($)		1 Months Ended						12 Months Ended
	Jul. 20, 2009	Aug. 31, 2012	Jan. 19, 2012	Dec. 31, 2010	Jun. 30, 2007	Mar. 31, 2006	Oct. 31, 2002	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011	Oct. 31, 2011
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Purchase an aggregate shares of common stock								184,533,651	183,697,213
License, contract and collaboration reimbursement revenues								$ 16,321,000	$ 47,450,000	$ 289,636,000
Sanofi [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Proceeds from termination of agreement			$ 15,300,000
Upfront and milestone payments	$ 140,000,000.0
Upfront payment received for license	120,000,000.0
Upfront payment received for collaboration	20,000,000.0
Withholding taxes on upfront payments	7,000,000
Upfront payments, net of tax	$ 133,000,000
Maximum amount eligible for development and regulatory milestones								745,000,000.0
License, contract and collaboration reimbursement revenues								0	0	113,900,000
Glaxo SmithKline [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront and milestone payments							$ 65,000,000.0
Research and development funding and loans							$ 85,000,000.0
Purchase an aggregate shares of common stock							3,000,000				5,537,906
License, contract and collaboration reimbursement revenues								0	0	0
Merck [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment			$ 12,000,000
Maximum amount eligible for development and regulatory milestones								239,000,000
License, contract and collaboration reimbursement revenues								0	10,700,000	1,300,000
Daiichi Sankyo [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment						$ 20,000,000
Maximum amount eligible for development and regulatory milestones								145,000,000
Research and development fund					$ 1,500,000.0	$ 3,800,000
Original research term, years						15 months
Extended research term, years					6 months
Milestone payment		$ 5,500,000.0		$ 5,000,000.0
License, contract and collaboration reimbursement revenues								$ 0	$ 5,500,000	$ 0

Disposition of Artemis Pharmaceuticals (Details) - USD ($) $ in Millions	1 Months Ended
	Sep. 30, 2011	Nov. 30, 2007
Discontinued Operations and Disposal Groups [Abstract]
Cash received for sale of shares in subsidiary	$ 3.0	$ 19.8
Outstanding share capital of wholly-owned subsidiary sold	19.90%	80.10%
Minority interest	19.90%
Gain recognized	$ 2.3

Restructurings (Narrative) (Details) $ in Thousands	12 Months Ended				46 Months Ended
Restructurings (Narrative) (Details) $ in Thousands	Dec. 31, 2013 USD ($) employee	Dec. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)	Dec. 31, 2010 USD ($)	Dec. 31, 2013 USD ($) employee restructuring
Restructuring Cost and Reserve [Line Items]
Number of Restructurings Implemented \| restructuring					5
Aggregate reduction in headcount \| employee	429				429
Restructuring charge	$ 1,231	$ 9,171	$ 10,136	$ 32,744	$ 53,300
Proceeds from sale of property and equipment	143	1,943	1,526
Restructuring reserve	13,472	19,222	13,978	14,281	13,472
Expected additional payment for restructuring	900
Aggregate cash expenditures	6,765	6,267	10,851	14,277	35,400
Proceeds from Subtenants					10,200
Restructuring Reserve, Cash Settlement Net of Proceeds	6,700	5,300	9,300
Facility Charges [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charge	662	8,276	8,480	11,814	29,200
Restructuring reserve	13,460	19,202	13,921	8,688	13,460
Aggregate cash expenditures	6,331	5,299	3,469	3,739
Employee Severance [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charge	496	970	2,566	17,677	21,700
Restructuring reserve	7	0	6	5,523	7
Aggregate cash expenditures	434	965	7,366	10,528
Asset Impairment [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charge	88	(47)	(907)	3,173	2,300
Proceeds from sale of property and equipment					2,700
Restructuring reserve	0	0	0	0	$ 0
Aggregate cash expenditures	$ 0	$ 0	$ 0	$ 0

Restructurings (Schedule Of Outstanding Restructuring Liability) (Details) - USD ($) $ in Thousands	12 Months Ended				46 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2013
Restructuring Reserve [Roll Forward]
Ending accrual balance at beginning of period	$ 19,222	$ 13,978	$ 14,281
Restructuring charge	1,231	9,171	10,136	$ 32,744	$ 53,300
Cash payments	(6,765)	(6,267)	(10,851)	(14,277)	(35,400)
Adjustments or non-cash credits including stock compensation expense	311	1,402	(1,114)	(4,354)
Proceeds from sale of assets	95	938	1,526	168
Ending accrual balance at end of period	13,472	19,222	13,978	14,281	13,472
Employee Severance And Other Benefits [Member]
Restructuring Reserve [Roll Forward]
Ending accrual balance at beginning of period	0	6	5,523
Restructuring charge	496	970	2,566	17,677	21,700
Cash payments	(434)	(965)	(7,366)	(10,528)
Adjustments or non-cash credits including stock compensation expense	55	(11)	(717)	(1,626)
Proceeds from sale of assets	0	0	0	0
Ending accrual balance at end of period	7	0	6	5,523	7
Facility Charges [Member]
Restructuring Reserve [Roll Forward]
Ending accrual balance at beginning of period	19,202	13,921	8,688
Restructuring charge	662	8,276	8,480	11,814	29,200
Cash payments	(6,331)	(5,299)	(3,469)	(3,739)
Adjustments or non-cash credits including stock compensation expense	73	2,304	222	613
Proceeds from sale of assets	0	0	0	0
Ending accrual balance at end of period	13,460	19,202	13,921	8,688	13,460
Asset Impairment [Member]
Restructuring Reserve [Roll Forward]
Ending accrual balance at beginning of period	0	0	0
Restructuring charge	88	(47)	(907)	3,173	2,300
Cash payments	0	0	0	0
Adjustments or non-cash credits including stock compensation expense	183	(891)	(619)	(3,341)
Proceeds from sale of assets	95	938	1,526	168
Ending accrual balance at end of period	0	0	0	0	0
Other Restructuring [Member]
Restructuring Reserve [Roll Forward]
Ending accrual balance at beginning of period	20	51	70
Restructuring charge	(15)	(28)	(3)	80
Cash payments	0	(3)	(16)	(10)
Adjustments or non-cash credits including stock compensation expense	0	0	0	0
Proceeds from sale of assets	0	0	0	0
Ending accrual balance at end of period	$ 5	$ 20	$ 51	$ 70	$ 5

Cash and Investments Cash and Investments (Details)	12 Months Ended
Cash and Investments Cash and Investments (Details)	Dec. 31, 2013 USD ($) account affiliate investment	Dec. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 415,617,000	$ 634,053,000
Gross Unrealized Gains	300,000	99,000
Gross Unrealized Losses	(55,000)	(191,000)
Fair Value	415,862,000	633,961,000
Amortized Cost	409,721,000	628,357,000
Gross Unrealized Gains	300,000	99,000
Gross Unrealized Losses	(55,000)	(191,000)
Fair Value	$ 409,966,000	628,265,000
Number of required investment accounts \| account	1
Number of affiliate banks \| affiliate	1
Gain (Loss) on Sale of Investments	$ 0	0	$ 0
Number of investments in an unrealized loss position \| investment	38
Unrealized loss position	$ 65,300,000
Unrealized loss position of all securities in years	1 year
Silicon Valley Bank Loan And Security Agreement [Member]
Schedule of Available-for-sale Securities [Line Items]
Collateral balance	$ 83,700,000	87,000,000
Commercial paper [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	94,682,000	167,223,000
Gross Unrealized Gains	0	10,000
Gross Unrealized Losses	0	0
Fair Value	94,682,000	167,233,000
Mature within One Year	94,682,000
After One Year through Two Years	0
Corporate bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	239,937,000	222,106,000
Gross Unrealized Gains	190,000	30,000
Gross Unrealized Losses	(55,000)	(187,000)
Fair Value	240,072,000	221,949,000
Mature within One Year	155,290,000
After One Year through Two Years	84,782,000
U.S. Treasury and government sponsored enterprises [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	44,284,000	132,933,000
Gross Unrealized Gains	102,000	59,000
Gross Unrealized Losses	0	(1,000)
Fair Value	44,386,000	132,991,000
Mature within One Year	32,216,000
After One Year through Two Years	12,170,000
Municipal bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	6,005,000	30,047,000
Gross Unrealized Gains	8,000	0
Gross Unrealized Losses		(3,000)
Fair Value	6,013,000	30,044,000
Mature within One Year	0
After One Year through Two Years	6,013,000
Money market funds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	24,813,000	76,048,000
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	24,813,000	76,048,000
Mature within One Year	24,813,000
After One Year through Two Years	0
Cash Equivalents [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	103,978,000	170,070,000
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	(1,000)
Fair Value	103,978,000	170,069,000
Short-term investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	138,403,000	241,391,000
Gross Unrealized Gains	94,000	46,000
Gross Unrealized Losses	(22,000)	(66,000)
Fair Value	138,475,000	241,371,000
Short-term restricted cash and investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	12,173,000	12,242,000
Gross Unrealized Gains	40,000	4,000
Gross Unrealized Losses	0	0
Fair Value	12,213,000	12,246,000
Long-term investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	144,226,000	182,407,000
Gross Unrealized Gains	106,000	28,000
Gross Unrealized Losses	(33,000)	(124,000)
Fair Value	144,299,000	182,311,000
Long-term restricted cash and investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	16,837,000	27,943,000
Gross Unrealized Gains	60,000	21,000
Gross Unrealized Losses	0	0
Fair Value	16,897,000	$ 27,964,000
Investments, excluding cash [Member]
Schedule of Available-for-sale Securities [Line Items]
Fair Value	409,966,000
Mature within One Year	307,001,000
After One Year through Two Years	$ 102,965,000

Inventory (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Inventory Disclosure [Abstract]
Raw materials	$ 529
Work in process	2,280
Finished goods	81
Total	$ 2,890	$ 0

Property And Equipment (Schedule Of Property And Equipment) (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Property, Plant and Equipment [Abstract]
Laboratory equipment	$ 15,453	$ 19,504
Computer equipment and software	14,462	11,897
Furniture and fixtures	3,691	3,230
Leasehold improvements	17,031	16,572
Construction-in-progress	68	1,409
Property and equipment, gross	50,705	52,612
Less accumulated depreciation and amortization	(45,795)	(46,553)
Property and equipment, net	$ 4,910	$ 6,059

Property And Equipment Property and Equipment Narrative (Details) - USD ($)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Property, Plant and Equipment [Line Items]
Depreciation	$ 3,100,000	$ 4,800,000	$ 6,800,000
Impairment charges	100,000	300,000	500,000
Gain on sale of assets	$ 0	$ 300,000	$ 1,400,000

Debt (Schedule Of Debt) (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Debt Instrument [Line Items]
Total debt	$ 347,237	$ 335,736
Less: current portion	(11,762)	(13,170)
Long-term debt	335,475	322,566
Senior Subordinated Notes [Member] \| Convertible Senior Subordinated Notes due August 15, 2019, 4.25% [Member]
Debt Instrument [Line Items]
Convertible Debt	165,296	149,800
Secured Debt [Member] \| Secured Convertible Notes due June 2015 [Member]
Debt Instrument [Line Items]
Convertible Debt	99,851	100,676
Term Loan [Member] \| Silicon Valley Bank Loan And Security Agreement [Member]
Debt Instrument [Line Items]
Silicon Valley Bank term loan	80,000	80,000
Line of Credit [Member] \| Silicon Valley Bank Loan And Security Agreement [Member]
Debt Instrument [Line Items]
Silicon Valley Bank Line of Credit	$ 2,090	$ 5,260

Debt (Narrative) (Details)				1 Months Ended										3 Months Ended	11 Months Ended	12 Months Ended			17 Months Ended	18 Months Ended
Debt (Narrative) (Details)	Aug. 14, 2012 USD ($) $ / shares shares	Jun. 30, 2010 USD ($) payment	Jun. 02, 2010 USD ($)	Jan. 31, 2014 $ / shares shares	Feb. 29, 2012 shares	Aug. 31, 2011	Jun. 30, 2011 USD ($)	Mar. 31, 2011 shares	Dec. 31, 2010 USD ($)	Jun. 30, 2010 USD ($) payment	Dec. 31, 2009 USD ($)	Jun. 30, 2008 USD ($)	Dec. 31, 2007 USD ($) payment	Dec. 31, 2012 USD ($)	Dec. 31, 2012 USD ($)	Dec. 31, 2013 USD ($) account affiliate payment shares	Dec. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)	Dec. 31, 2013 USD ($) payment shares	Jun. 30, 2011 USD ($)	Jan. 22, 2014 USD ($) shares
Debt Instrument [Line Items]
Sale of shares of common stock, shares \| shares	34,500,000				12,700,000			17,300,000
Share price (dollars per share) \| $ / shares	$ 4.25
Proceeds from Issuance of Common Stock and Convertible Debt, Net	$ 416,100,000
Proceeds from Convertible Debt, Net	277,700,000
Short-term restricted cash and investments														$ 12,246,000	$ 12,246,000	$ 12,213,000	$ 12,246,000		$ 12,213,000
Long-term restricted cash and investments														27,964,000	27,964,000	$ 16,897,000	27,964,000		$ 16,897,000
Adjustments to Additional Paid in Capital, Equity Component of Convertible Debt	4,900,000																137,785,000
Number of required investment accounts \| account																1
Number of affiliate banks \| affiliate																1
Class of Warrant or Right, Outstanding \| shares																1,441,215			1,441,215
Book value of debt outstanding														335,736,000	335,736,000	$ 347,237,000	335,736,000		$ 347,237,000
Minimum [Member]
Debt Instrument [Line Items]
Number of required investment accounts \| account																1
Subsequent Event [Member]
Debt Instrument [Line Items]
Sale of shares of common stock, shares \| shares				10,000,000
Share price (dollars per share) \| $ / shares				$ 8.00
Subsequent Event [Member] \| Warrants Issued On January Twenty Two Two Thousand and Fourteen[Member] [Member]
Debt Instrument [Line Items]
Warrant Repricing Terms on Exercise of Extension Option																					120.00%
Class of Warrant or Right, Outstanding \| shares																					1,000,000
Debt Payment [Member]
Debt Instrument [Line Items]
Restricted Cash and Investments	36,500,000
Restricted Cash and Investments Used for Debt Payments																			12,300,000
Short-term restricted cash and investments																$ 12,200,000			12,200,000
Long-term restricted cash and investments																16,900,000			16,900,000
Silicon Valley Bank Loan And Security Agreement [Member]
Debt Instrument [Line Items]
Debt, interest rate						6.00%
Collateral balance														87,000,000	87,000,000	83,700,000	87,000,000		83,700,000
Silicon Valley Bank Loan And Security Agreement [Member] \| Silicon Valley Bank [Member]
Debt Instrument [Line Items]
Book value of debt outstanding														85,300,000	85,300,000	82,100,000	85,300,000		82,100,000
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													287,500,000	287,500,000	287,500,000	287,500,000		287,500,000
Debt, interest rate	4.25%
Debt Instrument, Redemption Price Component, Percentage of Principal	100.00%
Convertible Debt														149,800,000	149,800,000	$ 165,296,000	149,800,000		$ 165,296,000
Debt Instrument, Convertible, Conversion Ratio	0.1882353
Debt Instrument, Convertible, Conversion Ratio, Principal Amount	$ 1,000
Debt Instrument, Convertible, Conversion Price (dollars per share) \| $ / shares	$ 5.31
Debt Instrument, Periodic Payment, Number of Payments Secured in Escrow \| payment																6			6
Debt Instrument, Interest Rate, Effective Percentage																10.09%			10.09%
Debt Instrument, Fair Value Disclosure	$ 144,300,000
Debt Instrument, Unamortized Discount	143,200,000
Unamortized debt issuance expense														137,700,000	137,700,000	$ 122,204,000	137,700,000		$ 122,204,000
Interest Expense, Debt														10,300,000		28,400,000
Interest Expense, Coupon Interest																12,200,000	4,600,000
Amortization of Financing Costs and Discounts																16,200,000	5,700,000
Balance of unamortized closing fees and expenses														4,700,000	4,700,000	4,000,000	4,700,000		4,000,000
Senior Subordinated Notes [Member] \| Convertible Senior Subordinated Notes due August 15, 2019, 4.25% [Member] \| Other Noncurrent Assets [Member]
Debt Instrument [Line Items]
Unamortized debt issuance expense	4,900,000
Secured Convertible Notes Due June 2015 [Member] \| Deerfield Financing [Member]
Debt Instrument [Line Items]
Debt, principal amount		$ 124,000,000.0								$ 124,000,000.0
Convertible Debt														124,000,000	124,000,000	114,000,000	124,000,000		114,000,000
Interest Expense, Debt															15,900,000	16,100,000		$ 14,300,000
Amortization of Financing Costs and Discounts															9,900,000	10,100,000		8,300,000
Debt instruments, purchase price		80,000,000.000
Debt instruments, closing fees and expenses		2,000,000
Debt Instrument, Amendment, Consent Fee, Amount	1,500,000.0
Annual interest		$ 6,000,000
Repayments of Notes Payable																$ 10,000,000.0
Percentage of revenues payable under collaborative arrangements in 2013, 2014 and 2015																15.00%
Maximum prepayment amount under collaborative arrangements in 2013 and 2014																$ 27,500,000.0
Debt instrument, minimum purchase amount for prepayment condition																$ 400,000,000
Percentage of assets minimum for prepayment condition																50.00%
Balance of unamortized closing fees and expenses														2,300,000	2,300,000	$ 1,400,000	2,300,000		1,400,000
Secured Convertible Notes Due June 2015 [Member] \| Deerfield Financing [Member] \| Subsequent Event [Member]
Debt Instrument [Line Items]
Principal Eligible for Extension Option																					$ 100,000,000
Debt Instrument, Interest Rate, Stated Percentage after Extension Option Election																					15.00%
Prepayment Price																					105.00%
Equipment Line Of Credit December 2007 [Member] \| Silicon Valley Bank Loan And Security Agreement [Member]
Debt Instrument [Line Items]
Line of credit, borrowing capacity													$ 30,000,000.0					$ 33,600,000
Draw down period													2 years
Number of installments \| payment													48
Annual rate of interest													0.75%
Increase in draw down period											18 months
Minimum draws											$ 2,500,000.0
Period of minimum draw											6 months
Draws on line of credit											$ 5,000,000.0	$ 13,600,000
Minimum draw down amount under facility							$ 2,500,000		$ 2,500,000	$ 2,500,000
Aggregate Minimum Draws Required Under Facility																				$ 7,500,000.0
Line Of Credit, Percentage Of Collateral Security On Outstanding Obligations											100.00%
Line of Credit [Member] \| Silicon Valley Bank Loan And Security Agreement [Member]
Debt Instrument [Line Items]
Silicon Valley Bank Line of Credit														$ 5,260,000	$ 5,260,000	$ 2,090,000	$ 5,260,000		$ 2,090,000
Seven-Year Term Loan [Member] \| Silicon Valley Bank Loan And Security Agreement [Member]
Debt Instrument [Line Items]
Debt, principal amount			$ 80,000,000.0
Debt, interest rate			1.00%
Principal balance payable in balloon payment			100.00%
Debt Instrument, Number of Balloon Payments \| payment		1								1
Percentage of security deposit on outstanding obligations			100.00%
Minimum percentage required for collateral balance						1
Maximum percentage required for collateral balance						1.07
Underwriting Discount [Member]
Debt Instrument [Line Items]
Payments of Debt Issuance Costs	9,300,000
Payments of stock issuance costs	7,700,000
Other Costs [Member]
Debt Instrument [Line Items]
Payments of Debt Issuance Costs	500,000
Payments of stock issuance costs	$ 500,000
Coupon Interest [Member] \| Secured Convertible Notes Due June 2015 [Member] \| Deerfield Financing [Member] \| Subsequent Event [Member]
Debt Instrument [Line Items]
Debt Instrument, Interest Rate, Stated Percentage after Extension Option Election																					7.50%
Payment-in-Kind Interest [Member] \| Secured Convertible Notes Due June 2015 [Member] \| Deerfield Financing [Member] \| Subsequent Event [Member]
Debt Instrument [Line Items]
Debt Instrument, Interest Rate, Stated Percentage after Extension Option Election																					7.50%

Debt (2019 Notes) (Details) - Senior Subordinated Notes [Member] - Convertible Senior Subordinated Notes due August 15, 2019, 4.25% [Member] - USD ($)	Dec. 31, 2013	Dec. 31, 2012	Aug. 14, 2012
Debt Instrument [Line Items]
Net carrying amount of the liability component	$ 165,296,000	$ 149,800,000
Unamortized discount of the liability component	122,204,000	137,700,000
Face amount	$ 287,500,000	$ 287,500,000	$ 287,500,000

Debt (Schedule Of Future Principal Payments Of Total Long-Term Debt) (Details)
$ in Thousands

Dec. 31, 2013

USD ($)

^[1]

Debt Disclosure [Abstract]

$ 11,762

104,328

80,000

$ 287,500

[1]

Common Stock And Warrants (Narrative) (Details) - USD ($)		1 Months Ended				12 Months Ended
	Aug. 14, 2012	Jan. 31, 2014	Feb. 29, 2012	Oct. 31, 2011	Mar. 31, 2011	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011	Jan. 22, 2014	Oct. 31, 2002
Class of Warrant or Right [Line Items]
Class of Warrant or Right, Outstanding						1,441,215
Public offering of common stock	34,500,000		12,700,000		17,300,000
Net proceeds from public offering	$ 138,400,000		$ 65,000,000		$ 179,400,000	$ 0	$ 203,479,000	$ 179,375,000
Share price (dollars per share)	$ 4.25
Common stock, shares issued						184,533,651	183,697,213
Glaxo SmithKline [Member]
Class of Warrant or Right [Line Items]
Sale of stock, price per share				$ 6.66
Common stock, shares issued				5,537,906						3,000,000
Repayment of loan from agreement				$ 36,900,000
Repayment of accrued interest from agreement				$ 8,000,000
Subsequent Event [Member]
Class of Warrant or Right [Line Items]
Public offering of common stock		10,000,000
Net proceeds from public offering		$ 75,600,000
Share price (dollars per share)		$ 8.00
Option to Purchase Additional Shares, Term		30 days
Option to Purchase Additional Shares, Number of Shares		1,500,000
Senior Subordinated Notes [Member] \| Convertible Senior Subordinated Notes due August 15, 2019, 4.25% [Member]
Class of Warrant or Right [Line Items]
Debt, principal amount	$ 287,500,000					$ 287,500,000	$ 287,500,000
Sale of stock, price per share	$ 5.31
Warrants Issued On January Twenty Two Two Thousand and Fourteen[Member] [Member] \| Subsequent Event [Member]
Class of Warrant or Right [Line Items]
Class of Warrant or Right, Outstanding									1,000,000

Common Stock And Warrants (Schedule Of Warrants To Purchase Common Stock Outstanding And Exercisable) (Details)	12 Months Ended
	Dec. 31, 2013 $ / warrant shares
Class of Warrant or Right [Line Items]
Number of Shares	1,441,215
Issued On June 4, 2008 [Member]
Class of Warrant or Right [Line Items]
Exercise Price per Share \| $ / warrant	7.40
Expiration Date	June 4, 2014
Number of Shares	1,000,000
Issued On June 10, 2009 [Member]
Class of Warrant or Right [Line Items]
Exercise Price per Share \| $ / warrant	6.05
Expiration Date	June 10, 2014
Number of Shares	441,215

Fair Value Measurements (Schedule of Estimated Fair Value of Outstanding Debt) (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
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	$ 165,296	$ 149,800
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	2,090	5,260
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	339,883	280,111
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	79,946	79,542
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	$ 2,090	$ 5,253

Employee Benefit Plans (Narrative) (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number	23,983,275	18,448,550	17,436,378	19,630,030
Options granted	6,694,174	3,442,696	2,545,625
Stock-based compensation expense	$ 12,018	$ 8,781	$ 12,019
Options, cancelled	79,942	358,360	1,021,323
Fair value of employee options vested and expensed	$ 7,400	$ 5,600	$ 8,400
Cash received from option exercises and purchases under the ESPP	$ 1,500	2,100
Retirement Plan, employee contribution (percentage)	50.00%
Employer matching contributions for first 4% of participant contributions	50.00%
Employer matching contributions for first 3% of participant contributions	100.00%
Percentage of company contribution to participant's compensation	4.00%
Percentage of participant contributions into the 401(k) Retirement Plan	3.00%
Expenses relating to stock match	$ 800	600	800
Non Employees [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation expense	$ 100	100	$ 100
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 (years)	P7Y		P10Y
Number of shares available for grant	1,709,233
Intrinsic value of options exercised	$ 0	100	$ 7,000
Total unrecognized compensation expense	$ 17,100
Unrecognized compensation expense weighted-average period for recognition (In years)	2 years 7 months 13 days
2009 Option Exchange Program [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Life of stock options granted (years)	P6Y2M12D
Performance Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Number	3,720,752
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	$ 7,300
Unrecognized compensation expense weighted-average period for recognition (In years)	3 years 3 months 10 days
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Discount rate from market value on purchase date	85.00%
Discount rate from market value on offering date	85.00%
Stock-based compensation expense	$ 600	$ 400	$ 700
Number of shares available for grant	2,040,839
Common stock issued (shares)	345,828	298,533	375,305
Average price per share	$ 4.13	$ 4.08	$ 4.62

Employee Benefit Plans (Schedule Of Allocated Employee Stock-Based Compensation Expense) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Employee stock-based compensation expense	$ 12,018	$ 8,781	$ 12,019
Research And Development Expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Employee stock-based compensation expense	6,021	4,536	5,935
General And Administrative Expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Employee stock-based compensation expense	5,948	4,245	5,459
Restructuring-Related Stock Compensation Expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Employee stock-based compensation expense	$ 49	$ 0	$ 625

Employee Benefit Plans (Schedule Of Fair Value Of Employee Share-Based Payments Awards ESPP Assumptions And Weighted Average Fair Values) (Details) - $ / shares	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant-date fair value	$ 2.97	$ 3.24	$ 3.50
Risk-free interest rate	1.51%	0.81%	1.07%
Dividend yield	0.00%	0.00%	0.00%
Volatility	61.00%	69.00%	70.00%
Expected life (in months/years)	5 years 7 months 17 days	5 years 7 months 17 days	5 years 6 months
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant-date fair value	$ 1.64	$ 2.07	$ 2.85
Risk-free interest rate	0.11%	0.10%	0.11%
Dividend yield	0.00%	0.00%	0.00%
Volatility	66.00%	68.00%	68.00%
Expected life (in months/years)	6 months	6 months	6 months

Employee Benefit Plans (Summary Of All Stock Option Activity) (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
Options outstanding at beginning of the year, Shares	18,448,550	17,436,378	19,630,030
Granted, Shares	6,694,174	3,442,696	2,545,625
Exercised, Shares	(13,311)	(181,979)	(2,161,804)
Forfeited, Shares	(79,942)	(358,360)	(1,021,323)
Expired, Shares	(1,066,196)	(1,890,185)	(1,556,150)
Options outstanding at ending of the year, Shares	23,983,275	18,448,550	17,436,378
Exercisable at December 31, 2013	13,818,615
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)	$ 6.85	$ 7.16	$ 7.52
Granted, Weighted Average Exercise Price (dollars per share)	5.44	5.45	5.86
Exercised, Weighted Average Exercise Price (dollars per share)	5.06	5.09	5.75
Forfeited, Weighted Average Exercise Price (dollars per share)	5.27	5.88	6.22
Expired, Weighted Average Exercise Price (dollars per share)	6.45	7.54	12.13
Options outstanding at ending of the year, Weighted Average Exercise Price (dollars per share)	6.48	$ 6.85	$ 7.16
Exercisable at December 31, 2013, Weighted Average Exercise Price (dollars per share)	$ 7.21
Options outstanding, Weighted Average Remaining Contractual Term	4 years 7 months 17 days
Exercisable at December 31, 2013, Weighted Average Remaining Contractual Term	3 years 5 months 8 days
Options outstanding, Aggregate Intrinsic Value	$ 8,079
Exercisable at December 31, 2013, Aggregate Intrinsic Value	$ 3,458

Employee Benefit Plans (Summary Of Information About Stock Options Outstanding) (Details)	12 Months Ended
	Dec. 31, 2013 $ / shares shares
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Options Outstanding, Number (shares) \| shares	23,983,275
Options Outstanding, Weighted Average Remaining Contractual Life (Years)	4 years 7 months 17 days
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 6.48
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	13,818,615
Options Outstanding and Exercisable, Weighted Average Exercise Price (dollars per share)	$ 7.21
$3.05 - $5.50 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower (dollars per share)	3.05
Exercise Price Range, upper (dollars per share)	$ 5.50
Options Outstanding, Number (shares) \| shares	4,735,373
Options Outstanding, Weighted Average Remaining Contractual Life (Years)	5 years 2 months 4 days
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 5.07
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	2,841,746
Options Outstanding and Exercisable, Weighted Average Exercise Price (dollars per share)	$ 5.04
$5.51 - $5.63 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower (dollars per share)	5.51
Exercise Price Range, upper (dollars per share)	$ 5.63
Options Outstanding, Number (shares) \| shares	10,369,851
Options Outstanding, Weighted Average Remaining Contractual Life (Years)	5 years 3 months
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 5.55
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	3,004,560
Options Outstanding and Exercisable, Weighted Average Exercise Price (dollars per share)	$ 5.62
$5.65 - $8.86 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower (dollars per share)	5.65
Exercise Price Range, upper (dollars per share)	$ 8.86
Options Outstanding, Number (shares) \| shares	3,877,697
Options Outstanding, Weighted Average Remaining Contractual Life (Years)	5 years 21 days
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 6.97
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	2,971,955
Options Outstanding and Exercisable, Weighted Average Exercise Price (dollars per share)	$ 7.32
$8.88 - $12.10 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower (dollars per share)	8.88
Exercise Price Range, upper (dollars per share)	$ 12.10
Options Outstanding, Number (shares) \| shares	5,000,354
Options Outstanding, Weighted Average Remaining Contractual Life (Years)	2 years 6 months
Options Outstanding, Weighted Average Exercise Price (dollars per share)	$ 9.34
Options Outstanding and Exercisable, Number of Exercisable (shares) \| shares	5,000,354
Options Outstanding and Exercisable, Weighted Average Exercise Price (dollars per share)	$ 9.34

Employee Benefit Plans (Summary Of All RSU Activity) (Details) - Restricted Stock Units (RSUs) [Member] - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
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	1,294,621	1,391,691	2,172,431
Awarded, Shares	1,119,733	733,958	356,498
Released, Shares	(517,874)	(596,397)	(648,437)
Forfeited, Shares	(85,959)	(234,631)	(488,801)
Awards outstanding at end of period, Shares	1,810,521	1,294,621	1,391,691
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)	$ 6.07	$ 6.92	$ 7.31
Awarded, Weighted Average Grant Date Fair Value (dollars per share)	5.45	5.50	6.17
Released, Weighted Average Grant Date Fair Value (dollars per share)	6.60	7.15	7.43
Forfeited, Weighted Average Grant Date Fair Value (dollars per share)	5.49	6.62	7.45
Awards outstanding at end of period, Weighted Average Grant Date Fair Value (dollars per share)	$ 5.56	$ 6.07	$ 6.92
ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsOutstandingWeightedAverageRemainingContractualTerms	2 years 18 days
Awards outstanding, Aggregate Intrinsic Value	$ 10,736

Income Taxes (Narrative) (Details) - USD ($)	12 Months Ended
Income Taxes (Narrative) (Details) - USD ($)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Income Tax Examination [Line Items]
Income tax (benefit) provision	$ (96,000)	$ 107,000	$ 1,295,000
Prior year income taxes		100,000	600,000
State tax expense	10,000	74,000	660,000
Valuation allowance increased/decreased	16,800,000	(6,800,000)	(49,700,000)
Tax benefit of stock option	15,700,000
Unrecognized tax benefit would affect the effective tax rate	100,000	100,000	100,000
Unrecognized Tax Benefits, Interest on Income Taxes Accrued	20,000	15,000	9,000
Unrecognized Tax Benefits, Interest on Income Taxes Expense	4,000	$ 6,000	$ 9,000
Internal Revenue Service (IRS) [Member]
Income Tax Examination [Line Items]
Net operating loss carryforwards	988,000,000
Research and development tax credits	75,000,000
State and Local Jurisdiction [Member]
Income Tax Examination [Line Items]
Net operating loss carryforwards	$ 918,000,000
Maximum [Member] \| Internal Revenue Service (IRS) [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards, expiration dates	Dec. 31, 2032
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, 2033
Minimum [Member] \| Internal Revenue Service (IRS) [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards, expiration dates	Dec. 31, 2018
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, 2014
Research Tax Credit Carryforward [Member] \| State and Local Jurisdiction [Member]
Income Tax Examination [Line Items]
Research and development tax credits	$ 25,000,000
Manufacturing Investment Credit [Member] \| State and Local Jurisdiction [Member]
Income Tax Examination [Line Items]
Research and development tax credits	$ 1,000,000

Income Taxes (Schedule Of Consolidated Net Income (Loss)) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Income Tax Disclosure [Abstract]
Domestic	$ (236,076)	$ (147,538)	$ 76,992
Foreign	(8,780)	0	0
(Loss) income before income taxes	$ (244,856)	$ (147,538)	$ 76,992

Income Taxes (Components of Income Tax Expense (Benefit)) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Current:
Federal	$ 0	$ 32	$ 636
State	12	75	659
Total current tax expense	12	107	1,295
Deferred:
Federal	(106)	0	0
State	(2)	0	0
Total deferred tax expense	(108)	0	0
Income tax (benefit) provision	$ (96)	$ 107	$ 1,295

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, 2013	Dec. 31, 2012	Dec. 31, 2011
Income Tax Disclosure [Abstract]
U.S. federal taxes (benefit) at statutory rate	$ (83,251)	$ (50,163)	$ 26,177
Unutilized net operating losses	(3,438)	46,324	(29,650)
Non-deductible interest	3,380	3,297	2,809
Stock based compensation	393	504	627
State tax expense	10	74	660
Refundable tax credit	0	32	636
Effective Income Tax Rate Reconciliation, Deduction, Other, Amount	106	0	0
Effective Income Tax Rate Reconciliation, Deduction, IP Transfer	82,858	0	0
Other	58	39	36
Income tax (benefit) provision	$ (96)	$ 107	$ 1,295

Income Taxes (Schedule Of Deferred Assets And Liabilities) (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Income Tax Disclosure [Abstract]
Net operating loss carryforwards	$ 358,372	$ 374,200
Tax credit carryforwards	64,635	65,232
Amortization of deferred stock compensation - non-qualified	24,279	26,469
Accruals and reserves not currently deductible	10,107	13,732
Deferred revenue	502	6,501
Book over tax depreciation and amortization	4,499	5,140
Total deferred tax assets	462,394	491,274
Valuation allowance	(421,426)	(438,266)
Net deferred tax assets	40,968	53,008
Convertible debt	(40,968)	(53,008)
Total deferred tax liabilities	(40,968)	(53,008)
Net deferred taxes	$ 0	$ 0

Income Taxes (Schedule Of Unrecognized Tax Benefits) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Reconciliation of Unrecognized Tax Benefits, Excluding Amounts Pertaining to Examined Tax Returns [Roll Forward]
Beginning balance	$ 47,298	$ 39,310	$ 46,381
Increase (decrease) relating to prior year provision	(112)	5,894	(9,782)
Increase relating to current year provision	7,891	2,094	2,711
Ending balance	$ 55,077	$ 47,298	$ 39,310

Net (Loss) Income Per Share (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Earnings Per Share [Abstract]
Net (loss) income	$ (70,746)	$ (67,124)	$ (62,161)	$ (44,729)	$ (52,193)	$ (32,814)	$ (36,487)	$ (26,151)	$ (244,760)	$ (147,645)	$ 75,697
Shares used in computing basic (loss) income per share amounts (in shares)									184,062	160,138	126,018
Shares issuable upon exercise of outstanding stock options									0	0	2,064
Shares issuable upon exercise of warrants									0	0	1,858
Shares issuable upon vesting of RSUs									0	0	515
Shares issuable upon purchase from ESPP contributions									0	0	24
Total dilutive securities									0	0	4,461
Shares used in computing diluted (loss) income per share amounts									184,062	160,138	130,479
Net (loss) income per share, basic (in dollars per share)									$ (1.33)	$ (0.92)	$ 0.60
Net (loss) income per share, diluted (in dollars per share)									$ (1.33)	$ (0.92)	$ 0.58
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Potentially dilutive shares									76,965	72,132	9,085
Convertible debt [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Potentially dilutive shares									54,123	54,123	0
Outstanding stock options, unvested RSUs and ESPP contributions [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Potentially dilutive shares									21,401	16,568	9,085
Warrants [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Potentially dilutive shares									1,441	1,441	0

Commitments (Schedule Of Aggregate Future Minimum Lease Payments Under Operating Leases) (Details)
$ in Thousands

Dec. 31, 2013

USD ($)

Commitments and Contingencies Disclosure [Abstract]

2014

$ 19,896

^[1]

2015

20,152

^[1]

2016

16,431

^[1]

2017

9,104

^[1]

2018

2,806

^[1]

Thereafter

^[1]

Total

68,389

^[1]

Future minimum rental under noncancelable subleases

$ 16,100

[1]	Minimum payments have not been reduced by minimum sublease rentals of $16.1 million due in the future under noncancelable subleases.

Commitments (Schedule Of Aggregate Future Minimum Lease Payments Under Operating Leases By Material Lease Agreements) (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2013 USD ($) renewal
Operating Leased Assets [Line Items]
Future Minimum Lease Payment	$ 68,389
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, in years	5 years
Future Minimum Lease Payment	$ 38,483
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, in years	5 years
Future Minimum Lease Payment	$ 21,070
Building Lease #4 [Member]
Operating Leased Assets [Line Items]
Original Term (Expiration)	Dec. 01, 2015
Number of Renewal Options \| renewal	1
Period of Renewal Option, in years	3 years
Future Minimum Lease Payment	$ 8,692
Other [Member]
Operating Leased Assets [Line Items]
Future Minimum Lease Payment	$ 144

Commitments (Narrative) (Details) - USD ($) $ in Millions	12 Months Ended
Commitments (Narrative) (Details) - USD ($) $ in Millions	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Operating Leased Assets [Line Items]
Rent expenses under operating leases	$ 9.1	$ 17.8	$ 21.3
Net of sublease rentals under operating leases	4.1	3.8	$ 1.9
Collateral provided for purchasing card program	3.5	2.5
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	$ 0.7	$ 0.6

Concentrations of Credit Risk (Details)	12 Months Ended
Concentrations of Credit Risk (Details)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Bristol-Myers Squibb [Member] \| Revenue, Rights Granted [Member] \| Customer Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration Risk, Percentage	52.00%	66.00%	59.00%
Diplomat Specialty Pharmacy [Member] \| Accounts Receivable [Member] \| Customer Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration Risk, Percentage	87.00%
Diplomat Specialty Pharmacy [Member] \| Revenue, Rights Granted [Member] \| Customer Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration Risk, Percentage	45.00%	0.00%	0.00%
Merck [Member] \| Revenue, Rights Granted [Member] \| Customer Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration Risk, Percentage	0.00%	22.00%	0.00%
Daiichi Sankyo [Member] \| Revenue, Rights Granted [Member] \| Customer Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration Risk, Percentage	0.00%	12.00%	0.00%
Sanofi [Member] \| Revenue, Rights Granted [Member] \| Customer Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration Risk, Percentage	0.00%	0.00%	39.00%
UNITED STATES \| Sales [Member] \| Geographic Concentration Risk [Member]
Concentration Risk [Line Items]
Concentration Risk, Percentage	97.00%	100.00%	100.00%

Subsequent Events (Details)		1 Months Ended			12 Months Ended
Subsequent Events (Details)	Aug. 14, 2012 USD ($) $ / shares shares	Jan. 31, 2014 USD ($) $ / shares shares	Feb. 29, 2012 USD ($) shares	Mar. 31, 2011 USD ($) shares	Dec. 31, 2013 USD ($) shares	Dec. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)	Jan. 22, 2014 USD ($) $ / warrant shares
Subsequent Event [Line Items]
Class of Warrant or Right, Outstanding					1,441,215
Sale of shares of common stock, shares	34,500,000		12,700,000	17,300,000
Share price (dollars per share) \| $ / shares	$ 4.25
Proceeds from issuance of common stock, net \| $	$ 138,400,000		$ 65,000,000	$ 179,400,000	$ 0	$ 203,479,000	$ 179,375,000
Subsequent Event [Member]
Subsequent Event [Line Items]
Sale of shares of common stock, shares		10,000,000
Share price (dollars per share) \| $ / shares		$ 8.00
Proceeds from issuance of common stock, net \| $		$ 75,600,000
Option to Purchase Additional Shares, Term		30 days
Option to Purchase Additional Shares, Number of Shares		1,500,000
Subsequent Event [Member] \| Warrants Issued On January Twenty Two Two Thousand and Fourteen[Member] [Member]
Subsequent Event [Line Items]
Class of Warrant or Right, Outstanding								1,000,000
Class of Warrant or Right, Exercise Price of Warrants or Rights \| $ / warrant								9.70
Subsequent Event [Member] \| Secured Convertible Notes Due June 2015 [Member] \| Deerfield Financing [Member]
Subsequent Event [Line Items]
Principal Eligible for Extension Option \| $								$ 100,000,000

Quarterly Financial Data (Unaudited) (Schedule Of Quarterly Financial Data) (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Quarterly Financial Information Disclosure [Abstract]
Revenues	$ 4,347	$ 5,466	$ 11,856	$ 9,669	$ 7,814	$ 13,313	$ 7,813	$ 18,510
Gross profit	4,084	5,176	11,571	9,389
Loss from operations	(59,514)	(55,913)	(51,295)	(34,010)	(41,974)	(25,443)	(32,723)	(22,296)
Net loss	$ (70,746)	$ (67,124)	$ (62,161)	$ (44,729)	$ (52,193)	$ (32,814)	$ (36,487)	$ (26,151)	$ (244,760)	$ (147,645)	$ 75,697
Net loss per share, basic and diluted (in dollars per share)	$ (0.38)	$ (0.36)	$ (0.34)	$ (0.24)	$ (0.28)	$ (0.20)	$ (0.25)	$ (0.18)

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