View Filing Data

Other comprehensive income (loss)

$ (147,645)

$ 75,697

$ (92,330)

^[1]

(150)

(143)

Comprehensive (loss) income

$ (147,599)

$ 75,547

$ (92,473)

[1]	Other comprehensive income (loss) consisted solely of unrealized gains (losses) on available for sale securities for the periods presented.

The change in equity [net assets] of a business enterprise during a period from transactions and other events and circumstances from non-owner sources which are attributable to noncontrolling interests. It includes all changes in equity during a period except those resulting from investments by owners and distributions to owners, which are directly or indirectly attributable to that ownership interest in subsidiary equity which is not attributable to the parent.

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=6943989&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=6880815&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=20435746&loc=d3e565-108580

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 38
-Subparagraph d
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 130
-Paragraph 10, 15
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph A7
-Appendix A

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Emerging Issues Task Force (EITF)
-Number 87-21
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 03
-Paragraph 19
-Article 5

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 38
-Subparagraph a
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 95
-Paragraph 28, 29, 30
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 16: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Paragraph 20
-Article 9

Net of tax amount of unrealized holding gain (loss) before reclassification adjustments and transfers on available-for-sale securities.

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 10A
-Subparagraph (e)
-URI http://asc.fasb.org/extlink&oid=20435746&loc=SL7669646-108580

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=20435746&loc=d3e637-108580

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 13
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 130
-Paragraph 17, 22
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 130
-Paragraph 24
-Subparagraph b
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 38
-Subparagraph c(3)
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Balance, shares at Dec. 31, 2009

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]

107,918,334

Balance at Dec. 31, 2009

$ (163,725)

$ 108

$ 925,736

$ 155

$ (1,089,724)

Other comprehensive (loss) income

(92,330)

(143)

^[1]

(143)

Issuance of common stock under stock plans, shares

1,368,826

Issuance of common stock under stock plans

6,761

$ 1

6,760

Stock-based compensation expense

21,112

Balance, shares at Dec. 31, 2010

109,287,160

Balance at Dec. 31, 2010

(228,325)

$ 109

953,608

(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)

Common stock, shares issued

135,563,735

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

Balance, shares at Dec. 31, 2012

183,697,213

Balance at Dec. 31, 2012

$ 296,434

$ 183

$ 1,550,345

$ (92)

$ (1,254,002)

Common stock, shares issued

183,697,213

[1]	Other comprehensive income (loss) consisted solely of unrealized gains (losses) on available for sale securities for the periods presented.

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Cash flows from operating activities:
Net (loss) income	$ (147,645)	$ 75,697	$ (92,330)
Adjustments to reconcile net (loss) income to net cash used in operating activities:
Depreciation and amortization	5,717	6,822	10,543
Stock-based compensation expense	8,833	12,099	21,112
Restructuring (credit) charge for property and equipment	(204)	497	3,327
Accretion of debt discount	14,752	7,989	3,596
Net gain on sale of property and equipment	(950)	0	0
Gain on sale of businesses	0	(2,254)	(8,197)
Other	4,989	4,801	3,234
Changes in assets and liabilities:
Other receivables	27,038	(24,294)	5,968
Prepaid expenses and other current assets	(1,764)	10,553	(66)
Other assets	(1,966)	405	(1,807)
Accounts payable and other accrued liabilities	6,318	(5,555)	(9,444)
Restructuring liability	5,244	(303)	14,281
Other long-term liabilities	(1,588)	(1,162)	(8,320)
Deferred revenue	(41,920)	(244,528)	(42,945)
Net cash used in operating activities	(123,146)	(159,233)	(101,048)
Cash flows from investing activities:
Purchases of property and equipment	(2,717)	(991)	(1,811)
Proceeds from sale of property and equipment	1,943	1,526	165
Proceeds from sale of businesses	0	3,010	9,000
Proceeds from maturities of restricted cash and investments	5,499	8,099	8,144
Purchase of restricted cash and investments	(41,485)	(5,899)	(8,099)
Proceeds from sale of investments	0	55,205	12,780
Proceeds from maturities of investments	310,765	124,800	127,569
Purchases of investments	(533,475)	(237,213)	(167,317)
Net cash used in investing activities	(259,470)	(51,463)	(19,569)
Cash flows from financing activities:
Proceeds from issuance of common stock, net	203,479	179,375	0
Proceeds from exercise of stock options and warrants	929	12,436	2,684
Proceeds from employee stock purchase plan	1,217	1,734	3,132
Proceeds from debt issuance, net	277,673	2,589	165,008
Principal payments on debt	(4,870)	(8,621)	(39,563)
Net cash provided by financing activities	478,428	187,513	131,261
Net increase (decrease) in cash and cash equivalents	95,812	(23,183)	10,644
Cash and cash equivalents at beginning of year	74,257	97,440	86,796
Cash and cash equivalents at end of year	170,069	74,257	97,440
Supplemental cash flow disclosure:
Cash paid for interest	6,982	6,835	11,059
Income Taxes Paid	1,118	0	0
Non-cash financing activity:
Issuance of common stock for settlement of convertible loan, including accrued interest	$ 0	$ 36,895	$ 0

Organization And Summary Of Significant Accounting Policies

12 Months Ended

Dec. 31, 2012

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. We are focusing our proprietary resources and development and commercialization efforts exclusively on COMETRIQ™ (cabozantinib), our wholly-owned inhibitor of multiple receptor tyrosine kinases. On November 29, 2012, the U.S. Food and Drug Administration approved COMETRIQ for the treatment of progressive, metastatic medullary thyroid cancer ("MTC"), in the United States. COMETRIQ is being evaluated in a variety of other cancer indications through a broad development program, including two ongoing phase 3 pivotal trials in metastatic castration-resistant prostate cancer ("CRPC") and two additional phase 3 pivotal trials in metastatic hepatocellular cancer and metastatic renal cell cancer that we plan to initiate in 2013. We believe COMETRIQ 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 COMETRIQ into a major oncology franchise, and we believe that the approval of COMETRIQ for the treatment of progressive, metastatic MTC provides us with the opportunity to establish a commercial presence in furtherance of this objective.

We have also established a portfolio of other novel compounds that we believe have the potential to address serious unmet medical needs. Many of these compounds are being advanced by partners as part of collaborations, at no cost to us but with significant retained economics to Exelixis in the event these compounds are commercialized. As disclosed on ClinicalTrials.gov (NCT01689519), a phase 3 clinical trial for one of these compounds, GDC-0973 (XL518), which we out-licensed to Genentech, Inc. (a wholly-owned member of the Roche Group) ("Genentech"), was initiated on November 1, 2012.

Basis of Consolidation

The consolidated financial statements include the accounts of Exelixis and those of our wholly-owned subsidiary. All intercompany balances and transactions have been eliminated.

Basis of Presentation

We have adopted a 52- or 53-week fiscal year that generally ends on the Friday closest to December 31. Fiscal year 2010, a 52-week year, ended on December 31, 2010, fiscal year 2011, a 52-week year, ended on December 30, 2011, and fiscal year 2012, a 52-week year, ended on December 28, 2012. For convenience, references in this report as of and for the fiscal years ended, December 31, 2010, December 30, 2011 and December 28, 2012 are indicated on a calendar year basis, ended December 31, 2010, 2011 and 2012, respectively.

Segment Information

We operate in one business segment. We have operations solely 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. In fiscal years 2012, 2011 and 2010, 100% of our revenues were earned in the United States and all of our long-lived assets were located in the United States.

Use of Estimates

The preparation of the consolidated financial statements is in conformity with accounting principles generally accepted in the United States which requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue and expenses, and related disclosures. On an ongoing basis, management evaluates its estimates including, but not limited to, those related to revenue recognition, long-lived assets, certain accrued liabilities, 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 are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results could differ materially from those estimates.

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.

Historically, all investments were viewed as available for use in current operations. Therefore, as of December 31, 2011 we classified certain investments as short-term investments even though their stated maturity dates may have been one year or more beyond the balance sheet date. As of December 31, 2012, due to the increase in our cash balances as a result of the financing activities we completed in February 2012 and in August 2012, we no longer require investments with original maturities in excess of 12 months for use in current operations, and have accordingly classified those investments that mature in more than 12 months as Long-term investments on our Consolidated Balance Sheets. As of December 31, 2012 and 2011, all 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, 2012, 2011, and 2010, we did not record any significant other-than-temporary impairment charges on its available-for-sale securities.

Foreign Currency Forward Contract

We have entered into foreign currency forward contracts to reduce our net exposure to Eurodollar currency fluctuations. In March 2010, we entered into a new foreign contract for a notional amount of $7.0 million that expired in December 2011. In December 2011, we received the $7.0 million from the French taxing authority relating to our 2009 Sanofi collaboration agreement and as a result, we settled all outstanding contracts for a net loss of $0.3 million and cash receipt of $6.7 million. The net unrealized loss on our foreign currency forward contracts, none of which were designated as a hedge, were recorded in our Consolidated Statements of Operations as Interest income and other, net. There were no foreign currency forward contracts outstanding as of December 31, 2012, December 31, 2011 or at any time during 2012.

Fair Value Measurements

We disclose the fair value of financial instruments for assets and liabilities for which the value is practicable to estimate. 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).

For those financial instruments which are measured and recorded at fair value on a recurring basis, we also provide fair value hierarchy information in these Notes to Consolidated Financial Statements. We currently exclude cash, but include investments classified as cash equivalents in this presentation; such investments are carried at fair value. Previously, we included cash in the presentation of fair value hierarchy information. Prior periods have been updated to reflect current presentation.

Inventory

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 are not capitalized as inventory but are expensed as research and development costs. When regulatory approval is obtained, we begin capitalization of inventory. 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.

Once we begin capitalization of inventory, it 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 sales in the Consolidated Statements of Operations.

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

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 as is consistent with our sole operating segment as of December 31, 2012 and 2011.

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

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, and contingent milestone payments and royalties. 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 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 is generally ratably over the period of the research and development obligation.

Milestone payments are non-refundable and recognized as revenues over the period of the research arrangement. This typically results in a portion of the milestone being recognized at the date the milestone is achieved, which portion is equal to the applicable percentage of the research term that has elapsed at the date the milestone is achieved, and the balance being recognized over the remaining research term of the agreement. In certain situations, we may receive milestone payments after the end of our period of continued involvement. In such circumstances, we would recognize 100% of the milestone revenues when the milestone is achieved. 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.

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, 2012, 2011 and 2010, we recorded a reduction related to prior periods of approximately $2.7 million, $1.6 million and $0.9 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 periods 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 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.

We have employee and director stock option plans that are more fully described in Note 10.

Need to Raise Additional Capital

We have incurred net losses since inception through the year ended December 31, 2012, 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, 2012, we had a net loss of $147.6 million; as of December 31, 2012, we had an accumulated deficit of $1.3 billion. As of December 31, 2012, we had not generated revenues from the sale of COMETRIQ, which was commercially launched for the treatment of progressive, metastatic MTC in the United States in January 2013. We have derived substantially all of our revenues to date from collaborative research and development agreements. Revenues from research and development collaborations depend upon continuation of the collaborations, 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, our collaborators fail to develop successful products or research funding we receive from collaborators decreases, 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 December 2011, Accounting Standards Codification ("ASC") Topic 350, Testing Goodwill for Impairment was amended to allow the option of performing a qualitative assessment in evaluating goodwill for impairment. We adopted this guidance beginning January 1, 2012, and it did not have a material effect on our consolidated financial statements.

In May 2011, ASC Topic 820, Fair Value Measurement was amended to converge U.S. and international accounting standards and provide more detailed disclosure. We adopted this guidance beginning January 1, 2012 and added additional disclosure as required. The amendment did not have a material effect on our consolidated financial statements.

Recently Issued Accounting Pronouncements Not Yet Adopted

In July 2012, 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 will be effective January 1, 2013. We do not expect the adoption of the amendment to have a material impact on our consolidated financial statements.

Research And Collaboration Agreements	12 Months Ended
Research And Collaboration Agreements	Dec. 31, 2012
Research And Collaboration Agreements [Abstract]
Research And Collaboration Agreements	RESEARCH AND COLLABORATION AGREEMENTS Genentech In December 2006, we entered into a worldwide co-development agreement with Genentech for the development and commercialization of GDC-0973 (XL518). GDC-0973 (XL518) 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 GDC-0973 (XL518) resulted in potent and sustained inhibition of MEK in RAS- or BRAF-mutant tumor models. Exelixis discovered GDC-0973 (XL518) 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 GDC-0973 (XL518). Under the terms of the agreement, we were responsible for developing GDC-0973 (XL518) through the end of a phase 1 clinical trial, and Genentech had the option to co-develop GDC-0973 (XL518), 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 achieved, we granted to Genentech an exclusive worldwide revenue-bearing license to GDC-0973 (XL518) 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 milestone payment in March 2010. Preliminary results from BRIM7, an ongoing phase 1b dose escalation study conducted by Roche and Genentech of the BRAF inhibitor ("BRAFi") vemurafenib in combination with GDC-0973 (XL518) in patients with locally advanced/unresectable or metastatic melanoma carrying a BRAFV600 mutation were presented at the European Society of Medical Oncologists Annual Meeting in September 2012. As disclosed on ClinicalTrials.gov (NCT01689519), a multicenter, randomized, double-blind, placebo-controlled phase 3 clinical trial evaluating the combination of vemurafenib with GDC-0973 (XL518) 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. Under the terms of our agreement with Genentech, we are entitled to an initial equal share of U.S. profits and losses for GDC-0973 (XL518), 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. We also have the option to co-promote in the United States. The co-promotion option would allow us to provide up to 25% of the total sales force for GDC-0973 (XL518) in the United States. We must exercise the co-promotion option within 12 months of receiving notification of the first patient dosed in the first phase 3 clinical trial of GDC-0973 (XL518). Our receipt of the notification of dosing from Genentech on January 14, 2013 triggered the beginning of the period in which we can exercise our co-promotion option. As a condition to exercise the co-promotion option, we must have the capability to co-promote, including an adequate internal sales and promotional infrastructure, and an experienced internal oncology sales force. 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. Bristol-Myers Squibb TGR5 License Agreement In October 2010, we entered into a global license agreement with Bristol-Myers Squibb pursuant to which we granted to Bristol-Myers Squibb a license to our small-molecule TGR5 agonist program, including rights to the program’s lead compound, XL475, as well as potential backups. The license agreement became effective in November 2010 following clearance under the Hart-Scott-Rodino Antitrust Improvement Act of 1976, as amended. The license agreement was amended and restated in April 2011 in connection with an assignment of patents to a wholly-owned subsidiary. Under the license agreement, Bristol-Myers Squibb received a worldwide exclusive license to XL475 and sole control and responsibility for all research, development, commercial and manufacturing activities. In November 2010 we received a nonrefundable upfront cash payment of $35.0 million from Bristol-Myers Squibb. Additionally, for each product developed by Bristol-Myers Squibb under the license, we will be eligible to receive development and regulatory milestones of up to $250.0 million in the aggregate and commercial milestones of up to $150.0 million in the aggregate, as well as royalties on commercial sales of any such products. Bristol-Myers Squibb may at any time, upon specified prior notice to us, terminate the license on a product-by-product and country-by-country basis. In addition, either party may terminate the license 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 from Bristol-Myers Squibb a license to develop and commercialize such product in the related country. Such license would be royalty-free if the agreement is terminated by Bristol-Myers Squibb at will, or royalty-bearing if the agreement is terminated by us for Bristol-Myers Squibb’s uncured material breach. In the event of termination by Bristol-Myers Squibb for our uncured material breach, Bristol-Myers Squibb would retain the right to such product and we would receive reduced royalties from Bristol-Myers Squibb on commercial sales of such product. 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 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 will be 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 will end on the earlier to occur of (i) July 8, 2013 if a compound has not satisfied certain specified criteria by such time or (ii) the date when such compound satisfied the next level of specified criteria, whichever is earlier. Following the collaborative research period, Bristol-Myers Squibb will 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. 2008 Cancer Collaboration In December 2008, we entered into a worldwide collaboration with Bristol-Myers Squibb for cabozantinib and XL281 (BMS-908662), a RAF inhibitor. Upon effectiveness of the collaboration agreement in December 2008, Bristol-Myers Squibb made a nonrefundable upfront cash payment of $195.0 million for the development and commercialization rights to both programs. The agreement required Bristol-Myers Squibb to make additional license payments to us of $45.0 million, which were received during 2009. On July 8, 2011, we received written notification from Bristol-Myers Squibb of its decision to terminate the collaboration agreement on a worldwide basis as to XL281. The termination was made pursuant to the terms of the collaboration agreement and became effective on October 8, 2011. Bristol-Myers Squibb informed us that the termination was based upon Bristol-Myers Squibb’s review of XL281 in the context of Bristol-Myers Squibb’s overall research and development priorities and pipeline products. Upon the effectiveness of the termination, Bristol-Myers Squibb’s license relating to XL281 terminated, and rights to XL281 reverted to us. We also received, subject to certain terms and conditions, licenses from Bristol-Myers Squibb to research, develop and commercialize XL281. We have discontinued activities related to XL281 and do not currently expect to further research, develop or commercialize XL281. On June 18, 2010, we regained full rights to develop and commercialize cabozantinib under the collaboration agreement following receipt of notice from Bristol-Myers Squibb of its decision to terminate the collaboration agreement, solely as to cabozantinib, on a worldwide basis. Bristol-Myers Squibb informed us that the termination was based upon its review of cabozantinib in the context of Bristol-Myers Squibb’s overall research and development priorities and pipeline products. On June 28, 2010, in connection with the termination, we received a $17.0 million transition payment from Bristol-Myers Squibb in satisfaction of its obligations under the collaboration agreement to continue to fund its share of development costs for cabozantinib for a period of three months following the notice of termination. 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. 2007 Cancer Collaboration In December 2006, we entered into a worldwide collaboration with Bristol-Myers Squibb, which became effective in January 2007, to discover, develop and commercialize novel targeted therapies for the treatment of cancer. We were responsible for discovery and preclinical development of small molecule drug candidates directed against mutually selected targets. In January 2007, Bristol-Myers Squibb made an upfront payment of $60.0 million to us for which we granted Bristol-Myers Squibb the right to select up to three IND candidates from six future Exelixis compounds. For each IND candidate selected, we were entitled to receive a $20.0 million selection milestone from Bristol-Myers Squibb. Once selected, Bristol-Myers Squibb became responsible for leading the further development and commercialization of the selected IND candidates. In addition, we had the right to opt in to co-promote the selected IND candidates, in which case we would equally share all development costs and profits in the United States. In January 2008 and November 2008, Bristol-Myers Squibb exercised its option under the collaboration to develop and commercialize BMS-833923 (XL139), a Hedgehog inhibitor, and BMS-863233 (XL413), a CDC7 inhibitor, respectively. Under the terms of the collaboration agreement, the selection of BMS-833923 (XL139) and BMS-863233 (XL413) by Bristol-Myers Squibb entitled us to milestone payments of $20.0 million each, which we received in February 2008 and December 2008, respectively. In addition, we exercised our option under the collaboration agreement to co-develop and co-commercialize each of BMS-833923 (XL139) and BMS-863233 (XL413) in the United States. However, in September 2010, we and Bristol-Myers Squibb terminated the BMS-863233 (XL413) program due to an unfavorable pharmacological profile observed in phase 1 clinical evaluation. Additionally, in connection with an amendment to the collaboration which became effective in November 2010, we exercised our right to opt-out of further co-development of BMS-833923 (XL139) in consideration for a cash payment of $20.0 million. As disclosed on ClinicalTrials.gov (NCT01218477), BMS is continuing to develop BMS-833923 (XL139) in combination with dasatinib in a phase 1/2 clinical trial in patients with chronic myeloid leukemia. The collaboration agreement was amended and restated in April 2011 in connection with an assignment of patents to a wholly-owned subsidiary. We have no further responsibility for conducting new activities or funding new development or commercialization activities with respect to BMS-833923 (XL139) and will therefore no longer be eligible to share profits on sales of any commercialized products under the collaboration. We will continue to be eligible to receive regulatory and commercial milestones of up to $260.0 million as well as double-digit royalties on any future sales of any products commercialized under the collaboration. As a result of the November 2010 amendment to the collaboration, the research term has ended, and we have no further obligation to deliver to Bristol-Myers Squibb a third IND candidate under the collaboration. Bristol-Myers Squibb may, upon notice to us, terminate the agreement as to any product containing or comprising the selected candidate. In the event of such termination election, Bristol-Myers Squibb’s license relating to such product would terminate and revert to us, and we would receive, subject to certain terms and conditions, licenses from Bristol-Myers Squibb to research, develop and commercialize certain collaboration compounds that were discovered. LXR Collaboration 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. 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 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 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 for achieving a development milestone with respect to BMS-852927 (XL041). 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 clinical trials in combination with an ErbB3 inhibitor in patients with solid tumors (NCT01436565) and in patients with advanced or recurrent endometrial cancer (NCT01013324). 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), and in combination with temozolomide (with or without radiation) in patients with malignant gliomas (NCT00704080). We will be eligible to receive 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 milestone 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. 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). 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. 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 will have 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 potential development and regulatory milestone payments for multiple indications of up to $239.0 million. We will also be eligible to receive combined sales performance milestones and royalties on net-sales of products emerging from the agreement. Milestones 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. Daiichi Sankyo In March 2006, we entered into a collaboration agreement with Daiichi Sankyo Company Limited ("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.

Dispositions	12 Months Ended
Dispositions	Dec. 31, 2012
Discontinued Operations and Disposal Groups [Abstract]
Dispositions	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 foreign currency 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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-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6391110&loc=d3e2941-110230

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 144
-Paragraph 43-48
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Restructurings

12 Months Ended

Dec. 31, 2012

Restructuring Charges [Abstract]

Restructurings

RESTRUCTURINGS

We implemented restructurings in March 2010 and December 2010 as a consequence of our decision to focus our proprietary resources and development efforts on the development and commercialization of cabozantinib. We implemented additional restructurings in March 2011 and May 2012 (the 2010, 2011 and 2012 restructurings are referred to collectively as the "Restructurings"). The aggregate reduction in headcount from the Restructurings is 422 employees.

During the three years ended December 31, 2012, we have recorded aggregate restructuring charges of $52.1 million in connection with the Restructurings, of which $21.2 million related to termination benefits, $28.6 million related to facility charges, $2.2 million net related to the impairment of excess equipment and other assets, and a minor amount of legal and other fees. Asset impairment charges were partially offset by cash proceeds of $2.6 million from the sale of such assets.

Our March 2010 restructuring charge was primarily related to termination benefits and facility related charges resulting from the closure of our facility in San Diego, California, and one of our South San Francisco facilities, which took into consideration a sublease that commenced in September 2010. The December 2010 restructuring charge was primarily related to termination benefits resulting from additional reductions in our workforce. Our 2011 restructuring charge was primarily facility-related charges that relate to portions of two additional buildings in South San Francisco and took into consideration our entry into two sublease agreements for the majority of one of these buildings in July 2011 as well as charges relating to the short-term exit of the second floor of another building in December 2011. The 2012 restructuring charge was primarily related to termination benefits in May 2012 and the December 2012 determination to extend disuse of most of the remaining space in one building for the remainder of the lease term.

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 years ended December 31, 2012, 2011 and 2010 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
Ending accrual balance as of December 31, 2012	$	—		$	19,202		$	—		$	20		$	19,222

We expect to pay the accrued facility charges of $19.2 million, net of cash received from our subtenants, through 2017, or the end of our lease terms of the buildings. With respect to our Restructurings, we expect to incur additional restructuring charges of $3.2 million relating to certain of our South San Francisco facilities that we planned to exit at a future date and which remained in use as of December 31, 2012). These charges will be recorded through the end the building lease terms, the last of which ends in 2017.

During the three years ended December 31, 2012, the Restructurings resulted in cash expenditures of $28.7 million, net of $2.6 million in cash received in connection with the sale of excess equipment and other assets.

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.

The entire disclosure for restructuring and related activities. Description of restructuring activities such as exit and disposal activities, include facts and circumstances leading to the plan, the expected plan completion date, the major types of costs associated with the plan activities, total expected costs, the accrual balance at the end of the period, and the periods over which the remaining accrual will be settled.

Investments, Debt and Equity Securities [Abstract]

Cash and Investments

12 Months Ended

Dec. 31, 2012

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, 2012 and 2011 (in thousands):



	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



	December 31, 2011
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
As reported:
Cash and cash equivalents	$	74,256	$	1	$	—		$	74,257
Short-term investments	120,143		35		(173		)	120,005
Long-term investments	85,260		—		—			85,260
Long-term restricted cash and investments	4,199		—		—			4,199
Total cash and investments	$	283,858	$	36	$	(173	)	$	283,721

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 and certain other designated financial institutions. The total collateral balances as of December 31, 2012 and 2011 were $87.0 million and $85.3 million, respectively and are reflected in our Consolidated Balance Sheets in Short- and Long-term investments. See "Note 7 - Debt" for more information regarding the collateral balance requirements under our Silicon Valley Bank loan and security agreement.

All of our cash and investments are classified as available-for-sale. The following table summarizes our cash and investments by security type as of December 31, 2012 and 2011 (in thousands):



	December 31, 2012
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Cash and money market funds	$	81,744	$	2	$	—		$	81,746
Commercial paper	167,223		8		—			167,231
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 cash and investments	$	634,053	$	99	$	(191	)	$	633,961



	December 31, 2011
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Cash and money market funds	$	81,986	$	—	$	—		$	81,986
Commercial paper	29,079		2		(1		)	29,080
Corporate bonds	116,068		22		(169		)	115,921
U.S. government sponsored enterprises	37,237		12		—			37,249
Municipal bonds	19,488		—		(3		)	19,485
Total cash and investments	$	283,858	$	36	$	(173	)	$	283,721

As of December 31, 2012, the fair value of investments that were in an unrealized loss position was $196.1 million, including $158.6 million in 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. 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, 2012 (in thousands):



	Mature within One Year		After One Year through Two Years		Fair Value
Money market funds	$	76,050	$	—	$	76,050
Commercial paper	167,231		—		167,231
Corporate bonds	126,896		95,053		221,949
U.S. Treasury and government sponsored enterprises	84,677		48,314		132,991
Municipal bonds	30,044		—		30,044
Total	$	484,898	$	143,367	$	628,265

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.

Property And Equipment

12 Months Ended

Dec. 31, 2012

Property, Plant and Equipment [Abstract]

Property And Equipment

PROPERTY AND EQUIPMENT

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



	December 31,
	2012			2011
Laboratory equipment	$	19,504		$	28,795
Computer equipment and software	11,897			11,743
Furniture and fixtures	3,230			3,230
Leasehold improvements	16,572			15,961
Construction-in-progress	1,409			155
	52,612			59,884
Less: accumulated depreciation and amortization	(46,553		)	(51,378		)
Property and equipment, net	$	6,059		$	8,506

For the years ended December 31, 2012, 2011 and 2010, we recorded depreciation expense of $4.8 million, $6.8 million and $10.5 million, respectively.

In 2012, 2011 and 2010, we recorded gross asset impairment charges in the amounts of approximately $0.3 million, $0.5 million and $3.2 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. Cash proceeds on those sales were $0.9 million, $1.5 million, and $0.2 million during 2012, 2011, and 2010, respectively.

The entire disclosure for long-lived, physical assets that are used in the normal conduct of business to produce goods and services and not intended for resale. Examples include land, buildings, machinery and equipment, and other types of furniture and equipment including, but not limited to, office equipment, furniture and fixtures, and computer equipment and software. This disclosure may include property plant and equipment accounting policies and methodology, a schedule of property, plant and equipment gross, additions, deletions, transfers and other changes, depreciation, depletion and amortization expense, net, accumulated depreciation, depletion and amortization expense and useful lives, income statement disclosures, assets held for sale and public utility disclosures.

Debt

12 Months Ended

Dec. 31, 2012

Debt Disclosure [Abstract]

Debt

DEBT

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



	December 31,
	2012			2011
Convertible Senior Subordinated Notes due 2019	$	149,800		$	—
Deerfield Notes	100,676			91,385
Silicon Valley Bank term loan	80,000			80,000
Silicon Valley Bank Line of Credit	5,260			10,130
Total debt	335,736			181,515
Less: current portion	(13,170		)	(4,870		)
Long-term debt	$	322,566		$	176,645

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.

In connection with the convertible debt offering, $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. The amount held in the escrow account is classified on our Consolidated Balance Sheets as Short-term restricted cash and investments and Restricted cash and investments of $12.2 million and $24.3 million, respectively, as of December 31, 2012. 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. We have adjusted the initially recorded balance of the liability component from $149.2 million to $144.3 million and the balance of equity component from $138.3 million to $143.2 million for the 2019 Notes along with the allocation of offering costs between debt and equity from the amounts originally reported in the Notes to our Condensed Consolidated Financial Statements included in our Quarterly Report on Form 10-Q for the period ended September 28, 2012 due to the finalization of the determination of the appropriate effective interest rate.

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



	December 31, 2012
Net carrying amount of the liability component	$	149,800
Unamortized discount of the liability component	137,700
Face amount of the 2019 Notes	$	287,500

The debt discount and debt issuance costs are amortized as interest expense through August 2019. During 2012, total interest expense related to the 2019 Notes was $10.3 million, relating to the 4.25% 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 during 2012 was $5.7 million.

The balance of unamortized fees and costs was $4.7 million as of December 31, 2012, 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 Management Company L.P. (“Deerfield”), pursuant to which, on July 1, 2010, we sold to Deerfield an aggregate of $124.0 million initial principal amount of our Secured Convertible Notes due June 2015 (the "Deerfield Notes") for an aggregate purchase price of $80.0 million, less closing fees and expenses of approximately $2.0 million. 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 Deerfield of a $1.5 million consent fee. As of December 31, 2012, all of the principal balance remains outstanding. The non-cash expense relating to the amortization of the debt discount and debt issuance costs during 2012 was $9.9 million. The outstanding principal amount of the Deerfield Notes bears interest in the annual amount of $6.0 million, payable quarterly in arrears. In January 2013, we made a mandatory prepayment of $10.0 million on the Deerfield Notes. We will be required to make additional mandatory prepayments on the Deerfield Notes on an annual basis in 2014 and 2015 equal to 15% of specified payments from our collaborative arrangements received during the prior fiscal year, subject to a maximum annual prepayment amount of $27.5 million. There is a minimum required prepayment amount of $10.0 million due in January 2014. There is no minimum prepayment due in 2015. We may also prepay all or a portion (not less than $5.0 million) of the principal amount of the Deerfield Notes at an optional prepayment price based on a discounted principal amount (during the first three years of the term, subject to a prepayment premium) determined as of the date of prepayment, plus accrued and unpaid interest, plus in the case of a prepayment of the full principal amount of the Deerfield Notes (other than prepayments upon the occurrence of specified transactions relating to a change of control or a substantial sale of assets), all accrued interest that would have accrued between the date of such prepayment and the next anniversary of the note purchase agreement. Pursuant to the amendment of the note purchase agreement, any optional prepayment of the Deerfield Notes made on or prior to July 2, 2013 will be determined as if such prepayment occurred as of July 3, 2013. In lieu of making any optional 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 optional prepayment amounts or mandatory prepayment amounts (other than the $10.0 million mandatory prepayment required in January 2014 and any optional prepayments made prior to July 3, 2013) 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 $400 million or a sale or transfer of more than 50% of our assets, Deerfield may require us to prepay the notes at the optional prepayment price, plus accrued and unpaid interest and any other accrued and reimbursable expenses (the “Put Price”). Upon an event of default, Deerfield may declare all or a portion of the Put Price to be immediately due and payable.

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

The balance of unamortized fees and costs was $2.3 million as of December 31, 2012, which is recorded in the accompanying Consolidated Balance Sheet as Other assets.

Silicon Valley Bank Loan and Security Agreement

The outstanding principal obligation under the Silicon Valley Bank Loan and Security Agreement, as amended, was $85.3 million and $90.1 million as of December 31, 2012 and 2011, 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 $5.3 million and $10.1 million as of December 31, 2012 and 2011, 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 and certain other designated financial institutions. 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, 2012 and 2011 was $87.0 million and $85.3 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, 2012 (in thousands):



Year Ending December 31, (1)
2013	$	13,170
2014	11,654
2015	104,436
2016	—
2017	80,000
Thereafter	287,500

____________________


(1)	Amounts include principal payments associated with the accretion of discounts and debt issuance costs. This table assumes we will make the minimum mandatory prepayment on the Deerfield Notes in January 2014 as required by the note purchase agreement. The actual timing of payments made may differ materially.

The entire disclosure for information about short-term and long-term debt arrangements, which includes amounts of borrowings under each line of credit, note payable, commercial paper issue, bonds indenture, debenture issue, own-share lending arrangements and any other contractual agreement to repay funds, and about the underlying arrangements, rationale for a classification as long-term, including repayment terms, interest rates, collateral provided, restrictions on use of assets and activities, whether or not in compliance with debt covenants, and other matters important to users of the financial statements, such as the effects of refinancing and noncompliance with debt covenants.

Warrants and Rights Note Disclosure [Abstract]

Common Stock And Warrants

12 Months Ended

Dec. 31, 2012

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. 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 7 - Debt" for more information regarding the 2019 Notes.

Conversion of Debt into Common Stock

In October 2011, we elected to repay the third and final installment of an outstanding loan from GlaxoSmithKline 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 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 7 - Debt" for more information regarding the conversion features of these instruments.

Warrants

At December 31, 2012, 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.

Fair Value Measurements

12 Months Ended

Dec. 31, 2012

Fair Value Disclosures [Abstract]

Fair Value Measurements

FAIR VALUE MEASUREMENTS

The fair value of our financial instruments 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). The fair value hierarchy has the following three levels:

Level 1 – quoted prices in active markets for identical assets and liabilities.

Level 2 – observable inputs other than quoted prices in active markets for identical assets and liabilities. 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. There were no transfers between any of the fair value hierarchies, as determined at the end of each reporting period.

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, 2012 and 2011. The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	December 31, 2012
	Level 1		Level 2		Level 3		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



	December 31, 2011
	Level 1		Level 2		Level 3		Total
Money market funds	$	78,702	$	—	$	—	$	78,702
Commercial paper	—		29,080		—		29,080
Corporate bonds	—		115,921		—		115,921
U.S. government sponsored enterprises	—		37,249		—		37,249
Municipal bonds	—		19,485		—		19,485
Total	$	78,702	$	201,735	$	—	$	280,437

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, 2012				December 31, 2011
	Carrying Amount		Fair Value		Carrying Amount		Fair Value
Convertible Senior Subordinated Notes due 2019	$	149,800	$	280,111	$	—	$	—
Silicon Valley Bank term loan	$	80,000	$	79,542	$	80,000	$	77,835
Silicon Valley Bank Line of Credit	$	5,260	$	5,253	$	10,130	$	10,066

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 1 input. The 2019 Notes are not marked-to-market 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 accompanying Consolidated Balance Sheets. See "Note 7 - 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.

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.

Reference 1: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 820
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=7578670&loc=d3e19207-110258

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Reference 7: http://www.xbrl.org/2003/role/presentationRef
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-Name Statement of Financial Accounting Standard (FAS)
-Number 107
-Paragraph 15B
-Subparagraph a, b
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 133
-Paragraph 44A, 44B
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 159
-Paragraph 17-22, 27, 28
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
-Paragraph 15C, 15D
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 157
-Paragraph 32, 33, 34
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

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-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
-Paragraph 3, 10, 14, 15
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

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

Employee Benefit Plans

12 Months Ended

Dec. 31, 2012

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. During 2012, 755,792 stock options 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, 2012, we have assumed that achievement of those performance objectives is probable. In the event a performance measure is not achieved at or above a specified threshold level, the portion of the award tied to such performance measure is forfeited. RSUs vest annually over a four year term.

In December 2005, our Board of Directors adopted a Change in Control and Severance Benefit Plan (the “Plan”) for executives and certain non-executives. Eligible 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 Plan participant is entitled to have the vesting of all of such participant’s stock options accelerated with the exercise period being extended to no more than one year.

Employee Stock Purchase Plan

In January 2000, we adopted the 2000 Employee Stock Purchase Plan (the “ESPP”). The ESPP allows for qualified employees (as defined in the ESPP) to purchase shares of our common stock at a price equal to the lower of 85% of the closing price at the beginning of the offering period or 85% of the closing price at the end of each six month purchase period. Compensation expense related to our ESPP was $0.4 million, $0.7 million, and $1.3 million for the years ended December 31, 2012, 2011 and 2010, respectively. As of December 31, 2012, we had 2,386,667 shares available for grant under our ESPP. We issued 298,533 shares, 375,305 shares, and 689,093 shares of common stock during the years ended December 31, 2012, 2011 and 2010, respectively, pursuant to the ESPP at an average price per share of $4.08, $4.62, and $4.55, respectively.

Stock-Based Compensation

We recorded and allocated employee stock-based compensation expense for the Plan and the ESPP as follows (in thousands):



	Year Ended December 31,
	2012		2011		2010
Research and development expense	$	4,536	$	5,935	$	11,535
General and administrative expense	4,245		5,459		7,931
Restructuring-related stock compensation expense	—		625		1,505
Total employee stock-based compensation expense	$	8,781	$	12,019	$	20,971

In addition, we recognized stock-based compensation expense of $0.1 million relating to nonemployees in each of the years ended December 31, 2012, 2011 and 2010.

In July 2010, our former Chief Executive Officer, George A. Scangos, Ph.D., resigned as an employee of Exelixis and in connection with such resignation agreed to cancel unvested stock options exercisable for 981,302 shares of our common stock and unvested RSUs with respect to 101,050 shares of our common stock. Due to Dr. Scangos’ continued services as a director of Exelixis he was entitled to retain his stock options and RSUs. Therefore, we treated the cancellation as a modification of his stock option and RSU agreements and in 2010 recorded a non-cash compensation charge of approximately $1.5 million to our Consolidated Statements of Operations.

We use the Black-Scholes 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 share-based payments awards was estimated using the following assumptions and weighted average fair values:



	Stock Options
	2012			2011			2010
Weighted average grant-date fair value	$	3.24		$	3.50		$	3.60
Risk-free interest rate	0.81		%	1.07		%	2.25		%
Dividend yield	—		%	—		%	—		%
Volatility	69		%	70		%	70		%
Expected life	5.6 years			5.5 years			5.2 years



	ESPP
	2012			2011			2010
Weighted average grant-date fair value	$	2.07		$	2.85		$	1.87
Risk-free interest rate	0.10		%	0.11		%	0.21		%
Dividend yield	—		%	—		%	—		%
Volatility	68		%	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, 2009	24,393,598		$	7.46
Granted	243,500		$	6.28
Exercised	(495,098	)	$	5.42
Cancelled	(4,511,970	)	$	7.35
Options outstanding at December 31, 2010	19,630,030		$	7.52
Granted	2,545,625		$	5.86
Exercised	(2,161,804	)	$	5.75
Cancelled	(2,577,473	)	$	9.79
Options outstanding at December 31, 2011	17,436,378		$	7.16
Granted	3,442,696		$	5.45
Exercised	(181,979	)	$	5.09
Cancelled	(2,248,545	)	$	7.28
Options outstanding at December 31, 2012	18,448,550		$	6.85	4.60 years	$	90,240
Exercisable at December 31, 2012	13,128,876		$	7.35	3.85 years	$	77,703

At December 31, 2012 a total of 8,632,907 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 2012 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, 2012. Total intrinsic value of options exercised was $0.1 million, $7.0 million, and $0.8 million during 2012, 2011 and 2010, respectively. Total fair value of employee options vested and expensed in 2012, 2011 and 2010 was $5.6 million, $8.4 million, and $16.2 million, respectively.

The following table summarizes information about stock options outstanding and exercisable at December 31, 2012:



	Options Outstanding				Options Outstanding and Exercisable
Exercise Price Range	Number	Weighted Average Remaining Contractual Life (Years)	Weighted Average Exercise Price		Number of Exercisable	Weighted Average Exercise Price
$3.05 - $4.99	913,013	6.29	$	4.47	642,101	$	4.43
$5.00 - $5.62	6,025,420	6.27	$	5.47	1,413,294	$	5.27
$5.63 - $5.99	2,976,329	3.34	$	5.68	2,931,042	$	5.67
$6.00 - $7.99	2,938,367	4.27	$	7.02	2,547,018	$	6.98
$8.00 - $8.99	3,774,399	2.87	$	8.85	3,774,399	$	8.85
$9.00 - $12.10	1,821,022	4.43	$	10.07	1,821,022	$	10.07
	18,448,550	4.60	$	6.85	13,128,876	$	7.35

As of December 31, 2012, $14.7 million of total unrecognized compensation expense related to stock options is expected to be recognized over a weighted-average period of 2.97 years.

Cash received from option exercises and purchases under the ESPP in 2012 and 2011 was $2.1 million and $14.2 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, 2009	2,679,224		$	7.46
Awarded	191,475		$	5.70
Forfeited	(698,268	)	$	7.44
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	1.78 years	$	5,839

As of December 31, 2012, $6.0 million of total unrecognized compensation expense related to employee RSUs was expected to be recognized over a weighted-average period of 2.92 years.

401(k) Retirement Plan

We sponsor a 401(k) Retirement 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) Retirement 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) Retirement 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) Retirement Plan in the form of our common stock. We recorded expense of $0.6 million, $0.8 million, and $1.0 million related to the stock match for the years ended December 31, 2012, 2011 and 2010, respectively.

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
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-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6406099&loc=d3e25284-112666

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Reference 5: http://www.xbrl.org/2003/role/presentationRef
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-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5444-113901

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 14

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 123R
-Paragraph 64, 65, A240
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Statement of Position (SOP)
-Number 93-6
-Paragraph 53
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Income Taxes

12 Months Ended

Dec. 31, 2012

Income Tax Disclosure [Abstract]

Income Taxes

INCOME TAXES

We recorded an income tax provision (benefit) of $0.1 million, $1.3 million and $(0.1) million for the periods ended December 31, 2012, 2011 and 2010, respectively. In 2010, we recorded an income tax benefit as a result of the enactment of the Housing and Economic Recovery Act of 2008. Under this Act, corporations otherwise eligible for bonus first-year depreciation could instead elect to claim a refundable credit for R&D tax credits generated prior to 2006. This tax benefit was extended for tax year 2009 with the enactment of the American Recovery and Reinvestment Tax Act of 2009. Approximately $0.1 million and $0.6 million of the 2012 and 2011 provisions, respectively, relate to adjustments of the refund received in 2009 and 2010 under these Acts after we further evaluated the qualified expenses from which the refund calculation was originally based. The remaining 2011 amount of $0.7 million relates to a tax deferred revenue adjustment that resulted in a state tax liability due to state net operating loss carryover limitations.

The income tax provision (benefit) is based on the following (loss) income before income taxes, all of which are from domestic sources (in thousands):



	Year Ended December 31,
	2012			2011		2010
(Loss) income before income taxes	$	(147,538	)	$	76,992	$	(92,402	)

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



	Year Ended December 31,
	2012			2011			2010
U.S. federal income tax provision (benefit) at statutory rate	$	(50,163	)	$	26,177		$	(31,417	)
Unutilized net operating losses	46,324			(29,650		)	29,636
Non-deductible interest	3,297			2,809			—
Stock-based compensation	504			627			1,709
State tax expense	74			660			—
Refundable tax credit	32			636			(72		)
Other	39			36			72
Income tax provision (benefit)	$	107		$	1,295		$	(72	)

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,
	2012			2011
Deferred tax assets:
Net operating loss carry-forwards	$	374,200		$	318,638
Tax credit carry-forwards	65,232			54,726
Amortization of deferred stock compensation – non-qualified	26,469			25,865
Accruals and reserves not currently deductible	13,732			6,522
Deferred revenue	6,501			18,400
Book over tax depreciation and amortization	5,140			6,543
Capitalized research and development costs	—			805
Total deferred tax assets	491,274			431,499
Valuation allowance	(438,266		)	(431,499		)
Net deferred tax assets	53,008			—
Deferred tax liabilities:
Convertible debt	(53,008		)	—
Total deferred tax liabilities	(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 increased by $6.8 million, decreased by $49.7 million, and increased by $25.2 million during 2012, 2011, and 2010, respectively.

At December 31, 2012, we had federal net operating loss carry-forwards of approximately $1,007 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 net operating loss carry-forwards for California of approximately $880 million, which expire in the years 2013 through 2032, and California research and development tax credits of approximately $26 million which have no expiration.

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 track the portion of our deferred tax assets attributable to stock option benefits; these amounts are no longer included in our gross or net deferred tax assets. The tax benefit of stock options total $6.2 million at December 31, 2012 and will only be recorded when we realize a reduction in taxes payable.

Accounting Standards Codification 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, 2012, 2011 and 2010 (in thousands):



	Year Ended December 31,
	2012		2011			2010
Beginning balance	$	39,310	$	46,381		$	32,171
Increase (decrease) relating to prior year provision	5,894		(9,782		)	10,472
Increase relating to current year provision	2,094		2,711			3,738
Ending balance	$	47,298	$	39,310		$	46,381

Included in the balance of unrecognized tax benefits as of December 31, 2012, 2011 and 2010 are $0.1 million, $0.1 million, and $0, 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, 2012, and 2011 we had an accrued interest balance of $15 thousand and $9 thousand, related to tax contingencies. Interest expense related to those tax contingencies was $6 thousand and $9 thousand during the years ended December 31, 2012, and 2011, respectively. There was no interest accrued as of December 31, 2010 and no penalties were recognized or accrued during any of the periods presented. Any tax-related interest and penalties are included in income tax provision (benefit) in the Consolidated Statements of Operations. We do not anticipate that the amount of unrecognized tax benefits existing as of December 31, 2012 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 1996 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.

The entire disclosure for income taxes. Disclosures may include net deferred tax liability or asset recognized in an enterprise's statement of financial position, net change during the year in the total valuation allowance, approximate tax effect of each type of temporary difference and carryforward that gives rise to a significant portion of deferred tax liabilities and deferred tax assets, utilization of a tax carryback, and tax uncertainties information.

Reference 1: 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.(h))
-URI http://asc.fasb.org/extlink&oid=6881521&loc=d3e23780-122690

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
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-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32559-109319

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 15
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32718-109319

Reference 4: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 740
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-Section 50
-Paragraph 9
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32639-109319

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32537-109319

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 109
-Paragraph 136, 172
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 08
-Paragraph h
-Article 4

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 109
-Paragraph 43, 44, 45, 46, 47, 48, 49
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Net (Loss) Income Per Share

Net (Loss) Income Per Share

12 Months Ended

Dec. 31, 2012

Earnings Per Share [Abstract]

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,
	2012			2011		2010
Numerator:
Net (loss) income	$	(147,645	)	$	75,697	$	(92,330	)
Denominator:
Shares used in computing basic (loss) income per share amounts	160,138			126,018		108,522
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	160,138			130,479		108,522
Net (loss) income per share, basic	$	(0.92	)	$	0.60	$	(0.85	)
Net (loss) income per share, diluted	$	(0.92	)	$	0.58	$	(0.85	)

Diluted net (loss) income per share gives effect to potential incremental common shares issuable upon the exercise of stock options and warrants, upon vesting of RSUs, upon the purchase from contributions to ESPP (calculated based on the treasury stock method), and upon conversion of our convertible debt (calculated using the if-converted method) and the effect is not anti-dilutive. The following table sets forth potential shares of common stock that are not included in the computation of diluted net loss per share because to do so would be antidilutive (in thousands):



	Year Ended December 31,
	2012	2011	2010
Convertible debt	54,123	—	6,725
Outstanding stock options, unvested RSUs and ESPP contributions	16,568	9,085	21,802
Warrants	1,441	—	2,250
Total potentially dilutive shares	72,132	9,085	30,777

Commitments and Contingencies

12 Months Ended

Dec. 31, 2012

Commitments and Contingencies Disclosure [Abstract]

Commitments

COMMITMENTS AND CONTINGENCIES

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 San Diego and South San Francisco. Aggregate future minimum lease payments under our operating leases are as follows (in thousands):



Year Ending December 31,	Operating Leases (1)
2013	$	19,486
2014	19,896
2015	20,152
2016	16,431
2017	9,104
Thereafter	2,806
	$	87,875

____________________


(1)	Minimum payments have not been reduced by minimum sublease rentals of $15.5 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, 2012 by material 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	$	49,216
Building Lease #3	July 2018	1 additional period of 5 years	25,378
Building Lease #4	December 2015	1 additional period of 3 years	13,058
Total			$	87,652

Rent expense under operating leases was $17.8 million, $21.3 million, and $28.0 million for the years ended December 31, 2012, 2011, and 2010, respectively. Rent expense was net of sublease rentals of $3.8 million, $1.9 million, and $0.3 million for the years ended December 2012, 2011 and 2010, 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 each of December 31, 2012 and 2011. We entered into two standby letters of credit with a bank in May 2007, which is related to our workers compensation insurance policy, for a combined credit limit of $0.6 million and $0.8 million at December 2012 and 2011, respectively. All three letters of credit are fully collateralized by long-term restricted cash and investments. As of December 31, 2012, 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, 2012 and 2011 was $2.5 million and $2.9 million, respectively. We recorded these amounts in the accompanying 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.

Contingencies

Pending Litigation

From time to time, we are party to legal proceedings, claims and investigations in the ordinary course of business, including the matter described below.

In December 2012, a former officer filed a lawsuit against us and our chief executive officer in California state court seeking unspecified monetary damages based on contract and tort claims in connection with the former officer's execution and revocation of a Rule 10b5-1 stock trading plan in December 2010. We have not responded to this complaint, and the time for us to respond has not expired. We intend to defend this claim vigorously. This matter is at a very early stage, and we are unable to reasonably estimate the possible loss or range of loss, if any.

The entire disclosure for commitments and contingencies.

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 825
-SubTopic 20
-Section 50
-Paragraph 1
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Reference 3: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 450
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Reference 4: 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 210.5-02.25)
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 440
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-URI http://asc.fasb.org/extlink&oid=6394976&loc=d3e25287-109308

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Interpretation (FIN)
-Number 14
-Paragraph 3
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 5
-Paragraph 9, 10, 11, 12
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Concentrations of Credit Risk

Concentrations of Credit Risk

12 Months Ended

Dec. 31, 2012

Risks and Uncertainties [Abstract]

CONCENTRATIONS OF CREDIT RISK

Financial instruments that potentially subject us to concentrations of credit risk are primarily cash and cash equivalents, other receivables and investments. Cash equivalents and 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 cash and cash equivalents, and investments are maintained with financial institutions that management believes are creditworthy.

Other receivables are typically 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.

The following table sets forth the percentage of revenues recognized under our collaboration agreements with collaborators that represent 10% or more of total revenues during the years ending December 31, 2012, 2011 and 2010:



Collaborator	2012		2011		2010
Bristol-Myers Squibb	66	%	59	%	50	%
Merck	22	%	—	%	—	%
Daiichi Sankyo	12	%	—	%	3	%
Sanofi	—	%	39	%	42	%

The entire disclosure for any concentrations existing at the date of the financial statements that make an entity vulnerable to a reasonably possible, near-term, severe impact. This disclosure informs financial statement users about the general nature of the risk associated with the concentration, and may indicate the percentage of concentration risk as of the balance sheet date.

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 275
-SubTopic 10
-Section 50
-Paragraph 16
-URI http://asc.fasb.org/extlink&oid=6927468&loc=d3e6327-108592

Reference 2: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 825
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-Paragraph 20
-URI http://asc.fasb.org/extlink&oid=7491637&loc=d3e13531-108611

Reference 3: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 275
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-Paragraph 20
-URI http://asc.fasb.org/extlink&oid=6927468&loc=d3e6404-108592

Reference 4: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 275
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Reference 5: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 275
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-URI http://asc.fasb.org/extlink&oid=6927468&loc=d3e6351-108592

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 825
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-Paragraph 21
-URI http://asc.fasb.org/extlink&oid=7491637&loc=d3e13537-108611

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Statement of Position (SOP)
-Number 94-6
-Paragraph 21, 22, 24
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
-Paragraph 15A
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Quarterly Financial Information Disclosure [Abstract]

Quarterly Financial Data

12 Months Ended

Dec. 31, 2012

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):



	2012 Quarter Ended
	March 31,			June 30,			September 30,			December 31,
Revenues	$	18,510		$	7,813		$	13,313		$	7,814
Loss from operations	$	(22,296	)	$	(32,723	)	$	(25,443	)	$	(41,974	)
Net loss	$	(26,151	)	$	(36,487	)	$	(32,814	)	$	(52,143	)
Net loss per share, basic and diluted	$	(0.18	)	$	(0.25	)	$	(0.20	)	$	(0.28	)



	2011 Quarter Ended
	March 31,			June 30,			September 30,		December 31,
Revenues	$	35,893		$	32,162		$	128,272	$	94,309
(Loss) income from operations	$	(23,730	)	$	(18,008	)	$	79,699	$	51,574
Net (loss) income	$	(27,490	)	$	(20,975	)	$	77,865	$	46,297
Net (loss) income per share, basic	$	(0.24	)	$	(0.16	)	$	0.60	$	0.35
Net (loss) income per share, diluted	$	(0.24	)	$	(0.16	)	$	0.59	$	0.35

The entire disclosure for the quarterly financial data in the annual financial statements. The disclosure may include a tabular presentation of financial information for each fiscal quarter for the current and previous year, including revenues, gross profit, income or loss before extraordinary items and earnings per share data. It also includes an indication if the information in the note is unaudited, comments on the aggregate effect of year-end adjustments, and an explanation of matters or transactions that affect comparability or are pertinent to an understanding of the information furnished.

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Organization And Summary Of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2012

Organization

Basis of Consolidation

The consolidated financial statements include the accounts of Exelixis and those of our wholly-owned subsidiary. All intercompany balances and transactions have been eliminated.

Basis of Presentation

Use of Estimates

Cash and Investments

Foreign Currency Forward Contract

Fair Value Measurements

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

Repairs and maintenance costs are charged to expense as incurred.

Goodwill

Long-Lived Assets

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

Revenue Recognition

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.

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

We have employee and director stock option plans that are more fully described in Note 10.

Liquidity Disclosure [Policy Text Block]

Need to Raise Additional Capital

Recently Adopted Accounting Pronouncements

Recently Issued Accounting Pronouncements Not Yet Adopted

Organization And Summary Of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2012

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

Repairs and maintenance costs are charged to expense as incurred.

Restructurings (Tables)

12 Months Ended

Dec. 31, 2012

Restructuring Charges [Abstract]

Schedule of outstanding restructuring liability

The components and changes of these liabilities during the years ended December 31, 2012, 2011 and 2010 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
Ending accrual balance as of December 31, 2012	$	—		$	19,202		$	—		$	20		$	19,222

Cash and Investments Cash and Investments (Tables)

12 Months Ended

Dec. 31, 2012

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, 2012 and 2011 (in thousands):



	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



	December 31, 2011
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
As reported:
Cash and cash equivalents	$	74,256	$	1	$	—		$	74,257
Short-term investments	120,143		35		(173		)	120,005
Long-term investments	85,260		—		—			85,260
Long-term restricted cash and investments	4,199		—		—			4,199
Total cash and investments	$	283,858	$	36	$	(173	)	$	283,721

Summary of Cash and Investments by Security Type

All of our cash and investments are classified as available-for-sale. The following table summarizes our cash and investments by security type as of December 31, 2012 and 2011 (in thousands):



	December 31, 2012
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Cash and money market funds	$	81,744	$	2	$	—		$	81,746
Commercial paper	167,223		8		—			167,231
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 cash and investments	$	634,053	$	99	$	(191	)	$	633,961



	December 31, 2011
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Cash and money market funds	$	81,986	$	—	$	—		$	81,986
Commercial paper	29,079		2		(1		)	29,080
Corporate bonds	116,068		22		(169		)	115,921
U.S. government sponsored enterprises	37,237		12		—			37,249
Municipal bonds	19,488		—		(3		)	19,485
Total cash and investments	$	283,858	$	36	$	(173	)	$	283,721

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, 2012 (in thousands):



	Mature within One Year		After One Year through Two Years		Fair Value
Money market funds	$	76,050	$	—	$	76,050
Commercial paper	167,231		—		167,231
Corporate bonds	126,896		95,053		221,949
U.S. Treasury and government sponsored enterprises	84,677		48,314		132,991
Municipal bonds	30,044		—		30,044
Total	$	484,898	$	143,367	$	628,265

Property And Equipment (Tables)

12 Months Ended

Dec. 31, 2012

Property, Plant and Equipment [Abstract]

Schedule Of Property And Equipment

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



	December 31,
	2012			2011
Laboratory equipment	$	19,504		$	28,795
Computer equipment and software	11,897			11,743
Furniture and fixtures	3,230			3,230
Leasehold improvements	16,572			15,961
Construction-in-progress	1,409			155
	52,612			59,884
Less: accumulated depreciation and amortization	(46,553		)	(51,378		)
Property and equipment, net	$	6,059		$	8,506

Debt (Tables)

12 Months Ended

Dec. 31, 2012

Debt Disclosure [Abstract]

Schedule Of Debt

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



	December 31,
	2012			2011
Convertible Senior Subordinated Notes due 2019	$	149,800		$	—
Deerfield Notes	100,676			91,385
Silicon Valley Bank term loan	80,000			80,000
Silicon Valley Bank Line of Credit	5,260			10,130
Total debt	335,736			181,515
Less: current portion	(13,170		)	(4,870		)
Long-term debt	$	322,566		$	176,645

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, 2012 (in thousands):



	December 31, 2012
Net carrying amount of the liability component	$	149,800
Unamortized discount of the liability component	137,700
Face amount of the 2019 Notes	$	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, 2012 (in thousands):



Year Ending December 31, (1)
2013	$	13,170
2014	11,654
2015	104,436
2016	—
2017	80,000
Thereafter	287,500

____________________


(1)	Amounts include principal payments associated with the accretion of discounts and debt issuance costs. This table assumes we will make the minimum mandatory prepayment on the Deerfield Notes in January 2014 as required by the note purchase agreement. The actual timing of payments made may differ materially

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
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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 835
-SubTopic 30
-Section 45
-Paragraph 1A
-URI http://asc.fasb.org/extlink&oid=6451184&loc=d3e28541-108399

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21506-112644

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

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

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, 2012

Schedule Of Warrants To Purchase Common Stock Outstanding And Exercisable

At December 31, 2012, 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

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.

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

Fair Value Measurements Fair Value Measurements (Tables)

12 Months Ended

Dec. 31, 2012

Fair Value Disclosures [Abstract]



	December 31, 2012
	Level 1		Level 2		Level 3		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



	December 31, 2011
	Level 1		Level 2		Level 3		Total
Money market funds	$	78,702	$	—	$	—	$	78,702
Commercial paper	—		29,080		—		29,080
Corporate bonds	—		115,921		—		115,921
U.S. government sponsored enterprises	—		37,249		—		37,249
Municipal bonds	—		19,485		—		19,485
Total	$	78,702	$	201,735	$	—	$	280,437

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, 2012				December 31, 2011
	Carrying Amount		Fair Value		Carrying Amount		Fair Value
Convertible Senior Subordinated Notes due 2019	$	149,800	$	280,111	$	—	$	—
Silicon Valley Bank term loan	$	80,000	$	79,542	$	80,000	$	77,835
Silicon Valley Bank Line of Credit	$	5,260	$	5,253	$	10,130	$	10,066

Tabular disclosure of assets, including [financial] instruments measured at fair value that are classified in stockholders' equity, if any, by class that are measured at fair value on a recurring basis. The disclosures contemplated herein include the fair value measurements at the reporting date by the level within the fair value hierarchy in which the fair value measurements in their entirety fall, segregating fair value measurements using quoted prices in active markets for identical assets (Level 1), significant other observable inputs (Level 2), and significant unobservable inputs (Level 3).

Tabular disclosure of liabilities, including [financial] instruments measured at fair value that are classified in stockholders' equity, if any, by class that are measured at fair value on a recurring basis. The disclosures contemplated herein include the fair value measurements at the reporting date by the level within the fair value hierarchy in which the fair value measurements in their entirety fall, segregating fair value measurements using quoted prices in active markets for identical assets (Level 1), significant other observable inputs (Level 2), and significant unobservable inputs (Level 3). Where the quoted price in an active market for the identical liability is not available, the Level 1 input is the quoted price of an identical liability when traded as an asset.

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

Employee Benefit Plans (Tables)

12 Months Ended

Dec. 31, 2012

Schedule Of Allocated Employee Stock-Based Compensation Expense

We recorded and allocated employee stock-based compensation expense for the Plan and the ESPP as follows (in thousands):



	Year Ended December 31,
	2012		2011		2010
Research and development expense	$	4,536	$	5,935	$	11,535
General and administrative expense	4,245		5,459		7,931
Restructuring-related stock compensation expense	—		625		1,505
Total employee stock-based compensation expense	$	8,781	$	12,019	$	20,971

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

The fair value of employee share-based payments awards was estimated using the following assumptions and weighted average fair values:



	Stock Options
	2012			2011			2010
Weighted average grant-date fair value	$	3.24		$	3.50		$	3.60
Risk-free interest rate	0.81		%	1.07		%	2.25		%
Dividend yield	—		%	—		%	—		%
Volatility	69		%	70		%	70		%
Expected life	5.6 years			5.5 years			5.2 years

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



	ESPP
	2012			2011			2010
Weighted average grant-date fair value	$	2.07		$	2.85		$	1.87
Risk-free interest rate	0.10		%	0.11		%	0.21		%
Dividend yield	—		%	—		%	—		%
Volatility	68		%	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, 2009	24,393,598		$	7.46
Granted	243,500		$	6.28
Exercised	(495,098	)	$	5.42
Cancelled	(4,511,970	)	$	7.35
Options outstanding at December 31, 2010	19,630,030		$	7.52
Granted	2,545,625		$	5.86
Exercised	(2,161,804	)	$	5.75
Cancelled	(2,577,473	)	$	9.79
Options outstanding at December 31, 2011	17,436,378		$	7.16
Granted	3,442,696		$	5.45
Exercised	(181,979	)	$	5.09
Cancelled	(2,248,545	)	$	7.28
Options outstanding at December 31, 2012	18,448,550		$	6.85	4.60 years	$	90,240
Exercisable at December 31, 2012	13,128,876		$	7.35	3.85 years	$	77,703

Summary Of Information About Stock Options Outstanding

The following table summarizes information about stock options outstanding and exercisable at December 31, 2012:



	Options Outstanding				Options Outstanding and Exercisable
Exercise Price Range	Number	Weighted Average Remaining Contractual Life (Years)	Weighted Average Exercise Price		Number of Exercisable	Weighted Average Exercise Price
$3.05 - $4.99	913,013	6.29	$	4.47	642,101	$	4.43
$5.00 - $5.62	6,025,420	6.27	$	5.47	1,413,294	$	5.27
$5.63 - $5.99	2,976,329	3.34	$	5.68	2,931,042	$	5.67
$6.00 - $7.99	2,938,367	4.27	$	7.02	2,547,018	$	6.98
$8.00 - $8.99	3,774,399	2.87	$	8.85	3,774,399	$	8.85
$9.00 - $12.10	1,821,022	4.43	$	10.07	1,821,022	$	10.07
	18,448,550	4.60	$	6.85	13,128,876	$	7.35

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, 2009	2,679,224		$	7.46
Awarded	191,475		$	5.70
Forfeited	(698,268	)	$	7.44
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	1.78 years	$	5,839

Tabular disclosure of the allocation of equity-based compensation costs to a given line item on the balance sheet and income statement for the period. This may include the reporting line for the costs and the amount capitalized and expensed.

Schedule Of Consolidated Net Income (Loss)

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2012

Income Tax Disclosure [Abstract]

The income tax provision (benefit) is based on the following (loss) income before income taxes, all of which are from domestic sources (in thousands):



	Year Ended December 31,
	2012			2011		2010
(Loss) income before income taxes	$	(147,538	)	$	76,992	$	(92,402	)

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 out income tax provision (benefit) included in the Consolidated Statements of Operations is as follows (in thousands):



	Year Ended December 31,
	2012			2011			2010
U.S. federal income tax provision (benefit) at statutory rate	$	(50,163	)	$	26,177		$	(31,417	)
Unutilized net operating losses	46,324			(29,650		)	29,636
Non-deductible interest	3,297			2,809			—
Stock-based compensation	504			627			1,709
State tax expense	74			660			—
Refundable tax credit	32			636			(72		)
Other	39			36			72
Income tax provision (benefit)	$	107		$	1,295		$	(72	)

Schedule Of Deferred Assets And Liabilities

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



	December 31,
	2012			2011
Deferred tax assets:
Net operating loss carry-forwards	$	374,200		$	318,638
Tax credit carry-forwards	65,232			54,726
Amortization of deferred stock compensation – non-qualified	26,469			25,865
Accruals and reserves not currently deductible	13,732			6,522
Deferred revenue	6,501			18,400
Book over tax depreciation and amortization	5,140			6,543
Capitalized research and development costs	—			805
Total deferred tax assets	491,274			431,499
Valuation allowance	(438,266		)	(431,499		)
Net deferred tax assets	53,008			—
Deferred tax liabilities:
Convertible debt	(53,008		)	—
Total deferred tax liabilities	(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, 2012, 2011 and 2010 (in thousands):



	Year Ended December 31,
	2012		2011			2010
Beginning balance	$	39,310	$	46,381		$	32,171
Increase (decrease) relating to prior year provision	5,894		(9,782		)	10,472
Increase relating to current year provision	2,094		2,711			3,738
Ending balance	$	47,298	$	39,310		$	46,381

Net (Loss) Income Per Share (Tables)

12 Months Ended

Dec. 31, 2012

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,
	2012			2011		2010
Numerator:
Net (loss) income	$	(147,645	)	$	75,697	$	(92,330	)
Denominator:
Shares used in computing basic (loss) income per share amounts	160,138			126,018		108,522
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	160,138			130,479		108,522
Net (loss) income per share, basic	$	(0.92	)	$	0.60	$	(0.85	)
Net (loss) income per share, diluted	$	(0.92	)	$	0.58	$	(0.85	)

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

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



	Year Ended December 31,
	2012	2011	2010
Convertible debt	54,123	—	6,725
Outstanding stock options, unvested RSUs and ESPP contributions	16,568	9,085	21,802
Warrants	1,441	—	2,250
Total potentially dilutive shares	72,132	9,085	30,777

Commitments and Contingencies (Tables)

12 Months Ended

Dec. 31, 2012

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)
2013	$	19,486
2014	19,896
2015	20,152
2016	16,431
2017	9,104
Thereafter	2,806
	$	87,875

____________________


(1)	Minimum payments have not been reduced by minimum sublease rentals of $15.5 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, 2012 by material 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	$	49,216
Building Lease #3	July 2018	1 additional period of 5 years	25,378
Building Lease #4	December 2015	1 additional period of 3 years	13,058
Total			$	87,652

Concentrations of Credit Risk (Tables)

12 Months Ended

Dec. 31, 2012

Risks and Uncertainties [Abstract]

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



Collaborator	2012		2011		2010
Bristol-Myers Squibb	66	%	59	%	50	%
Merck	22	%	—	%	—	%
Daiichi Sankyo	12	%	—	%	3	%
Sanofi	—	%	39	%	42	%

Tabular disclosure of the nature of a concentration, a benchmark to which it is compared, and the percentage that the risk is to the benchmark.

Quarterly Financial Information Disclosure [Abstract]

Quarterly Financial Data (Tables)

12 Months Ended

Dec. 31, 2012

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):



	2012 Quarter Ended
	March 31,			June 30,			September 30,			December 31,
Revenues	$	18,510		$	7,813		$	13,313		$	7,814
Loss from operations	$	(22,296	)	$	(32,723	)	$	(25,443	)	$	(41,974	)
Net loss	$	(26,151	)	$	(36,487	)	$	(32,814	)	$	(52,143	)
Net loss per share, basic and diluted	$	(0.18	)	$	(0.25	)	$	(0.20	)	$	(0.28	)



	2011 Quarter Ended
	March 31,			June 30,			September 30,		December 31,
Revenues	$	35,893		$	32,162		$	128,272	$	94,309
(Loss) income from operations	$	(23,730	)	$	(18,008	)	$	79,699	$	51,574
Net (loss) income	$	(27,490	)	$	(20,975	)	$	77,865	$	46,297
Net (loss) income per share, basic	$	(0.24	)	$	(0.16	)	$	0.60	$	0.35
Net (loss) income per share, diluted	$	(0.24	)	$	(0.16	)	$	0.59	$	0.35

Organization And Summary Of Significant Accounting Policies (Narrative) (Details) shares in Millions		1 Months Ended			3 Months Ended								12 Months Ended
	Aug. 14, 2012 shares	Feb. 29, 2012 shares	Dec. 31, 2011 USD ($)	Mar. 31, 2011 shares	Dec. 31, 2012 USD ($) phase	Sep. 30, 2012 USD ($)	Jun. 30, 2012 USD ($)	Mar. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)	Sep. 30, 2011 USD ($)	Jun. 30, 2011 USD ($)	Mar. 31, 2011 USD ($)	Dec. 31, 2012 USD ($) phase	Dec. 31, 2011 USD ($)	Dec. 31, 2010 USD ($)	Mar. 31, 2010 USD ($)
Organization And Summary Of Significant Policies [Line Items]
Annual operating cycle													P52W	P52W	P52W
Sale of shares of common stock, shares \| shares	34.5	12.7		17.3
Foreign currency forward contract, notional amount			$ 0		$ 0				$ 0				$ 0	$ 0		$ 7,000,000
Received from French taxing authority relating to our 2009 Sanofi Collaboration Agreement			7,000,000						7,000,000					7,000,000
Losses on fair values of the foreign currency forward contracts held			300,000
Cash receipt from foreign currency forward contracts									6,700,000
Inventory, net					0								0
Amount of reduction relating to prior periods													2,700,000	1,600,000	$ 900,000
Net (loss) income					(52,143,000)	$ (32,814,000)	$ (36,487,000)	$ (26,151,000)	46,297,000	$ 77,865,000	$ (20,975,000)	$ (27,490,000)	(147,645,000)	75,697,000	$ (92,330,000)
Accumulated Deficit			$ 1,106,357,000		$ 1,254,002,000				$ 1,106,357,000				$ 1,254,002,000	$ 1,106,357,000
United States [Member]
Organization And Summary Of Significant Policies [Line Items]
Percentage of geographic revenue over total revenue													100.00%	100.00%	100.00%
Minimum [Member]
Organization And Summary Of Significant Policies [Line Items]
Annual operating cycle													P52W
Maximum [Member]
Organization And Summary Of Significant Policies [Line Items]
Annual operating cycle													P53W
COMETRIQ [Member]
Organization And Summary Of Significant Policies [Line Items]
Number of phases in process \| phase					2								2
Number of phases planned to start in next fiscal year \| phase					2								2

Organization And Summary Of Significant Accounting Policies (Estimated Useful Lives Of Property Plant And Equipment) (Details)	12 Months Ended
	Dec. 31, 2012
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 (Genentech To Bristol-Meyers Squibb) (Details)		1 Months Ended											12 Months Ended
	Jun. 18, 2010 USD ($)	Jul. 31, 2011 USD ($)	Nov. 30, 2010 USD ($)	Mar. 31, 2010 USD ($)	Jan. 31, 2010 USD ($)	Jan. 31, 2009 USD ($)	Dec. 31, 2008 USD ($)	Mar. 31, 2008 USD ($)	Feb. 29, 2008 USD ($)	Dec. 31, 2007 USD ($)	Jan. 31, 2007 USD ($) compound	Dec. 31, 2006 USD ($)	Dec. 31, 2012 USD ($) years product	Dec. 31, 2010 USD ($)
Genentech [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront and milestone payments											$ 15,000,000	$ 25,000,000
Payment to use exercise of option related to co-development agreement								$ 3,000,000
Milestone payment				$ 7,000,000
Optional percent of total sales													25.00%
Period to elect co-promotion option													12 months
Genentech [Member] \| Profit Sharing Tier One [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of profits													50.00%
Profit threshold													$ 200,000,000
Genentech [Member] \| Profit Sharing Tier Two [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of profits													30.00%
Profit threshold													$ 400,000,000
Bristol-Myers Squibb [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Transition payment received	$ 17,000,000
Funding period following termination notice	3 months
TGR5 License Agreement [Member] \| Bristol-Myers Squibb [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment			$ 35,000,000
Maximum amount eligible for development and regulatory milestones			250,000,000
Maximum amount eligible for commercial milestones under collaborations agreement			150,000,000
ROR Collaboration Agreement [Member] \| Bristol-Myers Squibb [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
2008 Cancer Collaboration [Member] \| Bristol-Myers Squibb [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment							$ 195,000,000
Additional license payments														$ 45,000,000
2007 Cancer Collaboration [Member] \| Bristol-Myers Squibb [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment											$ 60,000,000
Selected milestone earnings entitled and received							$ 20,000,000		$ 20,000,000
Maximum amount eligible for development and regulatory milestones			260,000,000
Number of future drug compounds \| compound											3
Number of future drug compounds available \| compound											6
Collaboration agreement opt-out consideration payment			$ 20,000,000
LXR Collaboration [Member] \| Bristol-Myers Squibb [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment													$ 17,500,000
Number of years for initial research \| years													2
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
Income from development milestone										$ 5,000,000
Additional research fund						$ 7,700,000
Research and development fund					$ 5,800,000								$ 10,000,000

Research And Collaboration Agreements (Sanofi To Daiichi Sankyo) (Details) $ in Millions		1 Months Ended							12 Months Ended
	Jul. 20, 2009 USD ($)	Aug. 31, 2012 USD ($)	Jan. 19, 2012 USD ($)	Dec. 31, 2010 USD ($)	Jul. 31, 2008	Jun. 30, 2007 USD ($)	Mar. 31, 2006 USD ($)	Oct. 31, 2002 USD ($) agreements compound payment shares	Dec. 31, 2012 USD ($)	Oct. 27, 2011 shares
Sanofi [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Proceeds from termination of agreement									$ 15.3
Upfront and milestone payments	$ 140.0
Upfront payment received for license	120.0
Upfront payment received for collaboration	20.0
Withholding taxes on upfront payments	7.0
Upfront payments, net of tax	$ 133.0
Maximum amount eligible for development and regulatory milestones									745.0
Glaxo SmithKline [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Number of agreements \| agreements								3
Upfront and milestone payments								$ 65.0
Research and development funding and loans								$ 85.0
Number of installment payments \| payment								3
Purchase an aggregate shares of common stock \| shares								3,000,000		5,537,906
Percent of royalty on net sales					3.00%
Glaxo SmithKline [Member] \| Maximum [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Number of future drug compounds \| compound								2
Merck [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment			$ 12.0
Maximum amount eligible for development and regulatory milestones									239.0
Daiichi Sankyo [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment							$ 20.0
Maximum amount eligible for development and regulatory milestones									$ 145.0
Research and development fund						$ 1.5	$ 3.8
Original research term, years							15 months
Extended research term, years						6 months
Milestone payment		$ 5.5		$ 5.0

Dispositions (Details) - USD ($) $ in Millions	1 Months Ended
Dispositions (Details) - USD ($) $ in Millions	Dec. 31, 2011	Nov. 30, 2007	Sep. 30, 2011
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	1 Months Ended	12 Months Ended			36 Months Ended
Restructurings (Narrative) (Details) $ in Thousands	Jun. 30, 2011 sublease	Dec. 31, 2012 USD ($) employee	Dec. 31, 2011 USD ($) facility	Dec. 31, 2010 USD ($)	Dec. 31, 2012 USD ($) employee
Restructuring Cost and Reserve [Line Items]
Aggregate reduction in headcount \| employee		422			422
Restructuring charge		$ 9,171	$ 10,136	$ 32,744	$ 52,100
Proceeds from sale of property and equipment		1,943	1,526	165
Expected additional payment for restructuring		3,200
Aggregate cash expenditures					28,700
Termination Benefits [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charge					21,200
Facility Charges [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charge		8,276	8,480	11,814	28,600
Proceeds from sale of property and equipment		0	0	0
Number of resulting subleases \| sublease	2
Restructuring Reserve		19,202	13,921	8,688	19,202
Aggregate cash expenditures		5,299	$ 3,469	3,739
Facility Charges [Member] \| South San Francisco Facilities [Member]
Restructuring Cost and Reserve [Line Items]
Number of additional buildings \| facility			2
Impairment in Value of Asset [Domain]
Restructuring Cost and Reserve [Line Items]
Restructuring charge		(47)	$ (907)	3,173	2,200
Proceeds from sale of property and equipment					2,600
Restructuring Reserve		0	0	0	$ 0
Aggregate cash expenditures		$ 0	$ 0	$ 0

Restructurings (Schedule Of Outstanding Restructuring Liability) (Details) - USD ($) $ in Thousands	12 Months Ended			36 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012
Restructuring Cost and Reserve [Line Items]
Restructuring charge	$ 9,171	$ 10,136	$ 32,744	$ 52,100
Cash payments				(28,700)
Proceeds from sale of assets	1,943	1,526	165
Proceeds from Sale of Impaired Property, Plant, and Equipment	938	1,526	168
Employee Severance And Other Benefits [Member]
Restructuring Cost and Reserve [Line Items]
Ending accrual balance as of December 31, 2011	6	5,523
Restructuring charge	970	2,566	17,677
Cash payments	(965)	(7,366)	(10,528)
Adjustments or non-cash credits including stock compensation expense	(11)	(717)	(1,626)
Proceeds from sale of assets	0	0	0
Ending accrual balance as of December 31, 2012	0	6	5,523	0
Facility Charges [Member]
Restructuring Cost and Reserve [Line Items]
Ending accrual balance as of December 31, 2011	13,921	8,688
Restructuring charge	8,276	8,480	11,814	28,600
Cash payments	(5,299)	(3,469)	(3,739)
Adjustments or non-cash credits including stock compensation expense	2,304	222	613
Proceeds from sale of assets	0	0	0
Ending accrual balance as of December 31, 2012	19,202	13,921	8,688	19,202
Impairment in Value of Asset [Domain]
Restructuring Cost and Reserve [Line Items]
Ending accrual balance as of December 31, 2011	0	0
Restructuring charge	(47)	(907)	3,173	2,200
Cash payments	0	0	0
Adjustments or non-cash credits including stock compensation expense	(891)	(619)	(3,341)
Proceeds from sale of assets				2,600
Ending accrual balance as of December 31, 2012	0	0	0	0
Proceeds from Sale of Impaired Property, Plant, and Equipment	938	1,526	168
Legal And Other Fees [Member]
Restructuring Cost and Reserve [Line Items]
Ending accrual balance as of December 31, 2011	51	70
Restructuring charge	(28)	(3)	80
Cash payments	(3)	(16)	(10)
Adjustments or non-cash credits including stock compensation expense	0	0	0
Proceeds from sale of assets	0	0	0
Ending accrual balance as of December 31, 2012	20	51	70	20
Total Restructuring [Member]
Restructuring Cost and Reserve [Line Items]
Ending accrual balance as of December 31, 2011	13,978	14,281
Restructuring charge	9,171	10,136	32,744
Cash payments	(6,267)	(10,851)	(14,277)
Adjustments or non-cash credits including stock compensation expense	1,402	(1,114)	(4,354)
Proceeds from sale of assets	938	1,526	168
Ending accrual balance as of December 31, 2012	$ 19,222	$ 13,978	$ 14,281	$ 19,222

Cash and Investments Cash and Investments (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2012 USD ($) affiliate	Dec. 31, 2011 USD ($)
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 634,053	$ 283,858
Gross Unrealized Gains	99	36
Gross Unrealized Losses	(191)	(173)
Fair Value	$ 633,961	283,721
Number of affiliate banks \| affiliate	1
Unrealized loss position	$ 196,100
Available-For-Sale Securities, Unrealized Loss Position, Term	1 year
Silicon Valley Bank Loan And Security Agreement [Member]
Schedule of Available-for-sale Securities [Line Items]
Collateral balance	$ 87,000	85,300
Money Market Funds [Member]
Schedule of Available-for-sale Securities [Line Items]
Fair Value	76,050
Mature within One Year	76,050
After One Year through Two Years	0
Cash and cash equivalents [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	170,070	74,256
Gross Unrealized Gains	0	1
Gross Unrealized Losses	(1)	0
Fair Value	170,069	74,257
Short-term investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	241,391	120,143
Gross Unrealized Gains	46	35
Gross Unrealized Losses	(66)	(173)
Fair Value	241,371	120,005
Short-term restricted cash and investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	12,242
Gross Unrealized Gains	4
Gross Unrealized Losses	0
Fair Value	12,246
Long-term investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	182,407	85,260
Gross Unrealized Gains	28	0
Gross Unrealized Losses	(124)	0
Fair Value	182,311	85,260
Long-term restricted cash and investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	27,943	4,199
Gross Unrealized Gains	21	0
Gross Unrealized Losses	0	0
Fair Value	27,964	4,199
Cash and money market funds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	81,744	81,986
Gross Unrealized Gains	2	0
Gross Unrealized Losses	0	0
Fair Value	81,746	81,986
Commercial paper [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	167,223	29,079
Gross Unrealized Gains	8	2
Gross Unrealized Losses	0	(1)
Fair Value	167,231	29,080
Mature within One Year	167,231
After One Year through Two Years	0
Corporate bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	222,106	116,068
Gross Unrealized Gains	30	22
Gross Unrealized Losses	(187)	(169)
Fair Value	221,949	115,921
Unrealized loss position	158,600
Mature within One Year	126,896
After One Year through Two Years	95,053
U.S. Treasury and government sponsored enterprises [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	132,933	37,237
Gross Unrealized Gains	59	12
Gross Unrealized Losses	(1)	0
Fair Value	132,991	37,249
Mature within One Year	84,677
After One Year through Two Years	48,314
Municipal bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	30,047	19,488
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(3)	(3)
Fair Value	30,044	$ 19,485
Mature within One Year	30,044
After One Year through Two Years	0
Investments, excluding cash [Member]
Schedule of Available-for-sale Securities [Line Items]
Fair Value	628,265
Mature within One Year	484,898
After One Year through Two Years	$ 143,367

Property And Equipment (Schedule Of Property And Equipment) (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Property, Plant and Equipment [Abstract]
Laboratory equipment	$ 19,504	$ 28,795
Computer equipment and software	11,897	11,743
Furniture and fixtures	3,230	3,230
Leasehold improvements	16,572	15,961
Construction-in-progress	1,409	155
Property and equipment, gross	52,612	59,884
Less accumulated depreciation and amortization	(46,553)	(51,378)
Property and equipment, net	$ 6,059	$ 8,506

The cumulative amount of depreciation, depletion and amortization (related to property, plant and equipment, but not including land) that has been recognized in the income statement.

Property And Equipment Property and Equipment Narrative (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Property, Plant and Equipment [Abstract]
Depreciation	$ 4,808	$ 6,822	$ 10,500
Impairment charges	300	500	3,173
Gain on sale of assets	300	1,400
Cash proceeds from sale of assets	$ 938	$ 1,526	$ 168

Debt (Narrative) (Details)				1 Months Ended									12 Months Ended		18 Months Ended
Debt (Narrative) (Details)	Aug. 14, 2012 USD ($) shares $ / shares	Jun. 30, 2010 USD ($) payment	Jun. 02, 2010 USD ($)	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, 2013 USD ($)	Dec. 31, 2012 USD ($) account affiliate payment	Jun. 30, 2011 USD ($)	Dec. 31, 2011 USD ($)	Sep. 27, 2011 USD ($)
Debt Instrument [Line Items]
Sale of shares of common stock, shares \| shares	34,500,000			12,700,000			17,300,000
Share price \| $ / shares	$ 4.25
Proceeds from Issuance of Common Stock and Convertible Debt, Net	$ 416,100,000
Proceeds from Convertible Debt, Net	277,700,000
Payments for Underwriting Discount, Debt	9,300,000
Payments of Debt Issuance Costs	500,000
Net proceeds from issuance of stock	138,400,000
Underwriting discount	7,700,000
Payments of stock issuance costs	500,000
Short-term restricted cash and investments														$ 12,246,000		$ 0
Long-term restricted cash and investments														27,964,000		4,199,000
Adjustments to Additional Paid in Capital, Equity Component of Convertible Debt	4,900,000													$ 137,785,000
Number of affiliate banks \| affiliate														1
Book value of debt outstanding														$ 335,736,000		181,515,000
Minimum [Member]
Debt Instrument [Line Items]
Number of required investment accounts \| account														1
Silicon Valley Bank [Member]
Debt Instrument [Line Items]
Book value of debt outstanding														$ 85,300,000
Debt Payment [Member]
Debt Instrument [Line Items]
Restricted Cash and Investments	36,500,000
Short-term restricted cash and investments														12,200,000
Long-term restricted cash and investments														24,300,000
Silicon Valley Bank Loan And Security Agreement [Member]
Debt Instrument [Line Items]
Debt, interest rate					6.00%
Collateral balance														87,000,000		85,300,000
Silicon Valley Bank Loan And Security Agreement [Member] \| Silicon Valley Bank [Member]
Debt Instrument [Line Items]
Book value of debt outstanding																90,100,000
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
Debt, interest rate	4.25%
Debt Instrument, Convertible, Conversion Ratio \| shares	188.2353
Debt Instrument, Convertible, Conversion Ratio, Principal Amount	$ 1,000
Debt Instrument, Convertible, Conversion Price \| $ / shares	$ 5.31
Debt Instrument, Fair Value Disclosure	$ 144,300,000
Debt Instrument, Fair Value of Equity Component, initial estimate	138,300,000
Debt Instrument, Unamortized Discount	143,200,000
Unamortized debt issuance expense														137,700,000
Debt Instrument, Fair Value of Debt Component, initial estimate	$ 149,200,000
Balance of unamortized closing fees and expenses														$ 4,700,000
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
Senior Notes [Member] \| Convertible Senior Subordinated Notes due August 15, 2019, 4.25% [Member]
Debt Instrument [Line Items]
Debt Instrument, Redemption Price Component, Percentage of Principal	100.00%
Debt Instrument, Periodic Payment, Number of Payments Secured in Escrow \| payment														6
Debt Instrument, Convertible, Effective Interest Rate														10.09%
Interest Expense, Debt														$ 10,300,000
Amortization of Financing Costs and Discounts														5,700,000
Secured Convertible Notes Due June 2015 [Member] \| Deerfield Financing [Member]
Debt Instrument [Line Items]
Debt, principal amount		$ 124,000,000							$ 124,000,000
Amortization of Financing Costs and Discounts														$ 9,900,000
Debt instruments, purchase price		80,000,000
Debt instruments, closing fees and expenses		2,000,000
Debt Instrument, Amendment, Consent Fee, Amount	$ 1,500,000
Annual interest		$ 6,000,000
Repayments of Notes Payable													$ 10,000,000
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
Minimum prepayment amount under collaborative arrangements														10,000,000
Minimum limit on prepayments														5,000,000
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
Equipment Line Of Credit December 2007 [Member] \| Silicon Valley Bank Loan And Security Agreement [Member]
Debt Instrument [Line Items]
Line of credit, borrowing capacity								$ 33,600,000				$ 30,000,000
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
Period of minimum draw										6 months
Minimum draws															$ 7,500,000
Percentage of collateral on outstanding obligations										100.00%
Draws on line of credit										$ 5,000,000	$ 13,600,000
Minimum draw down amount under facility						$ 2,500,000		$ 2,500,000	$ 2,500,000
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		$ 10,130,000
Seven-Year Term Loan [Member] \| Silicon Valley Bank Loan And Security Agreement [Member]
Debt Instrument [Line Items]
Debt, principal amount			$ 80,000,000
Debt, interest rate			1.00%
Debt Instrument, Number of Balloon Payments \| payment		1							1
Principal balance payable in balloon payment			100.00%
Percentage of security deposit on outstanding obligations			100.00%
Minimum percentage required for collateral balance					1
Maximum percentage required for collateral balance					1.07

Debt (Schedule Of Debt) (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Debt Instrument [Line Items]
Total debt	$ 335,736	$ 181,515
Less: current portion	(13,170)	(4,870)
Long-term debt	322,566	176,645
Senior Subordinated Notes [Member] \| Convertible Senior Subordinated Notes due August 15, 2019, 4.25% [Member]
Debt Instrument [Line Items]
Convertible Debt	149,800	0
Secured Debt [Member] \| Secured Convertible Notes due June 2015 [Member]
Debt Instrument [Line Items]
Convertible Debt	100,676	91,385
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	$ 5,260	$ 10,130

Debt (2019 Notes) (Details) - Senior Subordinated Notes [Member] - Convertible Senior Subordinated Notes due August 15, 2019, 4.25% [Member] - USD ($) $ in Thousands	Dec. 31, 2012	Aug. 14, 2012	Dec. 31, 2011
Debt Instrument [Line Items]
Net carrying amount of the liability component	$ 149,800		$ 0
Unamortized discount of the liability component	137,700
Face amount	$ 287,500	$ 287,500

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

Dec. 31, 2012

USD ($)

^[1]

Debt Disclosure [Abstract]

$ 13,170

11,654

104,436

80,000

$ 287,500

[1]

Amounts include principal payments associated with the accretion of discounts and debt issuance costs. This table assumes we will make the minimum mandatory prepayment on the Deerfield Notes in January 2014 as required by the note purchase agreement. The actual timing of payments made may differ materially

Common Stock And Warrants (Narrative) (Details) - USD ($) $ / shares in Units, $ in Thousands			1 Months Ended		12 Months Ended
	Aug. 14, 2012	Oct. 27, 2011	Feb. 29, 2012	Mar. 31, 2011	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Oct. 31, 2002
Class of Warrant or Right [Line Items]
Public offering of common stock	34,500,000		12,700,000	17,300,000
Net proceeds from public offering			$ 65,000	$ 179,400	$ 203,479	$ 179,375	$ 0
Share price	$ 4.25
Net proceeds from issuance of stock	$ 138,400
Underwriting discount	7,700
Payments of stock issuance costs	500
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
Repayment of accrued interest from agreement		$ 8,000
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				$ 287,500
Sale of stock, price per share	$ 5.31

Common Stock And Warrants (Schedule Of Warrants To Purchase Common Stock Outstanding And Exercisable) (Details)	12 Months Ended
	Dec. 31, 2012 $ / shares 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 \| $ / shares	$ 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 \| $ / shares	$ 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, 2012	Dec. 31, 2011
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, Fair Value Disclosure	$ 149,800	$ 0
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, Fair Value Disclosure	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, Fair Value Disclosure	5,260	10,130
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, Fair Value Disclosure	280,111	0
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, Fair Value Disclosure	79,542	77,835
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, Fair Value Disclosure	$ 5,253	$ 10,066

Employee Benefit Plans (Narrative) (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	12 Months Ended
	Jul. 31, 2010	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Life of stock option granted (years)		7 years
Life of stock options granted (years)		10 years
Options granted		3,442,696	2,545,625	243,500
Stock-based compensation expense		$ 8,781	$ 12,019	$ 20,971
Options, cancelled		2,248,545	2,577,473	4,511,970
Fair value of employee options vested and expensed		$ 5,600	$ 8,400	$ 16,200
Cash received from option exercises and purchases under the ESPP		$ 2,100	14,200
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		$ 600	800	1,000
Chief Executive Officer [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation expense	$ 1,500
Unvested RSUs (shares)	101,050
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
Number of shares available for grant		8,632,907
Intrinsic value of options exercised		$ 100	7,000	800
Total unrecognized compensation expense		$ 14,700
Unrecognized compensation expense weighted-average period for recognition (In years)		2 years 11 months 19 days
Performance Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options granted		755,792
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		$ 400	$ 700	$ 1,300
Number of shares available for grant		2,386,667
Common stock issued (shares)		298,533	375,305	689,093
Average price per share		$ 4.08	$ 4.62	$ 4.55
Unvested [Member] \| Chief Executive Officer [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options, cancelled	981,302
Restricted Stock Units (RSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total unrecognized compensation expense		$ 6,000
Unrecognized compensation expense weighted-average period for recognition (In years)		2 years 11 months 1 day
Option Exchange Program [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Life of stock option granted (years)		6 years 2 months 12 days

Employee Benefit Plans (Schedule Of Allocated Employee Stock-Based Compensation Expense) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Employee stock-based compensation expense	$ 8,781	$ 12,019	$ 20,971
Research And Development Expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Employee stock-based compensation expense	4,536	5,935	11,535
General And Administrative Expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Employee stock-based compensation expense	4,245	5,459	7,931
Restructuring-Related Stock Compensation Expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Employee stock-based compensation expense	$ 0	$ 625	$ 1,505

Represents the expense recognized during the period arising from equity-based compensation arrangements (for example, shares of stock, unit, stock options or other equity instruments) with employees, directors and certain consultants qualifying for treatment as employees.

Employee Benefit Plans (Schedule Of Fair Value Of Employee Share-Based Payments Awards ESPP Assumptions And Weighted Average Fair Values) (Details) - $ / shares	3 Months Ended		12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant-date fair value	$ 3.24	$ 3.50			$ 3.60
Risk-free interest rate	0.81%	1.07%			2.25%
Dividend yield	0.00%	0.00%			0.00%
Volatility	69.00%	70.00%			70.00%
Expected life (in months/years)	5 years 7 months 6 days	5 years 6 months			5 years 2 months 12 days
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant-date fair value			$ 2.07	$ 2.85	$ 1.87
Risk-free interest rate			0.10%	0.11%	0.21%
Dividend yield			0.00%	0.00%	0.00%
Volatility			68.00%	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, 2012	Dec. 31, 2011	Dec. 31, 2010
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Options outstanding at beginning of the year, Shares	17,436,378	19,630,030	24,393,598
Granted, Shares	3,442,696	2,545,625	243,500
Exercised, Shares	(181,979)	(2,161,804)	(495,098)
Cancelled, Shares	(2,248,545)	(2,577,473)	(4,511,970)
Options outstanding at ending of the year, Shares	18,448,550	17,436,378	19,630,030
Exercisable at December 31, 2012	13,128,876
Options outstanding at beginning of the year, Weighted Average Exercise Price	$ 7.16	$ 7.52	$ 7.46
Granted, Weighted Average Exercise Price	5.45	5.86	6.28
Exercised, Weighted Average Exercise Price	5.09	5.75	5.42
Cancelled, Weighted Average Exercise Price	7.28	9.79	7.35
Options outstanding at ending of the year, Weighted Average Exercise Price	6.85	$ 7.16	$ 7.52
Exercisable at December 31, 2012, Weighted Average Exercise Price	$ 7.35
SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageRemainingContractualTerm2	4 years 7 months 6 days
SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageRemainingContractualTerm2	4 years 7 months 6 days
Exercisable at December 31, 2012, Weighted Average Remaining Contractual Term (years)	3 years 10 months 6 days
Options outstanding at ending of the year, Aggregate Intrinsic Value	$ 90,240
Exercisable at December 31, 2012, Aggregate Intrinsic Value	$ 77,703

Employee Benefit Plans (Summary Of Information About Stock Options Outstanding) (Details)	12 Months Ended
	Dec. 31, 2012 $ / shares shares
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Options Outstanding, Number \| shares	18,448,550
Options Outstanding, Weighted Average Remaining Contractual Life (Years)	4 years 7 months 6 days
Options Outstanding, Weighted Average Exercise Price	$ 6.85
Options Outstanding and Exercisable, Number of Exercisable \| shares	13,128,876
Options Outstanding and Exercisable, Weighted Average Exercise Price	$ 7.35
$3.05 - $4.99 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower	3.05
Exercise Price Range, upper	$ 4.99
Options Outstanding, Number \| shares	913,013
Options Outstanding, Weighted Average Remaining Contractual Life (Years)	6 years 3 months 15 days
Options Outstanding, Weighted Average Exercise Price	$ 4.47
Options Outstanding and Exercisable, Number of Exercisable \| shares	642,101
Options Outstanding and Exercisable, Weighted Average Exercise Price	$ 4.43
$5.00 - $5.62 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower	5.00
Exercise Price Range, upper	$ 5.62
Options Outstanding, Number \| shares	6,025,420
Options Outstanding, Weighted Average Remaining Contractual Life (Years)	6 years 3 months 7 days
Options Outstanding, Weighted Average Exercise Price	$ 5.47
Options Outstanding and Exercisable, Number of Exercisable \| shares	1,413,294
Options Outstanding and Exercisable, Weighted Average Exercise Price	$ 5.27
$5.63 - $5.99 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower	5.63
Exercise Price Range, upper	$ 5.99
Options Outstanding, Number \| shares	2,976,329
Options Outstanding, Weighted Average Remaining Contractual Life (Years)	3 years 4 months 2 days
Options Outstanding, Weighted Average Exercise Price	$ 5.68
Options Outstanding and Exercisable, Number of Exercisable \| shares	2,931,042
Options Outstanding and Exercisable, Weighted Average Exercise Price	$ 5.67
$6.00 - $7.99 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower	6.00
Exercise Price Range, upper	$ 7.99
Options Outstanding, Number \| shares	2,938,367
Options Outstanding, Weighted Average Remaining Contractual Life (Years)	4 years 3 months 7 days
Options Outstanding, Weighted Average Exercise Price	$ 7.02
Options Outstanding and Exercisable, Number of Exercisable \| shares	2,547,018
Options Outstanding and Exercisable, Weighted Average Exercise Price	$ 6.98
$8.00 - $8.99 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower	8.00
Exercise Price Range, upper	$ 8.99
Options Outstanding, Number \| shares	3,774,399
Options Outstanding, Weighted Average Remaining Contractual Life (Years)	2 years 10 months 13 days
Options Outstanding, Weighted Average Exercise Price	$ 8.85
Options Outstanding and Exercisable, Number of Exercisable \| shares	3,774,399
Options Outstanding and Exercisable, Weighted Average Exercise Price	$ 8.85
$9.00 - $12.10 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price Range, lower	9.00
Exercise Price Range, upper	$ 12.10
Options Outstanding, Number \| shares	1,821,022
Options Outstanding, Weighted Average Remaining Contractual Life (Years)	4 years 5 months 5 days
Options Outstanding, Weighted Average Exercise Price	$ 10.07
Options Outstanding and Exercisable, Number of Exercisable \| shares	1,821,022
Options Outstanding and Exercisable, Weighted Average Exercise Price	$ 10.07

Employee Benefit Plans (Summary Of All RSU Activity) (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Awards outstanding at December 31, 2012, Shares	1,294,621
Restricted Stock Units (RSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
RSUs outstanding at December 31, 2011, Shares	1,391,691	2,172,431	2,679,224
Awarded, Shares	733,958	356,498	191,475
Released, Shares	(596,397)	(648,437)
Forfeited, Shares	(234,631)	(488,801)	(698,268)
Awards outstanding at December 31, 2012, Shares		1,391,691	2,172,431
RSUs outstanding at December 31, 2011, Weighted Average Grant Date Fair Value	$ 6.92	$ 7.31	$ 7.46
Awarded, Weighted Average Grant Date Fair Value	5.50	6.17	5.70
Released, Weighted Average Grant Date Fair Value	7.15	7.43
Forfeited, Weighted Average Grant Date Fair Value	6.62	7.45	7.44
Awards outstanding at December 31, 2012, Weighted Average Grant Date Fair Value	$ 6.07	$ 6.92	$ 7.31
ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsOutstandingWeightedAverageRemainingContractualTerms	1 year 9 months 11 days
Awards outstanding at December 31, 2012, Aggregate Intrinsic Value	$ 5,839

Income Taxes (Narrative) (Details) - USD ($) $ in Thousands		12 Months Ended
Income Taxes (Narrative) (Details) - USD ($) $ in Thousands	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Income Tax Examination [Line Items]
Income tax provision (benefit)		$ 107	$ 1,295	$ (72)
Prior year income taxes		100	600
Valuation allowance increased/decreased		6,800	(49,700)	25,200
Tax benefit of stock option		6,200
Unrecognized tax benefit would affect the effective tax rate	$ 126	100	126	0
Unrecognized Tax Benefits, Interest on Income Taxes Accrued	9	15	9
Unrecognized Tax Benefits, Interest on Income Taxes Expense		6	9
Accrued interest				0
Income Tax Reconciliation, State and Local Income Taxes		74	$ 660	$ 0
Federal [Member]
Income Tax Examination [Line Items]
Net operating loss carryforwards		1,007,000
Research and development tax credits	75,000
California [Member]
Income Tax Examination [Line Items]
Net operating loss carryforwards		$ 880,000
Research and development tax credits	$ 26,000
Maximum [Member] \| Federal [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards, expiration dates		2032
Maximum [Member] \| Research And Development Expense [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards, expiration dates		2029
Maximum [Member] \| California [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards, expiration dates		2032
Minimum [Member] \| Federal [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards, expiration dates		2018
Minimum [Member] \| Research And Development Expense [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards, expiration dates		2020
Minimum [Member] \| California [Member]
Income Tax Examination [Line Items]
Operating loss carryforwards, expiration dates		2013

Income Taxes (Schedule Of Consolidated Net Income (Loss)) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Income Tax Disclosure [Abstract]
(Loss) income before income taxes	$ (147,538)	$ 76,992	$ (92,402)

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, 2012	Dec. 31, 2011	Dec. 31, 2010
Income Tax Disclosure [Abstract]
U.S. federal taxes (benefit) at statutory rate	$ (50,163)	$ 26,177	$ (31,417)
Unutilized net operating losses	46,324	(29,650)	29,636
Non-deductible interest	3,297	2,809	0
Stock based compensation	504	627	1,709
State tax expense	74	660	0
Refundable tax credit	32	636	(72)
Other	39	36	72
Total	$ 107	$ 1,295	$ (72)

The sum of the current income tax expense or benefit and the deferred income tax expense or benefit pertaining to pretax Income or Loss from continuing operations; income tax expense or benefit may include interest and penalties on tax uncertainties based on the entity's accounting policy.

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 9
-Subparagraph (a),(b)
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32639-109319

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 45
-Paragraph 25
-URI http://asc.fasb.org/extlink&oid=21917399&loc=d3e32247-109318

Reference 3: 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.(h))
-URI http://asc.fasb.org/extlink&oid=6881521&loc=d3e23780-122690

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 10
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32672-109319

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 109
-Paragraph 45, 46
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 08
-Paragraph h
-Article 4

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Interpretation (FIN)
-Number 48
-Paragraph 15, 16, 19
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Commitments and Contingencies Disclosure [Abstract]

Income Taxes (Schedule Of Deferred Assets And Liabilities) (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Income Tax Disclosure [Abstract]
Net operating loss carryforwards	$ 374,200	$ 318,638
Tax credit carryforwards	65,232	54,726
Amortization of deferred stock compensation - non-qualified	26,469	25,865
Accruals and reserves not currently deductible	13,732	6,522
Deferred revenue	6,501	18,400
Book over tax depreciation and amortization	5,140	6,543
Capitalized research and development costs	0	805
Total deferred tax assets	491,274	431,499
Valuation allowance	(438,266)	(431,499)
Net deferred tax assets	53,008	0
Convertible debt	(53,008)	0
Total deferred tax liabilities	(53,008)	0
Net deferred taxes	$ 0	$ 0

Income Taxes (Schedule Of Unrecognized Tax Benefits) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Income Tax Disclosure [Abstract]
Beginning balance	$ 39,310	$ 46,381	$ 32,171
Increase (decrease) relating to prior year provision	5,894	(9,782)	10,472
Increase relating to current year provision	2,094	2,711	3,738
Ending balance	$ 47,298	$ 39,310	$ 46,381

Net (Loss) Income Per Share (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net (loss) income	$ (52,143)	$ (32,814)	$ (36,487)	$ (26,151)	$ 46,297	$ 77,865	$ (20,975)	$ (27,490)	$ (147,645)	$ 75,697	$ (92,330)
Shares used in computing basic (loss) income per share amounts									160,138	126,018	108,522
Shares issuable upon exercise of outstanding stock options									0	2,064	0
Shares issuable upon exercise of warrants									0	1,858	0
Shares issuable upon vesting of RSUs									0	515	0
Shares issuable upon purchase from ESPP contributions									0	24	0
Total dilutive securities									0	4,461	0
Shares used in computing diluted (loss) income per share amounts									160,138	130,479	108,522
Net (loss) income per share, basic					$ 0.35	$ 0.60	$ (0.16)	$ (0.24)	$ (0.92)	$ 0.60	$ (0.85)
Net (loss) income per share, diluted					$ 0.35	$ 0.59	$ (0.16)	$ (0.24)	$ (0.92)	$ 0.58	$ (0.85)
Potentially dilutive shares									72,132	9,085	30,777
Convertible debt [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Potentially dilutive shares									54,123	0	6,725
Outstanding stock options, unvested RSUs and ESPP contributions [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Potentially dilutive shares									16,568	9,085	21,802
Warrants [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Potentially dilutive shares									1,441	0	2,250

Commitments and Contingencies (Narrative) (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Operating Leased Assets [Line Items]
Rent expenses under operating leases	$ 17.8	$ 21.3	$ 28.0
Net of sublease rentals under operating leases	3.8	1.9	$ 0.3
Collateral provided for purchasing card program	2.5	2.9
Building Lease [Member]
Operating Leased Assets [Line Items]
Standby letter of credit, amount	0.5	0.5
Workers Compensation Insurance Policy [Member]
Operating Leased Assets [Line Items]
Standby letter of credit, amount	$ 0.6	$ 0.8

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

Dec. 31, 2012

USD ($)

2013

$ 19,486

^[1]

2014

19,896

^[1]

2015

20,152

^[1]

2016

16,431

^[1]

2017

9,104

^[1]

Thereafter

2,806

^[1]

Total

87,875

^[1]

Future minimum rental under noncancelable subleases

$ 15,500

[1]	Minimum payments have not been reduced by minimum sublease rentals of $15.5 million due in the future under noncancelable subleases.

Commitments and Contingencies (Schedule Of Aggregate Future Minimum Lease Payments Under Operating Leases By Material Lease Agreements) (Details)
$ in Thousands

12 Months Ended

Dec. 31, 2012

USD ($)

renewal

Building Lease #1&2 [Member]

$ 87,652

^[1]

Original Term (Expiration)

May 01, 2017

Number of Renewal Options | renewal

Period of Renewal Option, in years

5 years

Building Lease #3 [Member]

$ 49,216

Original Term (Expiration)

Jul. 01, 2018

Number of Renewal Options | renewal

Period of Renewal Option, in years

5 years

Building Lease #4 [Member]

$ 25,378

Original Term (Expiration)

Dec. 01, 2015

Number of Renewal Options | renewal

Period of Renewal Option, in years

3 years

$ 13,058

[1]	Minimum payments have not been reduced by minimum sublease rentals of $15.5 million due in the future under noncancelable subleases.

Concentrations of Credit Risk (Details) - Revenue, Rights Granted [Member] - Revenue from Rights Concentration Risk [Member]	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Bristol-Myers Squibb [Member]
Concentration Risk [Line Items]
Concentration Risk, Percentage	66.00%	59.00%	50.00%
Merck [Member]
Concentration Risk [Line Items]
Concentration Risk, Percentage	22.00%	0.00%	0.00%
Daiichi Sankyo [Member]
Concentration Risk [Line Items]
Concentration Risk, Percentage	12.00%	0.00%	3.00%
Sanofi [Member]
Concentration Risk [Line Items]
Concentration Risk, Percentage	0.00%	39.00%	42.00%

Quarterly Financial Data (Schedule Of Quarterly Financial Data) (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Quarterly Financial Information Disclosure [Abstract]
Total revenues	$ 7,814	$ 13,313	$ 7,813	$ 18,510	$ 94,309	$ 128,272	$ 32,162	$ 35,893
Income (loss) from operations	(41,974)	(25,443)	(32,723)	(22,296)	51,574	79,699	(18,008)	(23,730)
Net (loss) income	$ (52,143)	$ (32,814)	$ (36,487)	$ (26,151)	$ 46,297	$ 77,865	$ (20,975)	$ (27,490)	$ (147,645)	$ 75,697	$ (92,330)
Net loss per share, basic and diluted	$ (0.28)	$ (0.20)	$ (0.25)	$ (0.18)
Net (loss) income per share, basic					$ 0.35	$ 0.60	$ (0.16)	$ (0.24)	$ (0.92)	$ 0.60	$ (0.85)
Net (loss) income per share, diluted					$ 0.35	$ 0.59	$ (0.16)	$ (0.24)	$ (0.92)	$ 0.58	$ (0.85)

The amount of net income (loss) for the period per each share of common stock or unit outstanding during the reporting period.

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 225
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SX 210.5-03.21)
-URI http://asc.fasb.org/extlink&oid=6880815&loc=d3e20235-122688

Reference 2: 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 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 55
-Paragraph 52
-URI http://asc.fasb.org/extlink&oid=16381557&loc=d3e4984-109258

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=7655603&loc=d3e1252-109256

Reference 5: 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 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 225
-Section S99
-Paragraph 1
-Subparagraph (SX 210.9-04.23)
-URI http://asc.fasb.org/extlink&oid=6879574&loc=d3e536633-122882

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Paragraph 18
-Article 7

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 128
-Paragraph 36, 37, 38
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Emerging Issues Task Force (EITF)
-Number 07-4
-Paragraph 4
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 03
-Paragraph 20
-Article 5

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Paragraph 21
-Article 9

The amount of net income (loss) for the period available to each share of common stock or common unit outstanding during the reporting period and to each share or unit that would have been outstanding assuming the issuance of common shares or units for all dilutive potential common shares or units outstanding during the reporting period.

Amount of income (loss) from continuing operations attributable to the parent. Also defined as revenue less expenses and taxes from ongoing operations before extraordinary items but after deduction of those portions of income or loss from continuing operations that are allocable to noncontrolling interests.

Reference 1: 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=6943989&loc=d3e3602-108585

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 50
-Paragraph 1
-Subparagraph (a)
-URI http://asc.fasb.org/extlink&oid=6371337&loc=d3e3550-109257

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 225
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SX 210.5-03.13)
-URI http://asc.fasb.org/extlink&oid=6880815&loc=d3e20235-122688

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 810
-SubTopic 10
-Section 45
-Paragraph 18
-URI http://asc.fasb.org/extlink&oid=7656940&loc=SL4613673-111683

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 38
-Subparagraph b(1)
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 29
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 28
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

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