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Document and Entity Information - USD ($)	12 Months Ended
Document and Entity Information - USD ($)	Dec. 31, 2012	Feb. 14, 2013	Jun. 30, 2012
Document and Entity Information
Entity Registrant Name	THERAVANCE INC
Entity Central Index Key	0001080014
Document Type	10-K
Document Period End Date	Dec. 31, 2012
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	Yes
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes
Entity Filer Category	Large Accelerated Filer
Entity Public Float			$ 940,773,069
Entity Common Stock, Shares Outstanding		98,451,008
Document Fiscal Year Focus	2012
Document Fiscal Period Focus	FY

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Current assets:
Cash and cash equivalents	$ 94,849	$ 44,778
Short-term investments	153,640	196,137
Receivables from collaboration partners (including amounts from a related party of $123 at December 31, 2012 and $223 at December 31, 2011)	1,064	223
Notes receivable, current	100	100
Prepaid and other current assets	3,966	3,525
Inventories	7,514
Total current assets	261,133	244,763
Long-term marketable securities	95,194
Restricted cash	833	893
Property and equipment, net	9,154	10,372
Notes receivable, non-current	140	240
Other assets, non-current	2,128	2,514
Total assets	368,582	258,782
Current liabilities:
Accounts payable	5,377	5,813
Accrued personnel-related expenses	9,002	9,643
Accrued clinical and development expenses	6,550	6,956
Accrued interest on convertible subordinated notes	2,372	2,372
Other accrued liabilities	2,072	1,946
Note payable and capital lease, current		69
Deferred revenue, current	4,593	18,697
Total current liabilities	29,966	45,496
Convertible subordinated notes	172,500	172,500
Deferred rent	5,074	5,821
Deferred revenue, non-current	6,014	122,017
Commitments and contingencies (Notes 3, 8 and 10)
Stockholders' equity (net capital deficiency):
Preferred stock, $0.01 par value, 230 shares authorized, no shares issued and outstanding
Additional paid-in capital	1,488,447	1,228,037
Accumulated other comprehensive income	99	16
Accumulated deficit	(1,334,502)	(1,315,960)
Total stockholders' equity (net capital deficiency)	155,028	(87,052)
Total liabilities and stockholders' equity (net capital deficiency)	368,582	258,782
Common stock
Stockholders' equity (net capital deficiency):
Common stock	984	855
Class A common stock
Stockholders' equity (net capital deficiency):
Common stock

Consolidated Balance Sheets (Parenthetical) - USD ($) shares in Thousands, $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Receivable from related party	$ 123	$ 223
Preferred stock, par value (in dollars per share)	$ 0.01	$ 0.01
Preferred stock, shares authorized	230	230
Common stock
Common stock, par value (in dollars per share)	$ 0.01	$ 0.01
Common stock, authorized shares	200,000	200,000
Common stock, outstanding shares	98,379	85,543
Class A common stock
Common stock, par value (in dollars per share)	$ 0.01	$ 0.01
Common stock, authorized shares	30,000	30,000

- Definition

The aggregate amount of receivables to be collected from related parties where one party can exercise control or significant influence over another party; including affiliates, owners or officers and their immediate families, pension trusts, and so forth, at the financial statement date. which are usually due within one year (or one business cycle).

+ References + Details

Consolidated Statements of Operations - USD ($) shares in Thousands, $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Consolidated Statements of Operations
Revenue (including amounts from a related party of $5,613 in 2012, $9,658 in 2011, and $9,826 in 2010)	$ 135,758	$ 24,512	$ 24,223
Operating expenses:
Research and development	117,898	103,568	75,070
General and administrative	30,859	30,681	27,476
Total operating expenses	148,757	134,249	102,546
Loss from operations	(12,999)	(109,737)	(78,323)
Interest and other income	460	415	505
Interest expense	(6,003)	(6,022)	(6,044)
Net loss	$ (18,542)	$ (115,344)	$ (83,862)
Basic and diluted net loss per share (in dollars per share)	$ (0.20)	$ (1.41)	$ (1.16)
Shares used in computing basic and diluted net loss per share (in shares)	90,909	82,051	72,070

Consolidated Statements of Operations (Parenthetical) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Consolidated Statements of Operations
Revenue from a related party	$ 5,613	$ 9,658	$ 9,826

- Definition

Amount of revenue, fees and commissions earned from transactions between (a) a parent company and its subsidiaries; (b) subsidiaries of a common parent; (c) an entity and trusts for the benefit of employees, for example, but not limited to, pension and profit-sharing trusts that are managed by or under the trusteeship of the entity's management; (d) an entity and its principal, owners, management, or members of their immediate families; and (e) affiliates.

+ References + Details

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Consolidated Statements of Comprehensive Loss
Net loss	$ (18,542)	$ (115,344)	$ (83,862)
Other comprehensive income (loss):
Net unrealized gain (loss) on available-for-sale securities, net of tax	83	(17)	(2)
Comprehensive loss	$ (18,459)	$ (115,361)	$ (83,864)

- Definition

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 the reporting entity. It includes all changes in equity during a period except those resulting from investments by owners and distributions to owners, but excludes any and all transactions which are directly or indirectly attributable to that ownership interest in subsidiary equity which is not attributable to the parent.

+ References + Details

- Definition

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

+ References

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.

+ Details

Consolidated Statements of Stockholders' Equity (Net Capital Deficiency) - USD ($) shares in Thousands, $ in Thousands	Total	Common Stock	Common Stock Common Stock	Common Stock Class A Common Stock	Additional Paid-In Capital	Accumulated Other Comprehensive Income	Accumulated Deficit
Balance at Dec. 31, 2009	$ (188,994)		$ 549	$ 94	$ 927,082	$ 35	$ (1,116,754)
Balance (in shares) at Dec. 31, 2009			54,830	9,402
Increase (Decrease) in Stockholders' Equity
Exercise of stock options, and issuance of common stock in settlement of restricted stock units, stock awards and purchase plan	8,761		$ 17		8,744
Exercise of stock options, and issuance of common stock in settlement of restricted stock units, stock awards and purchase plan (in shares)			1,745
Issuance of common stock for cash in secondary stock offering, net of expenses of $5.7 million	93,478		$ 86		93,392
Issuance of common stock for cash in secondary stock offering, expenses (in shares)			8,625
Issuance of common stock in private placement to a related party, net of expenses of $0.4 and $0.2 million for the year ended 2012 and 2010, respectively	129,190		$ 58		129,132
Issuance of common stock in private placement to a related party, expenses (in shares)			5,750
Stock-based compensation	19,009				19,009
Net loss	(83,862)						(83,862)
Net unrealized gain (loss) on marketable securities	(2)					(2)
Balance at Dec. 31, 2010	(22,420)		$ 710	$ 94	1,177,359	33	(1,200,616)
Balance (in shares) at Dec. 31, 2010			70,950	9,402
Increase (Decrease) in Stockholders' Equity
Exercise of stock options, and issuance of common stock in settlement of restricted stock units, stock awards and purchase plan	12,195		$ 46		12,149
Exercise of stock options, and issuance of common stock in settlement of restricted stock units, stock awards and purchase plan (in shares)			4,617
Issuance of common stock in private placement to a related party, net of expenses of $0.4 and $0.2 million for the year ended 2012 and 2010, respectively	13,618		$ 5		13,613
Issuance of common stock in private placement to a related party, expenses (in shares)			574
Conversion of Class A common stock (Note 3)			$ 94	$ (94)
Conversion of Class A common stock (Note 3) (in shares)			9,402	(9,402)
Stock-based compensation	24,916				24,916
Net loss	(115,344)						(115,344)
Net unrealized gain (loss) on marketable securities	(17)					(17)
Balance at Dec. 31, 2011	(87,052)		$ 855		1,228,037	16	(1,315,960)
Balance (in shares) at Dec. 31, 2011		85,543	85,543
Increase (Decrease) in Stockholders' Equity
Exercise of stock options, and issuance of common stock in settlement of restricted stock units, stock awards and purchase plan	7,081		$ 22		7,059
Exercise of stock options, and issuance of common stock in settlement of restricted stock units, stock awards and purchase plan (in shares)			2,151
Issuance of common stock in private placement to a related party, net of expenses of $0.4 and $0.2 million for the year ended 2012 and 2010, respectively	229,296		$ 107		229,189
Issuance of common stock in private placement to a related party, expenses (in shares)			10,685
Stock-based compensation	24,162				24,162
Net loss	(18,542)						(18,542)
Net unrealized gain (loss) on marketable securities	83					83
Balance at Dec. 31, 2012	$ 155,028		$ 984		$ 1,488,447	$ 99	$ (1,334,502)
Balance (in shares) at Dec. 31, 2012		98,379	98,379

Consolidated Statements of Stockholders' Equity (Net Capital Deficiency) (Parenthetical) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2010
Consolidated Statements of Stockholders' Equity (Net Capital Deficiency)
Issuance of common stock for cash in secondary stock offering, expenses		$ 5.7
Issuance of common stock in private placement to a related party, expenses	$ 0.4	$ 0.2

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	$ (18,542)	$ (115,344)	$ (83,862)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	7,326	7,583	6,336
(Gain) loss on sales of available-for-sale securities	(9)	2	(3)
Stock-based compensation	23,783	24,916	19,009
Loss on disposal of equipment	196		33
Forgiveness of notes receivable		16	8
Changes in operating assets and liabilities:
Receivables from collaboration partners	(841)	(29)	81
Prepaid and other current assets	(441)	2,288	652
Inventories	(4,822)
Other assets, non-current	(441)
Accounts payable	(1,480)	3,310	(236)
Accrued personnel-related expenses and other accrued liabilities	(1,829)	5,124	3,321
Deferred rent	(747)	2,429	1,446
Deferred revenue	(130,107)	(18,633)	(21,801)
Other long-term liabilities			(128)
Net cash used in operating activities	(127,954)	(88,338)	(75,144)
Cash flows from investing activities
Purchases of property and equipment	(2,590)	(3,628)	(861)
Purchases of short-term investments and marketable securities	(330,484)	(301,563)	(183,899)
Maturities of short-term investments and marketable securities	224,902	231,476	131,855
Sales of short-term investments and marketable securities	49,729	17,321	12,024
Sale of equipment			12
Release of restricted cash	60		417
Issuance of notes receivable	(140)	(140)
Payments received on notes receivable	240	715	140
Net cash used in investing activities	(58,283)	(55,819)	(40,312)
Cash flows from financing activities
Payments on note payable and capital leases	(69)	(206)	(184)
Proceeds from issuances of common stock, net	236,377	25,808	231,429
Net cash provided by financing activities	236,308	25,602	231,245
Net increase (decrease) in cash and cash equivalents	50,071	(118,555)	115,789
Cash and cash equivalents at beginning of period	44,778	163,333	47,544
Cash and cash equivalents at end of period	94,849	44,778	163,333
Supplemental Disclosure of Cash Flow Information
Cash paid for interest	$ 5,177	$ 5,195	$ 5,217

Description of Operations and Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2012

Description of Operations and Summary of Significant Accounting Policies

Description of Operations and Summary of Significant Accounting Policies

1. Description of Operations and Summary of Significant Accounting Policies

Description of Operations

Theravance, Inc. (the Company or Theravance) is a biopharmaceutical company with a pipeline of internally discovered product candidates and strategic collaborations with pharmaceutical companies. Theravance is focused on the discovery, development and commercialization of small molecule medicines across a number of therapeutic areas including respiratory disease, bacterial infections, and central nervous system (CNS)/pain.

Principles of Consolidation

The consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation.

Use of Management's Estimates

The preparation of consolidated financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the consolidated financial statements and accompanying notes. Actual results could differ materially from those estimates.

Segment Reporting

The Company has determined that it operates in a single segment which is the discovery (research), development and commercialization of human therapeutics. Revenues are generated primarily from the Company's collaboration arrangements with GlaxoSmithKline plc (GSK), located in the United Kingdom, Astellas Pharma Inc. (Astellas) (through January 6, 2012), located in Japan, and Merck located in the United States. All long-lived assets, which were comprised of property and equipment, are maintained in the United States.

Cash and Cash Equivalents

The Company considers all highly liquid investments purchased with a maturity of three months or less on the date of purchase to be cash equivalents. Cash equivalents are carried at cost, which approximates fair value.

Under certain lease agreements and letters of credit, the Company has pledged cash and cash equivalents as collateral. Restricted cash related to such agreements was $0.8 million as of December 31, 2012 and $0.9 million as of December 31, 2011.

Marketable Securities

The Company's management determines the appropriate classification of its marketable securities, which consist of debt securities, at the time of purchase and reevaluates such designation at each balance sheet date. All of the marketable securities are classified as available-for-sale and carried at estimated fair values and reported in cash equivalents, short-term investments or long-term marketable securities. Unrealized gains and losses on available-for-sale securities are reported in the consolidated statements of comprehensive loss. Interest, amortization of purchase premiums and discounts, and realized gains and losses on sales of securities are included in interest and other income. The cost of securities sold is based on the specific identification method.

The Company regularly reviews all of its investments for other-than-temporary declines in estimated fair value. The Company's review includes the consideration of the cause of the impairment, including the creditworthiness of the security issuers, the number of securities in an unrealized loss position, the severity and duration of the unrealized losses, whether the Company has the intent to sell the securities and whether it is more likely than not that the Company will be required to sell the securities before the recovery of their amortized cost basis. When the Company's management determines that the decline in estimated fair value of an investment is below the amortized cost basis and the decline is other-than-temporary, the Company reduces the carrying value of the security and records a loss for the amount of such decline.

Fair Value of Financial Instruments

Financial instruments include cash equivalents, marketable securities, related party receivables, accounts payable, accrued liabilities and convertible subordinated notes. Marketable securities are carried at estimated fair value. The carrying value of cash equivalents, receivables from related party, accounts payable and accrued liabilities approximate their estimated fair value due to the relatively short nature of these instruments. Convertible subordinated notes are described in Note 7.

Concentration of Credit Risks

The Company invests in a variety of financial instruments and, by its policy, limits the amount of credit exposure with any one issuer, industry or geographic area for investments other than instruments backed by the U.S. federal government.

Notes Receivable

The Company provided loans to certain employees to assist them primarily with the purchase of a primary residence, which collateralizes the resulting loans. There was no interest receivable related to the loans as of December 31, 2012 and December 31, 2011. The outstanding loans have maturity dates ranging from January 2013 through May 2014.

Inventories

Inventories are stated at the lower of cost or market value. Inventories include VIBATIV® active pharmaceutical ingredient and other raw materials of $5.7 million and work-in-process of $1.8 million at December 31, 2012. Work-in-process consists of third party manufacturing and associated labor costs relating to the Company's personnel directly involved in the production process. VIBATIV® is a U.S. Food and Drug Administration (FDA) approved drug. If information becomes available that suggests the inventories may not be realizable, the Company may be required to expense a portion or all of the previously capitalized inventories.

Property and Equipment

Property, equipment and leasehold improvements are stated at cost and depreciated using the straight-line method as follows:


Leasehold improvements		Shorter of remaining lease terms or useful life
Equipment, furniture and fixtures		5 - 7 years
Software and computer equipment		3 years

Capitalized Software

The Company capitalizes certain costs related to direct material and service costs for software obtained for internal use. Capitalized software costs are depreciated over 3 years.

Impairment of Long-Lived Assets

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

Bonus Accruals

The Company has short-term bonus programs for eligible employees. Bonuses are determined based on various criteria, including the achievement of corporate, departmental and individual goals. Bonus accruals are estimated based on various factors, including target bonus percentages per level of employee and probability of achieving the goals upon which bonuses are based. The Company's management periodically reviews the progress made towards the goals under the bonus programs. As bonus accruals are dependent upon management's judgments of the likelihood of achieving the various goals, it is possible for bonus expense to vary significantly in future periods if changes occur in those management estimates.

In 2011, the Company granted special long-term retention and incentive cash bonus awards to certain employees. The awards have dual triggers of vesting based upon the achievement of certain performance conditions over a six-year timeframe from 2011 through December 31, 2016 and continued employment. As of December 31, 2012, the Company's management determined that the achievement of the requisite performance conditions was not probable and, as a result, no compensation expense has been recognized.

Deferred Rent

Deferred rent consists of the difference between cash payments and the recognition of rent expense on a straight-line basis for the buildings the Company occupies. Rent expense is being recognized ratably over the life of the leases. Because the Company's facility operating leases provide for rent increases over the terms of the leases, average annual rent expense during the first 1.5 years of the leases exceeded the Company's actual cash rent payments. Also included in deferred rent are lease incentives of $2.6 million as of December 31, 2012, which is being recognized ratably over the life of the leases.

Revenue Recognition

The Company's revenues are related primarily to its collaboration arrangements. The Company's arrangements provide for various types of payments to the Company, including non-refundable upfront fees, milestone and other contingent payments and royalty payments.

Beginning in January 1, 2011, the Company accounts for new multiple element arrangements, such as license and development agreements in which a customer may purchase several deliverables, in accordance with Financial Accounting Standards Board (FASB) Subtopic ASC 605-25, "Multiple Element Arrangements". For new or materially amended multiple element arrangements, at the inception of the arrangement each deliverable within a multiple deliverable revenue arrangement is accounted for as a separate unit of accounting if both of the following criteria are met: (1) the delivered item or items have value to the customer on a standalone basis and (2) for an arrangement that includes a general right of return relative to the delivered item(s), delivery or performance of the undelivered item(s) is considered probable and substantially in the Company's control. The Company allocates revenue to each non-contingent element based on the relative selling price of each element. When applying the relative selling price method, the Company's management determines the selling price for each deliverable using vendor-specific objective evidence (VSOE) of selling price, if it exists, or third-party evidence (TPE) of selling price, if it exists. If neither VSOE nor TPE of selling price exist for a deliverable, the Company uses best estimated selling price for that deliverable. Revenue allocated to each element is then recognized based on when the basic four revenue recognition criteria are met for each element.

For multiple-element arrangements entered into prior to January 1, 2011, the Company's management determined the deliverables under its collaboration agreements which did not meet the criteria to be considered for separate accounting units for the purposes of revenue recognition. As a result, the Company recognized revenue from non-refundable, upfront fees and development milestone payments ratably over the term of its performance under the agreements. These upfront or milestone payments received, pending recognition as revenue, are recorded as deferred revenue and are classified as a short-term or long-term liability on the Company's consolidated balance sheet and amortized over the estimated period of performance. The Company periodically reviews the estimated performance periods of its contracts based on the progress of its programs.

Where a portion of non-refundable upfront fees or other payments received are allocated to continuing performance obligations under the terms of a collaboration agreement, they are be recorded as deferred revenue and recognized as revenue or as an accrued liability and recognized as a reduction of research and development expenses ratably over the term of its estimated performance period under the agreement. The Company's management determines the estimated performance periods and they are periodically reviewed based on the progress of the related program. The effect of any change made to an estimated performance period and therefore revenue recognized would occur on a prospective basis in the period that the change was made.

Under certain collaboration arrangements, the Company has been reimbursed for a portion of its research and development expenses. These reimbursements have been reflected as a reduction of research and development expense in the Company's consolidated statements of operation, as the Company does not consider performing research and development services to be a part of its ongoing and central operations. Therefore, the reimbursement of research and developmental services and any amounts allocated to the Company's research and development services are recorded as a reduction of research and development expense.

Amounts deferred under a collaboration agreement in which the performance obligations are terminated will result in an immediate recognition of any remaining deferred revenue and accrued liability in the period that termination occurred, provided that all performance obligations have been satisfied.

Beginning in 2011, the Company accounts for milestones in accordance with FASB Subtopic ASC 605-28 "Revenue Recognition-Milestone Method". The Company recognizes revenue from milestone payments when (i) the milestone event is substantive and its achievability was not reasonably assured at the inception of the agreement and (ii) the Company does not have ongoing performance obligations related to the achievement of the milestone. Milestone payments are considered substantive if all of the following conditions are met: the milestone payment (a) is commensurate with either the Company's performance to achieve the milestone or the enhancement of the value of the delivered item or items as a result of a specific outcome resulting from the Company's performance to achieve the milestone, (b) relates solely to past performance, and (c) is reasonable relative to all of the deliverables and payment terms (including other potential milestone consideration) within the arrangement. See Note 3, "Collaboration Arrangements," for analysis of each milestone event deemed to be substantive or non-substantive.

In accordance with ASC Subtopic 808-10, "Collaborative Arrangement," and pursuant to the Company's agreement with Astellas, the Company recognized as revenue the net impact of transactions with Astellas related to VIBATIV® inventories including revenue specifically attributable to any sales, and cost of inventories either transferred or expensed as unrealizable.

The Company recognizes royalty revenue on licensee net sales in the period in which the royalties are earned.

Research and Development Costs

Research and development costs are expensed in the period that services are rendered or goods are received. Research and development costs consist of salaries and benefits, laboratory supplies and facility costs, as well as fees paid to third parties that conduct certain research and development activities on behalf of the Company, net of certain external research and development costs reimbursed under the Company's collaboration arrangements.

Preclinical Study and Clinical Study Expenses

A substantial portion of the Company's preclinical studies and all of its clinical studies have been performed by third-party contract research organizations (CROs). Some CROs bill monthly for services performed, while others bill based upon milestones achieved. The Company reviews the activities performed under the significant contracts each quarter. For preclinical studies, the significant factors used in estimating accruals include the percentage of work completed to date and contract milestones achieved. For clinical study expenses, the significant factors used in estimating accruals include the number of patients enrolled and percentage of work completed to date. Vendor confirmations are obtained for contracts with longer duration when necessary to validate the Company's estimate of expenses. The Company's estimates are highly dependent upon the timeliness and accuracy of the data provided by its CROs regarding the status of each program and total program spending and adjustments are made when deemed necessary.

Fair Value of Stock-Based Compensation Awards

The Company uses the Black-Scholes-Merton option pricing model to estimate the fair value of options granted under its equity incentive plans and rights to acquire stock granted under its employee stock purchase plan (ESPP). The Black-Scholes-Merton option valuation model requires the use of assumptions, including the expected term of the award and the expected stock price volatility. The Company used the "simplified" method as described in Staff Accounting Bulletin No. 107, "Share-Based Payment", for the expected option term because the usage of its historical option exercise data is limited due to post-IPO exercise restrictions. Beginning April 1, 2011, the Company used its historical volatility to estimate expected stock price volatility. Prior to April 1, 2011, the Company used peer company price volatility to estimate expected stock price volatility due to the Company's limited historical common stock price volatility since its initial public offering in 2004.

Restricted Stock Units (RSUs) and Restricted Stock Awards (RSAs) are measured based on the fair market values of the underlying stock on the dates of grant.

Stock-based compensation expense was calculated based on awards ultimately expected to vest and was reduced for estimated forfeitures at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differed from those estimates. The Company's estimated annual forfeiture rates for stock options, RSUs and RSAs are based on its historical forfeiture experience.

The estimated fair value of stock options, RSUs and RSAs is expensed on a straight-line basis over the expected term of the grant and the estimated fair value of performance-contingent RSUs and RSAs is expensed using an accelerated method over the term of the award once the Company's management has determined that it is probable that performance milestones will be achieved. Compensation expense for RSUs and RSAs that contain performance conditions is based on the grant date fair value of the award. Compensation expense is recorded over the requisite service period based on management's best estimate as to whether it is probable that the shares awarded are expected to vest. The Company's management assesses the probability of the performance milestones being met on a continuous basis.

Compensation expense for purchases under the ESPP is recognized based on the fair value of the common stock on the date of offering, less the purchase discount percentage provided for in the plan.

The Company has not recognized, and does not expect to recognize in the near future, any tax benefit related to employee stock-based compensation expense as a result of the full valuation allowance on the Company's deferred tax assets including deferred tax assets related to its net operating loss carryforwards.

Income Taxes

The Company utilizes the asset and liability method of accounting for income taxes. Under this method, deferred tax assets and liabilities are determined based on differences between financial reporting and tax basis of assets and liabilities and are measured using enacted tax rates and laws that will be in effect when the differences are expected to reverse. A valuation allowance is provided when it is more likely than not that some portion or all of a deferred tax asset will not be realized.

None of the Company's currently unrecognized tax benefits would affect its effective income tax rate if recognized, due to the valuation allowance that currently offsets the Company's deferred tax assets. The Company does not anticipate the total amount of unrecognized income tax benefits relating to tax positions existing at December 31, 2012 will significantly increase or decrease in the next 12 months.

The Company's management assesses all material positions taken in any income tax return, including all significant uncertain positions, in all tax years that are still subject to assessment or challenge by relevant taxing authorities. Assessing an uncertain tax position begins with the initial determination of the position's sustainability and is measured at the largest amount of benefit that is greater than 50% likely to be realized upon ultimate settlement. As of each balance sheet date, unresolved uncertain tax positions must be reassessed, and the Company's management will determine whether: the factors underlying the sustainability assertion have changed; and the amount of the recognized tax benefit is still appropriate.

The recognition and measurement of tax benefits requires significant judgment. Judgments concerning the recognition and measurement of a tax benefit might change as new information becomes available.

Foreign Currency

The Company uses the U.S. dollar as the functional currency for its foreign subsidiary. Monetary and non-monetary assets and liabilities are remeasured into U.S. dollars at the applicable period end exchange rate. Operating expenses are remeasured at average exchange rates in effect during each period, except for those expenses related to non-monetary assets which are remeasured at historical exchange rates. Gains or losses from remeasurement of foreign currency financial statements into U.S. dollars are included in the condensed consolidated statements of operations and were insignificant for all periods presented, as was the effect of exchange rate changes on cash and cash equivalents.

Comprehensive Loss

Comprehensive loss is comprised of net loss and other comprehensive income (loss). Other comprehensive income (loss) consists of changes in unrealized gains and losses on the Company's available-for-sale securities, net of tax.

Related Parties

Transactions with GSK are described in Note 3, "Collaboration Arrangements".

Robert V. Gunderson, Jr. is a director of the Company. The Company has engaged Gunderson Dettmer Stough Villeneuve Franklin & Hachigian, LLP, of which Mr. Gunderson is a partner, as its primary legal counsel. Fees incurred in the ordinary course of business were $1.2 million in 2012, $0.3 million in 2011, and $0.7 million in 2010.

- Definition

The entire disclosure for the organization, consolidation and basis of presentation of financial statements disclosure, and significant accounting policies of the reporting entity. May be provided in more than one note to the financial statements, as long as users are provided with an understanding of (1) the significant judgments and assumptions made by an enterprise in determining whether it must consolidate a VIE and/or disclose information about its involvement with a VIE, (2) the nature of restrictions on a consolidated VIE's assets reported by an enterprise in its statement of financial position, including the carrying amounts of such assets, (3) the nature of, and changes in, the risks associated with an enterprise's involvement with the VIE, and (4) how an enterprise's involvement with the VIE affects the enterprise's financial position, financial performance, and cash flows. Describes procedure if disclosures are provided in more than one note to the financial statements.

+ References + Details

Net Loss per Share

12 Months Ended

Dec. 31, 2012

Net Loss per Share

Net Loss per Share

2. Net Loss per Share

Basic net loss per share (basic EPS) is computed by dividing net loss by the weighted-average number of common shares outstanding during the period, less unvested RSAs subject to forfeiture. Diluted net loss per share (diluted EPS) is computed by dividing net loss by the weighted-average number of common shares outstanding during the period, less unvested RSAs subject to forfeiture, plus dilutive potential common shares. Diluted EPS is identical to basic EPS for all periods presented since potential common shares are excluded from the calculation, as their effect is anti-dilutive.

Weighted-Average Shares Outstanding

The following table sets forth the computation of basic and diluted net loss and the weighted-average number of shares used in computing basic and diluted net loss per share:

	Year Ended December 31,

(in thousands, except for per share data)	2012			2011			2010
Basic and diluted:
Net loss	$	(18,542	)	$	(115,344	)	$	(83,862	)

Weighted-average shares of common stock outstanding		93,410			84,493			72,103
Less: unvested RSAs		(2,501	)		(2,442	)		(33	)

Weighted-average shares used in computing basic and diluted net loss per common share		90,909			82,051			72,070

Basic and diluted net loss per share	$	(0.20	)	$	(1.41	)	$	(1.16	)

Anti-dilutive Securities

Securities that were not included in the computation of diluted EPS because their effect would have been anti-dilutive were as follows:

	Year Ended December 31,

(in thousands)	2012		2011		2010
Shares issuable under Equity Incentive Plans and ESPP		5,367		5,464		6,636
Shares issuable upon the conversion of convertible subordinated notes		6,668		6,668		6,668

Total anti-dilutive securities		12,035		12,132		13,304

Collaboration Arrangements

12 Months Ended

Dec. 31, 2012

Collaboration Arrangements

Collaboration Arrangements

3. Collaboration Arrangements

GSK

LABA collaboration

In November 2002, the Company entered into its long-acting beta₂ agonist (LABA) collaboration with GSK to develop and commercialize once-daily LABA products for the treatment of chronic obstructive pulmonary disease (COPD) and asthma. For the treatment of COPD, the collaboration is developing two combination products: (1) RELVAR™ or BREO™ (FF/VI), an investigational once-daily combination medicine consisting of a LABA, vilanterol (VI), and an inhaled corticosteroid (ICS), fluticasone furoate (FF) and (2) ANORO™ (UMEC/VI), a once-daily investigational medicine combining a long-acting muscarinic antagonist (LAMA), umeclidinium bromide (UMEC), with a LABA, VI. For the treatment of asthma, the collaboration is developing FF/VI.

In the event that a product containing VI is successfully developed and commercialized, the Company will be obligated to make milestone payments to GSK which could total as much as $220.0 million if both a single-agent and a combination product or two different combination products are launched in multiple regions of the world. Of these potential milestone payments, the Company estimates up to $140.0 million could be payable during 2013 and all the milestone payments could be payable by the end of 2014. The Company is entitled to receive annual royalties from GSK of 15% on the first $3.0 billion of annual global net sales and 5% for all annual global net sales above $3.0 billion. Sales of single-agent LABA medicines and combination medicines would be combined for the purposes of this royalty calculation. For other products combined with a LABA from the LABA collaboration, such as ANORO™, royalties are upward tiering and range from the mid-single digits to 10%. However, if GSK is not selling a LABA/ICS combination product at the time that the first other LABA combination is launched, then the royalties described above for the LABA/ICS combination medicine would be applicable.

2004 Strategic Alliance

In March 2004, the Company entered into its strategic alliance with GSK. Under this alliance, GSK received an option to license exclusive development and commercialization rights to product candidates from certain of the Company's discovery programs on pre-determined terms and on an exclusive, worldwide basis. Upon GSK's decision to license a program, GSK is responsible for funding all future development, manufacturing and commercialization activities for product candidates in that program. In addition, GSK is obligated to use diligent efforts to develop and commercialize product candidates from any program that it licenses. If the program is successfully advanced through development by GSK, the Company is entitled to receive clinical, regulatory and commercial milestone payments and royalties on any sales of medicines developed from the program. If GSK chooses not to license a program, the Company retains all rights to the program and may continue the program alone or with a third party.

In 2005, GSK licensed the Company's bifunctional muscarinic antagonist-beta₂ agonist (MABA) program for the treatment of COPD, and in October 2011, the Company and GSK expanded the MABA program by adding six additional Theravance-discovered preclinical MABA compounds (the "Additional MABAs"). GSK's development, commercialization, milestone and royalty obligations under the strategic alliance remain the same with respect to '081, the lead compound in the MABA program. GSK is obligated to use diligent efforts to develop and commercialize at least one MABA within the MABA program, but may terminate progression of any or all Additional MABAs at any time and return them to the Company, at which point the Company may develop and commercialize such Additional MABAs alone or with a third party. Both GSK and the Company have agreed not to conduct any MABA clinical studies outside of the strategic alliance so long as GSK is in possession of the Additional MABAs. If a single-agent MABA medicine containing '081 is successfully developed and commercialized, the Company is entitled to receive royalties from GSK of between 10% and 20% of annual global net sales up to $3.5 billion, and 7.5% for all annual global net sales above $3.5 billion. If a MABA medicine containing '081 is commercialized only as a combination product, such as a MABA/ICS, the royalty rate is 70% of the rate applicable to sales of the single-agent MABA medicine. For single-agent MABA medicines containing an Additional MABA, the Company is entitled to receive royalties from GSK of between 10% and 15% of annual global net sales up to $3.5 billion, and 10% for all annual global net sales above $3.5 billion. For combination products containing an Additional MABA, such as a MABA/ICS, the royalty rate is 50% of the rate applicable to sales of the single-agent MABA medicine. If a MABA medicine containing '081 is successfully developed and commercialized in multiple regions of the world, the Company could earn total milestone payments of up to $125.0 million for a single-agent medicine and up to $250.0 million for both a single-agent and a combination medicine. If a MABA medicine containing an Additional MABA is successfully developed and commercialized in multiple regions of the world, the Company could earn total milestone payments of up to $129.0 million. GSK has no further option rights on any of the Company's research or development programs under the strategic alliance.

Purchases of Common Stock under the Company's Governance Agreement and Common Stock Purchase Agreements with GSK; GSK Conversion of the Company's Class A Common Stock

On May 16, 2012, the Company issued and Glaxo Group Limited, an affiliate of GSK, purchased 10,000,000 shares of the Company's common stock at a price of $21.2887 per share, for a total investment of $212.9 million.

In addition, Glaxo Group Limited purchased shares of the Company's common stock pursuant to its periodic "top-up" rights under the Company's governance agreement with GSK dated June 4, 2004, as amended, as follows:

	Through December 31, 2012

	Common Stock Shares Purchased		Aggregate Amounts (in thousands)
Purchase dates
February 18, 2011		152,278	$	3,609
May 3, 2011		261,299	$	6,689
August 2, 2011		102,466	$	2,020
November 1, 2011		58,411	$	1,298
February 14, 2012		88,468	$	1,603
August 3, 2012		316,334	$	8,924
November 2, 2012		280,348	$	6,266

In July 2011, GSK converted all of the shares of the Company's Class A common stock held by its affiliates into 9,401,499 shares of the Company's common stock on a one share-for-one share basis in accordance with the terms of the Company's restated certificate of incorporation.

GSK Contingent Payments and Revenue

The potential future contingent payments related to the MABA program of $102.0 million are not deemed substantive milestones due to the fact that the achievement of the event underlying the payment predominantly relates to GSK's performance of future development, manufacturing and commercialization activities for product candidates after licensing the program.

Revenue recognized from GSK under the LABA collaboration and strategic alliance agreements was as follows:

	Year Ended December 31,

(in thousands)	2012		2011		2010
LABA collaboration(1)	$	3,629	$	4,718	$	5,081
Strategic alliance agreement		—		1,858		2,738
Strategic alliance—MABA program license(2)		1,984		3,082		2,007

Total revenue	$	5,613	$	9,658	$	9,826

(1): The Company revised the estimated performance period for the LABA program based on its progress in the fourth quarter of 2011, resulting in an increase to net loss of $0.4 million for the year ended December 31, 2011. The Company does not expect that the revision will have a material impact on future revenue recognized under this program.
(2): The Company revised the estimated performance period for the MABA program based on its progress as follows: (i) in the first quarter of 2010, resulting in an increase to net loss of $1.0 million for the year ended December 31, 2010; (ii) in the fourth quarter of 2011, resulting in an increase to net loss of $0.2 million for the year ended December 31, 2011; and (iii) in the fourth quarter of 2012, resulting in an increase to net loss of $0.1 million for the year ended December 31, 2012. The Company does not expect that the revision will have a material impact on future revenue recognized under this program.

Under the GSK collaboration arrangements, the Company is reimbursed for research and development expenses. These reimbursements have been reflected as a reduction of research and development expense of $0.2 million for the year ended December 31, 2012, and $0.4 million for each of the years ended December 31, 2011 and 2010.

Merck

Research Collaboration and License Agreement with Merck

In October 2012, the Company signed a collaboration agreement with Merck, known as MSD outside the United States and Canada, to discover, develop and commercialize novel small molecule therapeutics directed towards a target being investigated for the treatment of hypertension and heart failure. In exchange for granting Merck a worldwide, exclusive license to the Company's therapeutic candidates, the Company received a $5.0 million upfront payment in November 2012. Also, the Company will receive funding for research and be eligible for potential future contingent payments totaling up to $148.0 million for the first indication and royalties on worldwide annual net sales of any products derived from the collaboration. The contingent payments are not deemed substantive milestones due to the fact that the achievement of the event underlying the payment predominantly relates to Merck's performance of future development and commercialization activities. The initial research term is twelve months, with optional extensions by mutual agreement, and Merck can terminate the agreement at any time.

The Company identified all of the deliverables at the inception of the agreement. The significant deliverables were determined to be the license, research services and committee participation. The Company's management determined that the license represents a separate unit of accounting as the license, which includes rights to the underlying technologies for the Company's therapeutic candidates, has standalone value because the rights conveyed permit Merck to perform all efforts necessary to use the Company's technologies to bring a therapeutic candidate through development, commercialization and begin selling the drug upon regulatory approval. Also, the Company's management determined that the research services and committee participation each represent individual units of accounting. The Company's management determined the best estimate of selling price for the license based on potential future cash flows under the arrangement over the estimated development period. The Company's management determined the best estimate of selling price of the research services and committee participation based on the nature and timing of the services to be performed.

The $5.0 million upfront payment received in November 2012 was allocated to the three units of accounting based on the relative selling price method as follows: $4.4 million to the license, $0.4 million to the research services and $0.2 million to the committee participation. The Company recognized revenue from the license in 2012 as the technical transfer activities were complete and the associated unit of accounting was deemed delivered. The amount allocated to the committee participation was deferred and will be recognized as revenue over the estimated performance period. The amount allocated to the research services was deferred and will be recognized as an offset to research and development expense as the underlying services are performed, as the nature of the research services is more appropriately characterized as research and development expense, consistent with the research reimbursements being received. Revenue recognized from Merck under the collaboration agreement was $4.4 million in 2012. Deferred research services of $0.4 million were included in other accrued liabilities at December 31, 2012. Amounts associated with deferred committee participation of $19,000 were included in deferred revenue, current and $0.2 million were included in deferred revenue, non-current at December 31, 2012.

The Company recognized $0.8 million in research reimbursement due from Merck as a reduction of research and development expense in 2012, which receivable was included in receivables from collaboration partners at December 31, 2012.

Alfa Wassermann

Development and Commercialization Agreement with Alfa Wassermann

In October 2012, the Company entered into a development and commercialization agreement with Alfa Wassermann società per azioni (S.p.A.) for velusetrag (or TD-5108), the Company's investigational 5-HT4 agonist in development for gastrointestinal motility disorders. Under the agreement, the companies will collaborate in the execution of a two-part Phase 2 program to test the efficacy, safety and tolerability of velusetrag in the treatment of patients with gastroparesis. Alfa Wassermann has an exclusive option to develop and commercialize velusetrag in the European Union, Russia, China, Mexico and certain other countries, while the Company retains full rights to velusetrag in the US, Canada, Japan and certain other countries. In October 2012, the Company entered into a development and commercialization agreement with Alfa Wassermann società per azioni (S.p.A.) for velusetrag (or TD-5108), the Company's investigational 5-HT4 agonist in development for gastrointestinal motility disorders. Under the agreement, the Company will collaborate in the execution of a two-part Phase 2 program to test the efficacy, safety and tolerability of velusetrag in the treatment of patients with gastroparesis. Alfa Wassermann has an exclusive option to develop and commercialize velusetrag in the European Union, Russia, China, Mexico and certain other countries, while the Company retains full rights to velusetrag in the US, Canada, Japan and certain other countries. The Company is entitled to receive funding for the Phase 2a study and a subsequent Phase 2b study if the parties agree to proceed. If Alfa Wassermann exercises its license option at the completion of the Phase 2 program, then the Company is entitled to receive a $10.0 million option fee. If velusetrag is successfully developed and commercialized, the Company is entitled to receive potential future contingent payments totaling up to $53.5 million, and royalties on net sales by Alfa Wassermann ranging from the low teens to 20%. The contingent payments are not deemed substantive milestones due to the fact that the achievement of the event underlying the payment predominantly relates to Alfa Wassermann's performance of future development and commercialization activities. At December 31, 2012, Alfa Wassermann's option right had not been exercised. The option right could be exercised within the next two years. The Company recognized $0.2 million in research reimbursement due from Alfa Wassermann as a reduction of research and development expense in 2012, which receivable was included in receivables from collaboration partners at December 31, 2012.

R-Pharm CJSC

Development and Commercialization Agreement with R-Pharm CJSC

In October 2012, the Company entered into two separate development and commercialization agreements with R-Pharm CJSC (R-Pharm). The first was for TD-1792, the Company's investigational glycopeptide-cephalosporin heterodimer antibiotic for the treatment of resistant Gram-positive infections, and the second was for telavancin. In exchange for granting R-Pharm exclusive development and commercialization rights in Russia, Ukraine, other member countries of the Commonwealth of Independent States, and Georgia under both agreements, the Company received $1.1 million in license and maintenance fees in November 2012. Also, the Company is eligible to receive an additional $1.0 million in near-term licensing fees, potential future contingent payments totaling up to $10.0 million and royalties on net sales by R-pharm of 15% from TD-1792 and 25% from telavancin. The contingent payments are not deemed substantive milestones due to the fact that the achievement of the event underlying the payment predominantly relates to R-Pharm's performance of future development and commercialization activities.

The Company identified all of the deliverables at the inception of the agreements. The significant deliverables were determined to be the licenses and committee participation for each agreement. The Company's management determined that the licenses represent a separate unit of accounting as the licenses, which include rights to the Company's underlying technologies for TD-1792 and telavancin, have standalone value because the rights conveyed permit R-Pharm to use the Company's technologies to bring the compounds through development, commercialization and begin selling the drugs upon regulatory approval. Also, the Company's management determined that the committee participation represents a separate unit of accounting under each agreement. The amounts received in license and maintenance fees of $1.1 million are included in deferred revenue, current at December 31, 2012, as the completion of the technical transfer to R-Pharm was not completed. The technical transfer is expected to be completed during the first quarter of 2013.

Astellas

License, Development and Commercialization Agreement with Astellas

In November 2005, the Company entered into a global collaboration arrangement with Astellas for the development and commercialization of VIBATIV®. On January 6, 2012, Astellas exercised its right to terminate this agreement. The rights previously granted to Astellas ceased upon termination of the agreement and Astellas stopped all promotional sales efforts. Pursuant to the terms of the agreement, Astellas is entitled to a ten-year, 2% royalty on future net sales of VIBATIV®. The Company continues to evaluate global commercialization alternatives for VIBATIV® either with partners or alone, and the Company intends to reintroduce VIBATIV® in the U.S. later in 2013 provided the Company can assure a reasonable source of VIBATIV® drug product.

In 2012, the Company issued purchase orders to Astellas for the purchase of VIBATIV® active pharmaceutical ingredient and other raw materials of up to $7.7 million, and as of December 31, 2012 the Company had purchased $5.8 million pursuant to these orders. The remaining active pharmaceutical ingredient and other raw materials will not be purchased. Also in 2012, the Company issued purchase orders to Astellas for the purchase of VIBATIV® finished goods inventories of up to $4.2 million, and as of December 31, 2012 these finished goods inventories remained subject to release.

In addition, beginning July 1, 2012, the Company was responsible to fund governmental rebate and governmental chargeback claims for Astellas-labeled product sales. As a result of the termination of the VIBATIV® collaboration agreement, the Company recognized $31,000 in governmental rebate and governmental chargeback claims in 2012.

Through January 6, 2012, the Company had received $191.0 million in upfront license, contingent payments and other fees from Astellas. The Company previously recorded these payments as deferred revenue and amortized them ratably over its estimated performance period (development and commercialization period). As a result of the termination of the VIBATIV® collaboration agreement, the development and commercialization period ended on January 6, 2012. As such, the Company recognized into revenue $125.8 million of deferred revenue related to Astellas in the first quarter of 2012, and the Company is no longer eligible to receive any further contingent payments from Astellas.

Net revenue recognized under this collaboration agreement was as follows:

	Year Ended December 31,

(in thousands)	2012			2011			2010
Recognition of deferred revenue	$	125,819		$	—		$	—
Amortization of deferred revenue		—			12,975			12,975
Royalties from net sales of VIBATIV®		—			2,422			1,123
Proceeds from VIBATIV® delivered to Astellas		—			1,171			2,058
Cost of VIBATIV® delivered to Astellas		—			(1,177	)		(938	)
Cost of unrealizable VIBATIV® inventories		—			(537	)		(821	)
Astellas-labeled product sales allowance		(31	)		—			—

Total net revenue	$	125,788		$	14,854		$	14,397

Under the Astellas collaboration arrangement, the Company was reimbursed for a portion of the Company's research and development expenses. These reimbursements have been reflected as a reduction of research and development expense of $0.4 million for the year ended December 31, 2011 and $0.3 million for the year ended December 31, 2010.

Marketable Securities

12 Months Ended

Dec. 31, 2012

Marketable Securities

Marketable Securities

4. Marketable Securities

The following table is a summary of available-for-sale debt securities and money market funds recorded in cash equivalents or marketable securities in the Company's Consolidated Balance Sheets. Estimated fair values of available-for-sale securities are generally based on prices obtained from commercial pricing services:

	December 31, 2012

(in thousands)	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
U.S. government securities	$	27,197	$	10	$	(2	)	$	27,205
U.S. government agencies		115,397		85		(16	)		115,466
U.S. corporate notes		91,544		32		(10	)		91,566
U.S. commercial paper		23,082		—		—			23,082
Money market funds		78,646		—		—			78,646

Total	$	335,866	$	127	$	(28	)	$	335,965

	December 31, 2011

(in thousands)	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
U.S. government securities	$	66,150	$	24	$	—		$	66,174
U.S. government agencies		93,183		9		(17	)		93,175
U.S. corporate notes		2,707		—		(2	)		2,705
U.S. commercial paper		34,973		3		—			34,976
Money market funds		38,721		—		—			38,721

Total	$	235,734	$	36	$	(19	)	$	235,751

The following table summarizes the classification of the available-for-sale debt securities on the Company's condensed consolidated balance sheets:

(in thousands)	December 31, 2012		December 31, 2011

Cash and cash equivalents	$	86,298	$	38,721
Short-term investments		153,640		196,137
Long-term marketable securities		95,194		—
Restricted cash		833		893

Total	$	335,965	$	235,751

The following table provides the net realized gains (losses) on marketable securities for the periods presented:

	Year Ended December 31,

(in thousands)	2012		2011			2010
Realized gains	$	9	$	—		$	3
Realized losses		—		(2	)		—

Net realized gains (losses)	$	9	$	(2	)	$	3

The Company realized no gains or losses in 2012 and 2011 that were previously classified as unrealized gains and losses in accumulated other comprehensive income at December 31, 2011 and 2010, respectively.

The following table provides the breakdown of the marketable securities with unrealized losses at December 31, 2012:

	In loss position for less than 12 months					In loss position for more than 12 months				Total

(in thousands)	Estimated Fair Value		Estimated Gross Unrealized Losses			Estimated Fair Value		Estimated Gross Unrealized Losses		Estimated Fair Value		Estimated Gross Unrealized Losses
U.S. government securities	$	7,002	$	(2	)	$	—	$	—	$	7,002	$	(2	)
U.S. government agencies		10,499		(16	)		—		—		10,499		(16	)
U.S. corporate notes		34,693		(10	)		—		—		34,693		(10	)

Total	$	52,194	$	(28	)	$	—	$	—	$	52,194	$	(28	)

At December 31, 2012, all of the available-for-sale debt securities had contractual maturities within twenty-four months and the average duration of marketable securities was approximately 9 months. The Company does not intend to sell the investments which are in an unrealized loss position and it is unlikely that the Company will be required to sell the investments before recovery of their amortized cost basis, which may be maturity. The Company has determined that the gross unrealized losses on its marketable securities at December 31, 2012 were temporary in nature.

- Definition

The entire disclosure for investments in certain debt and equity securities.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-Glossary Debt Security
-URI http://asc.fasb.org/extlink&oid=6509901

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 310
-SubTopic 30
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6379141&loc=d3e15032-111544

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27290-111563

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-Glossary Equity Security
-URI http://asc.fasb.org/extlink&oid=6511694

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27232-111563

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 320
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6957658&loc=d3e62557-112803

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 9
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27357-111563

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27161-111563

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 10
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27405-111563

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 3, 19, 20, 21, 22, 137
-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.

+ Details

Fair Value Measurements

12 Months Ended

Dec. 31, 2012

Fair Value Measurements

Fair Value Measurements

5. Fair Value Measurements

The Company defines estimated fair value as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date.

The Company's valuation techniques are based on observable and unobservable inputs. Observable inputs reflect readily obtainable data from independent sources, while unobservable inputs reflect the Company's market assumptions. The Company classifies these inputs into the following hierarchy:

        Level 1 Inputs—Quoted prices for identical instruments in active markets.

        Level 2 Inputs—Quoted prices for similar instruments in active markets; quoted prices for identical or similar instruments in markets that are not active; and model-derived valuations whose inputs are observable or whose significant value drivers are observable.

        Level 3 Inputs—Unobservable inputs and little, if any, market activity for the assets.

The estimated fair values of the Company's financial assets were as follows:

	Estimated Fair Value Measurements at Reporting Date Using:

	Quoted Prices in Active Markets for Identical Assets		Significant Other Observable Inputs		Significant Unobservable Inputs
Types of Instruments (in thousands)	Level 1		Level 2		Level 3		Total
Assets at December 31, 2012:
U.S. government securities	$	27,205	$	—	$	—	$	27,205
U.S. government agency securities		56,969		58,497		—		115,466
U.S. corporate notes		40,472		51,094		—		91,566
U.S. commercial paper		—		23,082		—		23,082
Money market funds		78,646		—		—		78,646

Total assets measured at estimated fair value	$	203,292	$	132,673	$	—	$	335,965

Liabilities at December 31 , 2012:
Convertible subordinated notes	$	—	$	194,050	$	—	$	194,050

	Estimated Fair Value Measurements at Reporting Date Using:

	Quoted Prices in Active Markets for Identical Assets		Significant Other Observable Inputs		Significant Unobservable Inputs
Types of Instruments (in thousands)	Level 1		Level 2		Level 3		Total
Assets at December 31, 2011:
U.S. government securities	$	66,174	$	—	$	—	$	66,174
U.S. government agency securities		55,901		37,274		—		93,175
U.S. corporate notes		2,705		—		—		2,705
U.S. commercial paper		—		34,976		—		34,976
Money market funds		38,721		—		—		38,721

Total assets measured at estimated fair value	$	163,501	$	72,250	$	—	$	235,751

Liabilities at December 31, 2011:
Convertible subordinated notes	$	—	$	189,588	$	—	$	189,588

At December 31, 2012, there were no transfers from Level 1 to Level 2 or from Level 2 to Level 1 in comparison to December 31, 2011.

- Definition

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

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-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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-Topic 825
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Reference 3: http://www.xbrl.org/2003/role/presentationRef
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Reference 4: http://www.xbrl.org/2003/role/presentationRef
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-SubTopic 10
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Reference 5: http://www.xbrl.org/2003/role/presentationRef
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-SubTopic 10
-Section 50
-Paragraph 16
-URI http://asc.fasb.org/extlink&oid=7491637&loc=d3e13504-108611

Reference 6: http://www.xbrl.org/2003/role/presentationRef
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-SubTopic 10
-Section 50
-Paragraph 10
-URI http://asc.fasb.org/extlink&oid=7491637&loc=d3e13433-108611

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-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
-Paragraph 15A
-Subparagraph a-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 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.

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-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.

+ Details

Property and Equipment

12 Months Ended

Dec. 31, 2012

Property and Equipment

Property and Equipment

6. Property and Equipment

Property and equipment consists of the following:

	December 31,

(in thousands)	2012			2011
Computer equipment	$	3,027		$	3,158
Software		5,073			4,628
Furniture and fixtures		3,829			3,821
Laboratory equipment		29,229			28,894
Leasehold improvements		17,416			17,263

		58,574			57,764
Less accumulated depreciation and amortization		(49,420	)		(47,392	)

Property and equipment, net	$	9,154		$	10,372

Depreciation expense was $3.3 million in 2012, $3.8 million in 2011 and $3.9 million in 2010. The change in accumulated depreciation is net of asset retirements. In 2012, the Company recognized a write-off of $0.2 million related to assets that could no longer be used in operations.

- Definition

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.

+ References + Details

Long-Term Obligations

12 Months Ended

Dec. 31, 2012

Long-Term Obligations

Long-Term Obligations

7. Long-Term Obligations

Long-term obligations are as follows:

(in thousands)		December 31, 2012			December 31, 2011

Convertible subordinated notes		$	172,500		$	172,500

Convertible Subordinated Notes Due 2015

In January 2008, the Company closed an underwritten public offering of $172.5 million aggregate principal amount of unsecured convertible subordinated notes which will mature on January 15, 2015. The financing raised proceeds, net of issuance costs, of $166.7 million. The notes bear interest at the rate of 3.0% per year, that is payable semi-annually in arrears in cash on January 15 and July 15 of each year, beginning on July 15, 2008.

The notes are convertible, at the option of the holder, into shares of the Company's common stock at an initial conversion rate of 38.6548 shares per $1,000 principal amount of the notes, subject to adjustment in certain circumstances, which represents an initial conversion price of approximately $25.87 per share. The debt issuance costs, which are included in other long-term assets, are being amortized on a straight-line basis over the life of the notes. Unamortized debt issuance costs totaled $1.7 million as of December 31, 2012. Amortization expense was $0.8 million in 2012, 2011 and 2010.

Holders of the notes will be able to require the Company to repurchase some or all of their notes upon the occurrence of a fundamental change (as defined) at 100% of the principal amount of the notes being repurchased plus accrued and unpaid interest. The Company may not redeem the notes prior to January 15, 2012. On or after January 15, 2012 and prior to the maturity date, the Company, upon notice of redemption, may redeem for cash all or part of the notes if the last reported sale price of its common stock has been greater than or equal to 130% of the conversion price then in effect for at least 20 trading days during any 30 consecutive trading day period prior to the date on which it provides notice of redemption. The redemption price will equal 100% of the principal amount of the notes to be redeemed, plus accrued and unpaid interest up to but excluding the redemption date.

Stock-Based Compensation

12 Months Ended

Dec. 31, 2012

Stock-Based Compensation

Stock-Based Compensation

8. Stock-Based Compensation

Equity Incentive Plans

In May 2012, the Company adopted the 2012 Equity Incentive Plan (2012 Plan). The number of shares of the Company's common stock available for issuance under the 2012 Plan is equal to 6,500,000 shares plus up to 12,667,411 additional shares that may be added to the 2012 Plan in connection with the forfeiture, repurchase, cash settlement or termination of awards outstanding under the 2004 Equity Incentive Plan (2004 Plan), the 2008 New Employee Equity Incentive Plan, the 1997 Stock Plan and the Long-Term Stock Option Plan (collectively, the "Prior Plans") as of December 31, 2011. While a maximum of 12,667,411 shares could be added to the 2012 Plan from the Prior Plans, since this assumes that all the awards outstanding on December 31, 2011 will be forfeited, repurchased, cash settled or terminated, the actual number to be added to the 2012 Plan share reserve may be less. The Company reserved 6,500,000 shares of common stock for issuance under the 2012 Plan. No additional awards have been or will be made after May 15, 2012 under the 2004 Plan. Stock options and SARs will reduce the 2012 Plan reserve by one share for every share granted, and stock awards other than options and SARs granted will reduce the 2012 Plan share reserve by 1.45 shares for every share granted. The 2012 Plan share reserve was also reduced by the number of stock awards granted under the 2004 Plan on or after January 1, 2012, using the same ratios described. As of December 31, 2012, approximately 5,023,370 shares remained available for issuance under the 2012 Plan.

The 2012 Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards, stock unit awards and stock appreciation rights ("SARs") to employees, non-employee directors and consultants of the Company. Stock options may be granted with an exercise price not less than the fair market value of the common stock on the grant date. Stock options granted to employees generally have a maximum term of 10 years and vest over a four year period from the date of grant; 25% vest at the end of one year, and 75% vest monthly over the remaining three years. The Company may grant options with different vesting terms from time to time. Unless an employee's termination of service is due to disability or death, upon termination of service, any unexercised vested options will be forfeited at the end of three months or the expiration of the option, whichever is earlier.

Employee Stock Purchase Plan

Under the 2004 Employee Stock Purchase Plan (ESPP), the Company's non-officer employees may purchase common stock through payroll deductions at a price equal to 85 percent of the lower of the fair market value of the stock at the beginning of the offering period or at the end of each applicable purchase period. The ESPP provides for consecutive and overlapping offering periods of 24 months in duration, with each offering period composed of four consecutive six-month purchase periods. The purchase periods end on either May 15^th or November 15^th. ESPP contributions are limited to a maximum of 15 percent of an employee's eligible compensation.

The Company's ESPP plan also includes a feature that provides for a new offering period to begin when the fair market value of the Company's common stock on any purchase date during an offering period falls below the fair market value of the Company's common stock on the first day of such offering period. This feature is called a reset. The Company had resets for new twenty-four month offering periods starting on May 16, 2008, November 16, 2008, May 16, 2010, November 16, 2011, May 16, 2012 and November 16, 2012. The Company applied modification accounting to determine the incremental fair value associated with the ESPP resets and recognized the related incremental stock- based compensation expense.

As of December 31, 2012, a total of 2,025,000 shares of common stock were approved and authorized for issuance under the ESPP. Through December 31, 2012, the Company had issued 1,601,425 shares under the ESPP at an average price of $10.75 per share. As of December 31, 2012, total shares remaining available for issuance under the ESPP were 423,575.

Performance-Contingent Restricted Stock Awards

In 2012, the Compensation Committee of the Company's Board of Directors approved the grant of 44,500 performance-contingent RSAs to senior management. These awards have dual triggers of vesting based upon the achievement of one of three possible performance goals by December 31, 2013, as well as a requirement for continued employment through early 2016. As of December 31, 2012, one of the performance goals had been deemed achieved and time-based vesting commenced with respect to these awards. As a result, compensation expense of $0.4 million was recognized in 2012, and the remaining unrecognized expense will be recognized over the remaining vesting period using the graded vesting expense attribution method.

In 2011, the Compensation Committee of the Company's Board of Directors approved the grant of 1,290,000 performance-contingent RSAs to senior management. These awards have dual triggers of vesting based upon the achievement of certain performance conditions over a six-year timeframe from 2011-2016 and continued employment, both of which must be satisfied in order for the RSAs to vest. Expense associated with these RSAs would be recognized, if at all, during these years depending on the probability of meeting the performance conditions. The maximum potential expense associated with the RSAs could be up to approximately $31.9 million (allocated as $6.3 million for research and development expense and $25.6 million for general and administrative expense) if all of the performance conditions are achieved on time. As of December 31, 2012, the Company had determined that the achievement of the requisite performance conditions was not probable and, as a result, no compensation expense has been recognized. As the RSAs are dependent upon the achievement of certain performance conditions, the expense associated with the RSAs may vary significantly from period to period.

In 2011, the Compensation Committee of the Company's Board of Directors approved the grant of a 25,000 performance-contingent RSA to a non-executive officer that has dual triggers of vesting based upon the achievement of a performance condition over a timeframe from 2012-2013 and continued employment through 2014, both of which must be satisfied in order for the award to vest in full. The maximum potential expense associated with this award is approximately $475,000, which would be recognized in increments based on the achievement of the performance condition. As of December 31, 2012, the Company had determined that the achievement of the requisite performance condition was not probable and, as a result, no compensation expense has been recognized. As the vesting of the RSAs is contingent upon the achievement of the performance condition, the expense associated with the RSA may vary significantly from period to period.

Performance-Contingent Restricted Stock Units

In 2010, the Compensation Committee of the Company's Board of Directors approved the grant of 210,000 performance-contingent RSUs to senior management. These awards have dual triggers of vesting based upon the successful achievement of certain corporate operating milestones during 2010 and 2011, as well as a requirement for continued employment through early 2014. As of February 11, 2011, both performance milestones had been deemed achieved, and time-based vesting commenced with respect to all of the performance-contingent RSU shares. As a result, compensation expense was $0.3 million in 2012 and $ 1.3 million in 2011, and the remaining unrecognized expense will be recognized over the remaining vesting period using the graded vesting expense attribution method.

Director Compensation Program

Non-employee directors of the Company receive compensation for services provided as a director. Each member of the Company's Board who is not an employee receives an annual retainer as well as a fee for each board and committee meeting attended. Commencing on April 27, 2011, chairpersons of the various committees of the Board, the Audit Committee, the Compensation Committee, Nominating/Corporate Governance Committee and the Science and Technology Advisory Committee receives a fixed retainer. The lead independent director also receives a fixed retainer.

Each of the Company's independent directors receives periodic automatic grants of equity awards under a program implemented under the 2004 Plan. These grants are non-discretionary. Only independent directors of the Company or affiliates of such directors are eligible to receive automatic grants under the 2004 Plan. Under the program, as amended in July 2010, each individual who first becomes an independent director will, on the date such individual joins the Board, automatically be granted (i) a one-time grant of RSUs covering 6,000 shares of the Company's common stock and (ii) a one-time nonstatutory stock option grant covering 6,000 shares of the Company's common stock.

These initial equity grants vest monthly over the director's first two years of service. In addition, on the date of joining the Board, the new director will also receive the standard annual equity awards (if joining on the date of the Company's Annual Meeting of Stockholders) or pro-rated annual equity awards (if joining on any other date). The pro-ration is based upon the number of months of service the new board member will provide during the 12-month period ending on the one-year anniversary of the most recent annual meeting of stockholders. Annually, upon his or her re-election to the Board at the Annual Meeting of Stockholders, each independent director is automatically granted both an RSU covering 6,000 shares of the Company's common stock and a nonstatutory stock option covering 6,000 shares of the Company's common stock. These standard annual equity awards vest monthly over the twelve month period of service following the date of grant. In addition, all automatic equity awards vest in full if the Company is subject to a change in control or the Board member dies while in service.

Stock-Based Compensation Expense

The allocation of stock-based compensation expense included in the consolidated statements of operations was as follows:

	Year Ended December 31,

(in thousands)	2012		2011		2010
Research and development	$	13,667	$	13,422	$	10,322
General and administrative		10,116		11,494		8,687

Total stock-based compensation expense	$	23,783	$	24,916	$	19,009

Stock-based compensation expense included in the consolidated statements of operations by award type was as follows:

	Year Ended December 31,

(in thousands)	2012		2011		2010
Employee stock options	$	3,417	$	4,528	$	7,003
Employee RSUs		11,546		13,290		9,783
Employee RSAs		7,968		5,498		398
Non-employee options and RSUs		—		307		1,186
ESPP		852		1,293		639

Total stock-based compensation expense	$	23,783	$	24,916	$	19,009

Total stock-based compensation expense capitalized to inventory was $0.4 million for the year ended December 31, 2012, and none for each of the years ended December 31, 2011 and 2010.

In connection with the retirement of the Company's former chairman of the Board of Directors in April 2010, the Company entered into a consulting agreement that provided for, among other things, the acceleration of an RSU that was scheduled to vest through April 2012 and an extension of the period of time in which vested stock options may be exercised until to the stated expiration date of the stock options. As a result of the stock option modification, the Company recorded an expense of $0.9 million in June 2010.

As of December 31, 2012, the unrecognized stock-based compensation cost, net of expected forfeitures, and the estimated weighted-average amortization period, using the straight-line attribution method, was as follows:

(in thousands, except amortization period)	Unrecognized Compensation Cost

Stock options	$	6,442	2.6
RSUs		14,027	2.1
RSAs		23,525	3.5

Total unrecognized stock-based compensation expense	$	43,994

Compensation Awards

The following table summarizes equity award activity under the 2008 Plan and the 2004 Plan, and related information:

(in thousands, except per share data)			Weighted- average Exercise Price of Outstanding Options				Weighted- average Fair Value per Share at Grant				Weighted- average Fair Value per Share at Grant

Balance at December 31, 2009	8,414		$	16.63	2,042		$	14.15	57		$	25.87
Granted	321			14.90	1,170			10.55	—			—
Exercised	(784	)		9.60	—			—	—			—
Released RSUs/RSAs	—			—	(657	)		13.20	(24	)		25.55
Forfeited	(297	)		26.17	(658	)		26.26	—			—

Balance at December 31, 2010	7,654			16.91	1,897			12.45	33			26.10
Granted	629			21.98	471			24.96	2,483			24.61
Exercised	(1,265	)		8.87	—			—	—			—
Released RSUs/RSAs	—			—	(797	)		13.89	(74	)		24.96
Forfeited	(127	)		29.15	(29	)		15.35	—			—

Balance at December 31, 2011	6,891			18.62	1,542			15.47	2,442			24.62
Granted	335			21.91	528			18.45	447			18.11
Exercised	(947	)		7.98	—			—	—			—
Released RSUs/RSAs	—			—	(752	)		14.19	(388	)		24.77
Forfeited	(159	)		24.43	(78	)		18.48	—			—

Balance at December 31, 2012	6,120			20.30	1,240			17.32	2,501			23.43

As of December 31, 2012, the aggregate intrinsic value of the options outstanding was $30.0 million and the aggregate intrinsic value of the options exercisable was $28.1 million.

The total intrinsic value of the options exercised was $15.2 million in 2012, $17.1 million in 2011, and $7.2 million in 2010. The total estimated fair value of options vested was $4.1 million in 2012, $6.4 million in 2011, and $8.2 million in 2010.

Valuation Assumptions

The Company based the range of weighted-average estimated values of employee stock option grants and rights granted under the employee stock purchase plan, as well as the weighted-average assumptions used in calculating these values, on estimates at the date of grant, as follows:

	Year Ended December 31,

	2012	2011	2010
*Employee stock options*
Risk-free interest rate	0.74% - 1.17%	1.10% - 2.57%	1.11% - 2.82%
Expected life (in years)	5 - 6	5 - 6	5 - 6
Volatility	55% - 60%	49% - 55%	48% - 52%
Dividend yield	—%	—%	—%
Weighted-average estimated fair value of stock options granted	$11.50	$11.11	$7.41
*Employee stock purchase plan issuances*
Risk-free interest rate	0.14% - 0.29%	0.05% - 0.54%	0.19% - 0.79%
Expected life (in years)	0.5 - 2	0.5 - 2	0.5 - 2
Volatility	51% - 64%	48% - 59%	50% - 69%
Dividend yield	—%	—%	—%
Weighted-average estimated fair value of ESPP issuances	$8.07	$9.46	$7.63

Range of Stock Option Exercise Prices

As of December 31, 2012, all outstanding options to purchase common stock of the Company are summarized in the following table (in thousands, except years and per share data):

	Options Outstanding						Options Exercisable

Range of Exercise Prices	Number Outstanding		Weighted- average Remaining Contractual Life in Years		Weighted- average Exercise Prices		Options Exercisable		Weighted- average Remaining Contractual Life in Years		Weighted- average Exercise Price
$3.10		191		0.8	$	3.10		191		0.8	$	3.10
$6.15 - $6.70		25		5.9		6.15		25		5.9		6.15
$9.69		1,140		1.3		9.69		1,140		1.3		9.69
$9.70 - $16.00		839		4.1		14.71		768		3.8		14.87
$16.01 - $19.80		1,228		4.5		18.17		956		3.3		18.13
$19.81 - $24.71		594		7.2		22.16		316		5.7		22.38
$24.72 - $29.70		1,124		4.1		28.29		1,038		3.6		28.42
$29.71 - $35.46		979		4.1		33.52		979		4.1		33.52

Total		6,120		3.8		20.30		5,413		3.2		20.31

- Definition

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.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-Paragraph 4
-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.

+ Details

Income Taxes

12 Months Ended

Dec. 31, 2012

Income Taxes

Income Taxes

9. Income Taxes

Due to ongoing operating losses and the inability to recognize any income tax benefit, there is no provision for income taxes for any periods presented.

Deferred income taxes reflect the net tax effects of temporary differences between the carrying amounts of assets and liabilities for financial reporting purposes and the amounts used for income tax purposes. Significant components of the Company's deferred tax assets are as follows:

	December 31,

(in thousands)	2012			2011
Deferred tax assets:
Net operating loss carryforwards	$	411,000		$	359,000
Deferred revenues		4,000			56,000
Capitalized research and development expenditures		35,000			35,000
Research and development tax credit carryforwards		38,000			37,000
Other		33,000			31,000
Valuation allowance		(521,000	)		(518,000	)

Net deferred tax assets	$	—		$	—

The differences between the U.S. federal statutory income tax rate to the Company's effective tax rate are as follows:

	Year Ended December 31,

	2012			2011			2010
U.S. federal statutory income tax rate		34.00	%		34.00	%		34.00	%
State income taxes, net of federal benefit		—			—			5.83
Federal and state research credits		(4.21	)		1.67			2.91
Non-deductible executive compensation		(13.24	)		—			—
Stock-based compensation		(1.36	)		(0.32	)		2.29
Expiration of net operating loss		(1.81	)		(0.42	)		—
Other		(2.09	)		0.75			(0.05	)
Change in valuation allowance		(11.29	)		(35.68	)		(44.98	)

Effective tax rate		(0.00	)%		(0.00	)%		(0.00	)%

Realization of deferred tax assets is dependent on future taxable income, if any, the timing and the amount of which are uncertain. Accordingly, the deferred tax assets have been fully offset by a valuation allowance. The valuation allowance increased by $3.0 million in 2012, $50.0 million in 2011, and $35.0 million in 2010.

As of December 31, 2012, the Company had federal net operating loss carryforwards of approximately $1,221.4 million, which will expire from 2018 through 2032, and federal research and development tax credit carryforwards of approximately $43.2 million, which will expire from 2018 through 2031. The Company also had state net operating loss carryforwards of approximately $563.4 million expiring in the years 2014 through 2032 and state research tax credits of approximately $52.2 million, which do not expire.

The net operating loss deferred tax asset balances as of December 31, 2012 and 2011 do not include excess tax benefits from stock option exercises. Stockholders' equity (net capital deficiency) will be credited if and when such excess tax benefits are ultimately realized.

Utilization of net operating loss and tax credit carryforwards may be subject to a substantial annual limitation due to ownership change limitations provided by the Internal Revenue Code and similar state provisions. Annual limitations may result in expiration of net operating loss and tax credit carryforwards before some or all of such amounts have been utilized.

The Company's practice is to recognize interest and/or penalties related to income tax matters in income tax expense. As of December 31, 2012 and 2011, the Company had no accrued interest or penalties due to the Company's net operating losses available to offset any tax adjustment.

The Company conducted an analysis through 2012 to determine whether an ownership change had occurred since inception. The analysis indicated that two ownership changes occurred in prior years. However, notwithstanding the applicable annual limitations, no portion of the net operating loss or credit carryforwards are expected to expire before becoming available to reduce federal and state income tax liabilities.

Uncertain Tax Positions

A reconciliation of the beginning and ending balances of the total amounts of unrecognized tax benefits are as follows (in thousands):


Unrecognized tax benefits as of December 31, 2009	$	39,600
Gross decrease for tax positions for prior years		—
Gross increase in tax positions for current year		3,000

Unrecognized tax benefits as of December 31, 2010		42,600
Gross decrease for tax positions for prior years		—
Gross increase in tax positions for current year		4,300

Unrecognized tax benefits as of December 31, 2011		46,900
Gross decrease for tax positions for prior years		—
Gross increase in tax positions for current year		5,600

Unrecognized tax benefits as of December 31, 2012	$	52,500

If the Company eventually is able to recognize these uncertain positions, most of the $52.5 million of the unrecognized benefit would reduce the effective tax rate, except for excess tax benefits related to stock-based payments. The Company currently has a full valuation allowance against its deferred tax asset which would impact the timing of the effective tax rate benefit should any of these uncertain positions be favorably settled in the future. The Company does not believe it is reasonably possible that its unrecognized tax benefits will significantly change within the next twelve months.

The Company is subject to taxation in the U.S. and various state jurisdictions. The tax years 1996 and forward remain open to examination by the federal and most state tax authorities due to net operating loss and overall credit carryforward positions.

- Definition

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.

+ References

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
-SubTopic 10
-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
-SubTopic 10
-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.

+ Details

Commitments and Contingencies

12 Months Ended

Dec. 31, 2012

Commitments and Contingencies

Commitments and Contingencies

10. Commitments and Contingencies

Operating Leases and Subleases

The Company entered into amendments to its South San Francisco, CA facility leases in June 2010. These amendments extend the lease terms through May 2020 and the Company may extend the terms for two additional five-year periods. The Company leases approximately 130,000 square feet of office and laboratory space in two buildings.

The Company leases its South San Francisco, California, facilities under a non-cancelable operating lease. Future minimum lease payments under this lease, exclusive of executory costs, at December 31, 2012, were as follows:

(in thousands)

Years ending December 31:
2013	$	5,029
2014		4,859
2015		5,005
2016		5,155
2017		5,310
Thereafter		13,497

Total	$	38,855

Expenses and income associated with operating leases were as follows:

	Year Ended December 31,

(in thousands)	2012			2011			2010
Rent expense	$	5,720		$	6,702		$	6,779
Sublease income, net		(160	)		(637	)		(622	)

Purchase Obligations

As of December 31, 2012, the Company had outstanding purchase obligations on commercially reasonable terms, primarily for services under contract research, development and clinical and commercial supply agreements totaling $2.5 million.

Special Long-Term Retention and Incentive Equity Awards Program

In 2011, the Company granted special long-term retention and incentive RSAs to members of senior management and special long-term retention and incentive cash bonus awards to certain employees. The awards have dual triggers of vesting based upon the achievement of certain performance conditions over a six-year timeframe from 2011 through December 31, 2016 and continued employment. The maximum potential expense associated with this program is $31.9 million related to stock-based compensation expense and $38.2 million related to cash bonus expense, which would be recognized in increments based on achievement of the performance conditions. As of December 31, 2012, the Company's management determined that the achievement of the requisite performance conditions was not probable and, as a result, no compensation expense has been recognized. If sufficient performance conditions are achieved in 2013, then the Company would recognize up to $15.6 million in stock-based compensation expense associated with these RSAs and $18.7 million related to cash bonus expense in 2013.

Guarantees and Indemnifications

The Company indemnifies its officers and directors for certain events or occurrences, subject to certain limits. The Company believes the fair value of these indemnification agreements is minimal. Accordingly, the Company has not recognized any liabilities relating to these agreements as of December 31, 2012.

- Definition

The entire disclosure for commitments and contingencies.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 825
-SubTopic 20
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6449706&loc=d3e16207-108621

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 460
-SubTopic 10
-Section 50
-Paragraph 8
-URI http://asc.fasb.org/extlink&oid=6398077&loc=d3e12565-110249

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 450
-SubTopic 20
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6952336&loc=d3e14435-108349

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02.25)
-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
-SubTopic 10
-Section 50
-Paragraph 2
-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.

+ Details

Subsequent Events	12 Months Ended
Subsequent Events	Dec. 31, 2012
Subsequent Events
Subsequent Events	11. Subsequent Events Convertible Subordinated Notes Due 2023 On January 24, 2013, the Company completed an underwritten public offering of $287.5 million aggregate principal amount of unsecured 2.125% convertible subordinated notes due 2023, which includes the full exercise of the underwriters' over-allotment option for $37.5 million aggregate principal amount. The financing raised proceeds, net of issuance costs, of approximately $244.4 million. The notes are convertible into shares of the Company's common stock at an initial conversion rate of 35.9903 shares per $1,000 principal amount of the notes, subject to adjustment in certain circumstances, which represents an initial conversion price of approximately $27.79 per share. In connection with the offering of the notes, the Company entered into privately-negotiated capped call option transactions. The capped call option transaction is an integrated instrument consisting of a call option purchased by the Company with a strike price equal to the conversion price of $27.79 per share for the underlying number of shares and a cap price of $38.00 per share. The cap component is economically equivalent to a call option sold by the Company for the underlying number of shares with a strike price of $38.00 per share. As an integrated instrument, the settlement of the capped call coincides with the due date of the convertible debt. At settlement, the Company will receive from its hedge counterparty a number of our common shares that will range from zero, if the stock price is below $27.79 per share, to a maximum of 2,779,659 shares, if the stock price is above $38.00 per share. However, if the market price of our common stock, as measured under the terms of the capped call transactions, exceeds $38.00 per share, there is no incremental anti-dilutive benefit from the capped call. The aggregate cost of the capped call options was $36.8 million. Sale of Stock On February 15, 2013, the Company and GSK entered into an agreement pursuant to which GSK agreed to purchase through an affiliate, in a private placement, 116,527 shares of the Company's common stock at $22.03 per share, for an aggregate purchase price of approximately $2.6 million, pursuant to its rights under the Company's governance agreement with GSK dated June 4, 2004, as amended.

Description of Operations and Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2012

Description of Operations and Summary of Significant Accounting Policies

Principles of Consolidation

Principles of Consolidation

The consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation.

Use of Management's Estimates

Use of Management's Estimates

Segment Reporting

Segment Reporting

Cash and Cash Equivalents

Cash and Cash Equivalents

Marketable Securities

Marketable Securities

Fair Value of Financial Instruments

Fair Value of Financial Instruments

Concentration of Credit Risks

Concentration of Credit Risks

Notes Receivable

Notes Receivable

Inventories

Inventories

Property and Equipment

Property and Equipment

Property, equipment and leasehold improvements are stated at cost and depreciated using the straight-line method as follows:


Leasehold improvements		Shorter of remaining lease terms or useful life
Equipment, furniture and fixtures		5 - 7 years
Software and computer equipment		3 years

Capitalized Software

Capitalized Software

The Company capitalizes certain costs related to direct material and service costs for software obtained for internal use. Capitalized software costs are depreciated over 3 years.

Impairment of Long-Lived Assets

Impairment of Long-Lived Assets

Bonus Accruals

Bonus Accruals

Deferred Rent

Deferred Rent

Revenue Recognition

Revenue Recognition

The Company recognizes royalty revenue on licensee net sales in the period in which the royalties are earned.

Research and Development Costs

Research and Development Costs

Preclinical Study and Clinical Study Expenses

Preclinical Study and Clinical Study Expenses

Fair Value of Stock-Based Compensation Awards

Fair Value of Stock-Based Compensation Awards

Restricted Stock Units (RSUs) and Restricted Stock Awards (RSAs) are measured based on the fair market values of the underlying stock on the dates of grant.

Compensation expense for purchases under the ESPP is recognized based on the fair value of the common stock on the date of offering, less the purchase discount percentage provided for in the plan.

Income Taxes

Income Taxes

The recognition and measurement of tax benefits requires significant judgment. Judgments concerning the recognition and measurement of a tax benefit might change as new information becomes available.

Foreign Currency

Foreign Currency

Comprehensive Loss

Comprehensive Loss

Related Parties

Related Parties

Transactions with GSK are described in Note 3, "Collaboration Arrangements".

Description of Operations and Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2012

Description of Operations and Summary of Significant Accounting Policies

Property and Equipment


Leasehold improvements		Shorter of remaining lease terms or useful life
Equipment, furniture and fixtures		5 - 7 years
Software and computer equipment		3 years

Net Loss per Share (Tables)

12 Months Ended

Dec. 31, 2012

Net Loss per Share

Computation of basic and diluted net income (loss) and the weighted-average number of shares used in computing basic and diluted net income (loss) per share

	Year Ended December 31,

(in thousands, except for per share data)	2012			2011			2010
Basic and diluted:
Net loss	$	(18,542	)	$	(115,344	)	$	(83,862	)

Weighted-average shares of common stock outstanding		93,410			84,493			72,103
Less: unvested RSAs		(2,501	)		(2,442	)		(33	)

Weighted-average shares used in computing basic and diluted net loss per common share		90,909			82,051			72,070

Basic and diluted net loss per share	$	(0.20	)	$	(1.41	)	$	(1.16	)

Schedule of anti-dilutive securities

	Year Ended December 31,

(in thousands)	2012		2011		2010
Shares issuable under Equity Incentive Plans and ESPP		5,367		5,464		6,636
Shares issuable upon the conversion of convertible subordinated notes		6,668		6,668		6,668

Total anti-dilutive securities		12,035		12,132		13,304

Collaboration Arrangements (Tables)

12 Months Ended

Dec. 31, 2012

Collaboration Arrangements

Schedule of common stock shares purchased in private placements by the affiliate of GSK

	Through December 31, 2012

	Common Stock Shares Purchased		Aggregate Amounts (in thousands)
Purchase dates
February 18, 2011		152,278	$	3,609
May 3, 2011		261,299	$	6,689
August 2, 2011		102,466	$	2,020
November 1, 2011		58,411	$	1,298
February 14, 2012		88,468	$	1,603
August 3, 2012		316,334	$	8,924
November 2, 2012		280,348	$	6,266

Schedule of revenue recognized from GSK under the LABA collaboration and strategic alliance agreements

	Year Ended December 31,

(in thousands)	2012		2011		2010
LABA collaboration(1)	$	3,629	$	4,718	$	5,081
Strategic alliance agreement		—		1,858		2,738
Strategic alliance—MABA program license(2)		1,984		3,082		2,007

Total revenue	$	5,613	$	9,658	$	9,826

(1): The Company revised the estimated performance period for the LABA program based on its progress in the fourth quarter of 2011, resulting in an increase to net loss of $0.4 million for the year ended December 31, 2011. The Company does not expect that the revision will have a material impact on future revenue recognized under this program.
(2): The Company revised the estimated performance period for the MABA program based on its progress as follows: (i) in the first quarter of 2010, resulting in an increase to net loss of $1.0 million for the year ended December 31, 2010; (ii) in the fourth quarter of 2011, resulting in an increase to net loss of $0.2 million for the year ended December 31, 2011; and (iii) in the fourth quarter of 2012, resulting in an increase to net loss of $0.1 million for the year ended December 31, 2012. The Company does not expect that the revision will have a material impact on future revenue recognized under this program.

Schedule of revenue recognized under the Astellas collaboration agreement

	Year Ended December 31,

(in thousands)	2012			2011			2010
Recognition of deferred revenue	$	125,819		$	—		$	—
Amortization of deferred revenue		—			12,975			12,975
Royalties from net sales of VIBATIV®		—			2,422			1,123
Proceeds from VIBATIV® delivered to Astellas		—			1,171			2,058
Cost of VIBATIV® delivered to Astellas		—			(1,177	)		(938	)
Cost of unrealizable VIBATIV® inventories		—			(537	)		(821	)
Astellas-labeled product sales allowance		(31	)		—			—

Total net revenue	$	125,788		$	14,854		$	14,397

Marketable Securities (Tables)

12 Months Ended

Dec. 31, 2012

Marketable Securities

Schedule of amortized cost and estimated fair values for available-for-sale securities

	December 31, 2012

(in thousands)	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
U.S. government securities	$	27,197	$	10	$	(2	)	$	27,205
U.S. government agencies		115,397		85		(16	)		115,466
U.S. corporate notes		91,544		32		(10	)		91,566
U.S. commercial paper		23,082		—		—			23,082
Money market funds		78,646		—		—			78,646

Total	$	335,866	$	127	$	(28	)	$	335,965

	December 31, 2011

(in thousands)	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
U.S. government securities	$	66,150	$	24	$	—		$	66,174
U.S. government agencies		93,183		9		(17	)		93,175
U.S. corporate notes		2,707		—		(2	)		2,705
U.S. commercial paper		34,973		3		—			34,976
Money market funds		38,721		—		—			38,721

Total	$	235,734	$	36	$	(19	)	$	235,751

Schedule of classification of the available-for-sale debt securities

(in thousands)	December 31, 2012		December 31, 2011

Cash and cash equivalents	$	86,298	$	38,721
Short-term investments		153,640		196,137
Long-term marketable securities		95,194		—
Restricted cash		833		893

Total	$	335,965	$	235,751

Schedule of net realized gains (losses) on marketable securities

	Year Ended December 31,

(in thousands)	2012		2011			2010
Realized gains	$	9	$	—		$	3
Realized losses		—		(2	)		—

Net realized gains (losses)	$	9	$	(2	)	$	3

Summary of marketable securities with unrealized losses

	In loss position for less than 12 months					In loss position for more than 12 months				Total

(in thousands)	Estimated Fair Value		Estimated Gross Unrealized Losses			Estimated Fair Value		Estimated Gross Unrealized Losses		Estimated Fair Value		Estimated Gross Unrealized Losses
U.S. government securities	$	7,002	$	(2	)	$	—	$	—	$	7,002	$	(2	)
U.S. government agencies		10,499		(16	)		—		—		10,499		(16	)
U.S. corporate notes		34,693		(10	)		—		—		34,693		(10	)

Total	$	52,194	$	(28	)	$	—	$	—	$	52,194	$	(28	)

- Definition

Tabular disclosure of available-for-sale securities which includes, but is not limited to, changes in the cost basis and fair value, fair value and gross unrealized gain (loss), fair values by type of security, contractual maturity and classification, amortized cost basis, contracts to acquire securities to be accounted for as available-for-sale, debt maturities, transfers to trading, change in net unrealized holding gain (loss) net of tax, continuous unrealized loss position fair value, aggregate losses qualitative disclosures, other than temporary impairment (OTTI) losses or other disclosures related to available for sale securities.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 320
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6957658&loc=d3e62557-112803

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
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-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27337-111563

Reference 3: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27198-111563

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
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-URI http://asc.fasb.org/extlink&oid=6957658&loc=d3e62586-112803

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-Name Accounting Standards Codification
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Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27357-111563

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
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-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27290-111563

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 19, 20, 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 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Staff Position (FSP)
-Number FAS115-1/124-1
-Paragraph 17
-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 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Emerging Issues Task Force (EITF)
-Number 03-1
-Paragraph 21
-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.

+ Details

Fair Value Measurements (Tables)

12 Months Ended

Dec. 31, 2012

Fair Value Measurements

Estimated fair values of the financial assets

	Estimated Fair Value Measurements at Reporting Date Using:

	Quoted Prices in Active Markets for Identical Assets		Significant Other Observable Inputs		Significant Unobservable Inputs
Types of Instruments (in thousands)	Level 1		Level 2		Level 3		Total
Assets at December 31, 2012:
U.S. government securities	$	27,205	$	—	$	—	$	27,205
U.S. government agency securities		56,969		58,497		—		115,466
U.S. corporate notes		40,472		51,094		—		91,566
U.S. commercial paper		—		23,082		—		23,082
Money market funds		78,646		—		—		78,646

Total assets measured at estimated fair value	$	203,292	$	132,673	$	—	$	335,965

Liabilities at December 31 , 2012:
Convertible subordinated notes	$	—	$	194,050	$	—	$	194,050

	Estimated Fair Value Measurements at Reporting Date Using:

	Quoted Prices in Active Markets for Identical Assets		Significant Other Observable Inputs		Significant Unobservable Inputs
Types of Instruments (in thousands)	Level 1		Level 2		Level 3		Total
Assets at December 31, 2011:
U.S. government securities	$	66,174	$	—	$	—	$	66,174
U.S. government agency securities		55,901		37,274		—		93,175
U.S. corporate notes		2,705		—		—		2,705
U.S. commercial paper		—		34,976		—		34,976
Money market funds		38,721		—		—		38,721

Total assets measured at estimated fair value	$	163,501	$	72,250	$	—	$	235,751

Liabilities at December 31, 2011:
Convertible subordinated notes	$	—	$	189,588	$	—	$	189,588

- Definition

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).

+ References + Details

Property and Equipment (Tables)

12 Months Ended

Dec. 31, 2012

Property and Equipment

Schedule of property and equipment

	December 31,

(in thousands)	2012			2011
Computer equipment	$	3,027		$	3,158
Software		5,073			4,628
Furniture and fixtures		3,829			3,821
Laboratory equipment		29,229			28,894
Leasehold improvements		17,416			17,263

		58,574			57,764
Less accumulated depreciation and amortization		(49,420	)		(47,392	)

Property and equipment, net	$	9,154		$	10,372

Long-Term Obligations (Tables)

12 Months Ended

Dec. 31, 2012

Long-Term Obligations

Schedule of long-term obligations

(in thousands)		December 31, 2012			December 31, 2011

Convertible subordinated notes		$	172,500		$	172,500

- Definition

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

+ References

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

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 470
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6479336&loc=d3e64711-112823

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

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08.(e),(f))
-URI http://asc.fasb.org/extlink&oid=6881521&loc=d3e23780-122690

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 835
-SubTopic 30
-Section 55
-Paragraph 8
-URI http://asc.fasb.org/extlink&oid=6584090&loc=d3e28878-108400

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

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 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

+ Details

Stock-Based Compensation (Tables)

12 Months Ended

Dec. 31, 2012

Stock-Based Compensation

Allocation of stock-based compensation expense included in the consolidated statements of operations

	Year Ended December 31,

(in thousands)	2012		2011		2010
Research and development	$	13,667	$	13,422	$	10,322
General and administrative		10,116		11,494		8,687

Total stock-based compensation expense	$	23,783	$	24,916	$	19,009

Schedule of stock-based compensation expense by award type included in the consolidated statements of operations

	Year Ended December 31,

(in thousands)	2012		2011		2010
Employee stock options	$	3,417	$	4,528	$	7,003
Employee RSUs		11,546		13,290		9,783
Employee RSAs		7,968		5,498		398
Non-employee options and RSUs		—		307		1,186
ESPP		852		1,293		639

Total stock-based compensation expense	$	23,783	$	24,916	$	19,009

Schedule of unrecognized compensation cost, net of expected forfeitures, and estimated weighted-average amortization period

(in thousands, except amortization period)	Unrecognized Compensation Cost

Stock options	$	6,442	2.6
RSUs		14,027	2.1
RSAs		23,525	3.5

Total unrecognized stock-based compensation expense	$	43,994

Summary of equity award activity under the 2008 and 2004 Plan

(in thousands, except per share data)			Weighted- average Exercise Price of Outstanding Options				Weighted- average Fair Value per Share at Grant				Weighted- average Fair Value per Share at Grant

Balance at December 31, 2009	8,414		$	16.63	2,042		$	14.15	57		$	25.87
Granted	321			14.90	1,170			10.55	—			—
Exercised	(784	)		9.60	—			—	—			—
Released RSUs/RSAs	—			—	(657	)		13.20	(24	)		25.55
Forfeited	(297	)		26.17	(658	)		26.26	—			—

Balance at December 31, 2010	7,654			16.91	1,897			12.45	33			26.10
Granted	629			21.98	471			24.96	2,483			24.61
Exercised	(1,265	)		8.87	—			—	—			—
Released RSUs/RSAs	—			—	(797	)		13.89	(74	)		24.96
Forfeited	(127	)		29.15	(29	)		15.35	—			—

Balance at December 31, 2011	6,891			18.62	1,542			15.47	2,442			24.62
Granted	335			21.91	528			18.45	447			18.11
Exercised	(947	)		7.98	—			—	—			—
Released RSUs/RSAs	—			—	(752	)		14.19	(388	)		24.77
Forfeited	(159	)		24.43	(78	)		18.48	—			—

Balance at December 31, 2012	6,120			20.30	1,240			17.32	2,501			23.43

Schedule of weighted-average assumptions used to estimate the fair value of stock options granted and employee stock purchase plan issuances

	Year Ended December 31,

	2012	2011	2010
*Employee stock options*
Risk-free interest rate	0.74% - 1.17%	1.10% - 2.57%	1.11% - 2.82%
Expected life (in years)	5 - 6	5 - 6	5 - 6
Volatility	55% - 60%	49% - 55%	48% - 52%
Dividend yield	—%	—%	—%
Weighted-average estimated fair value of stock options granted	$11.50	$11.11	$7.41
*Employee stock purchase plan issuances*
Risk-free interest rate	0.14% - 0.29%	0.05% - 0.54%	0.19% - 0.79%
Expected life (in years)	0.5 - 2	0.5 - 2	0.5 - 2
Volatility	51% - 64%	48% - 59%	50% - 69%
Dividend yield	—%	—%	—%
Weighted-average estimated fair value of ESPP issuances	$8.07	$9.46	$7.63

Schedule of outstanding options to purchase common stock based on range of stock option exercise prices

As of December 31, 2012, all outstanding options to purchase common stock of the Company are summarized in the following table (in thousands, except years and per share data):

	Options Outstanding						Options Exercisable

Range of Exercise Prices	Number Outstanding		Weighted- average Remaining Contractual Life in Years		Weighted- average Exercise Prices		Options Exercisable		Weighted- average Remaining Contractual Life in Years		Weighted- average Exercise Price
$3.10		191		0.8	$	3.10		191		0.8	$	3.10
$6.15 - $6.70		25		5.9		6.15		25		5.9		6.15
$9.69		1,140		1.3		9.69		1,140		1.3		9.69
$9.70 - $16.00		839		4.1		14.71		768		3.8		14.87
$16.01 - $19.80		1,228		4.5		18.17		956		3.3		18.13
$19.81 - $24.71		594		7.2		22.16		316		5.7		22.38
$24.72 - $29.70		1,124		4.1		28.29		1,038		3.6		28.42
$29.71 - $35.46		979		4.1		33.52		979		4.1		33.52

Total		6,120		3.8		20.30		5,413		3.2		20.31

- Definition

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.

+ References + Details

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2012

Income Taxes

Significant components of the Company's deferred tax assets

	December 31,

(in thousands)	2012			2011
Deferred tax assets:
Net operating loss carryforwards	$	411,000		$	359,000
Deferred revenues		4,000			56,000
Capitalized research and development expenditures		35,000			35,000
Research and development tax credit carryforwards		38,000			37,000
Other		33,000			31,000
Valuation allowance		(521,000	)		(518,000	)

Net deferred tax assets	$	—		$	—

Schedule of the differences between the U.S. federal statutory income tax rate to the Company's effective tax rate

	Year Ended December 31,

	2012			2011			2010
U.S. federal statutory income tax rate		34.00	%		34.00	%		34.00	%
State income taxes, net of federal benefit		—			—			5.83
Federal and state research credits		(4.21	)		1.67			2.91
Non-deductible executive compensation		(13.24	)		—			—
Stock-based compensation		(1.36	)		(0.32	)		2.29
Expiration of net operating loss		(1.81	)		(0.42	)		—
Other		(2.09	)		0.75			(0.05	)
Change in valuation allowance		(11.29	)		(35.68	)		(44.98	)

Effective tax rate		(0.00	)%		(0.00	)%		(0.00	)%

Reconciliation of gross unrecognized tax benefits

A reconciliation of the beginning and ending balances of the total amounts of unrecognized tax benefits are as follows (in thousands):


Unrecognized tax benefits as of December 31, 2009	$	39,600
Gross decrease for tax positions for prior years		—
Gross increase in tax positions for current year		3,000

Unrecognized tax benefits as of December 31, 2010		42,600
Gross decrease for tax positions for prior years		—
Gross increase in tax positions for current year		4,300

Unrecognized tax benefits as of December 31, 2011		46,900
Gross decrease for tax positions for prior years		—
Gross increase in tax positions for current year		5,600

Unrecognized tax benefits as of December 31, 2012	$	52,500

- Definition

Tabular disclosure of tax positions taken in the tax returns filed or to be filed for which it is more likely than not that the tax position will not be sustained upon examination by taxing authorities (i.e., uncertain tax positions) and other types of income tax contingencies, including: (1) the policy on classification of interest and penalties; (2) a tabular reconciliation of the total amounts of unrecognized tax benefits at the beginning and end of the period; the total amount(s) of: (3) unrecognized tax benefits that, if recognized, would affect the effective tax rate, and (4) interest and penalties recognized in each of the income statement and balance sheet; (5) for positions for which it is reasonably possible that the total amounts unrecognized will significantly change within 12 months of the reporting date the: (i) nature of the uncertainty, (ii) nature of the event that could occur that would cause the change, and (iii) an estimate of the range of the reasonably possible change or a statement that an estimate of the range cannot be made; and (6) a description of tax years that remain subject to examination by major tax jurisdictions.

+ References + Details

Commitments and Contingencies (Tables)

12 Months Ended

Dec. 31, 2012

Commitments and Contingencies

Schedule of future minimum lease payments under non-cancelable operating lease

(in thousands)

Years ending December 31:
2013	$	5,029
2014		4,859
2015		5,005
2016		5,155
2017		5,310
Thereafter		13,497

Total	$	38,855

Schedule of expenses and income associated with operating leases

	Year Ended December 31,

(in thousands)	2012			2011			2010
Rent expense	$	5,720		$	6,702		$	6,779
Sublease income, net		(160	)		(637	)		(622	)

Description of Operations and Summary of Significant Accounting Policies (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Cash, Cash Equivalents and Restricted Cash
Restricted cash	$ 833	$ 893
VIBATIV
Description of operations and summary of significant accounting policies
Inventories of active pharmaceutical ingredient and other raw materials	5,700
Inventories of work-in-process	$ 1,800

Description of Operations and Summary of Significant Accounting Policies (Details 2) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011
Deferred rent
Period over which average annual rent expense exceeded actual cash rent payments	1 year 6 months
Lease incentives	$ 2.6
Performance-contingent
Bonus Accruals
Timeframe for achievement of performance conditions		6 years
Equipment, furniture and fixtures \| Maximum
Information related to useful life of property and equipment
Estimated useful life	7 years
Equipment, furniture and fixtures \| Minimum
Information related to useful life of property and equipment
Estimated useful life	5 years
Software and computer equipment
Information related to useful life of property and equipment
Estimated useful life	3 years
Capitalized software
Information related to useful life of property and equipment
Estimated useful life	3 years

Description of Operations and Summary of Significant Accounting Policies (Details 3) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Gunderson law firm
Related parties
Fees incurred related to related party	$ 1.2	$ 0.3	$ 0.7

Net Loss per Share (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Basic and diluted
Net loss	$ (18,542)	$ (115,344)	$ (83,862)
Weighted-average common shares outstanding	93,410	84,493	72,103
Less: unvested RSAs (in shares)	(2,501)	(2,442)	(33)
Weighted-average shares used in computing basic net loss per share	90,909	82,051	72,070
Basic and diluted net loss per share (in dollars per share)	$ (0.20)	$ (1.41)	$ (1.16)
Securities that could potentially dilute basic EPS in the future
Anti-dilutive securities (in shares)	12,035	12,132	13,304
Equity Incentive Plans and ESPP
Securities that could potentially dilute basic EPS in the future
Anti-dilutive securities (in shares)	5,367	5,464	6,636
Convertible subordinated notes
Securities that could potentially dilute basic EPS in the future
Anti-dilutive securities (in shares)	6,668	6,668	6,668

Collaboration Arrangements (Details)				1 Months Ended									12 Months Ended
Collaboration Arrangements (Details)	Oct. 31, 2012 USD ($) Item	Oct. 03, 2012	May 16, 2012 USD ($) $ / shares	Nov. 30, 2012 USD ($) Item shares	Aug. 31, 2012 USD ($) shares	May 31, 2012 shares	Feb. 29, 2012 USD ($) shares	Nov. 30, 2011 USD ($) shares	Aug. 31, 2011 USD ($) shares	Jul. 31, 2011 shares	May 31, 2011 USD ($) shares	Feb. 28, 2011 USD ($) shares	Dec. 31, 2012 USD ($) Item	Dec. 31, 2011 USD ($)	Dec. 31, 2010 USD ($)	Oct. 01, 2012 USD ($)
Information related to collaboration arrangements
Company's stock purchased by related party													$ 229,296,000	$ 13,618,000	$ 129,190,000
Net revenue recognized under the collaboration
Revenue													135,758,000	24,512,000	24,223,000
Deferred revenue, non-current													6,014,000	122,017,000
Accounts payable													5,377,000	5,813,000
Deferred revenue, current													4,593,000	18,697,000
Deferred revenue, non-current													6,014,000	122,017,000
GSK
Net revenue recognized under the collaboration
Revenue													5,613,000	9,658,000	9,826,000
Research reimbursement recognized as a reduction of research and development expense													200,000	400,000	400,000
Class A common stock \| GSK
Information related to collaboration arrangements
Number of shares of common stock converted \| shares										9,401,499
Conversion ratio										1
MABA \| GSK
Net revenue recognized under the collaboration
Potential future contingent payments that may be received													102,000,000
VIBATIV \| Astellas
Information related to collaboration arrangements
Purchases of active pharmaceutical ingredient and other raw materials													5,800,000
VIBATIV \| Astellas \| Maximum
Information related to collaboration arrangements
Amount of purchase agreements for pharmaceutical ingredient and raw materials													7,700,000
Amount of finished goods inventories													$ 4,200,000
Long-acting beta agonist (LABA) collaboration \| GSK
Information related to collaboration arrangements
Number of combination products \| Item													2
Long-acting beta agonist (LABA) collaboration \| GSK \| Maximum
Information related to collaboration arrangements
Obligation for milestone payments to GSK													$ 220,000,000
Portion of potential milestone payments payable by end of 2014													$ 140,000,000
Long-acting beta agonist (LABA) collaboration \| LABA collaboration \| GSK
Information related to collaboration arrangements
Royalty rate for first level of annual global net sales (as a percent)													15.00%
Royalty rate for sales above first level of annual global net sales (as a percent)													5.00%
Annual global sales level used to determine royalty rate													$ 3,000,000,000
Net revenue recognized under the collaboration
Revenue													$ 3,629,000	4,718,000	5,081,000
Increase in net loss due to revised estimated performance period														400,000
Long-acting beta agonist (LABA) collaboration \| Other products combined with LABA \| GSK \| Maximum
Net revenue recognized under the collaboration
Royalty rate, as a percentage of net sales													10.00%
2004 Strategic alliance \| MABA \| GSK
Information related to collaboration arrangements
Number of combination products to be developed and commercialized \| Item													1
Net revenue recognized under the collaboration
Revenue													$ 1,984,000	3,082,000	2,007,000
Increase in net loss due to revised estimated performance period													100,000	200,000	1,000,000
2004 Strategic alliance \| MABA containing '081 \| GSK
Information related to collaboration arrangements
Potential upfront license and milestone payments that Company could receive in respect of combination medicines													$ 250,000,000
2004 Strategic alliance \| MABA containing '081 - single-agent \| GSK
Information related to collaboration arrangements
Royalty rate for sales above first level of annual global net sales (as a percent)													7.50%
Annual global sales level used to determine royalty rate													$ 3,500,000,000
Potential upfront license and milestone payments that Company could receive													$ 125,000,000
2004 Strategic alliance \| MABA containing '081 - single-agent \| GSK \| Maximum
Information related to collaboration arrangements
Royalty rate for first level of annual global net sales (as a percent)													20.00%
2004 Strategic alliance \| MABA containing '081 - single-agent \| GSK \| Minimum
Information related to collaboration arrangements
Royalty rate for first level of annual global net sales (as a percent)													10.00%
2004 Strategic alliance \| MABA containing '081 - combination product \| GSK
Information related to collaboration arrangements
Royalty rate for combination products as a percentage of the rate applied to single products													70.00%
Annual global sales level used to determine royalty rate													$ 3,500,000,000
2004 Strategic alliance \| MABA containing additional MABA \| GSK
Information related to collaboration arrangements
Number of products which Company is obligated to use diligent efforts to discover after license of a program \| Item													6
2004 Strategic alliance \| MABA containing additional MABA \| GSK \| Maximum
Information related to collaboration arrangements
Potential milestone payments that Company could receive													$ 129,000,000
2004 Strategic alliance \| MABA containing additional MABA - single-agent \| GSK
Information related to collaboration arrangements
Royalty rate for sales above first level of annual global net sales (as a percent)													10.00%
2004 Strategic alliance \| MABA containing additional MABA - single-agent \| GSK \| Maximum
Information related to collaboration arrangements
Royalty rate for first level of annual global net sales (as a percent)													15.00%
2004 Strategic alliance \| MABA containing additional MABA - single-agent \| GSK \| Minimum
Information related to collaboration arrangements
Royalty rate for first level of annual global net sales (as a percent)													10.00%
2004 Strategic alliance \| MABA containing additional MABA - combination product \| GSK
Information related to collaboration arrangements
Royalty rate for combination products as a percentage of the rate applied to single products													50.00%
2004 Strategic alliance \| Non-license specific \| GSK
Net revenue recognized under the collaboration
Revenue														1,858,000	2,738,000
Governance agreement \| Common stock \| GSK
Information related to collaboration arrangements
Company's stock purchased by related party (in shares) \| shares				280,348	316,334		88,468	58,411	102,466		261,299	152,278
Company's stock purchased by related party				$ 6,266,000	$ 8,924,000		$ 1,603,000	$ 1,298,000	$ 2,020,000		$ 6,689,000	$ 3,609,000
Common stock purchase agreement \| Common stock \| GSK
Information related to collaboration arrangements
Company's stock purchased by related party (in shares) \| shares						10,000,000
Company's stock purchased by related party, price (in dollars per share) \| $ / shares			$ 21.2887
Company's stock purchased by related party			$ 212,900,000
License, Development and Commercialization Agreement With Astellas \| VIBATIV \| Astellas
Information related to collaboration arrangements
Percentage of royalties payable to Astellas													2.00%
Amount recognized in governmental rebate and governmental chargeback claims													$ 31,000
Term of royalty payment													10 years
Information related to collaboration arrangements
Upfront license, milestone and other fees received													$ 191,000,000
Net revenue recognized under the collaboration
Revenue													125,788,000	14,854,000	14,397,000
Recognition of remaining deferred revenue													125,819,000
Amortization of deferred revenue														12,975,000	12,975,000
Royalties from net sales of VIBATIV														2,422,000	1,123,000
Proceeds from VIBATIV delivered to Astellas														1,171,000	2,058,000
Cost of VIBATIV delivered to Astellas														(1,177,000)	(938,000)
Cost of unrealizable VIBATIV inventories														(537,000)	(821,000)
Astellas-labeled product sales allowance													(31,000)
Research reimbursement recognized as a reduction of research and development expense														$ 400,000	$ 300,000
Development and Commercialization Agreement \| R-Pharm CJSC
Net revenue recognized under the collaboration
Deferred revenue, current													1,100,000
Number of separate development and commercialization agreements \| Item	2
Arrangement consideration, license and maintenance fees received				1,100,000
Potential additional near-term licensing fees	$ 1,000,000
Potential future contingent payments that may be received	$ 10,000,000
Development and Commercialization Agreement \| Velusetrag (or TD-5108) \| Alfa Wassermann
Net revenue recognized under the collaboration
Research reimbursement recognized as a reduction of research and development expense													$ 200,000
Option fee funding amount																$ 10,000,000
GSK Upfront License Fees, Milestone Payments and Revenue
Option right exercise period													2 years
Development and Commercialization Agreement \| Velusetrag (or TD-5108) \| Alfa Wassermann \| Maximum
Net revenue recognized under the collaboration
Potential development, regulatory and sales milestone payments eligible to receive																$ 53,500,000
Royalty rate, as a percentage of net sales		20.00%
Development and Commercialization Agreement \| TD-1792 \| R-Pharm CJSC
Net revenue recognized under the collaboration
Royalty rate, as a percentage of net sales	15.00%
Development and Commercialization Agreement \| Telavancin \| R-Pharm CJSC
Net revenue recognized under the collaboration
Royalty rate, as a percentage of net sales	25.00%
Research Collaboration and License Agreement \| Novel small molecule therapeutics \| Merck
Net revenue recognized under the collaboration
Deferred revenue, non-current													$ 200,000
Upfront payment received allocated to license				4,400,000
Upfront payment received allocated to research services				400,000
Upfront payment received allocated to committee participation				200,000
Deferred revenue, current													19,000
Deferred revenue, non-current													200,000
Research reimbursement recognized as a reduction of research and development expense													$ 800,000
Arrangement consideration, upfront license payment received				$ 5,000,000
Number of units of accounting based on the relative selling price method \| Item				3
Research Collaboration and License Agreement \| Novel small molecule therapeutics \| Merck \| Maximum
Net revenue recognized under the collaboration
Potential future payments to be received	$ 148,000,000

Marketable Securities (Details) - USD ($) $ in Thousands	12 Months Ended
Marketable Securities (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Available-for-sale securities
Amortized Cost	$ 335,866	$ 235,734
Gross Unrealized Gains	127	36
Gross Unrealized Losses	(28)	(19)
Estimated Fair Value	335,965	235,751
Net realized gains (losses) on marketable securities
Realized gains	9		$ 3
Realized losses		(2)
Net realized gains (losses)	9	(2)	$ 3
Fair Value
Fair Value, In loss position for less than 12 months	52,194
Fair Value, Total	52,194
Gross Unrealized Losses
Estimated Gross Unrealized Losses, In loss position for less than 12 months	(28)
Gross Unrealized Losses, Total	$ (28)
Maturity period for marketable securities
Average contractual maturity period	9 months
Maximum
Maturity period for marketable securities
Maximum contractual maturity period	24 months
Cash and cash equivalents
Available-for-sale securities
Estimated Fair Value	$ 86,298	38,721
Short-term investments
Available-for-sale securities
Estimated Fair Value	153,640	196,137
Long-term marketable securities
Available-for-sale securities
Estimated Fair Value	95,194
Restricted cash
Available-for-sale securities
Estimated Fair Value	833	893
U.S. government securities
Available-for-sale securities
Amortized Cost	27,197	66,150
Gross Unrealized Gains	10	24
Gross Unrealized Losses	(2)
Estimated Fair Value	27,205	66,174
Fair Value
Fair Value, In loss position for less than 12 months	7,002
Fair Value, Total	7,002
Gross Unrealized Losses
Estimated Gross Unrealized Losses, In loss position for less than 12 months	(2)
Gross Unrealized Losses, Total	(2)
U.S. government agencies
Available-for-sale securities
Amortized Cost	115,397	93,183
Gross Unrealized Gains	85	9
Gross Unrealized Losses	(16)	(17)
Estimated Fair Value	115,466	93,175
Fair Value
Fair Value, In loss position for less than 12 months	10,499
Fair Value, Total	10,499
Gross Unrealized Losses
Estimated Gross Unrealized Losses, In loss position for less than 12 months	(16)
Gross Unrealized Losses, Total	(16)
U.S. corporate notes
Available-for-sale securities
Amortized Cost	91,544	2,707
Gross Unrealized Gains	32
Gross Unrealized Losses	(10)	(2)
Estimated Fair Value	91,566	2,705
Fair Value
Fair Value, In loss position for less than 12 months	34,693
Fair Value, Total	34,693
Gross Unrealized Losses
Estimated Gross Unrealized Losses, In loss position for less than 12 months	(10)
Gross Unrealized Losses, Total	(10)
U.S. commercial paper
Available-for-sale securities
Amortized Cost	23,082	34,973
Gross Unrealized Gains		3
Estimated Fair Value	23,082	34,976
Money market funds
Available-for-sale securities
Amortized Cost	78,646	38,721
Estimated Fair Value	$ 78,646	$ 38,721

Fair Value Measurements (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	$ 335,965	$ 235,751
U.S. government securities
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	27,205	66,174
U.S. government agency securities
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	115,466	93,175
U.S. corporate notes
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	91,566	2,705
U.S. commercial paper
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	23,082	34,976
Money market funds
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	78,646	38,721
Recurring basis \| Quoted Prices in Active Markets for Identical Assets, Level 1
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	203,292	163,501
Recurring basis \| Quoted Prices in Active Markets for Identical Assets, Level 1 \| U.S. government securities
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	27,205	66,174
Recurring basis \| Quoted Prices in Active Markets for Identical Assets, Level 1 \| U.S. government agency securities
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	56,969	55,901
Recurring basis \| Quoted Prices in Active Markets for Identical Assets, Level 1 \| U.S. corporate notes
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	40,472	2,705
Recurring basis \| Quoted Prices in Active Markets for Identical Assets, Level 1 \| Money market funds
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	78,646	38,721
Recurring basis \| Significant Other Observable Inputs, Level 2
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	132,673	72,250
Recurring basis \| Significant Other Observable Inputs, Level 2 \| U.S. government agency securities
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	58,497	37,274
Recurring basis \| Significant Other Observable Inputs, Level 2 \| U.S. corporate notes
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	51,094
Recurring basis \| Significant Other Observable Inputs, Level 2 \| U.S. commercial paper
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	23,082	34,976
Recurring basis \| Significant Other Observable Inputs, Level 2 \| Convertible subordinated notes
Estimated fair values of entity's financial assets and liabilities
Total liabilities measured at fair value	194,050	189,588
Recurring basis \| Total
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	335,965	235,751
Recurring basis \| Total \| U.S. government securities
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	27,205	66,174
Recurring basis \| Total \| U.S. government agency securities
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	115,466	93,175
Recurring basis \| Total \| U.S. corporate notes
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	91,566	2,705
Recurring basis \| Total \| U.S. commercial paper
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	23,082	34,976
Recurring basis \| Total \| Money market funds
Estimated fair values of entity's financial assets and liabilities
Total assets measured at fair value	78,646	38,721
Recurring basis \| Total \| Convertible subordinated notes
Estimated fair values of entity's financial assets and liabilities
Total liabilities measured at fair value	$ 194,050	$ 189,588

Property and Equipment (Details) - USD ($) $ in Thousands	12 Months Ended
Property and Equipment (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Property and Equipment
Property and equipment, gross	$ 58,574	$ 57,764
Less accumulated depreciation and amortization	(49,420)	(47,392)
Property and equipment, net	9,154	10,372
Depreciation expense	3,300	3,800	$ 3,900
Amount of write-off recognized related to assets that could no longer be used in operations	200
Computer equipment
Property and Equipment
Property and equipment, gross	3,027	3,158
Software
Property and Equipment
Property and equipment, gross	5,073	4,628
Furniture and fixtures
Property and Equipment
Property and equipment, gross	3,829	3,821
Laboratory equipment
Property and Equipment
Property and equipment, gross	29,229	28,894
Leasehold improvements
Property and Equipment
Property and equipment, gross	$ 17,416	$ 17,263

Long-Term Obligations (Details)		12 Months Ended
Long-Term Obligations (Details)	Jan. 31, 2008 USD ($)	Dec. 31, 2012 USD ($) shares $ / shares	Dec. 31, 2011 USD ($)	Dec. 31, 2010 USD ($)
Information related to long-term obligations
Convertible subordinated notes		$ 172,500,000	$ 172,500,000
Convertible subordinated notes
Debt disclosures
Loan amount	$ 172,500,000
Proceeds from issuance of debt, net of issuance costs	$ 166,700,000
Interest rate (as a percent)		3.00%
Conversion rate, number of shares to be issued per $1000 of principal amount of notes \| shares		38.6548
Principal amount used for debt instrument conversion ratio		$ 1,000
Initial conversion price of convertible notes into common stock (in dollars per share) \| $ / shares		$ 25.87
Unamortized debt issuance costs		$ 1,700,000
Amortization expense		$ 800,000	$ 800,000	$ 800,000
Percentage of principal amount at which the entity may redeem some or all notes		100.00%
Percentage of closing sales price of the entity's common stock the conversion price must exceed in order for the notes to be convertible		130.00%
Number of days within 30 consecutive trading days in which the closing price of the entity's common stock must exceed the conversion price for the notes to be redeemable		20 days
Number of consecutive trading days during which the closing price of the entity's common stock must exceed the conversion price for at least 20 days in order for the notes to be redeemable		30 days

Stock-Based Compensation (Details)	12 Months Ended
Stock-Based Compensation (Details)	Dec. 31, 2012 Item $ / shares shares	Dec. 31, 2011 shares	May 31, 2012 shares	Dec. 31, 2010 shares
Employee stock purchase plan
Information related to stock-based compensation
Shares of common stock approved and authorized for issuance	2,025,000
Shares remaining available for issuance	423,575
Purchase price as a percentage of fair market value of stock	85.00%
Consecutive and overlapping offering periods	24 months
Number of offering periods \| Item	4
Duration of purchase period	6 months
Maximum contributions as a percentage of employee's eligible compensation	15.00%
Stock issued during period (in shares)	1,601,425
Cumulative average sale price per share as of the period end (in dollars per share) \| $ / shares	$ 10.75
Stock options
Information related to stock-based compensation
Maximum term for stock options	10 years
Vesting term for stock option	4 years
Percentage of stock options to be vested at end of year one	25.00%
Percentage of stock options to be vested monthly over remaining three years	75.00%
RSUs \| Performance-contingent \| Senior management \| Employee
Information related to stock-based compensation
Shares of common stock approved and authorized for issuance				210,000
RSAs \| Performance-contingent \| Senior management \| Employee
Information related to stock-based compensation
Shares of common stock approved and authorized for issuance	44,500	1,290,000
Number of possible performance conditions, achievement of which not probable \| Item	1
Number of possible performance conditions \| Item	3
RSAs \| Performance-contingent \| Non-executive officer \| Non-employee
Information related to stock-based compensation
Shares of common stock approved and authorized for issuance		25,000
2012 Employee Incentive Plan
Information related to stock-based compensation
Shares of common stock approved and authorized for issuance			6,500,000
Reduction in number of shares 2012 plan reserve for each stock option and SAR granted	1
Reduction in number of shares 2012 plan reserve for each stock award other than option and SAR granted	1.45
Shares remaining available for issuance	5,023,370
Prior Plans
Information related to stock-based compensation
Additional number of shares of common stock approved and authorized for issuance		12,667,411

Stock-Based Compensation (Details 2) - USD ($)	1 Months Ended	12 Months Ended
Stock-Based Compensation (Details 2) - USD ($)	Jun. 30, 2010	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Allocation of stock-based compensation expense
Stock-based compensation expense		$ 23,783,000	$ 24,916,000	$ 19,009,000
Total stock-based compensation expense capitalized to inventory		400,000
Information related to share-based compensation
Total unrecognized compensation cost related to unvested stock-based compensation		43,994,000
Performance-contingent
Information related to share-based compensation
Timeframe for achievement of performance conditions			6 years
Stock options
Allocation of stock-based compensation expense
Stock-based compensation expense		3,417,000	$ 4,528,000	7,003,000
Information related to share-based compensation
Expense recorded in connection with stock option modification	$ 900,000
Total unrecognized compensation cost related to unvested stock-based compensation		$ 6,442,000
Weighted-average remaining service period of recognition of unrecognized compensation cost		2 years 7 months 6 days
RSUs
Allocation of stock-based compensation expense
Stock-based compensation expense		$ 11,546,000	13,290,000	9,783,000
Information related to share-based compensation
Total unrecognized compensation cost related to unvested stock-based compensation		$ 14,027,000
Weighted-average remaining service period of recognition of unrecognized compensation cost		2 years 1 month 6 days
RSUs \| Employee \| Performance-contingent \| Senior management
Allocation of stock-based compensation expense
Stock-based compensation expense		$ 300,000	1,300,000
RSAs
Allocation of stock-based compensation expense
Stock-based compensation expense		7,968,000	$ 5,498,000	398,000
Information related to share-based compensation
Total unrecognized compensation cost related to unvested stock-based compensation		$ 23,525,000
Weighted-average remaining service period of recognition of unrecognized compensation cost		3 years 6 months
RSAs \| Employee \| Performance-contingent \| Senior management
Allocation of stock-based compensation expense
Stock-based compensation expense		$ 400,000
Information related to share-based compensation
Timeframe for achievement of performance conditions			6 years
Maximum potential expense associated with incentive compensation program			$ 31,900,000
RSAs \| Non-employee \| Performance-contingent \| Non-executive officer
Information related to share-based compensation
Maximum potential expense associated with incentive compensation program			475,000
Non-employee options and RSUs
Allocation of stock-based compensation expense
Stock-based compensation expense			307,000	1,186,000
ESPP
Allocation of stock-based compensation expense
Stock-based compensation expense		852,000	1,293,000	639,000
Research and development
Allocation of stock-based compensation expense
Stock-based compensation expense		13,667,000	13,422,000	10,322,000
Research and development \| RSAs \| Employee \| Performance-contingent \| Senior management
Information related to share-based compensation
Maximum potential expense associated with incentive compensation program			6,300,000
General and administrative
Allocation of stock-based compensation expense
Stock-based compensation expense		$ 10,116,000	11,494,000	$ 8,687,000
General and administrative \| RSAs \| Employee \| Performance-contingent \| Senior management
Information related to share-based compensation
Maximum potential expense associated with incentive compensation program			$ 25,600,000

Stock-Based Compensation (Details 3) - USD ($) $ / shares in Units, shares in Thousands, $ in Millions	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Stock options
Number of shares outstanding (in shares)
Balance at the beginning of the period (in shares)	6,891	7,654	8,414
Granted (in shares)	335	629	321
Exercised (in shares)	(947)	(1,265)	(784)
Forfeited (in shares)	(159)	(127)	(297)
Balance at the end of the period (in shares)	6,120	6,891	7,654
Weighted-Average Exercise Price of Outstanding Options (in dollars per share)
Balance at the beginning of the period, Weighted-Average Exercise Price of Outstanding Options (in dollars per share)	$ 18.62	$ 16.91	$ 16.63
Granted, Weighted-Average Exercise Price of Outstanding Options (in dollars per share)	21.91	21.98	14.90
Exercised, Weighted-Average Exercise Price of Outstanding Options (in dollars per share)	7.98	8.87	9.60
Forfeited, Weighted-Average Exercise Price of Outstanding Options (in dollars per share)	24.43	29.15	26.17
Balance at the end of the period, Weighted-Average Exercise Price of Outstanding Options (in dollars per share)	$ 20.30	$ 18.62	$ 16.91
Weighted-average assumptions
Risk-free interest rate, minimum (as a percent)	0.74%	1.10%	1.11%
Risk-free interest rate, maximum (as a percent)	1.17%	2.57%	2.82%
Volatility rate, minimum (as a percent)	55.00%	49.00%	48.00%
Volatility rate, maximum (as a percent)	60.00%	55.00%	52.00%
Weighted-average estimated fair value of ESPP issuances (in dollars per share)	$ 11.50	$ 11.11	$ 7.41
Aggregate intrinsic value of options outstanding	$ 30.0
Aggregate intrinsic value of options exercisable	28.1
Total intrinsic value of options exercised	15.2	$ 17.1	$ 7.2
Total estimated fair value of options vested	$ 4.1	$ 6.4	$ 8.2
Stock options \| Minimum
Weighted-average assumptions
Expected life	5 years	5 years	5 years
Stock options \| Maximum
Weighted-average assumptions
Expected life	6 years	6 years	6 years
RSUs
Number of shares outstanding, RSUs and RSAs
Balance at the beginning of the period (in shares)	1,542	1,897	2,042
Granted (in shares)	528	471	1,170
Released RSUs and RSAs (in shares)	(752)	(797)	(657)
Forfeited (in shares)	(78)	(29)	(658)
Balance at the end of the period (in shares)	1,240	1,542	1,897
Weighted-Average Exercise Price of Outstanding Awards (in dollars per share)
Balance at the beginning of the period (in dollars per share)	$ 15.47	$ 12.45	$ 14.15
Granted (in dollars per share)	18.45	24.96	10.55
Released RSUs and RSAs (in dollars per share)	14.19	13.89	13.20
Forfeited (in dollars per share)	18.48	15.35	26.26
Balance at the end of the period (in dollars per share)	$ 17.32	$ 15.47	$ 12.45
RSUs and RSAs performance-contingent
Number of shares outstanding, RSUs and RSAs
Balance at the beginning of the period (in shares)	2,442	33	57
Granted (in shares)	447	2,483
Released RSUs and RSAs (in shares)	(388)	(74)	(24)
Balance at the end of the period (in shares)	2,501	2,442	33
Weighted-Average Exercise Price of Outstanding Awards (in dollars per share)
Balance at the beginning of the period (in dollars per share)	$ 24.62	$ 26.10	$ 25.87
Granted (in dollars per share)	18.11	24.61
Released RSUs and RSAs (in dollars per share)	24.77	24.96	25.55
Balance at the end of the period (in dollars per share)	$ 23.43	$ 24.62	$ 26.10
Employee stock purchase plan issuances
Weighted-average assumptions
Risk-free interest rate, minimum (as a percent)	0.14%	0.05%	0.19%
Risk-free interest rate, maximum (as a percent)	0.29%	0.54%	0.79%
Volatility rate, minimum (as a percent)	51.00%	48.00%	50.00%
Volatility rate, maximum (as a percent)	64.00%	59.00%	69.00%
Weighted-average estimated fair value of ESPP issuances (in dollars per share)	$ 8.07	$ 9.46	$ 7.63
Employee stock purchase plan issuances \| Minimum
Weighted-average assumptions
Expected life	6 months	6 months	6 months
Employee stock purchase plan issuances \| Maximum
Weighted-average assumptions
Expected life	2 years	2 years	2 years

Stock-Based Compensation (Details 4)	12 Months Ended
Stock-Based Compensation (Details 4)	Dec. 31, 2012 $ / shares shares
Non-employee director
Options outstanding and exercisable
Vesting period of initial grant to newly appointed director	2 years
Vesting period of annual grant upon re-election as director	12 months
Proration vesting period of annual grant upon re-election as director	12 months
Stock options
Options outstanding and exercisable
Number Outstanding (in shares) \| shares	6,120,000
Weighted-average Remaining Contractual Life in Years, Options Outstanding	3 years 9 months 18 days
Weighted-average Exercise Price, Options Outstanding (in dollars per share)	$ 20.30
Options Exercisable (in shares) \| shares	5,413,000
Weighted-average Remaining Contractual Life in Years, Options Exercisable	3 years 2 months 12 days
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$ 20.31
Stock options \| Non-employee director
Options outstanding and exercisable
One-time grant of shares \| shares	6,000
Annual grant of shares upon re-election to the Board \| shares	6,000
Stock options \| Exercise price, $3.10
Options outstanding and exercisable
Exercise price range, low end of range (in dollars per share)	$ 3.10
Number Outstanding (in shares) \| shares	191,000
Weighted-average Remaining Contractual Life in Years, Options Outstanding	9 months 18 days
Weighted-average Exercise Price, Options Outstanding (in dollars per share)	$ 3.10
Options Exercisable (in shares) \| shares	191,000
Weighted-average Remaining Contractual Life in Years, Options Exercisable	9 months 18 days
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$ 3.10
Stock options \| Exercise price range, $6.15 - $6.70
Options outstanding and exercisable
Exercise price range, low end of range (in dollars per share)	6.15
Exercise price range, high end of range (in dollars per share)	$ 6.70
Number Outstanding (in shares) \| shares	25,000
Weighted-average Remaining Contractual Life in Years, Options Outstanding	5 years 10 months 24 days
Weighted-average Exercise Price, Options Outstanding (in dollars per share)	$ 6.15
Options Exercisable (in shares) \| shares	25,000
Weighted-average Remaining Contractual Life in Years, Options Exercisable	5 years 10 months 24 days
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$ 6.15
Stock options \| Exercise price, $9.69
Options outstanding and exercisable
Exercise price range, low end of range (in dollars per share)	$ 9.69
Number Outstanding (in shares) \| shares	1,140,000
Weighted-average Remaining Contractual Life in Years, Options Outstanding	1 year 3 months 18 days
Weighted-average Exercise Price, Options Outstanding (in dollars per share)	$ 9.69
Options Exercisable (in shares) \| shares	1,140,000
Weighted-average Remaining Contractual Life in Years, Options Exercisable	1 year 3 months 18 days
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$ 9.69
Stock options \| Exercise price range, $9.70 - $16.00
Options outstanding and exercisable
Exercise price range, low end of range (in dollars per share)	9.70
Exercise price range, high end of range (in dollars per share)	$ 16.00
Number Outstanding (in shares) \| shares	839,000
Weighted-average Remaining Contractual Life in Years, Options Outstanding	4 years 1 month 6 days
Weighted-average Exercise Price, Options Outstanding (in dollars per share)	$ 14.71
Options Exercisable (in shares) \| shares	768,000
Weighted-average Remaining Contractual Life in Years, Options Exercisable	3 years 9 months 18 days
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$ 14.87
Stock options \| Exercise price range, $16.01- $19.80
Options outstanding and exercisable
Exercise price range, low end of range (in dollars per share)	16.01
Exercise price range, high end of range (in dollars per share)	$ 19.80
Number Outstanding (in shares) \| shares	1,228,000
Weighted-average Remaining Contractual Life in Years, Options Outstanding	4 years 6 months
Weighted-average Exercise Price, Options Outstanding (in dollars per share)	$ 18.17
Options Exercisable (in shares) \| shares	956,000
Weighted-average Remaining Contractual Life in Years, Options Exercisable	3 years 3 months 18 days
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$ 18.13
Stock options \| Exercise price range, $19.81- $24.71
Options outstanding and exercisable
Exercise price range, low end of range (in dollars per share)	19.81
Exercise price range, high end of range (in dollars per share)	$ 24.71
Number Outstanding (in shares) \| shares	594,000
Weighted-average Remaining Contractual Life in Years, Options Outstanding	7 years 2 months 16 days
Weighted-average Exercise Price, Options Outstanding (in dollars per share)	$ 22.16
Options Exercisable (in shares) \| shares	316,000
Weighted-average Remaining Contractual Life in Years, Options Exercisable	5 years 8 months 12 days
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$ 22.38
Stock options \| Exercise price range, $24.72 - $29.70
Options outstanding and exercisable
Exercise price range, low end of range (in dollars per share)	24.72
Exercise price range, high end of range (in dollars per share)	$ 29.70
Number Outstanding (in shares) \| shares	1,124,000
Weighted-average Remaining Contractual Life in Years, Options Outstanding	4 years 1 month 6 days
Weighted-average Exercise Price, Options Outstanding (in dollars per share)	$ 28.29
Options Exercisable (in shares) \| shares	1,038,000
Weighted-average Remaining Contractual Life in Years, Options Exercisable	3 years 7 months 6 days
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$ 28.42
Stock options \| Exercise price range, $29.71 - $35.46
Options outstanding and exercisable
Exercise price range, low end of range (in dollars per share)	29.71
Exercise price range, high end of range (in dollars per share)	$ 35.46
Number Outstanding (in shares) \| shares	979,000
Weighted-average Remaining Contractual Life in Years, Options Outstanding	4 years 1 month 6 days
Weighted-average Exercise Price, Options Outstanding (in dollars per share)	$ 33.52
Options Exercisable (in shares) \| shares	979,000
Weighted-average Remaining Contractual Life in Years, Options Exercisable	4 years 1 month 6 days
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$ 33.52
RSUs \| Non-employee director
Options outstanding and exercisable
One-time grant of shares \| shares	6,000
Annual grant of shares upon re-election to the Board \| shares	6,000

Income Taxes (Details) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Deferred tax assets:
Net operating loss carryforwards	$ 411,000	$ 359,000
Deferred revenues	4,000	56,000
Capitalized research and development expenditures	35,000	35,000
Research and development tax credit carryforwards	38,000	37,000
Other	33,000	31,000
Valuation allowance	(521,000)	(518,000)
Information related to valuation allowance
Increase in valuation allowance	$ 3,000	$ 50,000	$ 35,000
The differences between the U.S. federal statutory income tax rate to the Company's effective tax rate
U.S. federal statutory income tax rate (as a percent)	34.00%	34.00%	34.00%
State income taxes, net of federal benefit (as a percent)			5.83%
Federal and state research credits	(4.21%)	1.67%	2.91%
Non-deductible executive compensation	(13.24%)
Stock-based compensation (as a percent)	(1.36%)	(0.32%)	2.29%
Expiration of net operating loss (as a percent)	(1.81%)	(0.42%)
Other (as a percent)	(2.09%)	0.75%	(0.05%)
Change in valuation allowance	(11.29%)	(35.68%)	(44.98%)
Effective tax rate (as a percent)	(0.00%)	(0.00%)	(0.00%)
Gross unrecognized tax benefits
Gross unrecognized tax benefits at the beginning of the period	$ 46,900	$ 42,600	$ 39,600
Gross increase in tax positions for current year	5,600	4,300	3,000
Gross unrecognized tax benefits at the end of the period	52,500	$ 46,900	$ 42,600
Federal
Operating Loss and Tax Credit Carryforward
Net operating loss carryfowards	1,221,400
Federal \| Research and Development
Operating Loss and Tax Credit Carryforward
Tax credit carryforward amount	43,200
State
Operating Loss and Tax Credit Carryforward
Net operating loss carryfowards	563,400
State \| Research
Operating Loss and Tax Credit Carryforward
Tax credit carryforward amount	$ 52,200

Commitments and Contingencies (Details) $ in Thousands	12 Months Ended
Commitments and Contingencies (Details) $ in Thousands	Dec. 31, 2012 USD ($) ft²	Dec. 31, 2011 USD ($)	Dec. 31, 2010 USD ($)
VIBATIV \| Astellas
Information related to commitment and contingencies
Purchases of active pharmaceutical ingredient and other raw materials	$ 5,800
Purchase Obligations
Information related to commitment and contingencies
Total purchase obligations for services, development and supply agreements	2,500
Maximum \| VIBATIV \| Astellas
Information related to commitment and contingencies
Amount of purchase agreements for pharmaceutical ingredient and raw materials	7,700
Amount of finished goods inventories	$ 4,200
Operating Leases
Operating Leases
Number of lease terms \| ft²	2
Additional lease period	5 years
Area of buildings in South San Francisco, California (in square feet) \| ft²	130,000
Number of buildings \| ft²	2
Future minimum lease payments
2013	$ 5,029
2014	4,859
2015	5,005
2016	5,155
2017	5,310
Thereafter	13,497
Total	38,855
Information related to commitment and contingencies
Rent expense	5,720	$ 6,702	$ 6,779
Sublease income, net	$ (160)	$ (637)	$ (622)

Commitments and Contingencies (Details 2) - Special Long-Term Retention and Incentive Equity Awards Program - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2011	Dec. 31, 2012
Special Long-Term Retention and Incnetive Equity Awards Program
Timeframe for achievement of performance conditions	6 years
Stock-based compensation
Special Long-Term Retention and Incnetive Equity Awards Program
Compensation expenses to be recognized if sufficient performance conditions are achieved		$ 31.9
Compensation expenses related to cash bonus to be recognized in next fiscal year if sufficient performance conditions are achieved		15.6
Cash bonus expense
Special Long-Term Retention and Incnetive Equity Awards Program
Compensation expenses to be recognized if sufficient performance conditions are achieved		38.2
Compensation expenses related to cash bonus to be recognized in next fiscal year if sufficient performance conditions are achieved		$ 18.7

Subsequent Events (Details) - Subsequent events	Feb. 15, 2013 USD ($) $ / shares shares	Jan. 24, 2013 USD ($) shares $ / shares
Maximum
Subsequent event
Net shares settlement payable to the entity \| shares		2,779,659
Minimum
Subsequent event
Net shares settlement payable to the entity \| shares		0
Common stock \| Future Sale of Stock \| GSK
Subsequent event
Stock price (in dollars per share) \| $ / shares	$ 22.03
Agreement to issue stock, number of shares \| shares	116,527
Agreement to issue stock in private placement, aggregate purchase price	$ 2,600,000
Privately-negotiated capped call option
Subsequent event
Aggregate cost of the capped call options		$ 36,800,000
Stock prices below $27.79 per share \| Common stock
Subsequent event
Strike price for the underlying number of shares (in dollars per share) \| $ / shares		27.79
Cap price for the underlying number of shares (in dollars per share) \| $ / shares		38.00
Stock prices above $38.00 per share \| Common stock
Subsequent event
Strike price for the underlying number of shares (in dollars per share) \| $ / shares		38.00
2.125% convertible subordinated notes
Subsequent event
Loan amount		$ 287,500,000
Interest rate (as a percent)		2.125%
Full exercise of the underwriters' over-allotment option principal amount		$ 37,500,000
Proceeds from issuance of debt, net of issuance costs		$ 244,400,000
2.125% convertible subordinated notes \| Common stock
Subsequent event
Conversion rate, number of shares to be issued per $1000 of principal amount of notes \| shares		35.9903
Principal amount used for debt instrument conversion ratio		$ 1,000
Initial conversion price of convertible notes into common stock (in dollars per share) \| $ / shares		$ 27.79