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Document and Entity Information - shares	6 Months Ended
Document and Entity Information - shares	Jun. 30, 2012	Jul. 31, 2012
Document and Entity Information [Abstract]
Entity Registrant Name	BIOCRYST PHARMACEUTICALS INC
Entity Central Index Key	0000882796
Document Type	10-Q
Document Period End Date	Jun. 30, 2012
Amendment Flag	false
Document Fiscal Year Focus	2012
Document Fiscal Period Focus	Q2
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		50,493,786

Consolidated Balance Sheets - USD ($)	Jun. 30, 2012	Dec. 31, 2011
Assets
Cash and cash equivalents	$ 21,924,000	$ 16,444,000
Restricted cash	2,230,000	625,000
Investments	12,958,000	25,274,000
Receivables from collaborations	5,084,000	5,831,000
Interest reserve	1,742,000	1,742,000
Inventories	263,000	263,000
Prepaid expenses and other current assets	344,000	378,000
Deferred collaboration expense	519,000	2,301,000
Total current assets	45,064,000	52,858,000
Investments	16,351,000	15,382,000
Furniture and equipment, net	882,000	1,098,000
Deferred collaboration expense	5,235,000	5,437,000
Other assets	8,704,000	7,433,000
Total assets	76,236,000	82,208,000
Liabilities and Stockholders' Equity
Accounts payable	3,328,000	2,497,000
Accrued expenses	8,206,000	12,616,000
Interest payable	3,500,000	1,400,000
Deferred collaboration revenue	4,072,000	9,786,000
Total current liabilities	19,106,000	26,299,000
Deferred collaboration revenue	6,512,000	7,103,000
Foreign currency derivative	4,959,000	4,000,000
Non-recourse notes payable	30,000,000	30,000,000
Commitments and contingencies
Stockholders' equity:
Preferred stock, $0.001 par value; shares authorized - 5,000; no shares issued and outstanding
Common stock, $.01 par value: shares authorized 95,000; shares issued and outstanding 50,129 in 2012 and 45,662 in 2011	501,000	457,000
Additional paid-in capital	386,966,000	367,829,000
Accumulated other comprehensive income	40,000	40,000
Accumulated deficit	(371,848,000)	(353,520,000)
Total stockholders' equity	15,659,000	14,806,000
Total liabilities and stockholders' equity	$ 76,236,000	$ 82,208,000

Consolidated Balance Sheets (Parenthetical) - $ / shares shares in Thousands	Jun. 30, 2012	Dec. 31, 2011
Consolidated Balance Sheets [Abstract]
Preferred stock, par value	$ 0.001	$ 0.001
Preferred stock, shares authorized	5,000	5,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value	$ 0.01	$ 0.01
Common stock, shares authorized	95,000	95,000
Common stock, shares issued	50,129	45,662
Common stock, shares outstanding	50,129	45,662

Consolidated Statements of Comprehensive Loss (Unaudited) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Revenues
Collaborative and other research and development	$ 4,210	$ 3,735	$ 16,431	$ 9,170
Total revenues	4,210	3,735	16,431	9,170
Expenses
Research and development	12,777	14,442	28,302	27,941
General and administrative	1,609	3,536	3,306	6,971
Total expenses	14,386	17,978	31,608	34,912
Loss from operations	(10,176)	(14,243)	(15,177)	(25,742)
Interest and other income	57	136	128	239
Interest expense	(1,160)	(1,166)	(2,320)	(1,455)
Loss on foreign currency derivative	(997)	(998)	(959)	(2,340)
Net loss	$ (12,276)	$ (16,271)	$ (18,328)	$ (29,298)
Basic and diluted net loss per common share	$ (0.25)	$ (0.36)	$ (0.38)	$ (0.65)
Weighted average shares outstanding	49,218	45,111	48,161	45,063
Unrealized gain (loss) on investments	$ (9)	$ 9		$ (14)
Comprehensive loss	$ (12,285)	$ (16,262)	$ (18,328)	$ (29,312)

Consolidated Statements of Cash Flows (Unaudited) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011
Operating activities
Net loss	$ (18,328)	$ (29,298)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	325	445
Stock-based compensation expense	2,178	2,728
Amortization of debt issuance costs	220	137
Change in fair value of foreign currency derivative	959	2,340
Changes in operating assets and liabilities:
Receivables from collaborations	747	14,266
Prepaid expenses and other current assets	105	745
Deferred collaboration expense	1,984	977
Accounts payable and accrued expenses	(2,575)	(8,031)
Interest payable	2,100	1,318
Interest reserve		(3,000)
Deferred collaboration revenue	(6,305)	(425)
Net cash used in operating activities	(18,590)	(17,798)
Investing activities
Acquisitions of furniture and equipment	(109)	(53)
Change in restricted cash	(1,605)	(791)
Purchases of investments	(14,534)	(27,676)
Sales and maturities of investments	25,811	26,189
Net cash provided by (used in) investing activities	9,563	(2,331)
Financing activities
Exercise of stock options	510	238
Employee stock purchase plan sales	148	170
Purchases of treasury stock		(61)
Sale of common stock,net	15,339	(73)
Issuance of non-recourse notes payable		25,691
Payment of foreign currency derivative collateral	(1,490)	(2,450)
Net cash provided by financing activities	14,507	23,515
Increase in cash and cash equivalents	5,480	3,386
Cash and cash equivalents at beginning of period	16,444	13,622
Cash and cash equivalents at end of period	$ 21,924	$ 17,008

Significant Accounting Policies

6 Months Ended

Jun. 30, 2012

Significant Accounting Policies [Abstract]

Significant Accounting Policies

Note 1 — Significant Accounting Policies

The Company

BioCryst Pharmaceuticals, Inc. (the “Company”) is a biotechnology company that designs, optimizes and develops novel drugs that block key enzymes involved in the pathogenesis of disease related to therapeutic areas with unmet medical needs aligned with its capabilities and expertise. The Company was incorporated in Delaware in 1986 and its headquarters is located in Durham, North Carolina. Areas of interest for the Company are determined primarily by the scientific discoveries and the potential advantages that its experienced drug discovery group identifies, as well as by the associated potential commercial opportunity of those discoveries. The Company integrates the disciplines of biology, crystallography, medicinal chemistry and computer modeling to discover and develop small molecule pharmaceuticals through the process known as structure-guided drug design.

Basis of Presentation

Beginning in March 2011, the consolidated financial statements include the accounts of the Company and its wholly-owned subsidiary, JPR Royalty Sub LLC (“Royalty Sub”). Royalty Sub was formed in connection with a $30,000 financing transaction the Company completed on March 9, 2011. See Note 4, Royalty Monetization, for a further description of this transaction. All intercompany transactions and balances have been eliminated.

The Company’s financial statements became consolidated beginning in March 2011 with the creation of Royalty Sub, and have been prepared in accordance with accounting principles generally accepted in the United States (“U.S. GAAP”) for interim financial reporting and the instructions to Form 10-Q and do not include all of the information and footnotes required by U.S. GAAP for complete financial statements. Such financial statements reflect all adjustments that are, in management’s opinion, necessary to present fairly, in all material respects, the Company’s financial position, results of operations, and cash flows. There were no adjustments other than normal recurring adjustments.

These financial statements should be read in conjunction with the financial statements for the year ended December 31, 2011 and the notes thereto included in the Company’s 2011 Annual Report on Form 10-K. Interim operating results are not necessarily indicative of operating results for the full year. The balance sheet as of December 31, 2011 has been derived from the audited consolidated financial statements included in the Company’s most recent Annual Report on Form 10-K.

Reclassifications

In the fourth quarter of 2011, the Company changed its classification of patent costs. This change resulted in $387 and $858 of patent expenses reclassified from general and administrative expense to research and development expense for the three months and six months ended June 30, 2011, respectively. Additionally, during the second quarter of 2012, the Company changed its classification of facilities costs and other costs directly related to its laboratory facility in Birmingham, Alabama from general and administrative expense to research and development expense. This change resulted in $80 and $176 of expenses being reclassified from general and administrative expense to research and development expense for the three months and six months ended June 30, 2011, respectively. These reclassifications had no effect on previously reported operating expenses or net loss amounts. Certain other balance sheet amounts as of December 31, 2011 have been reclassified to conform to the 2012 presentation.

Cash and Cash Equivalents

The Company generally considers cash equivalents to be all cash held in commercial checking accounts, money market accounts or investments in debt instruments with maturities of three months or less at the time of purchase. The carrying value of cash and cash equivalents approximates fair value due to the short-term nature of these items.

Restricted Cash

Restricted cash as of June 30, 2012 includes $300 ($625 as of December 31, 2011) the Company is required to maintain in an interest bearing money market account to serve as collateral for a corporate credit card program and $1,930 in royalty receipts paid by Shionogi & Co., Ltd. (“Shionogi”) designated for interest on the PhaRMA Notes (defined in Note 4).

Investments

The Company invests in high credit quality investments in accordance with its investment policy, which is designed to minimize the possibility of loss. The objective of the Company’s investment policy is to ensure the safety and preservation of invested funds, as well as maintaining liquidity sufficient to meet cash flow requirements. The Company places its excess cash with high credit quality financial institutions, commercial companies, and government agencies in order to limit the amount of its credit exposure. Per its policy, the Company is able to invest in marketable debt securities that may consist of U.S. government and government agency securities, money market and mutual fund investments, municipal and corporate notes and bonds, commercial paper and asset or mortgage-backed securities, among others. The Company’s investment policy requires it to purchase high-quality marketable securities with a maximum individual maturity of three years and requires an average portfolio maturity of no more than two years. Some of the securities the Company invests in may have market risk. This means that a change in prevailing interest rates may cause the principal amount of the investment to fluctuate. To minimize this risk, the Company schedules its investments with maturities that coincide with expected cash flow needs, thus avoiding the need to redeem an investment prior to its maturity date. Accordingly, the Company does not believe it has a material exposure to interest rate risk arising from its investments. Generally, the Company’s investments are not collateralized. The Company has not realized any significant losses from its investments.

The Company classifies all of its investments as available-for-sale. Unrealized gains and losses on investments are recognized in comprehensive income/(loss), unless an unrealized loss is considered to be other than temporary, in which case the unrealized loss is charged to operations. The Company periodically reviews its investments for other than temporary declines in fair value below cost basis and whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable. The Company believes the individual unrealized losses represent temporary declines primarily resulting from interest rate changes. Realized gains and losses are reflected in interest and other income in the Consolidated Statements of Comprehensive Loss and are determined using the specific identification method with transactions recorded on a settlement date basis. Investments with original maturities at date of purchase beyond three months and which mature at or less than 12 months from the balance sheet date are classified as current. Investments with a maturity beyond 12 months from the balance sheet date are classified as long-term. At June 30, 2012, the Company believes that the costs of its investments are recoverable in all material respects.

The following tables summarize the fair value of the Company’s investments by type. The estimated fair value of the Company’s fixed income investments are classified as Level 2 in the fair value hierarchy as defined in U.S. GAAP. These valuations are based on observable direct and indirect inputs, primarily quoted prices of similar, but not identical, instruments in active markets or quoted prices for identical or similar instruments in markets that are not active. These fair values are obtained from independent pricing services which utilize Level 2 inputs.


	June 30, 2012
					Gross		Gross
	Amortized		Accrued		Unrealized		Unrealized			Estimated
	Cost		Interest		Gains		Losses			Fair Value
U.S. Treasury securities	$	1,999	$	2	$	7	$	—		$	2,008
Obligations of U.S. government and its agencies		10,213		12		—		(3	)		10,222
Corporate debt securities		6,872		34		15		—			6,921
Commercial paper		1,399		—		—		—			1,399
Certificate of deposit		800		—		—		—			800
Municipal obligations		7,895		43		21		—			7,959

Total investments	$	29,178	$	91	$	43	$	(3	)	$	29,309


	December 31, 2011
					Gross		Gross
	Amortized		Accrued		Unrealized		Unrealized			Estimated
	Cost		Interest		Gains		Losses			Fair Value
U.S. Treasury securities	$	1,998	$	2	$	14	$	—		$	2,014
Obligations of U.S. government and its agencies		5,000		10		—		—			5,010
Corporate debt securities		10,924		80		15		(9	)		11,010
Commercial paper		10,939		—		2		(1	)		10,940
Asset-backed securities		611		—		—		—			611
Certificate of deposit		801		1		—		—			802
Municipal obligations		10,182		68		21		(2	)		10,269

Total investments	$	40,455	$	161	$	52	$	(12	)	$	40,656

The following table summarizes the scheduled maturity for the Company’s investments at June 30, 2012.


Maturing in one year or less	$	12,958
Maturing after one year through two years		16,351

Total investments	$	29,309

Receivables from Collaborations

Receivables are recorded for amounts due to the Company, primarily related to reimbursable research and development costs. These receivables are evaluated to determine if any reserve or allowance should be established at each reporting date. At June 30, 2012, the Company had the following receivables from collaborations.


	Billed		Unbilled		Total
U.S. Department of Health and Human Services	$	681	$	4,403	$	5,084

Total receivables from collaborations	$	681	$	4,403	$	5,084

Monthly invoices are submitted to the U.S. Department of Health and Human Services Biomedical Advanced Research and Development Authority (“BARDA/HHS”) related to reimbursable research and development costs. The Company is also entitled to monthly reimbursement of indirect costs based on rates stipulated in the underlying contract. The Company’s calculations of its indirect cost rates are subject to audit by the federal government.

Inventory

At June 30, 2012 and December 31, 2011, the Company’s inventory consisted of peramivir finished goods inventory and supplies for the manufacture of peramivir. Inventory is stated at the lower of cost, determined under the first-in, first-out (“FIFO”) method, or market. The Company expenses costs related to the production of inventories as research and development expenses in the period incurred until such time it is believed that future economic benefit is expected to be recognized, which generally is reliant upon receipt of regulatory approval. Upon regulatory approval, the Company capitalizes subsequent costs related to the production of inventories.

During 2011, based on the annual variability of influenza, which impacts potential clinical and commercial demand and timing for peramivir administration as well as the costs to store and maintain supplies, the Company decided for economic reasons to reduce its supplies inventory, resulting in a $635 charge in 2011. Upon disposal of this inventory in early January 2012, the supplies inventory and related reserve were reduced by $635.

The Company’s inventory consisted of the following as of June 30, 2012 and December 31, 2011:


	2012			2011
Supplies	$	263		$	898
Finished goods		3,980			3,980
Reserve for finished goods		(3,980	)		(4,615	)

Net inventories	$	263		$	263

Patents and Licenses

The Company seeks patent protection on all internally developed processes and products. All patent related costs are expensed to research and development expenses when incurred as recoverability of such expenditures is uncertain.

Accrued Expenses

The Company generally enters into contractual agreements with third-party vendors who provide research and development, manufacturing, and other services in the ordinary course of business. Some of these contracts are subject to milestone-based invoicing and services are completed over an extended period of time. The Company records liabilities under these contractual commitments when it determines an obligation has been incurred, regardless of the timing of the invoice. This process involves reviewing open contracts and purchase orders, communicating with applicable Company personnel to identify services that have been performed on its behalf and estimating the level of service performed and the associated cost incurred for the service when the Company not yet been invoiced or otherwise notified of actual cost. The majority of service providers invoice the Company monthly in arrears for services performed. The Company makes estimates of accrued expenses as of each balance sheet date in its financial statements based on the facts and circumstances. The Company periodically confirms the accuracy of its estimates with the service providers and makes adjustments if necessary. Examples of estimated accrued expenses include:

•

fees paid to Clinical Research Organization (“CROs”) in connection with preclinical and toxicology studies and clinical trials;

•

fees paid to investigative sites in connection with clinical trials;

•

fees paid to contract manufacturers in connection with the production of our raw materials, drug substance and drug products; and

•

professional fees.

The Company bases its expenses related to clinical trials on its estimates of the services received and efforts expended pursuant to contracts with multiple research institutions and CROs that conduct and manage clinical trials on the Company’s behalf. The financial terms of these agreements are subject to negotiation, vary from contract to contract and may result in uneven payment flows. Payments under some of these contracts depend on factors such as the successful enrollment of patients and the completion of clinical trial milestones. In accruing service fees, the Company estimates the time period over which services will be performed and the level of effort to be expended in each period. If the actual timing of the performance of services or the level of effort varies from the estimate, the Company will adjust the accrual accordingly. Accrued expenses as of June 30, 2012 and December 31, 2011 included $5,459 and $8,622, respectively, of research and development costs.

Income Taxes

The liability method is used in the Company’s accounting for income taxes. Under this method, deferred tax assets and liabilities are determined based on differences between financial reporting and tax bases of assets and liabilities and are measured using the enacted tax rates and laws that will be in effect when the differences are expected to reverse.

Accumulated Other Comprehensive (Loss) Income

Accumulated other comprehensive (loss) income is comprised of unrealized gains and losses on investments available-for-sale and is disclosed as a separate component of stockholders’ equity.

Revenue Recognition

The Company recognizes revenues from collaborative and other research and development arrangements and product sales.

Collaborative and Other Research and Development Arrangements and Royalties

Revenue from license fees, royalty payments, event payments, and research and development fees are recognized as revenue when the earnings process is complete and the Company has no further continuing performance obligations or the Company has completed the performance obligations under the terms of the agreement. Fees received under licensing agreements that are related to future performance are deferred and recognized over an estimated period determined by management based on the terms of the agreement and the products licensed. In the event a license agreement contains multiple deliverables, the Company evaluates whether the deliverables are separate or combined units of accounting. Revisions to revenue or profit estimates as a result of changes in the estimated revenue period are recognized prospectively.

Under certain of our license agreements, the Company receives royalty payments based upon our licensees’ net sales of covered products. Generally, under these agreements, the Company receives royalty reports from our licensees approximately one quarter in arrears, that is, generally in the second month of the quarter after the licensee has sold the royalty-bearing product. The Company recognizes royalty revenues when it can reliably estimate such amounts and collectability is reasonably assured.

Royalty revenue paid by Shionogi on their product sales is subject to returns. RAPIACTA^® is a newly introduced product and there is not sufficient historical experience that can be used to reasonably estimate product returns. Therefore, the Company defers recognition of RAPIACTA^® royalty revenue from Shionogi until the earlier of (1) a right of return no longer exists or (2) the Company has developed sufficient historical experience to estimate product returns. RAPIACTA^® royalty payments received from Shionogi sales in 2011 were $1,216 and during the six months ended June 30, 2012 were $1,666.

Reimbursements received for direct out-of-pocket expenses related to research and development costs are recorded as revenue in the Consolidated Statements of Comprehensive Loss rather than as a reduction in expenses. Event payments are recognized as revenue upon the achievement of specified events if (1) the event is substantive in nature and the achievement of the event was not reasonably assured at the inception of the agreement and (2) the fees are non-refundable and non-creditable. Any event payments received prior to satisfying these criteria are recorded as deferred revenue. Under the Company’s contract with BARDA/HHS, revenue is recognized as reimbursable direct and indirect costs are incurred.

Product Sales

Sales are recognized when there is persuasive evidence that an arrangement exists, title has passed, the price was fixed and determinable, and collectability is reasonably assured. Product sales are recognized net of estimated allowances, discounts, sales returns, chargebacks and rebates.

The Company recorded the following revenues for the three and six months ended June 30, 2012 and 2011:


	Three Months				Six Months
	2012		2011		2012		2011
Collaborative and other research and development revenues:
U.S. Department of Health and Human Services	$	3,914	$	3,111	$	8,073	$	7,772
Shionogi (Japan)		296		296		592		592
Mundipharma (United Kingdom)		—		328		7,766		720
Grants (United States)		—		—		—		86

Total revenues	$	4,210	$	3,735	$	16,431	$	9,170

Research and Development Expenses

The Company’s research and development costs are charged to expense when incurred. Research and development expenses include all direct and indirect development costs related to the development of the Company’s portfolio of drug candidates. Advance payments for goods or services that will be used or rendered for future research and development activities are deferred and capitalized. Such amounts are recognized as expense when the related goods are delivered or the related services are performed. Research and development expenses include, among other items, personnel costs, including salaries and benefits, manufacturing costs, clinical, regulatory, and toxicology services performed by CROs, materials and supplies, and overhead allocations consisting of various administrative and facilities related costs. Most of the Company’s manufacturing and clinical and preclinical studies are performed by third-party CROs. Costs for studies performed by CROs are accrued by the Company over the service periods specified in the contracts and estimates are adjusted, if required, based upon the Company’s on-going review of the level of services actually performed.

Additionally, the Company has license agreements with third parties, such as Albert Einstein College of Medicine of Yeshiva University (“AECOM”), Industrial Research, Ltd. (“IRL”), and the University of Alabama at Birmingham (“UAB”), which require fees related to sublicense agreements or maintenance fees. The Company expenses sublicense payments as incurred unless they are related to revenues that have been deferred, in which case the expenses are deferred and recognized over the related revenue recognition period. The Company expenses maintenance payments as incurred.

Deferred collaboration expenses represent sub-license payments, paid to the Company’s academic partners upon receipt of consideration from various commercial partners, and other consideration paid to our academic partners for modification to existing license agreements. These deferred expenses would not have been incurred without receipt of such payments or modifications from the Company’s commercial partners and are being expensed in proportion to the related revenue being recognized. The Company believes that this accounting treatment appropriately matches expenses with the associated revenue.

Stock-Based Compensation

All share-based payments, including grants of stock option awards and restricted stock awards, are recognized in the Company’s Consolidated Statement of Comprehensive Loss based on their fair values. The fair value of stock option awards is estimated using the Black-Scholes option pricing model. The fair value of restricted stock awards is based on the grant date closing price of the common stock. Stock-based compensation cost is recognized as expense on a straight-line basis over the requisite service period of the award.

Interest Expense and Deferred Financing Costs

Interest expense for the three months ended June 30, 2012 and 2011 was $1,160 and $1,166, respectively, and $2,320 and $1,455 for the six months ended June 30, 2012 and 2011, respectively, and relates to the issuance of the PhaRMA Notes (defined in Note 4). Costs directly associated with the issuance of the PhaRMA Notes have been capitalized and are included in other non-current assets on the consolidated balance sheet. These costs are being amortized to interest expense over the term of the PhaRMA Notes using the effective interest rate method. Amortization of deferred financing costs included in interest expense was $110 and $105 for the three months ended June 30, 2012 and 2011, respectively, and $220 and $136 for the six months ended June 30, 2012 and 2011, respectively.

Currency Hedge Agreement

In connection with the issuance by Royalty Sub of the PhaRMA Notes, the Company entered into a Currency Hedge Agreement (defined in Note 4) to hedge certain risks associated with changes in the value of the Japanese yen relative to the U.S. dollar. The Currency Hedge Agreement does not qualify for hedge accounting treatment; therefore, mark-to-market adjustments are recognized in the Company’s Consolidated Statement of Comprehensive Loss. Cumulative mark-to-market adjustments resulted in a loss of $997 and $998 for the three months ended June 30, 2012 and 2011, respectively, and a loss of $959 and $2,340 for the six months ended June 30, 2012 and 2011, respectively. Mark-to-market adjustments are determined by a third party pricing model which uses quoted prices in markets that are not actively traded and for which significant inputs are observable directly or indirectly, representing Level 2 in the fair value hierarchy as defined by U.S. GAAP. The Company is also required to post collateral in connection with the mark-to-market adjustments based on thresholds defined in the Currency Hedge Agreement. As of June 30, 2012, $4,970 of hedge collateral was posted under the agreement and is recorded in other assets.

Net Loss Per Share

Net loss per share is based upon the weighted average number of common shares outstanding during the period. Diluted loss per share is equivalent to basic net loss per share for all periods presented herein because common equivalent shares from unexercised stock options, outstanding warrants, and common shares expected to be issued under the Company’s employee stock purchase plan were anti-dilutive. The calculation of diluted earnings per share for the six months ended June 30, 2012 and 2011 does not include 9,172 and 8,128, respectively, of such potential common shares, as their impact would be anti-dilutive.

Use of Estimates

The preparation of financial statements in conformity with U.S. GAAP requires the Company to make estimates and assumptions that affect the amounts reported in the financial statements. Actual results could differ from those estimates.

Concentration of Market Risk

The Company’s primary source of revenue is reimbursement of peramivir development expenses, which was earned under the cost-plus-fixed-fee contract with BARDA/HHS. The Company relies on BARDA/HHS to reimburse predominantly all of the development costs for its peramivir program. Accordingly, reimbursement of these expenses represents a significant portion of the Company’s collaborative and other research and development revenues. The completion or termination of this program/collaboration could negatively impact the Company’s future Consolidated Statements of Comprehensive Loss and Cash Flows. The Company’s drug development activities are performed by a limited group of third party vendors. If any of these vendors were unable to perform their services, this could significantly impact the Company’s ability to complete its drug development activities.

Credit Risk

Cash equivalents and investments are financial instruments which potentially subject the Company to concentration of risk to the extent recorded on the Consolidated Balance Sheet. The Company deposits excess cash with major financial institutions in the United States. Balances may exceed the amount of insurance provided on such deposits. The Company believes it has established guidelines for investment of its excess cash relative to diversification and maturities that maintain safety and liquidity. To minimize the exposure due to adverse shifts in interest rates, the Company maintains a portfolio of investments with an average maturity of approximately 24 months or less.

Recent Accounting Pronouncements

In May 2011, the Financial Accounting Standards Board (the “FASB”) issued Accounting Standards Update (“ASU”) 2011-04, “Fair Value Measurement (Topic 820): Amendments to Achieve Common Fair Value Measurements and Disclosure Requirement in U.S. GAAP and IFRS.” This ASU modifies the existing standards to include disclosure of all transfers between Level 1 and Level 2 asset and liability fair value categories. In addition, the ASU provides guidance on measuring the fair value of financial instruments managed within a portfolio and the application of premiums and discounts on fair value measurements. The ASU requires additional disclosure for Level 3 measurements regarding the sensitivity of fair value to changes in unobservable inputs and any interrelationships between those inputs. The Company adopted this guidance effective January 2012. The adoption of this ASU did not have a material impact on the Company’s consolidated financial statements.

In June 2011, the FASB issued ASU 2011-05, “Comprehensive Income (Topic 220): Presentation of Comprehensive Income.” This ASU eliminates the current option to report other comprehensive income and its components in the statement of changes in equity. Under this new ASU, an entity can elect to present items of net income, other comprehensive income and total comprehensive income in one continuous statement or in two separate, but consecutive statements. The Company adopted this guidance effective January 1, 2012.

In December 2011, the FASB issued ASU 2011-12, “Comprehensive Income (Topic 220): Deferral of the Effective Date for Amendments to the Presentation of Reclassifications of Items Out of Accumulated Other Comprehensive Income in Accounting Standards Update No. 2011-05.” This ASU defers the requirement in ASU 2011-05 to present reclassification adjustments for each component of accumulated other comprehensive income in both net income and other comprehensive income on the face of the financial statements. This ASU does not affect the requirement to present items of net income, other comprehensive income and total comprehensive income in one continuous statement or in two separate, but consecutive statements.

Stock-Based Compensation

6 Months Ended

Jun. 30, 2012

Stock-Based Compensation [Abstract]

Stock-Based Compensation

Note 2 — Stock-Based Compensation

As of June 30, 2012, the Company had two stock-based employee compensation plans, the Stock Incentive Plan (“Incentive Plan”), which was amended and restated in March 2012 and approved by the Company’s stockholders in May 2012, and the Employee Stock Purchase Plan (“ESPP”), which was amended and restated in March 2012 and approved by the Company’s stockholders in May 2012. In addition, during 2007, the Company made an inducement grant outside of the Incentive Plan and ESPP to recruit a new employee to a key position within the Company. Stock-based compensation expense of $2,178 ($2,108 of expense related to the Incentive Plan and $70 of expense related to the ESPP) was recognized during the first six months of 2012, while $2,728 ($2,603 of expense related to the Incentive Plan, $88 of expense related to the ESPP, and $37 of expense related to the inducement grant) was recognized during the first six months of 2011.

There was approximately $9,912 of total unrecognized compensation cost related to non-vested stock option awards and restricted stock awards granted by the Company as of June 30, 2012. That cost is expected to be recognized as follows: $2,041 during the remainder of 2012, $3,709 in 2013, $2,538 in 2014, $1,428 in 2015, and $196 in 2016.

Stock Incentive Plan

The Company grants stock option awards and restricted stock awards to its employees, directors, and consultants under the Incentive Plan. Under the Incentive Plan, stock option awards are granted with an exercise price equal to the closing market price of the Company’s stock at the date of grant. Prior to March 1, 2011, stock option awards granted to employees generally vest 25% after one year and monthly thereafter on a pro rata basis over the next three years until fully vested after four years. Commencing March 1, 2011, stock option awards granted to employees generally vest 25% each year until fully vested after four years. Stock option awards granted to non-employee directors of the Company generally vest monthly over one year. All stock option awards have contractual terms of 10 years. The vesting exercise provisions of all awards granted under the Incentive Plan are subject to acceleration in the event of certain stockholder-approved transactions, or upon the occurrence of a change in control as defined in the Incentive Plan.

Related activity under the Incentive Plan is as follows:


	Awards Available			Options Outstanding			Weighted Average Exercise Price
Balance December 31, 2011		2,010			7,858		$	6.21
Plan amendment		1,700			—			—
Restricted stock awards granted		(415	)		—			—
Restricted stock awards cancelled		13			—			—
Stock option awards granted		(1,563	)		1,563			4.66
Stock option awards exercised		—			(303	)		1.66
Stock option awards cancelled		419			(419	)		8.32

Balance June 30, 2012		2,164			8,699		$	5.99

For stock option awards granted under the Incentive Plan during the first six months of 2012 and 2011, the fair value was estimated on the date of grant using a Black-Scholes option pricing model and the assumptions noted in the table below. The weighted average grant date fair value per share of the awards granted during the first six months of 2012 and 2011 was $3.04 and $2.75, respectively. The fair value of the stock option awards is amortized to expense over the vesting periods using a straight-line expense attribution method. The following table summarizes the key assumptions used by the Company to value the stock option awards granted during the first six months of 2012 and 2011. The expected life is based on the average of the assumption that all outstanding stock option awards will be exercised at full vesting and the assumption that all outstanding stock option awards will be exercised at the midpoint of the current date (if already vested) or at full vesting (if not yet vested) and the full contractual term. The expected volatility represents the historical volatility on the Company’s publicly traded common stock. The Company has assumed no expected dividend yield, as dividends have never been paid to stock or option holders and will not be paid for the foreseeable future. The weighted average risk-free interest rate is the implied yield currently available on zero-coupon government issues with a remaining term equal to the expected term.

Weighted Average Assumptions for Stock Option Awards Granted to

Employees and Directors under the Incentive Plan


	2012			2011
Expected Life in Years		5.5			5.5
Expected Volatility		87	%		80	%
Expected Dividend Yield		0.0	%		0.0	%
Risk-Free Interest Rate		0.88	%		2.20	%

Employee Stock Purchase Plan

The Company has reserved a total of 975 shares of common stock to be purchased under the ESPP, of which 234 shares remain available for purchase at June 30, 2012. Eligible employees may authorize up to 15% of their salary to purchase common stock at the lower of 85% of the beginning or 85% of the ending price during six-month purchase intervals. No more than 3 shares may be purchased by any one employee at the six-month purchase dates and no employee may purchase stock having a fair market value at the commencement date of $25 or more in any one calendar year. The Company issued 52 shares during the first six months of 2012 under the ESPP. Compensation expense for shares purchased under the ESPP related to the purchase discount and the “look-back” option were determined using a Black-Scholes option pricing model.

- 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
-Topic 505
-SubTopic 50
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6406099&loc=d3e25284-112666

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 40
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6418621&loc=d3e17540-113929

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5070-113901

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5047-113901

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-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

Collaborative and Other Research and Development Contracts

6 Months Ended

Jun. 30, 2012

Collaborative and Other Research and Development Contracts [Abstract]

Collaborative and Other Research and Development Contracts

Note 3 — Collaborative and Other Research and Development Contracts

U.S. Department of Health and Human Services (“BARDA/HHS”). In January 2007, BARDA/HHS awarded the Company a $102,661, four-year contract for the advanced development of peramivir for the treatment of influenza. During 2009, peramivir clinical development shifted to focus on intravenous delivery and the treatment of hospitalized patients. To support this focus, a September 2009 contract modification was awarded to extend the intravenous (“i.v.”) peramivir program by 12 months and to increase funding by $77,191. On February 24, 2011, the Company announced that BARDA/HHS had awarded it a $55,000 contract modification, intended to fund completion of the Phase 3 development of i.v. peramivir for the treatment of patients hospitalized with influenza. This contract modification brings the total award from BARDA/HHS to $234,852 and extends the contract term by 24 months through December 31, 2013, providing funding through completion of Phase 3 and to support the filing of a new drug application (“NDA”) to seek regulatory approval for i.v. peramivir in the U.S.

The contract with BARDA/HHS is a cost-plus-fixed-fee contract. That is, the Company is entitled to receive reimbursement for all costs incurred in accordance with the contract provisions that are related to the development of peramivir plus a fixed fee, or profit. BARDA/HHS will make periodic assessments of progress and the continuation of the contract is based on the Company’s performance, the timeliness and quality of deliverables, and other factors. The contract is terminable by BARDA/HHS at any time for breach or without cause.

Shionogi & Co., Ltd. (“Shionogi”). In March 2007, the Company entered into an exclusive license agreement with Shionogi to develop and commercialize peramivir in Japan for the treatment of seasonal and potentially life-threatening human influenza (the “Shionogi Agreement”). Under the terms of the Shionogi Agreement, Shionogi obtained rights to injectable formulations of peramivir in Japan. The Company developed peramivir under a license from UAB and will owe sublicense payments to UAB on any future milestone payments and/or royalties received by the Company from Shionogi. In October 2008, the Company and Shionogi amended the license agreement to expand the territory covered by the agreement to include Taiwan and to provide rights for Shionogi to perform a Phase 3 clinical trial in Hong Kong. Shionogi has commercially launched peramivir under the commercial name RAPIACTA^® in Japan.

Green Cross Corporation (“Green Cross”). In June 2006, the Company entered into an agreement with Green Cross to develop and commercialize peramivir in Korea. Under the terms of the agreement, Green Cross will be responsible for all development, regulatory, and commercialization costs in Korea. The Company received a one-time license fee of $250. The license also provides that the Company will share in profits resulting from the sale of peramivir in Korea, including the sale of peramivir to the Korean government for stockpiling purposes. Furthermore, Green Cross will pay the Company a premium over its cost to supply peramivir for development and any future marketing of peramivir products in Korea.

Mundipharma International Holdings Limited (“Mundipharma”). In February 2006, the Company entered into an exclusive, royalty bearing right and license agreement with Mundipharma for the development and commercialization of forodesine, a Purine Nucleoside Phosphorylase (“PNP”) inhibitor, for use in oncology (the “Original Agreement”). Under the terms of the Original Agreement, Mundipharma obtained rights to forodesine in markets across Europe, Asia, and Australasia in exchange for a $10,000 up-front payment.

The Company deferred revenue recognition of the $10,000 up-front payment that was received from Mundipharma in February 2006 because the Company was involved in the continued development of forodesine. Amortization of this revenue commenced in February 2006 and was initially scheduled to end in October 2017, which is the date of expiration for the last-to-expire patent covered by the agreement. The Company also deferred revenue recognition of a $5,000 payment received from Mundipharma in connection with the initiation of a clinical trial in 2007. Amortization of this deferred revenue commenced in 2007 and was initially scheduled to end in October 2017. Under its agreement with AECOM/IRL, the Company paid sublicense payments related to these upfront cash payments received from Mundipharma. Expense recognition of these sublicense payments was deferred and recognized under the same term as the related deferred revenue.

On November 11, 2011, the Company entered into the Amended and Restated License and Development Agreement (the “Amended and Restated Agreement”) with Mundipharma, amending and restating the Original Agreement. Under the terms of the Amended and Restated Agreement, Mundipharma obtained worldwide rights to forodesine. Commencing on November 11, 2011, Mundipharma controls the development and commercialization of forodesine and assumes all future development and commercialization costs. Since the Company is no longer associated with the development of forodesine, amortization of the deferred revenue and expense associated with the Original Agreement ceased immediately. Mundipharma also purchased from the Company certain drug substance for forodesine at a cost of approximately $901. The Amended and Restated Agreement provides for the possibility of future event payments totaling $15,000 for achieving specified regulatory events for certain indications and tiered royalties ranging from mid to high single-digit percentages of net product sales in each country where forodesine is sold by Mundipharma. These royalties are subject to downward adjustments based on the then-existing patent coverage and/or the availability of generic compounds in each country.

The Amended and Restated Agreement is a multiple element arrangement for accounting purposes, in which the Company is required to deliver to Mundipharma both the worldwide rights to forodesine in the field of oncology and the transfer of product data and know-how to permit Mundipharma to develop and commercialize forodesine (the “Knowledge Transfer”). Without completion of the Knowledge Transfer, Mundipharma would not be able to develop and commercialize forodesine in the U.S. The Company accounted for these elements as a combined unit of accounting as they do not have stand-alone value to Mundipharma. The worldwide license rights were granted to Mundipharma on November 11, 2011. The Knowledge Transfer commenced in 2011 and was completed during the first quarter of 2012. Completion of the Knowledge Transfer concludes the Company’s obligations under the Amended and Restated Agreement and resulted in the recognition of the unamortized deferred revenue and expense of $7,766 and $1,864, respectively, in the Consolidated Statements of Comprehensive Loss for the six months ended June 30, 2012. Recognition of these deferred amounts resulted in a $2,337 decrease in the Company’s deferred tax assets, with an equal reduction to the valuation allowance, resulting in no impact to net deferred tax assets.

Albert Einstein College of Medicine of Yeshiva University and Industrial Research, Ltd. (“AECOM” and “IRL” respectively). In June 2000, the Company licensed a series of potent inhibitors of PNP from AECOM and IRL (collectively, the “Licensors”). The lead drug candidates from this collaboration are forodesine and ulodesine (formerly referred to as “BCX4208”). The Company has obtained worldwide exclusive rights to develop and ultimately distribute these, or any other, drug candidates that might arise from research on these inhibitors. The Company has since granted the worldwide license rights to develop forodesine to Mundipharma. The Company has the option to expand the agreement to include other inventions in the field made by the investigators or employees of the Licensors. The Company agreed to use commercially reasonable efforts to develop these drugs. In addition, the Company has agreed to pay certain milestone payments for each licensed product (which range in the aggregate from $1,400 to almost $4,000 per indication) for future development of these inhibitors, single digit royalties on net sales of any resulting product made by the Company, and to share approximately one quarter of future payments received from other third-party partners, if any. In addition, the Company has agreed to pay annual license fees, which can range from $150 to $500, that are creditable against actual royalties and other payments due to the Licensors. This agreement may be terminated by the Company at any time by giving 60 days advance notice or in the event of material uncured breach by the Licensors.

In May 2010, the Company amended the license agreement through which the Company obtained worldwide exclusive rights to develop and ultimately distribute any drug candidates that might arise from research on a series of PNP inhibitors, including forodesine and ulodesine. Under the terms of the amendment, the Licensors agreed to accept a reduction of one-half in the percentage of future payments received from third-party sublicensees of the licensed PNP inhibitors that must be paid to the Licensors. This reduction does not apply to (i) any milestone payments the Company may receive in the future under its license agreement dated February 1, 2006 with Mundipharma and (ii) royalties received from its sublicensees in connection with the sale of licensed products, for which the original payment rate will remain in effect. The rate of royalty payments to the Licensors based on net sales of any resulting product made by the Company remains unchanged.

In consideration for these modifications in 2010, the Company issued to the Licensors shares of its common stock with an aggregate value of $5,911 and paid the Licensors $90 in cash. Additionally, at the Company’s sole option and subject to certain agreed-upon conditions, any future non-royalty payments due to be paid by it to the Licensors under the license agreement may be made either in cash, in shares of its common stock, or in a combination of cash and shares.

On November 17, 2011, the Company further amended its agreements with the Licensors whereby the Licensors agreed to accept a reduction of one-half in the percentage of Net Proceeds (as defined in the license agreement) received by the Company under its Amended and Restated Agreement with Mundipharma that will be paid to AECOM/IRL.

On June 19, 2012, the Company further amended its agreement with the Licensors to include a compound for use in the field of antivirals and to clarify the exclusion of certain compounds for use as antibacterials.

The University of Alabama at Birmingham (“UAB”). The Company currently has agreements with UAB for influenza neuraminidase and complement inhibitors. Under the terms of these agreements, UAB performed specific research for the Company in return for research payments and license fees. UAB has granted the Company certain rights to any discoveries in these areas resulting from research developed by UAB or jointly developed with the Company. The Company has agreed to pay single digit royalties on sales of any resulting product and to share in future payments received from other third-party partners. The Company has completed the research under the UAB agreements. These two agreements have initial 25-year terms, are automatically renewable for five-year terms throughout the life of the last patent and are terminable by the Company upon three months notice and by UAB under certain circumstances. Upon termination, both parties shall cease using the other parties’ proprietary and confidential information and materials, the parties shall jointly own joint inventions and UAB shall resume full ownership of all UAB licensed products. There is currently no activity between the Company and UAB on these agreements, but when the Company licenses this technology, such as in the case of the Shionogi and Green Cross agreements, or commercializes products related to these programs, the Company will owe sublicense fees or royalties on amounts it receives.

Emory University (“Emory”). In June 2000, the Company licensed intellectual property from Emory related to the hepatitis C polymerase target associated with hepatitis C viral infections. Under the original terms of the agreement, the research investigators from Emory provided the Company with materials and technical insight into the target. The Company has agreed to pay Emory single digit royalties on sales of any resulting product and to share in future payments received from other third party partners, if any. The Company can terminate this agreement at any time by giving 90 days advance notice. Upon termination, the Company will cease using the licensed technology.

Royalty Monetization

6 Months Ended

Jun. 30, 2012

Royalty Monetization [Abstract]

Royalty Monetization

Note 4 — Royalty Monetization

Overview

On March 9, 2011, the Company completed a $30,000 financing transaction to monetize certain future royalty and milestone payments under the Shionogi Agreement, pursuant to which Shionogi licensed from the Company the rights to market RAPIACTA^® in Japan and, if approved for commercial sale, Taiwan. The Company received net proceeds of $22,691 from the transaction after transaction costs of $4,309 and the establishment of a $3,000 interest reserve account by Royalty Sub, which will be available to help cover interest shortfalls in the future. As of June 30, 2012, $1,742 remains in the interest reserve account for future interest payments.

As part of the transaction, the Company entered into a purchase and sale agreement dated as of March 9, 2011 with Royalty Sub, whereby the Company transferred to Royalty Sub, among other things, (i) its rights to receive certain royalty and milestone payments from Shionogi arising under the Shionogi Agreement, and (ii) the right to receive payments under a Japanese yen/US dollar foreign currency hedge arrangement (as further described below, the “Currency Hedge Agreement”) put into place by the Company in connection with the transaction. Royalty payments will be paid by Shionogi in Japanese yen and milestone payments will paid in U.S. dollars. The Company’s collaboration with Shionogi was not impacted as a result of this transaction.

Non-Recourse Notes Payable

On March 9, 2011, Royalty Sub completed a private placement to institutional investors of $30,000 in aggregate principal amount of its PhaRMA Senior Secured 14.0% Notes due 2020 (the “PhaRMA Notes”). The PhaRMA Notes were issued by Royalty Sub under an Indenture, dated as of March 9, 2011 (the “Indenture”), by and between Royalty Sub and U.S. Bank National Association, as Trustee. Principal and interest on the PhaRMA Notes issued are payable from, and are secured by, the rights to royalty and milestone payments under the Shionogi Agreement transferred by the Company to Royalty Sub and payments, if any, made to Royalty Sub under the Currency Hedge Agreement. The PhaRMA Notes bear interest at 14% per annum, payable annually in arrears on September 1^st of each year, beginning on September 1, 2011 (the “Payment Date”). The Company remains entitled to receive any royalties and milestone payments related to sales of RAPIACTA^® by Shionogi following repayment of the PhaRMA Notes.

Royalty Sub’s obligations to pay principal and interest on the PhaRMA Notes are obligations solely of Royalty Sub and are without recourse to any other person, including the Company, except to the extent of the Company’s pledge of its equity interests in Royalty Sub in support of the PhaRMA Notes. The Company may, but is not obligated to, make capital contributions to a capital account that may be used to redeem, or on up to one occasion pay any interest shortfall on, the PhaRMA Notes.

On September 1, 2012, $4,200 of interest will be due and payable on the PhaRMA Notes. Based on royalty payments received from RAPIACTA^® sales of $1,930 (from September 2, 2011 through June 30, 2012) and the $1,742 remaining balance in the interest reserve account, the Company currently estimates that there will be an interest shortfall of approximately $528 on September 1, 2012 Payment Date. As stipulated under the PhaRMA Notes Indenture, if the amounts available for payment on any Payment Date are insufficient to pay all of the interest due on a Payment Date, unless sufficient capital is contributed to Royalty Sub by the Company as permitted under the Indenture or the interest reserve account is available to make such payment, the shortfall in interest will accrue interest at the interest rate applicable to the PhaRMA Notes compounded annually. Under the terms of the Indenture, Royalty Sub’s inability to pay the full amount of interest payable on September 1, 2012 will not constitute an event of default under the PhaRMA Notes unless Royalty Sub fails to pay such unpaid interest, plus interest thereon, on or prior to the next succeeding Payment Date for the PhaRMA Notes, which is September 1, 2013.

The Indenture does not contain any financial covenants. The Indenture includes customary representations and warranties of Royalty Sub, affirmative and negative covenants of Royalty Sub, Events of Default and related remedies, and provisions regarding the duties of the Trustee, indemnification of the Trustee, and other matters typical for indentures used in structured financings of this type.

As of June 30, 2012, the aggregate fair value of the PhaRMA Notes approximate the carrying value of $30,000 since the stated rate and terms are representative of current rates and terms available to the Company. The fair value was determined by a quoted price in a not actively traded market representing Level 2 in the fair value hierarchy as defined by U. S. GAAP.

Beginning on March 9, 2012, the PhaRMA Notes became redeemable by Royalty Sub. Accordingly, the PhaRMA Notes are redeemable at the option of Royalty Sub at any time at a redemption price equal to the percentage of the outstanding principal balance of the PhaRMA Notes being redeemed specified below for the period in which the redemption occurs, plus accrued and unpaid interest through the redemption date on the PhaRMA Notes being redeemed:


Payment Dates (Between Indicated Dates)	Redemption Percentage
From and including March 9, 2012 to and including March 8, 2013		107.0	%
From and including March 9, 2013 to and including March 8, 2014		103.5	%
From and including March 9, 2014 and thereafter		100.0	%

Foreign Currency Hedge

In connection with the issuance by Royalty Sub of the PhaRMA Notes, the Company entered into a “Currency Hedge Agreement” to hedge certain risks associated with changes in the value of the Japanese yen relative to the U.S. dollar. Under the Currency Hedge Agreement, the Company has the right to purchase dollars and sell yen at a rate of 100 yen per dollar for which the Company may be required to pay a premium in each year from 2014 through 2020, provided the Currency Hedge Agreement remains in effect. A payment of $1,950 will be required if, on May 18 of the relevant year, the U.S. dollar is worth 100 yen or less as determined in accordance with the Currency Hedge Agreement.

The Currency Hedge Agreement does not qualify for hedge accounting treatment; therefore, mark-to-market adjustments are recognized in the Company’s Consolidated Statement of Comprehensive Loss. Mark-to-market adjustments for the three months ended June 30, 2012 and 2011 resulted in a loss of $997 and $998, respectively, a loss of $959 and $2,340 for the six months ended June 30, 2012 and 2011, respectively. The Company is also required to post collateral in connection with the mark-to-market adjustments based on defined thresholds. As of June 30, 2012, $4,970 was posted under the Currency Hedge Agreement. The Company will not be required at any time to post collateral exceeding the maximum premium payments remaining payable under the Currency Hedge Agreement. Subject to certain obligations the Company has in connection with the PhaRMA Notes, the Company has the right to terminate the Currency Hedge Agreement with respect to the 2016 through 2020 period by giving notice to the counterparty prior to May 18, 2014 and paying a $1,950 termination fee.

Stockholders' Equity

6 Months Ended

Jun. 30, 2012

Stockholders' Equity [Abstract]

Stockholders' Equity

Note 5 — Stockholders’ Equity

In June 2011, the Company entered into an At Market Issuance Sales Agreement (the “ATM Agreement”) with McNicoll, Lewis & Vlak (“MLV”) pursuant to which the Company may issue and sell $70,000 in shares of its common stock at current market prices under a Form S-3 registration statement with MLV acting as the sales agent. Subject to the terms and conditions of the ATM Agreement, MLV will use commercially reasonable efforts to sell the Company’s common stock from time to time, based upon the Company’s instruction, including any price, time or size limits or other customary parameters or conditions the Company may impose. The Company will pay MLV an aggregate commission rate of 2% or 3% of the gross proceeds of the sales price per share of any common stock sold under the ATM Agreement depending on the number of shares sold. On June 28, 2011, the Company filed a Registration Statement on Form S-3, which became effective on July 13, 2011, for the issuance and sale of up to $70,000 of equity or other securities. During the six months ended June 30, 2012, the Company sold an aggregate of 3,879 shares of common stock at an average per share price of $4.09 pursuant to the ATM Agreement for net proceeds of $15,339.

On March 15, 2012, the Company issued 193 shares of restricted common stock in lieu of a cash payment to employees as payment for their annual incentive award earned in 2011. The number of shares issued was based on the total value of the annual incentive earned in 2011 of $1,542, less $535 in withholding taxes paid in cash on the employees’ behalf, divided by the closing common stock price on March 15, 2012 of $5.23 per share.

Significant Accounting Policies (Policies)

6 Months Ended

Jun. 30, 2012

Significant Accounting Policies [Abstract]

Basis of Presentation

Reclassifications

Cash and Cash Equivalents

Restricted Cash

Investments

Receivables from Collaborations


	Billed		Unbilled		Total
U.S. Department of Health and Human Services	$	681	$	4,403	$	5,084

Total receivables from collaborations	$	681	$	4,403	$	5,084

Inventory

The Company’s inventory consisted of the following as of June 30, 2012 and December 31, 2011:


	2012			2011
Supplies	$	263		$	898
Finished goods		3,980			3,980
Reserve for finished goods		(3,980	)		(4,615	)

Net inventories	$	263		$	263

Patents and Licenses

Accrued Expenses

•

fees paid to Clinical Research Organization (“CROs”) in connection with preclinical and toxicology studies and clinical trials;

•

fees paid to investigative sites in connection with clinical trials;

•

fees paid to contract manufacturers in connection with the production of our raw materials, drug substance and drug products; and

•

professional fees.

Income Taxes

Accumulated Other Comprehensive (Loss) Income

Accumulated other comprehensive (loss) income is comprised of unrealized gains and losses on investments available-for-sale and is disclosed as a separate component of stockholders’ equity.

Revenue Recognition

The Company recognizes revenues from collaborative and other research and development arrangements and product sales.

Collaborative and Other Research and Development Arrangements and Royalties

Product Sales

Research and Development Expenses

Stock-Based Compensation

Interest Expense and Deferred Financing Costs

Currency Hedge Agreement

Net Loss Per Share

Use of Estimates

Concentration of Market Risk

Credit Risk

Recent Accounting Pronouncements

Significant Accounting Policies (Tables)

6 Months Ended

Jun. 30, 2012

Significant Accounting Policies [Abstract]

Fair value of the Company's investments by type


	June 30, 2012
					Gross		Gross
	Amortized		Accrued		Unrealized		Unrealized			Estimated
	Cost		Interest		Gains		Losses			Fair Value
U.S. Treasury securities	$	1,999	$	2	$	7	$	—		$	2,008
Obligations of U.S. government and its agencies		10,213		12		—		(3	)		10,222
Corporate debt securities		6,872		34		15		—			6,921
Commercial paper		1,399		—		—		—			1,399
Certificate of deposit		800		—		—		—			800
Municipal obligations		7,895		43		21		—			7,959

Total investments	$	29,178	$	91	$	43	$	(3	)	$	29,309


	December 31, 2011
					Gross		Gross
	Amortized		Accrued		Unrealized		Unrealized			Estimated
	Cost		Interest		Gains		Losses			Fair Value
U.S. Treasury securities	$	1,998	$	2	$	14	$	—		$	2,014
Obligations of U.S. government and its agencies		5,000		10		—		—			5,010
Corporate debt securities		10,924		80		15		(9	)		11,010
Commercial paper		10,939		—		2		(1	)		10,940
Asset-backed securities		611		—		—		—			611
Certificate of deposit		801		1		—		—			802
Municipal obligations		10,182		68		21		(2	)		10,269

Total investments	$	40,455	$	161	$	52	$	(12	)	$	40,656

Scheduled maturity for the Company's investments


Maturing in one year or less	$	12,958
Maturing after one year through two years		16,351

Total investments	$	29,309

Summary of receivables from collaborations


	Billed		Unbilled		Total
U.S. Department of Health and Human Services	$	681	$	4,403	$	5,084

Total receivables from collaborations	$	681	$	4,403	$	5,084

Components of inventories


	2012			2011
Supplies	$	263		$	898
Finished goods		3,980			3,980
Reserve for finished goods		(3,980	)		(4,615	)

Net inventories	$	263		$	263

Revenues from collaborations


	Three Months				Six Months
	2012		2011		2012		2011
Collaborative and other research and development revenues:
U.S. Department of Health and Human Services	$	3,914	$	3,111	$	8,073	$	7,772
Shionogi (Japan)		296		296		592		592
Mundipharma (United Kingdom)		—		328		7,766		720
Grants (United States)		—		—		—		86

Total revenues	$	4,210	$	3,735	$	16,431	$	9,170

- 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
-SubTopic 10
-Section 50
-Paragraph 7
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27337-111563

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 3
-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
-SubTopic 320
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6957658&loc=d3e62586-112803

Reference 5: 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 6: 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 7: 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 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

Stock-Based Compensation (Tables)

6 Months Ended

Jun. 30, 2012

Stock-Based Compensation [Abstract]


	Awards Available			Options Outstanding			Weighted Average Exercise Price
Balance December 31, 2011		2,010			7,858		$	6.21
Plan amendment		1,700			—			—
Restricted stock awards granted		(415	)		—			—
Restricted stock awards cancelled		13			—			—
Stock option awards granted		(1,563	)		1,563			4.66
Stock option awards exercised		—			(303	)		1.66
Stock option awards cancelled		419			(419	)		8.32

Balance June 30, 2012		2,164			8,699		$	5.99

Weighted Average Assumptions for Stock Option Awards Granted to Employees and Directors under the Incentive Plan


	2012			2011
Expected Life in Years		5.5			5.5
Expected Volatility		87	%		80	%
Expected Dividend Yield		0.0	%		0.0	%
Risk-Free Interest Rate		0.88	%		2.20	%

Royalty Monetization (Tables)

6 Months Ended

Jun. 30, 2012

Royalty Monetization [Abstract]

Accrued and unpaid interest through the redemption date


Payment Dates (Between Indicated Dates)	Redemption Percentage
From and including March 9, 2012 to and including March 8, 2013		107.0	%
From and including March 9, 2013 to and including March 8, 2014		103.5	%
From and including March 9, 2014 and thereafter		100.0	%

Significant Accounting Policies (Details) - USD ($) $ in Thousands	Jun. 30, 2012	Dec. 31, 2011
Fair value of the Company's investments by type
Amortized Cost	$ 29,178	$ 40,455
Accrued Interest	91	161
Gross Unrealized Gains	43	52
Gross Unrealized Losses	(3)	(12)
Estimated Fair Value	29,309	40,656
Level 2 [Member] \| U.S. Treasury securities [Member]
Fair value of the Company's investments by type
Amortized Cost	1,999	1,998
Accrued Interest	2	2
Gross Unrealized Gains	7	14
Gross Unrealized Losses
Estimated Fair Value	2,008	2,014
Level 2 [Member] \| Obligations of U.S. government and its agencies [Member]
Fair value of the Company's investments by type
Amortized Cost	10,213	5,000
Accrued Interest	12	10
Gross Unrealized Gains
Gross Unrealized Losses	(3)
Estimated Fair Value	10,222	5,010
Level 2 [Member] \| Corporate debt securities [Member]
Fair value of the Company's investments by type
Amortized Cost	6,872	10,924
Accrued Interest	34	80
Gross Unrealized Gains	15	15
Gross Unrealized Losses		(9)
Estimated Fair Value	6,921	11,010
Level 2 [Member] \| Commercial paper [Member]
Fair value of the Company's investments by type
Amortized Cost	1,399	10,939
Accrued Interest
Gross Unrealized Gains		2
Gross Unrealized Losses		(1)
Estimated Fair Value	1,399	10,940
Level 2 [Member] \| Asset-backed securities [Member]
Fair value of the Company's investments by type
Amortized Cost		611
Accrued Interest
Gross Unrealized Gains
Gross Unrealized Losses
Estimated Fair Value		611
Level 2 [Member] \| Certificate of deposit [Member]
Fair value of the Company's investments by type
Amortized Cost	800	801
Accrued Interest		1
Gross Unrealized Gains
Gross Unrealized Losses
Estimated Fair Value	800	802
Level 2 [Member] \| Municipal obligations [Member]
Fair value of the Company's investments by type
Amortized Cost	7,895	10,182
Accrued Interest	43	68
Gross Unrealized Gains	21	21
Gross Unrealized Losses		(2)
Estimated Fair Value	$ 7,959	$ 10,269

Significant Accounting Policies (Details 1) - USD ($) $ in Thousands	Jun. 30, 2012	Dec. 31, 2011
Scheduled maturity for the Company's investments
Maturing in one year or less	$ 12,958
Maturing after one year through two years	16,351
Total investments	$ 29,309	$ 40,656

- Definition

This element represents the portion of the balance sheet assertion valued at fair value by the entity whether such amount is presented as a separate caption or as a parenthetical disclosure. Additionally, this element may be used in connection with the fair value disclosures required in the footnote disclosures to the financial statements. The element may be used in both the balance sheet and disclosure in the same submission. This item represents Available-for-sale Securities which consist of all investments in certain debt and equity securities neither classified as trading or held-to-maturity securities. A debt security represents a creditor relationship with an enterprise. Debt securities include, among other items, US Treasury securities, US government securities, municipal securities, corporate bonds, convertible debt, commercial paper, and all securitized debt instruments. An equity security represents an ownership interest in an enterprise or the right to acquire or dispose of an ownership interest in an enterprise at fixed or determinable prices. Equity securities include, among other things, common stock, certain preferred stock, warrant rights, call options, and put options, but do not include convertible debt. An entity may opt to provide the reader with additional narrative text to better understand the nature of investments in debt and equity securities which are categorized as Available-for-sale.

+ References + Details

Significant Accounting Policies (Details 2) - USD ($) $ in Thousands	Jun. 30, 2012	Dec. 31, 2011
Summary of receivables from collaborations
U.S. Department of Health and Human Services	$ 5,084	$ 5,831
Total receivables from collaborations	5,084
Billed [Member]
Summary of receivables from collaborations
U.S. Department of Health and Human Services	681
Total receivables from collaborations	681
Unbilled [Member]
Summary of receivables from collaborations
U.S. Department of Health and Human Services	4,403
Total receivables from collaborations	$ 4,403

Significant Accounting Policies (Details 3) - USD ($) $ in Thousands	Jun. 30, 2012	Dec. 31, 2011
Components of inventories
Supplies	$ 263	$ 898
Finished goods	3,980	3,980
Reserve for finished goods	(3,980)	(4,615)
Net inventories	$ 263	$ 263

- Definition

The amount of the valuation account as of the balance sheet date which reduces the carrying amount of inventory to net realizable value; takes into consideration such factors as market value, excessive quantities based on expected sales, technological obsolescence, and shrinkage. May also provide for estimated product returns or price concessions pertaining to product cost.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 330
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SAB TOPIC 5.BB)
-URI http://asc.fasb.org/extlink&oid=6386940&loc=d3e100047-122729

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02.6(a))
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 4
-Subparagraph (SX 210.12-09)
-URI http://asc.fasb.org/extlink&oid=6881521&loc=d3e24092-122690

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 330
-SubTopic 10
-Section 35
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6386567&loc=d3e3927-108312

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 43
-Paragraph 14
-Chapter 4
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 43
-Paragraph 8, 9, 14
-Chapter 4
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 43
-Section A
-Paragraph 9
-Chapter 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 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 09
-Article 12

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 02
-Paragraph 6
-Subparagraph a
-Article 5

+ Details

Significant Accounting Policies (Details 4) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Revenues from collaborations
Total revenues	$ 4,210	$ 3,735	$ 16,431	$ 9,170
U.S. Department of Health and Human Services [Member]
Revenues from collaborations
Total revenues	3,914	3,111	8,073	7,772
Shionogi (Japan) [Member]
Revenues from collaborations
Total revenues	296	296	592	592
Mundipharma (United Kingdom) [Member]
Revenues from collaborations
Total revenues		328	7,766	720
Grants (United States) [Member]
Revenues from collaborations
Total revenues				$ 86

Significant Accounting Policies (Details Textual) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011	Dec. 31, 2011	Mar. 09, 2011
Significant Accounting Policies (Textual) [Abstract]
Royalty and milestone payments						$ 30,000
Manufacturing cost of finished goods	$ 3,980		$ 3,980		$ 3,980
Cumulative mark-to-market adjustments - loss	997	$ 998	959	$ 2,340
Hedge collateral under the agreement	4,970		$ 4,970
Potential common shares			9,172	8,128
Average maturity for portfolio investments			24 months
Gross Unrealized Gains	(9)	9		$ (14)
Significant Accounting Policies (Additional Textual) [Abstract]
Research and development expenses		387		858
Additional Research and development expenses		80		176
Restricted cash	300		$ 300
Maturity of investments			12 months
Reduction in supplies inventory and related reserve					635
Manufacturing cost of finished goods	3,980		$ 3,980		3,980
Accrued expenses	5,459		5,459		8,622
Interest expenses	1,160	1,166	2,320	1,455
Amortization of deferred financing costs	110	105	220	136
Cumulative mark-to-market adjustments - loss	997	$ 998	959	$ 2,340
Hedge collateral under the agreement	4,970		$ 4,970
Potential common shares			9,172	8,128
Average maturity for portfolio investments			24 months
Amortization of deferred financing costs			$ 220	$ 137
Maximum [Member]
Significant Accounting Policies (Textual) [Abstract]
Maturity period for high-quality marketable securities			3 years
Average portfolio maturity period for high-quality marketable securities			2 years
Maturity period of investments			12 months
Minimum [Member]
Significant Accounting Policies (Textual) [Abstract]
Maturity period of investments			3 months
JPR Royalty Sub LLC [Member]
Significant Accounting Policies (Textual) [Abstract]
Royalty and milestone payments						$ 30,000
Shionogi (Japan) [Member]
Significant Accounting Policies (Textual) [Abstract]
Collateral credit card program in royalty revenue paid	$ 1,930		$ 1,930
RAPIACTA [Member]
Significant Accounting Policies (Textual) [Abstract]
Royalty payments received			$ 1,666		$ 1,216

Stock-Based Compensation (Details) shares in Thousands	6 Months Ended
Stock-Based Compensation (Details) shares in Thousands	Jun. 30, 2012 $ / shares shares
Summary of related activity under Incentive Plan
Awards Available, Beginning balance	2,010
Plan amendment, Awards Available	1,700
Restricted stock awards granted, Awards Available	(415)
Restricted stock awards cancelled, Awards Available	13
Stock option awards granted, Awards Available	(1,563)
Stock option awards exercised, Awards Available
Stock option awards cancelled, Awards Available	419
Awards Available, Ending balance	2,164
Options Outstanding, Beginning balance	7,858
Plan amendment, Options Outstanding
Restricted stock awards granted, Options Outstanding
Restricted stock awards cancelled, Options Outstanding
Stock option awards granted, Options Outstanding	1,563
Stock option awards exercised, Options Outstanding	(303)
Stock option awards cancelled, Options Outstanding	(419)
Options Outstanding, Ending balance	8,699
Weighted Average Exercise Price, Beginning balance \| $ / shares	$ 6.21
Plan amendment, Weighted Average Exercise Price \| $ / shares
Restricted stock awards granted, Weighted Average Exercise Price \| $ / shares
Restricted stock awards cancelled, Weighted Average Exercise Price \| $ / shares
Stock option awards granted, Weighted Average Exercise Price \| $ / shares	4.66
Stock option awards exercised, Weighted Average Exercise Price \| $ / shares	1.66
Stock option awards cancelled, Weighted Average Exercise Price \| $ / shares	8.32
Weighted Average Exercise Price, Ending balance \| $ / shares	$ 5.99

Stock-Based Compensation (Details 1)	6 Months Ended
Stock-Based Compensation (Details 1)	Jun. 30, 2012	Jun. 30, 2011
Weighted Average Assumptions for Stock Option Awards Granted to Employees and Directors under the Incentive Plan
Expected Life in Years	5 years 6 months	5 years 6 months
Expected Volatility	87.00%	80.00%
Expected Dividend Yield	0.00%	0.00%
Risk-Free Interest Rate	0.89%	2.20%

Stock-Based Compensation (Details Textual) - USD ($) $ / shares in Units, $ in Thousands	6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Dec. 31, 2011
Stock-Based Compensation (Textual) [Abstract]
Stock-based compensation expense	$ 2,178
Share-based compensation	$ 2,178	$ 2,728
Stock option contractual terms	P10Y
Grant date fair value per share	$ 3.37	$ 2.75
Remaining common stock shares	2,164,000		2,010,000
Share Based Compensation (Additional) (Textual) [Abstract]
Stock option vesting period	4 years
Stock option granting period after granted	1 year
Vesting period after grant date	4 years
Stock option granted to non employee directors	1 year
Unrecognized compensation cost	$ 9,912
Recognized cost current year	2,041
Recognized cost, 2013	3,709
Recognized cost, 2014	2,538
Recognized cost, 2015	1,428
Recognized cost, 2016	196
Incentive Plan [Member]
Stock-Based Compensation (Textual) [Abstract]
Stock-based compensation expense	$ 2,108
Share-based compensation		$ 2,603
Stock option awards granted in percentage	25.00%	25.00%
ESPP [Member]
Stock-Based Compensation (Textual) [Abstract]
Stock-based compensation expense	$ 70
Share-based compensation		$ 88
Common stock shares reserved	975,000
Common stock, shares issued	234,000
Remaining common stock shares	84,000
Percentage of salary to purchase common stock	15.00%
Percentage of common stock shares Beginning	85.00%
Percentage of common stock shares Ending	85.00%
Purchase of common stock shares	3
Maximum number of shares per employee amount	$ 25
Inducement grant [Member]
Stock-Based Compensation (Textual) [Abstract]
Share-based compensation		$ 37

Collaborative and Other Research and Development Contracts (Details) - USD ($) $ in Thousands	1 Months Ended							3 Months Ended	6 Months Ended
	Feb. 28, 2011	May 31, 2010	Sep. 30, 2009	Jan. 31, 2007	Jun. 30, 2006	Feb. 28, 2006	Jun. 30, 2000	Mar. 31, 2012	Jun. 30, 2012
U.S. Department of Health and Human Services [Member]
Collaborative and Other Research and Development Contracts (Textual) [Abstract]
Collaborative agreement period of agreement				4 years
Collaborative agreement contract value				$ 102,661
Collaborative agreement adjusted contract value									$ 234,852
Collaborative agreement additional contract value	$ 55,000		$ 77,191
Collaborative agreement additional contract period			12 months
Contract term	24 months
Green Cross Corporation [Member]
Collaborative and Other Research and Development Contracts (Textual) [Abstract]
License fee received					$ 250
Mundipharma International Holdings Limited [Member]
Collaborative and Other Research and Development Contracts (Textual) [Abstract]
Up-front payment receivable amount						$ 10,000
Deferred revenue up-front payment receivable						10,000
Deferred revenue initiation of clinic trail payment received						5,000
Purchase of drug substance for forodesine						901
Potential milestone payments receivable						15,000
Unamortized deferred revenue, related to Amended and Restated Agreement								$ 7,766
Deferred amounts equal reduction to valuation						$ 2,337
Unamortized deferred expenses, related to Amended and Restated Agreement								$ 1,864
AECOM and IRL [Member]
Collaborative and Other Research and Development Contracts (Textual) [Abstract]
Advance notice period for termination of agreement							60 days
Milestone payment minimum							$ 1,400
Milestone payment maximum							4,000
Annual license fees minimum							150
Annual license fees maximum							$ 500
Stock issued during period value for modification of license agreement		$ 5,911
Payments for modification of license agreement		$ 90
UAB [Member]
Collaborative and Other Research and Development Contracts (Textual) [Abstract]
Period of agreement		25 years
Renewable period of agreement		5 years
Emory University [Member]
Collaborative and Other Research and Development Contracts (Textual) [Abstract]
Advance notice period for termination of agreement							90 days

Royalty Monetization (Details)	6 Months Ended
Royalty Monetization (Details)	Jun. 30, 2012
Accrued and unpaid interest through the redemption date
From and including March 9, 2012 to and including March 8, 2013	107.00%
From and including March 9, 2013 to and including March 8, 2014	103.50%
From and including March 9, 2014 and thereafter	100.00%

Royalty Monetization (Details Textual) $ in Thousands	3 Months Ended		6 Months Ended
Royalty Monetization (Details Textual) $ in Thousands	Jun. 30, 2012 USD ($)	Jun. 30, 2011 USD ($)	Jun. 30, 2012 USD ($) Rate	Jun. 30, 2011 USD ($)	Sep. 01, 2012 USD ($)	Mar. 31, 2012 USD ($)	Mar. 09, 2011 USD ($)
Royalty Monetization (Textual) [Abstract]
Royalty and milestone payments							$ 30,000
Royalty Monetization (Additional Textual) [Abstract]
Interest reserve account	$ 1,742		$ 1,742			$ 1,742
Interest Shortfall					$ 528
Royalty payments			$ 1,930
Yen rate per dollar \| Rate			100
Payment of premium			$ 1,950
Market adjustments loss	997	$ 998	959	$ 2,340
Cash collateral						$ 3,890
Termination fee			1,950
Currency Hedge Agreement	$ 4,970		4,970
JPR Royalty Sub LLC [Member]
Royalty Monetization (Textual) [Abstract]
Royalty and milestone payments							30,000
Net proceeds from transaction			22,691
Transaction costs			4,309
Establishment costs			$ 3,000
PhaRMA Notes [Member]
Royalty Monetization (Textual) [Abstract]
Aggregate principal amount							$ 30,000
Percentage of interest on notes secured							14.00%
Interest Payable					$ 4,200

Stockholders' Equity (Details) - USD ($)	6 Months Ended
Stockholders' Equity (Details) - USD ($)	Jun. 30, 2012	Mar. 15, 2012	Dec. 31, 2011	Jun. 30, 2011
Stockholders' Equity (Textual) [Abstract]
Selling of company aggregate shares of common stock	50,129,000		45,662,000
Stockholders' Equity (Additional Textual) [Abstract]
Issue of common stock	$ 501,000		$ 457,000	$ 70,000
Average price per share	$ 4.09
Net proceeds under the agreement	$ 15,339
Annual incentive earned	1,542
Taxes paid	535
Common stock price, Ending		$ 5.23
Common stock were issued and sales at market price	$ 70,000
Sales [Member]
Stockholders' Equity (Textual) [Abstract]
Selling of company aggregate shares of common stock	3,879
Restricted common stock [Member]
Stockholders' Equity (Textual) [Abstract]
Restricted common stock in shares	193
Maximum [Member]
Stockholders' Equity (Textual) [Abstract]
Commission rate	3.00%
Minimum [Member]
Stockholders' Equity (Textual) [Abstract]
Commission rate	2.00%