View Filing Data

Document and Entity Information - shares	6 Months Ended
Document and Entity Information - shares	Jun. 30, 2013	Jul. 31, 2013
Document Information [Line Items]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Jun. 30, 2013
Document Fiscal Year Focus	2013
Document Fiscal Period Focus	Q2
Trading Symbol	ZIOP
Entity Registrant Name	ZIOPHARM ONCOLOGY INC
Entity Central Index Key	0001107421
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		83,522,763

Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2013	Dec. 31, 2012
Current assets:
Cash and cash equivalents	$ 38,932	$ 73,306
Receivables	31	58
Prepaid expenses and other current assets	4,067	6,912
Total current assets	43,030	80,276
Property and equipment, net	1,713	1,994
Deposits	128	133
Other non-current assets	732	1,001
Total assets	45,603	83,404
Current liabilities:
Accounts payable	1,165	1,509
Accrued expenses	18,969	16,516
Deferred revenue - current portion	800	800
Deferred rent - current portion	63	39
Total current liabilities	20,997	18,864
Deferred revenue	2,333	2,733
Deferred rent	365	400
Warrant liabilities	2,576	12,962
Total liabilities	26,271	34,959
Commitments and contingencies (note 7)
Stockholders' equity:
Preferred stock, $0.001 par value; 30,000,000 shares authorized and no shares issued and outstanding
Common stock, $0.001 par value; 250,000,000 shares authorized; 83,540,682 and 83,236,840 shares issued and outstanding at June 30, 2013 and December 31, 2012, respectively	84	83
Additional paid-in capital - common stock	330,735	325,177
Additional paid-in capital - warrants issued	3,728	6,909
Deficit accumulated during the development stage	(315,215)	(283,724)
Total stockholders' equity	19,332	48,445
Total liabilities and stockholders' equity	$ 45,603	$ 83,404

Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2013	Dec. 31, 2012
Preferred stock, par value	$ 0.001	$ 0.001
Preferred stock, shares authorized	30,000,000	30,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value	$ 0.001	$ 0.001
Common stock, shares authorized	250,000,000	250,000,000
Common stock, shares issued	83,540,682	83,236,840
Common stock, shares outstanding	83,540,682	83,236,840

Statements of Operations - USD ($) $ in Thousands	3 Months Ended		6 Months Ended		118 Months Ended
Statements of Operations - USD ($) $ in Thousands	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013
Research contract revenue	$ 200	$ 200	$ 400	$ 400	$ 1,867
Operating expenses:
Research and development, including costs of research contracts	14,775	18,264	33,887	32,249	246,232
General and administrative	3,721	4,902	8,392	9,750	96,710
Total operating expenses	18,496	23,166	42,279	41,999	342,942
Loss from operations	(18,296)	(22,966)	(41,879)	(41,599)	(341,075)
Other income (expense), net	7	3	3	(23)	4,704
Change in fair value of warrants	(403)	(650)	10,385	(6,461)	21,156
Net loss	$ (18,692)	$ (23,613)	$ (31,491)	$ (48,083)	$ (315,215)
Net loss per share - basic and diluted	$ (0.22)	$ (0.30)	$ (0.38)	$ (0.62)
Weighted average common shares outstanding to compute net loss per share - basic and diluted	83,082,633	78,514,718	82,994,845	77,067,424

Statement of Stockholders' Equity - 6 months ended Jun. 30, 2013 - USD ($) $ in Thousands	Total	Common Stock	Additional Paid in Capital, Common Stock	Other Additional Capital	Accumulated Deficit during Development Stage
Beginning Balance (in shares) at Dec. 31, 2012		83,236,840
Beginning Balance at Dec. 31, 2012	$ 48,445	$ 83	$ 325,177	$ 6,909	$ (283,724)
Stock-based compensation	$ 1,673		1,673
Exercise of employee stock options (in shares)	455,168	455,168
Exercise of employee stock options	$ 854	$ 1	853
Exercise of warrants to purchase common stock (in shares)		49,315
Exercise of warrants to purchase common stock	101		172	(71)
Expired warrants			3,110	(3,110)
Cancelled restricted stock		(140,600)
Repurchase of shares of restricted common stock (in shares)		(60,041)
Repurchase of shares of restricted common stock	(250)		(250)
Net loss	(31,491)				(31,491)
Ending Balance (in shares) at Jun. 30, 2013		83,540,682
Ending Balance at Jun. 30, 2013	$ 19,332	$ 84	$ 330,735	$ 3,728	$ (315,215)

Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended		118 Months Ended
Statements of Cash Flows - USD ($) $ in Thousands	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013
Cash flows from operating activities:
Net loss	$ (31,491)	$ (48,083)	$ (315,215)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	396	265	2,970
Stock-based compensation	1,673	2,290	21,854
Change in fair value of warrants	(10,385)	6,461	(21,156)
Loss on disposal of fixed assets			57
Common stock issued in exchange for in-process research and development			36,151
(Increase) decrease in:
Receivables	27	79	(31)
Prepaid expenses and other current assets	2,845	(7,738)	(4,067)
Other noncurrent assets	269	(53)	(732)
Deposits	4	(41)	(130)
Increase (decrease) in:
Accounts payable	(344)	(258)	1,165
Accrued expenses	2,453	4,681	18,969
Deferred revenue	(400)	(400)	3,133
Deferred rent	(11)	172	428
Net cash used in operating activities	(34,964)	(42,625)	(256,604)
Cash flows from investing activities:
Purchases of property and equipment	(115)	(1,107)	(4,741)
Proceeds from sale of property and equipment			1
Net cash used in investing activities	(115)	(1,107)	(4,740)
Cash flows from financing activities:
Stockholders' capital contribution			500
Proceeds from exercise of stock options	854	30	2,227
Payments to employees for repurchase of common stock	(250)		(3,117)
Proceeds from exercise of warrants	101	210	13,180
Proceeds from issuance of common stock and warrants, net		49,170	270,726
Proceeds from issuance of preferred stock, net			16,760
Net cash provided by financing activities	705	49,410	300,276
Net increase (decrease) in cash and cash equivalents	(34,374)	5,678	38,932
Cash and cash equivalents, beginning of period	73,306	104,713
Cash and cash equivalents, end of period	38,932	110,391	38,932
Supplementary disclosure of cash flow information:
Cash paid for interest
Cash paid for income taxes
Supplementary disclosure of noncash investing and financing activities:
Warrants issued to placement agents and investors			47,276
Exercise of liability-classified warrants to common shares		412	352
Convertible Preferred Stock
Supplementary disclosure of noncash investing and financing activities:
Preferred stock conversion/exercise of equity-classified warrants to common stock			16,760
Warrant Exercise
Supplementary disclosure of noncash investing and financing activities:
Preferred stock conversion/exercise of equity-classified warrants to common stock	$ 72	$ 166	$ 9,396

Business

6 Months Ended

Jun. 30, 2013

Business

1. Business

Overview

ZIOPHARM Oncology, Inc. (“ZIOPHARM” or the “Company”) is a biopharmaceutical company that seeks to acquire, develop and commercialize, on its own or with other commercial partners, a diverse portfolio of cancer drugs that can address unmet medical needs through the development of a proprietary synthetic biology platform and small molecule drug candidates.

The Company’s operations to date have consisted primarily of raising capital and conducting research and development. Accordingly, the Company is considered to be in the development stage at June 30, 2013. The Company’s fiscal year ends on December 31.

The Company has operated at a loss since its inception in 2003 and has minimal revenues. The Company anticipates that losses will continue for the foreseeable future. At June 30, 2013, the Company’s accumulated deficit was approximately $315.2 million. Following the restructuring described in Note 3, the Company currently believes that it has sufficient capital to fund development and commercialization activities into the first quarter of 2014. The Company’s ability to continue operations after its current cash resources are exhausted depends on its ability to obtain additional financing or to achieve profitable operations, as to which no assurances can be given. Cash requirements may vary materially from those now planned because of changes in the Company’s focus and direction of its research and development programs, competitive and technical advances, patent developments, regulatory changes or other developments. Additional financing will be required to continue operations after the Company exhausts its current cash resources and to continue its long-term plans for clinical trials and new product development. There can be no assurance that any such financing can be realized by the Company, or if realized, what the terms thereof may be, or that any amount that the Company is able to raise will be adequate to support the Company’s working capital requirements until it achieves profitable operations.

Basis of Presentation

The accompanying unaudited interim financial statements have been prepared in accordance with the instructions to Form 10-Q pursuant to the rules and regulations of the Securities and Exchange Commission. Certain information and note disclosures required by generally accepted accounting principles in the United States have been condensed or omitted pursuant to such rules and regulations.

It is management’s opinion that the accompanying unaudited interim financial statements reflect all adjustments (which are normal and recurring) that are necessary for a fair statement of the results for the interim periods. The unaudited interim financial statements should be read in conjunction with the audited financial statements and the notes thereto for the year ended December 31, 2012, included in the Company’s Form 10-K for such fiscal year.

The year-end balance sheet data was derived from the audited financial statements but does not include all disclosures required by generally accepted accounting principles in the United States.

The results disclosed in the Statements of Operations for the three and six months ended June 30, 2013 are not necessarily indicative of the results to be expected for the full fiscal year.

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenues and expenses during the reporting period. Although the Company regularly assesses these estimates, actual results could differ from those estimates. Changes in estimates are recorded in the period in which they become known.

The Company’s most significant estimates and judgments used in the preparation of its financial statements are:

•

Clinical trial expenses;

•

Fair value measurements for stock based compensation and warrants; and

•

Income taxes.

Subsequent Events

The Company evaluated all events and transactions that occurred after the balance sheet date through the date of this filing. During this period, the Company did not have any material recognizable or disclosable subsequent events.

Summary of Significant Accounting Policies	6 Months Ended
Summary of Significant Accounting Policies	Jun. 30, 2013
Summary of Significant Accounting Policies	2. Summary of Significant Accounting Policies The Company’s significant accounting policies were identified in the Company’s Form 10-K for the fiscal year ended December 31, 2012 and are substantially unchanged.

Restructuring

6 Months Ended

Jun. 30, 2013

Restructuring

3. Restructuring

On April 3, 2013, the Company completed a workforce reduction plan to reduce costs as part of the Company’s decision to terminate development of palifosfamide in first-line metastatic soft tissue sarcoma and place exclusive strategic focus on its synthetic biology programs, which are being developed in partnership with Intrexon Corporation (Notes 6, 7 and 9). Pursuant to the workforce reduction plan, the Company eliminated a total of 65 positions, comprised of 40 filled positions and 25 unfilled positions across various functions and locations. Employees whose positions were eliminated as part of the plan were notified beginning on April 2, 2013. Affected employees were offered separation benefits, including severance payments, and temporary healthcare coverage assistance. In connection with the elimination of filled positions as part of the workforce reduction plan, the Company incurred charges of $1.6 million during the second quarter of 2013, primarily for one-time contractual severance benefits. Additionally, the Company is evaluating its facilities and the associated contractual obligations to determine the appropriate course of action and any associated charges for exit and disposal activities. The Company currently cannot estimate these amounts, but expects to file an amended Current Report on Form 8-K within four business days of making such determination.

On July 16, 2012, the Company announced that it restructured its management team and closed its Germantown, MD office. As a result of this action, the Company recorded a restructuring charge, consisting primarily of severance, stock based compensation associated with stock option modifications (see Note 9) and health benefit continuation costs of approximately $1.3 million. These costs are included in general and administrative expense for the period from inception (September 9, 2003) through June 30, 2013.

Fair Value Measurements

6 Months Ended

Jun. 30, 2013

Fair Value Measurements

4. Fair Value Measurements

The Company accounts for its financial assets and liabilities using fair value measurements. The accounting standard defines fair value, establishes a framework for measuring fair value under generally accepted accounting principles and enhances disclosures about fair value measurements. Fair value is defined as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. Valuation techniques used to measure fair value must maximize the use of observable inputs and minimize the use of unobservable inputs. The standard describes a fair value hierarchy based on three levels of inputs, of which the first two are considered observable and the last unobservable, that may be used to measure fair value which are the following:

•

Level 1—Quoted prices in active markets for identical assets or liabilities.

•

Level 2—Inputs other than Level 1 that are observable, either directly or indirectly, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.

•

Level 3—Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

Assets and liabilities measured at fair value on a recurring basis as of June 30, 2013 and December 31, 2012 are as follows:


($ in thousands)			Fair Value Measurements at Reporting Date Using
Description	Balance as of June 30, 2013		Quoted Prices in Active Markets for Identical Assets/Liabilities (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Cash equivalents	$	36,709	$	36,709	$	—	$	—


Warrant liability	$	2,576	$	—	$	2,576	$	—


($ in thousands)			Fair Value Measurements at Reporting Date Using
Description	Balance as of December 31, 2012		Quoted Prices in Active Markets for Identical Assets/Liabilities (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)

Cash equivalents	$	72,002	$	72,002	$	—	$	—


Warrant liability	$	12,962	$	—	$	12,962	$	—

The cash equivalents represent deposits in a short term U.S. treasury money market mutual fund quoted in an active market and classified as a Level 1 asset. The Company’s Level 2 financial liabilities consist of long-term investor and placement agent warrants issued in connection with its December 2009 public offering. The warrants were valued using Binomial/Monte Carlo valuation models. See Note 8 for additional disclosures on the valuation methodology and significant assumptions.

- Definition

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

+ References + Details

Net Loss per Share

6 Months Ended

Jun. 30, 2013

Net Loss per Share

5. Net Loss per Share

Basic net loss per share is computed by dividing net loss by the weighted average number of shares of common stock outstanding for the period. The Company’s potential dilutive shares, which include outstanding common stock options, unvested restricted stock and warrants, have not been included in the computation of diluted net loss per share for any of the periods presented as the result would be anti-dilutive. Such potential shares of common stock at June 30, 2013 and 2012 consist of the following:


	June 30,
	2013		2012
Stock options		6,538,419		5,397,154
Unvested restricted common stock		454,325		1,029,848
Warrants		10,441,431		11,268,678

		17,434,175		17,695,680

Related Party Transactions

6 Months Ended

Jun. 30, 2013

Related Party Transactions

6. Related Party Transactions

On January 6, 2011, the Company entered into an Exclusive Channel Partner Agreement (the “Channel Agreement”) with Intrexon Corporation (see Note 7 for additional disclosure relating to the Channel Agreement). Our director, Randall J. Kirk, is the CEO, a director, and the largest stockholder of Intrexon. During the six months ended June 30, 2012, the Company paid Intrexon approximately $10.7 million, of which $2.5 million was for services already incurred and the remaining $8.2 million expected to be incurred within a year. This amount has been included as part of prepaid expenses and other current assets on the balance sheet as of June 30, 2012. During the six months ended June 30, 2013, the Company was billed $3.7 million for services performed by Intrexon, which was applied against the prepaid balance. As of June 30, 2013, the prepaid balance in other current assets on the accompanying balance sheet was $1.1 million.

On January 25, 2012, Intrexon purchased 1,923,075 shares of common stock in the Company’s public offering (see Note 9).

On November 7, 2012, the Company issued 3,636,926 shares of common stock to Intrexon (see Note 9).

- Definition

The entire disclosure for related party transactions. Examples of related party transactions include transactions between (a) a parent company and its subsidiary; (b) subsidiaries of a common parent; (c) and entity and its principal owners; and (d) affiliates.

+ References + Details

Commitments and Contingencies

6 Months Ended

Jun. 30, 2013

Commitments and Contingencies

7. Commitments and Contingencies

Patent and Technology License Agreement – The University of Texas M. D. Anderson Cancer Center and the Texas A&M University System.

On August 24, 2004, the Company entered into a patent and technology license agreement with The Board of Regents of the University of Texas System, acting on behalf of The University of Texas M. D. Anderson Cancer Center and the Texas A&M University System (collectively, the “Licensors”). Under this agreement, the Company was granted an exclusive, worldwide license to rights (including rights to U.S. and foreign patent and patent applications and related improvements and know-how) for the manufacture and commercialization of two classes of organic arsenicals (water- and lipid-based) for human and animal use. The class of water-based organic arsenicals includes darinaparsin.

As partial consideration for the license rights obtained, the Company made an upfront payment in 2004 of $125 thousand and granted the Licensors 250,487 shares of the Company’s common stock. In addition, the Company issued options to purchase an additional 50,222 shares outside the 2003 Stock Option Plan for $0.002 per share following the successful completion of certain clinical milestones, which vested with respect to 12,555 shares upon the filing of an Investigation New Drug application (“IND”) for darinaparsin in 2005 and vested with respect to another 25,111 shares upon the completion of dosing of the last patient for both Phase 1 clinical trials in 2007. The Company recorded $120 thousand of stock based compensation expense related to the vesting in 2007. The remaining 12,556 shares will vest upon enrollment of the first patient in a multi-center pivotal clinical trial, i.e. a human clinical trial intended to provide the substantial evidence of efficacy necessary to support the filing of an approvable New Drug Application (“NDA”). In addition, the Licensors are entitled to receive certain milestone payments, including $100 thousand that was paid in 2005 upon the commencement of Phase 1 clinical trial and $250 thousand that was paid in 2006 upon the dosing of the first patient in the Company-sponsored Phase 2 clinical trial for darinaparsin. The Company may be required to make additional payments upon achievement of certain other milestones in varying amounts which on a cumulative basis could total up to an additional $4.5 million. In addition, the Licensors are entitled to receive single-digit percentage royalty payments on sales from a licensed product and will also be entitled to receive a portion of any fees that the Company may receive from a possible sublicense under certain circumstances.

The license agreement also contains other provisions customary and common in similar agreements within the industry, such as the right to sublicense the Company rights under the agreement. However, if the Company sublicenses its rights prior to the commencement of a pivotal study, i.e. a human clinical trial intended to provide the substantial evidence of efficacy necessary to support the filing of an approvable NDA, the Licensors will be entitled to receive a share of the payments received by the Company in exchange for the sublicense (subject to certain exceptions). The term of the license agreement extends until the expiration of all claims under patents and patent applications associated with the licensed technology, subject to earlier termination in the event of defaults by the Company or the Licensors under the license agreement, or if the Company becomes bankrupt or insolvent. No milestones under the license agreement were reached or expensed since 2006.

License Agreement with DEKK-Tec, Inc.

On October 15, 2004, the Company entered into a license agreement with DEKK-Tec, Inc., pursuant to which it was granted an exclusive, worldwide license for palifosfamide. As part of the signing of license agreement with DEKK-Tec, the Company expensed an upfront $50 thousand payment to DEKK-Tec in 2004.

In consideration for the license rights, DEKK-Tec is entitled to receive payments upon achieving certain milestones in varying amounts, which on a cumulative basis may total $4.0 million. Of the aggregate milestone payments, most will be creditable against future royalty payments as referenced below. The Company expensed a $100 thousand milestone payment upon achieving Phase 2 milestones during the year ended December 31, 2006. Additionally, in 2004 the Company issued DEKK-Tec an option to purchase 27,616 shares of the Company’s common stock for $0.02 per share. Upon the execution of the license agreement, 6,904 shares vested and were subsequently exercised in 2005 and the remaining options will vest upon certain milestone events, culminating with final FDA approval of the first NDA submitted by the Company (or by its sublicensee) for palifosfamide. DEKK-Tec is entitled to receive single-digit percentage royalty payments on the sales of palifosfamide should it be approved for commercial sale. On March 16, 2010, the Company expensed a $100 thousand milestone payment upon receiving a United States Patent for palifosfamide. In December 2010, the Company expensed a $300 thousand milestone payment and vested 6,904 stock options upon achieving Phase 3 milestones. These options were subsequently exercised in 2011. The Company’s obligation to pay royalties will terminate on a country-by-country basis upon the expiration of all valid claims of patents in such country covering licensed product, subject to earlier termination in the event of defaults by the parties under the license agreement. No milestones under the license agreement were reached or expensed since 2010.

Option Agreement with Southern Research Institute (“SRI”)

On December 22, 2004, the Company entered into an Option Agreement with SRI (the “Option Agreement”), pursuant to which the Company was granted an exclusive option to obtain an exclusive license to SRI’s interest in certain intellectual property, including exclusive rights related to certain isophosphoramide mustard analogs.

Also on December 22, 2004, the Company entered into a Research Agreement with SRI pursuant to which the Company agreed to spend a sum not to exceed $200 thousand between the execution of the agreement and December 21, 2006, including a $25 thousand payment that was made simultaneously with the execution of the agreement, to fund research and development work by SRI in the field of isophosphoramide mustard analogs. The Option Agreement was exercised on February 13, 2007. Under the license agreement entered into upon exercise of the option, the Company is required to remit minimum annual royalty payments of $25 thousand until the first commercial sale of a licensed product. These payments were made for the years ended December 31, 2008, 2009, 2010, 2011 and 2012. The Company may be required to make payments upon achievement of certain milestones in varying amounts which on a cumulative basis could total up to $775 thousand. In addition, SRI will be entitled to receive single digit percentage royalty payments on the sales of a licensed product in any country until all licensed patents rights in that country which are utilized in the product have expired. No milestones under the license agreement were reached or expensed since the agreement’s inception.

License Agreement with Baxter Healthcare Corporation

On November 3, 2006, the Company entered into a definitive Asset Purchase Agreement for indibulin and a License Agreement to proprietary nanosuspension technology with affiliates of Baxter Healthcare S.A. The purchase included the entire indibulin intellectual property portfolio as well as existing drug substance and capsule inventories. The terms of the Asset Purchase Agreement included an upfront cash payment of approximately $1.1 million and an additional $100 thousand payment for existing inventory, both of which were expensed in 2006. In addition to the upfront costs, the Asset Purchase Agreement includes additional diligence and milestone payments that could amount to approximately $8 million in the aggregate and royalties on net sales of products covered by a valid claim of a patent for the life of the patent on a country-by-country basis. The Company expensed a $625 thousand milestone payment upon the successful U.S. IND application for indibulin in 2007. The License Agreement requires payment of a $15 thousand annual patent and license prosecution/maintenance fee through the expiration of the last of the licensed patents, which is expected to expire in 2025, and single-digit royalties on net sales of licensed products covered by a valid claim of a patent for the life of the patent on a country-by-country basis. The term of the license agreement extends until the expiration of the last to expire of the patents covering the licensed products, subject to earlier termination in the event of defaults by the parties under the license agreement.

In October 2009, the Baxter License Agreement was amended to allow the Company to manufacture indibulin. During the year ended December 31, 2012, a milestone of $250 thousand was reached and expensed. No milestones under the license agreement were reached or expensed during the six months ended June 30, 2013.

Exclusive Channel Partner Agreement with Intrexon Corporation

On January 6, 2011, we entered into the Channel Agreement, with Intrexon that governs a “channel partnering” arrangement in which we use Intrexon’s technology directed towards in vivo expression of effectors in connection with the development of DC-RTS-IL-12 and Ad-RTS-IL-12 and generally to research, develop and commercialize products, in each case in which DNA is administered to humans for expression of anti-cancer effectors for the purpose of treatment or prophylaxis of cancer, which we collectively refer to as the Cancer Program. The Channel Agreement establishes committees comprised of representatives of us and Intrexon that govern activities related to the Cancer Program in the areas of project establishment, chemistry, manufacturing and controls, clinical and regulatory matters, commercialization efforts and intellectual property.

The Channel Agreement grants us a worldwide license to use patents and other intellectual property of Intrexon in connection with the research, development, use, importing, manufacture, sale, and offer for sale of products involving DNA administered to humans for expression of anti-cancer effectors for the purpose of treatment or prophylaxis of cancer (collectively the “ZIOPHARM Products”). Such license is exclusive with respect to any clinical development, selling, offering for sale or other commercialization of ZIOPHARM Products, and otherwise is non-exclusive. Subject to limited exceptions, we may not sublicense the rights described without Intrexon’s written consent.

Under the Channel Agreement, and subject to certain exceptions, we are responsible for, among other things, the performance of the Cancer Program, including development, commercialization and certain aspects of manufacturing of ZIOPHARM Products. Intrexon is responsible for the costs of establishing manufacturing capabilities and facilities for the bulk manufacture of products developed under the Cancer Program, certain other aspects of manufacturing and costs of discovery-stage research with respect to platform improvements and costs of filing, prosecution and maintenance of Intrexon’s patents.

Subject to certain expense allocations and other offsets provided in the Channel Agreement, we will pay Intrexon on a quarterly basis 50% of net profits derived in that quarter from the sale of ZIOPHARM Products, calculated on a ZIOPHARM Product-by- ZIOPHARM Product basis. We have likewise agreed to pay Intrexon on a quarterly basis 50% of revenue obtained in that quarter from a sublicensor in the event of a sublicensing arrangement. In addition, in partial consideration for each party’s execution and delivery of the Channel Agreement, we entered into a Stock Purchase Agreement with Intrexon.

Intrexon may terminate the Channel Agreement if we fail to use diligent efforts to develop and commercialize ZIOPHARM Products or if we elect not to pursue the development of a Cancer Program identified by Intrexon that is a “Superior Therapy” as defined in the Channel Agreement. We may voluntarily terminate the Channel Agreement upon 90 days written notice to Intrexon.

Upon termination of the Channel Agreement, we may continue to develop and commercialize any ZIOPHARM Product that, at the time of termination:

•

is being commercialized by us;

•

has received regulatory approval;

•

is a subject of an application for regulatory approval that is pending before the applicable regulatory authority; or

•

is the subject of at least an ongoing Phase 2 clinical trial (in the case of a termination by Intrexon due to an uncured breach or a voluntary termination by us), or an ongoing Phase 1 clinical trial in the field (in the case of a termination by us due to an uncured breach or a termination by Intrexon following an unconsented assignment by us or our election not to pursue development of a Superior Therapy).

Our obligation to pay 50% of net profits or revenue described above with respect to these “retained” products will survive termination of the Channel Agreement.

Also see Notes 6 and 9.

Collaboration Agreement with Harmon Hill, LLC

On April 8, 2008, the Company signed a collaboration agreement for Harmon Hill, LLC (“Harmon Hill”) to provide consulting and other services for the development and commercialization of oncology therapeutics by ZIOPHARM. Under the agreement the Company has agreed to pay Harmon Hill $20 thousand per month for the consulting services and has further agreed to pay Harmon Hill (a) $500 thousand upon the first patient dosing of the Specified Drug in a pivotal trial, which trial uses a dosing Regime introduced by Harmon Hill; and (b) provided that the Specified Drug receives regulatory approval from the FDA, the European Medicines Agency or another regulatory agency for the marketing of the Specified Drug, a 1% royalty of the Company’s net sales will be awarded to Harmon Hill. If the Specified Drug is sublicensed to a third party, the agreement entitles Harmon Hill to 1% award of royalties or other payments received from a sublicense. Subject to renewal or extension by the parties, the term of the agreement was for a one year period that expired April 8, 2009. Following such expiration, the parties continued to operate under the terms of the agreement and, in 2010, the agreement was formally extended through April 8, 2011 and again through April 8, 2012. The agreement was extended through November 8, 2012 upon which date it expired. The Company expensed $240 thousand during the years ended December 31, 2010 and 2011 and expensed $200 thousand during the year ended December 31, 2012 for consulting services per the aforementioned agreement. No milestones under the collaboration agreement were reached or expensed since the agreement’s inception.

On June 27, 2013, the Company signed a new collaboration agreement with Harmon Hill to provide consulting and other services for the development and commercialization of oncology therapeutics by ZIOPHARM. Under the agreement the Company has agreed to pay Harmon Hill $15 thousand per month for the consulting services. Subject to renewal or extension by the parties, the term of the agreement is for a one year period.

Collaboration Agreement with Solasia Pharma K.K.

On March 7, 2011, we entered into a License and Collaboration Agreement with Solasia Pharma K.K., (“Solasia”).

Pursuant to the License and Collaboration Agreement, we granted Solasia an exclusive license to develop and commercialize darinaparsin in both IV and oral forms and related organic arsenic molecules, in all indications for human use in a pan- Asian/Pacific territory comprised of Japan, China, Hong Kong, Macau, Republic of Korea, Taiwan, Singapore, Australia, New Zealand, Malaysia, Indonesia, Philippines and Thailand.

As consideration for the license, we received an upfront payment of $5.0 million to be used exclusively for further clinical development of darinaparsin outside of the pan-Asian/Pacific territory, and will be entitled to receive additional payments of up to $32.5 million in development-based milestones and up to $53.5 million in sales-based milestones. We will also be entitled to receive double-digit royalty payments from Solasia based upon net sales of licensed products in the applicable territories, once commercialized, and a percentage of sublicense revenues generated by Solasia.

The upfront payment for research and development funding is earned over the period of effort. We currently estimate this period to be 75 months, which could be adjusted in the future.

Under the License and Collaboration Agreement, we provide Solasia with drug product to conduct clinical trials. These transfers are accounted for as a reduction of research and development costs and an increase in collaboration receivables.

The agreement provides that Solasia will be responsible for the development and commercialization of darinaparsin in the pan-Asian/Pacific territory.

CRO Services Agreement with PPD Development, L. P.

We are party to a Master Clinical Research Organization Services Agreement with PPD Development, L.P., or PPD, dated January 29, 2010, a related work order dated June 25, 2010 and a related work order dated April 8, 2011 under which PPD provides clinical research organization, or CRO, services in support of our clinical trials. PPD is entitled to cumulative payments of up to $19.9 million under these arrangements, which is payable by us in varying amounts upon PPD achieving specified milestones. During the year ended December 31, 2010, we expensed $1.8 million upon contract execution and $1.1 million upon a clinical study commencement of enrollment in North America. During the year ended December 31, 2011, additional milestones related to commencing enrollment in Europe, Latin America and Asia along with enrollment based milestones were met and we recorded an aggregate $4.0 million expense. During the year ended December 31, 2012, additional enrollment-based and contract modification milestones were met and expensed totaling $3.8 million. During the six months ended June 30, 2013, patient progression and data based milestones were met and expensed totaling $9.1 million.

CRO Services Agreement with Pharmaceutical Research Associates, Inc.

On December 13, 2011, we entered into a Master Clinical Research Organization Services Agreement with Pharmaceutical Research Associates, Inc., or PRA, under which PRA provides CRO services in support of our clinical trials. PRA is entitled to cumulative payments of up to $9.5 million under these arrangements, which is payable by us in varying amounts upon PRA achieving specified milestones. During the year ended December 31, 2012, we expensed $7.3 million upon the achievement of various letter of intent and enrollment-based milestones. During the six months ended June 30, 2013, contract modification and patient enrollment based milestones were met and expensed totaling $2.2 million.

CRO Services Agreement with Novella Clinical, Inc.

On December 4, 2008, we entered into a Master Clinical Research Organization Services Agreement with Novella Clinical, Inc., or Novella, under which PRA provides CRO services in support of our clinical trials. The work order for the current trial being conducted by Novella was signed on November 2, 2012. Novella is entitled to cumulative payments of up to $790 thousand under these arrangements, which is payable by us in varying amounts upon Novella achieving specified milestones. During the year ended December 31, 2012, we expensed $256 thousand upon the achievement of various milestones. During the six months ended June 30, 2013, two database related milestones were met and expensed totaling $126 thousand.

Warrants

6 Months Ended

Jun. 30, 2013

Warrants

8. Warrants

The Company has issued both warrants that are accounted for as liabilities and warrants that are accounted for as equity instruments. The number of warrants outstanding at June 30, 2013 and December 31, 2012 were as follows:


	June 30, 2013		December 31, 2012
Liability-classified warrants		8,050,709		8,050,709
Equity-classified warrants		2,390,722		3,146,745


Total warrants		10,441,431		11,197,454

Liability-Classified Warrants

In May 2005, the Company issued 419,786 warrants to placement agents for services performed in connection with a 2005 private placement (the “2005 Warrants”), 11,083 of which were subsequently exercised. The remaining 408,703 warrants were originally valued at $1.6 million. Subject to certain exceptions, the 2005 Warrants provide for anti-dilution protection should common stock or common stock equivalents be subsequently issued at a price less than the exercise price of the 2005 Warrants then in effect, which was initially $4.75 per share. This provision was triggered when the Company sold stock in a 2006 private placement at $4.63 per share. Accordingly, the 2005 Warrants were re-priced at $4.69. The provision was triggered a second time upon completion of a 2009 private placement in which the Company sold stock at $1.825 per share and issued common stock purchase warrants with an exercise price of $2.04, and the 2005 Warrants were re-priced at $4.25. The provision was triggered again when the Company sold stock in a December 2009 public offering at $3.10 per share and the 2005 Warrants were re-priced at $3.93. Of the total warrant tranche, 419,207 were exercised and the remaining 579 expired on May 31, 2012.

Also, in connection with its December 2009 public securities offering, the Company issued warrants to purchase an aggregate of 8,206,520 shares of common stock (including the investor warrants and 464,520 warrants issued to the underwriters for the offering) (the “2009 Warrants”). The 2009 Warrants issued to investors were exercisable immediately and the warrants issued to underwriters became exercisable six months after the date of issuance. The 2009 Warrants have an exercise price of $4.02 per share and have a five-year term. The fair value of the 2009 Warrants was estimated at $22.9 million using a Black-Scholes model with the following assumptions: expected volatility of 105%, risk free interest rate of 2.14%, expected life of five years and no dividends.

The Company assessed whether the 2005 Warrants and the 2009 Warrants require accounting as derivatives. The Company determined that these warrants were not indexed to the Company’s own stock in accordance with accounting standards codification Topic 815, Derivatives and Hedging. As such, the Company has concluded these warrants did not meet the scope exception for determining whether the instruments require accounting as derivatives and were classified as liabilities.

The Company uses the Binomial/Monte Carlo pricing model to estimate the value of the liability-classified warrants. The following assumptions were used in the Binomial/Monte Carlo valuation model at June 30, 2013 and 2012:


	June 30, 2013			June 30, 2012
Risk-free interest rate		0.26	%		0.37	%
Expected life in years		1.44			2.44
Expected volatility		70	%		70	%
Expected dividend yield		0			0
Steps per year		12			12

The change in the fair value of the warrant liability resulted in a loss of $0.4 million and a gain of $10.4 million for the three and six months ended June 30, 2013, respectively. The change in the fair value of the warrant liability resulted in losses of $0.6 million and $6.4 million for the three and six months ended June 30, 2012, respectively. The change in the fair value of the warrant liability was charged to other income (expense) in the Statements of Operations.

During the six months ended June 30, 2013, warrant exercises were as follows:


(in thousands, except share data)	Equity Warrants		Liability Warrants		Common Stock Issued		Liability Reclassed to Equity		Cash Received
Cash exercises		49,315		—		49,315	$	—	$	101
Cashless exercises		—		—		—		—		—

		49,315		—		49,315	$	—	$	101

During the six months ended June 30, 2012, warrant exercises were as follows:


(in thousands, except share data)	Equity Warrants		Liability Warrants		Common Stock Issued		Liability Reclassed to Equity		Cash Received
Cash exercises		102,744		—		102,744	$	—	$	210
Cashless exercises		12,329		373,617		89,859		412		—

		115,073		373,617		192,603	$	412	$	210

During the six months ended June 30, 2013, 706,708 warrants issued on May 3, 2006, exercisable at $5.09, expired unexercised on May 3, 2013.

During the six months ended June 30, 2012, 1,359,317 warrants issued on February 23, 2007, exercisable at $5.75, expired unexercised on February 23, 2012 and 579 warrants issued on May 31, 2005, exercisable at $3.93, expired unexercised on May 31, 2012.

Common Stock

6 Months Ended

Jun. 30, 2013

Common Stock

9. Common Stock

On January 20, 2012, pursuant to an underwriting agreement between the Company and J. P. Morgan Securities LLC, as representative of the several underwriters named therein, the Company completed the sale of an aggregate 10,114,401 shares of the Company’s common stock at a price of $5.20 per share in a public offering. The total gross proceeds resulting from the 2012 public offering were approximately $52.6 million, before deducting selling commissions and expenses.

On November 7, 2012, the Company issued 3,636,926 shares of our common stock, which we refer to as the Milestone Shares, to Intrexon under the terms of its Stock Purchase Agreement with Intrexon dated January 6, 2011. Under the terms of the Stock Purchase Agreement with Intrexon, the Company agreed to issue the Milestone Shares under certain conditions upon dosing of the first patient in a ZIOPHARM-conducted Phase 2 clinical trial in the Unites States, or similar study as the parties may agree in a country other than the United States, of a product candidate that is created, produced, developed or identified directly or indirectly by us during the term of the Channel Agreement and that, subject to certain exceptions, involves DNA administered to humans for expression of anti-cancer effectors for the purpose of treatment or prophylaxis of cancer. On October 24, 2012, the Company initiated dosing in a Phase 2 study of Ad-RTS-IL-12 for unresectable Stage III or IV melanoma, triggering the issuance of the Milestone Shares.

Stock-Based Compensation

6 Months Ended

Jun. 30, 2013

Stock-Based Compensation

10. Stock-Based Compensation

The Company recognized stock-based compensation expense on all employee and non-employee awards as follows:


	For the three months ended June 30,					For the six months ended June 30,
(in thousands)	2013			2012		2013		2012
Research and development	$	(145	)	$	426	$	392	$	942
General and administrative		277			652		1,281		1,348

Stock-based employee compensation expense	$	132		$	1,078	$	1,673	$	2,290

The Company granted 1,315,500 and 1,426,400 stock options during the three and six months ended June 30, 2013 that had a weighted-average grant date fair value of $1.77 and $1.89 per share, respectively. The Company granted 361,900 and 425,400 stock options during the three and six months ended June 30, 2012 that had a weighted-average grant date fair value of $3.51 and $3.48 per share, respectively.

At June 30, 2013, total unrecognized compensation costs related to unvested stock options outstanding amounted to $6.3 million. The cost is expected to be recognized over a weighted-average period of 1.74 years.

On July 16, 2012, the Company extended the contractual life of 829,488 fully vested stock options held by 3 employees from 12 to 18 months, and extended the vesting period for 200,000 unvested stock options and 147,427 unvested shares of restricted stock held by 2 employees from 6 to 12 months (also see Note 3 Restructuring).

On May 31, 2013, the Company extended the contractual life of 66,667 fully vested stock options held by one employee from 3 to 12 months.

For the six months ended June 30, 2013 and 2012, the fair value of stock options was estimated on the date of grant using a Black-Scholes option valuation model with the following assumptions:


	For the three months ended June 30,
	2013			2012
Risk-free interest rate		1.65	%	0.93 - 1.10%
Expected life in years		6		6
Expected volatility		95.45	%	83.36 - 83.52%
Expected dividend yield		0		0

Stock option activity under the Company’s stock option plan for the six months ended June 30, 2013 is as follows:


(in thousands, except share and per share data)	Number of Shares			Weighted- Average Exercise Price		Weighted- Average Contractual Term (Years)		Aggregate Intrinsic Value
Outstanding, December 31, 2012		7,147,303		$	4.11

Granted		1,426,400			2.49
Exercised		(455,168	)		1.87
Cancelled		(1,580,116	)		4.73


Outstanding, June 30, 2013		6,538,419		$	3.76		7.11	$	956


Vested and unvested expected to vest at June 30, 2013		6,481,884		$	3.85		5.03	$	948


Options exercisable, June 30, 2013		3,406,985		$	3.85		5.03	$	956


Options exercisable, December 31, 2012		3,683,786		$	3.56		5.28	$	3,972


Options available for future grant		1,430,403

A summary of the status of unvested restricted stock for the six months ended June 30, 2013 is as follows:


	Number of Shares			Weighted-Average Grant Date Fair Value
Non-vested, December 31, 2012		733,739		$	4.37
Granted		—			—
Vested		(138,814	)		4.26
Cancelled		(140,600	)		4.42


Non-vested, June 30, 2013		454,325		$	4.38

At June 30, 2013, total unrecognized compensation costs related to unvested restricted stock outstanding amounted to $1.4 million. The cost is expected to be recognized over a weighted-average period of 1.44 years.

Fair Value Measurements (Tables)

6 Months Ended

Jun. 30, 2013

Assets and Liabilities Measured at Fair Value on Recurring Basis

Assets and liabilities measured at fair value on a recurring basis as of June 30, 2013 and December 31, 2012 are as follows:


($ in thousands)			Fair Value Measurements at Reporting Date Using
Description	Balance as of June 30, 2013		Quoted Prices in Active Markets for Identical Assets/Liabilities (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Cash equivalents	$	36,709	$	36,709	$	—	$	—


Warrant liability	$	2,576	$	—	$	2,576	$	—


($ in thousands)			Fair Value Measurements at Reporting Date Using
Description	Balance as of December 31, 2012		Quoted Prices in Active Markets for Identical Assets/Liabilities (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)

Cash equivalents	$	72,002	$	72,002	$	—	$	—


Warrant liability	$	12,962	$	—	$	12,962	$	—

Net Loss per Share (Tables)

6 Months Ended

Jun. 30, 2013

Potential Dilutive Shares Excluded from Computation of Diluted Net Loss Per Share

The Company’s potential dilutive shares, which include outstanding common stock options, unvested restricted stock and warrants, have not been included in the computation of diluted net loss per share for any of the periods presented as the result would be anti-dilutive. Such potential shares of common stock at June 30, 2013 and 2012 consist of the following:


	June 30,
	2013		2012
Stock options		6,538,419		5,397,154
Unvested restricted common stock		454,325		1,029,848
Warrants		10,441,431		11,268,678

		17,434,175		17,695,680

Warrants (Tables)

6 Months Ended

Jun. 30, 2013

Number of Warrants Outstanding

The number of warrants outstanding at June 30, 2013 and December 31, 2012 were as follows:


	June 30, 2013		December 31, 2012
Liability-classified warrants		8,050,709		8,050,709
Equity-classified warrants		2,390,722		3,146,745


Total warrants		10,441,431		11,197,454

Assumptions Used In Binomial and Monte Carlo Valuation Model

The following assumptions were used in the Binomial/Monte Carlo valuation model at June 30, 2013 and 2012:


	June 30, 2013			June 30, 2012
Risk-free interest rate		0.26	%		0.37	%
Expected life in years		1.44			2.44
Expected volatility		70	%		70	%
Expected dividend yield		0			0
Steps per year		12			12

Warrant Exercises

During the six months ended June 30, 2013, warrant exercises were as follows:


(in thousands, except share data)	Equity Warrants		Liability Warrants		Common Stock Issued		Liability Reclassed to Equity		Cash Received
Cash exercises		49,315		—		49,315	$	—	$	101
Cashless exercises		—		—		—		—		—

		49,315		—		49,315	$	—	$	101

During the six months ended June 30, 2012, warrant exercises were as follows:


(in thousands, except share data)	Equity Warrants		Liability Warrants		Common Stock Issued		Liability Reclassed to Equity		Cash Received
Cash exercises		102,744		—		102,744	$	—	$	210
Cashless exercises		12,329		373,617		89,859		412		—

		115,073		373,617		192,603	$	412	$	210

- Definition

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

+ References + Details

Stock-Based Compensation (Tables)

6 Months Ended

Jun. 30, 2013

Stock-Based Compensation Expense on All Employee and Non-Employee Awards

The Company recognized stock-based compensation expense on all employee and non-employee awards as follows:


	For the three months ended June 30,					For the six months ended June 30,
(in thousands)	2013			2012		2013		2012
Research and development	$	(145	)	$	426	$	392	$	942
General and administrative		277			652		1,281		1,348

Stock-based employee compensation expense	$	132		$	1,078	$	1,673	$	2,290

Fair Value of Stock Options Assumptions Using Black-Scholes Option Valuation Model

For the six months ended June 30, 2013 and 2012, the fair value of stock options was estimated on the date of grant using a Black-Scholes option valuation model with the following assumptions:


	For the three months ended June 30,
	2013			2012
Risk-free interest rate		1.65	%	0.93 - 1.10%
Expected life in years		6		6
Expected volatility		95.45	%	83.36 - 83.52%
Expected dividend yield		0		0

Stock Option Activity Under Stock Option Plan

Stock option activity under the Company’s stock option plan for the six months ended June 30, 2013 is as follows:


(in thousands, except share and per share data)	Number of Shares			Weighted- Average Exercise Price		Weighted- Average Contractual Term (Years)		Aggregate Intrinsic Value
Outstanding, December 31, 2012		7,147,303		$	4.11

Granted		1,426,400			2.49
Exercised		(455,168	)		1.87
Cancelled		(1,580,116	)		4.73


Outstanding, June 30, 2013		6,538,419		$	3.76		7.11	$	956


Vested and unvested expected to vest at June 30, 2013		6,481,884		$	3.85		5.03	$	948


Options exercisable, June 30, 2013		3,406,985		$	3.85		5.03	$	956


Options exercisable, December 31, 2012		3,683,786		$	3.56		5.28	$	3,972


Options available for future grant		1,430,403

Summary of Unvested Restricted Stock

A summary of the status of unvested restricted stock for the six months ended June 30, 2013 is as follows:


	Number of Shares			Weighted-Average Grant Date Fair Value
Non-vested, December 31, 2012		733,739		$	4.37
Granted		—			—
Vested		(138,814	)		4.26
Cancelled		(140,600	)		4.42


Non-vested, June 30, 2013		454,325		$	4.38

Business - Additional Information (Detail) - USD ($) $ in Thousands	Jun. 30, 2013	Dec. 31, 2012
Nature Of Business [Line Items]
Accumulated deficit	$ 315,215	$ 283,724

Restructuring - Additional Information (Detail) $ in Millions	1 Months Ended	3 Months Ended	118 Months Ended
	Apr. 03, 2013 Position	Jun. 30, 2013 USD ($)	Jun. 30, 2013 USD ($)
Restructuring Cost and Reserve [Line Items]
Total charges incurred related to workforce reduction \| $		$ 1.6
Number of positions eliminated	65
Severance and Health Benefit Continuation Costs
Restructuring Cost and Reserve [Line Items]
Restructuring charges relating to severance and other \| $			$ 1.3
Filled positions
Restructuring Cost and Reserve [Line Items]
Number of positions eliminated	40
Unfilled positions
Restructuring Cost and Reserve [Line Items]
Number of positions eliminated	25

Assets and Liabilities Measured at Fair Value on Recurring Basis (Detail) - USD ($) $ in Thousands	Jun. 30, 2013	Dec. 31, 2012
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Cash equivalents	$ 36,709	$ 72,002
Warrant liability	2,576	12,962
Quoted Prices in Active Markets for Identical Assets/Liabilities (Level 1)
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Cash equivalents	36,709	72,002
Significant Other Observable In puts (Level 2)
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Warrant liability	$ 2,576	$ 12,962

Potential Dilutive Shares Excluded from Computation of Diluted Net Loss Per Share (Detail) - shares	6 Months Ended
	Jun. 30, 2013	Jun. 30, 2012
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	17,434,175	17,695,680
Stock Option
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	6,538,419	5,397,154
Unvested Restricted Common Stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	454,325	1,029,848
Warrant Exercise
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	10,441,431	11,268,678

Related Party Transactions - Additional Information (Detail) - USD ($) $ in Thousands	1 Months Ended		6 Months Ended
	Nov. 07, 2012	Jan. 25, 2012	Jun. 30, 2013	Jun. 30, 2012	Dec. 31, 2012
Related Party Transaction [Line Items]
Remaining service expenses expected to be incurred			$ 4,067		$ 6,912
Intrexon Corporation
Related Party Transaction [Line Items]
Payments for services				$ 10,700
Amounts paid for services incurred			3,700	2,500
Remaining service expenses expected to be incurred			$ 1,100	$ 8,200
Issuance of common stock	3,636,926	1,923,075

Commitments and Contingencies - Additional Information (Detail) - USD ($)	1 Months Ended						3 Months Ended		6 Months Ended		12 Months Ended							24 Months Ended	118 Months Ended
	Jun. 27, 2013	Jan. 06, 2011	Mar. 16, 2010	Apr. 08, 2008	Nov. 03, 2006	Oct. 15, 2004	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2007	Dec. 31, 2006	Dec. 31, 2005	Dec. 31, 2004	Dec. 21, 2006	Jun. 30, 2013	Nov. 02, 2012	Dec. 13, 2011	Jan. 29, 2010
Commitments and Contingencies Disclosure [Line Items]
Shares of common stock granted							1,315,500	361,900	1,426,400	425,400
Stock based compensation expenses							$ 132,000	$ 1,078,000	$ 1,673,000	$ 2,290,000									$ 21,854,000
Research expenses							14,775,000	$ 18,264,000	33,887,000	$ 32,249,000									246,232,000
Milestones under the license agreement expense									0		$ 250,000
Harmon Hill LLC \| Collaboration Agreement
Commitments and Contingencies Disclosure [Line Items]
Percent of company net profit											1.00%
Other expense											$ 200,000	$ 240,000	$ 240,000
Agreement period	1 year
Harmon Hill LLC \| Collaboration Agreement \| Upon the dosing of the first patient
Commitments and Contingencies Disclosure [Line Items]
Payment for consulting services fee				$ 500,000
Harmon Hill LLC \| Monthly Payment \| Collaboration Agreement
Commitments and Contingencies Disclosure [Line Items]
Payment for consulting services fee	$ 15,000			$ 20,000
Solasia
Commitments and Contingencies Disclosure [Line Items]
Upfront payment received											5,000,000
Solasia \| Development-based milestones
Commitments and Contingencies Disclosure [Line Items]
Expected Additional milestone payments to be received											32,500,000
Solasia \| Sales-based milestones
Commitments and Contingencies Disclosure [Line Items]
Expected Additional milestone payments to be received											$ 53,500,000
DEKK Tec Inc
Commitments and Contingencies Disclosure [Line Items]
Option to purchase common stock																	27,616
Sale of stock, price per share																	$ 0.02
Shares vested																	$ 6,904
Milestone maximum payment						$ 4,000,000
DEKK Tec Inc \| Upon the dosing of the first patient
Commitments and Contingencies Disclosure [Line Items]
Milestone payment															$ 100,000
DEKK Tec Inc \| Phase 3
Commitments and Contingencies Disclosure [Line Items]
Shares vested													6,904
Milestone payment													300,000
DEKK Tec Inc \| Upon receiving a United States Patent for palifosfamide
Commitments and Contingencies Disclosure [Line Items]
Milestone payment			$ 100,000
DEKK Tec Inc \| Up Front Payment
Commitments and Contingencies Disclosure [Line Items]
Licensing fee						$ 50,000
Intrexon Corporation
Commitments and Contingencies Disclosure [Line Items]
Contract termination description											Our obligation to pay 50% of net profits or revenue described above with respect to these "retained" products will survive termination of the Channel Agreement
Intrexon Corporation \| Quarterly Payment
Commitments and Contingencies Disclosure [Line Items]
Percent of company net profit		50.00%
Percentage of revenue agreed to pay which is obtained from sublicensor		50.00%
Southern Research Institute
Commitments and Contingencies Disclosure [Line Items]
Milestone maximum payment							775,000		775,000										775,000
Royalty payment									25,000
Southern Research Institute \| Execution Agreement
Commitments and Contingencies Disclosure [Line Items]
Research expenses																		$ 25,000
Southern Research Institute \| Maximum
Commitments and Contingencies Disclosure [Line Items]
Research expenses																		$ 200,000
The University Of Texas M.D. Anderson Cancer Center And The Texas A& M University System
Commitments and Contingencies Disclosure [Line Items]
Shares of common stock granted																	250,487
Option to purchase common stock																	50,222
Sale of stock, price per share																	$ 0.002
Stock based compensation expenses														$ 120,000
Milestone maximum payment							$ 4,500,000		$ 4,500,000										$ 4,500,000
The University Of Texas M.D. Anderson Cancer Center And The Texas A& M University System \| Upon the commencement of Phase 1 clinical trial
Commitments and Contingencies Disclosure [Line Items]
Milestone payment																$ 100,000
The University Of Texas M.D. Anderson Cancer Center And The Texas A& M University System \| Upon the dosing of the first patient
Commitments and Contingencies Disclosure [Line Items]
Milestone payment															$ 250,000
The University Of Texas M.D. Anderson Cancer Center And The Texas A& M University System \| Upon the filing of an Investigation New Drug application (IND) for darinaparsin
Commitments and Contingencies Disclosure [Line Items]
Shares vested																$ 12,555
The University Of Texas M.D. Anderson Cancer Center And The Texas A& M University System \| Upon the completion of dosing of the last patient for both Phase 1 clinical trials
Commitments and Contingencies Disclosure [Line Items]
Shares vested														25,111
The University Of Texas M.D. Anderson Cancer Center And The Texas A& M University System \| Upon enrollment of the first patient in a multi-center pivotal clinical trial
Commitments and Contingencies Disclosure [Line Items]
Shares expected to vest							12,556		12,556										12,556
The University Of Texas M.D. Anderson Cancer Center And The Texas A& M University System \| Up Front Payment
Commitments and Contingencies Disclosure [Line Items]
Licensing fee																	$ 125,000
Baxter Healthcare Corporation
Commitments and Contingencies Disclosure [Line Items]
Annual patent and license prosecution/maintenance fee					$ 15,000
Baxter Healthcare Corporation \| Upon the successful U.S. IND application for indibulin
Commitments and Contingencies Disclosure [Line Items]
Milestone payment														$ 625,000
Baxter Healthcare Corporation \| Assets
Commitments and Contingencies Disclosure [Line Items]
Asset Purchase Agreement, upfront cash payment					1,100,000
Baxter Healthcare Corporation \| Inventories
Commitments and Contingencies Disclosure [Line Items]
Asset Purchase Agreement, upfront cash payment					100,000
Baxter Healthcare Corporation \| Royalty Payments
Commitments and Contingencies Disclosure [Line Items]
Milestone maximum payment					$ 8,000,000
PPD Development L. P.
Commitments and Contingencies Disclosure [Line Items]
Milestone maximum payment																						$ 19,900,000
PPD Development L. P. \| Upon the achievement of various milestones
Commitments and Contingencies Disclosure [Line Items]
Milestone payment									$ 9,100,000
PPD Development L. P. \| Upon contract execution
Commitments and Contingencies Disclosure [Line Items]
Milestone payment													1,800,000
PPD Development L. P. \| Upon a clinical study commencement of enrollment in North America
Commitments and Contingencies Disclosure [Line Items]
Milestone payment													$ 1,100,000
PPD Development L. P. \| Upon initial clinical study enrollment
Commitments and Contingencies Disclosure [Line Items]
Milestone payment											$ 3,800,000	$ 4,000,000
Pharmaceutical Research Associates Inc
Commitments and Contingencies Disclosure [Line Items]
Milestone maximum payment																					$ 9,500,000
Pharmaceutical Research Associates Inc \| Upon the achievement of various milestones
Commitments and Contingencies Disclosure [Line Items]
Milestone payment									2,200,000		7,300,000
Novella Clinical, Inc.
Commitments and Contingencies Disclosure [Line Items]
Milestone maximum payment																				$ 790,000
Novella Clinical, Inc. \| Upon the achievement of various milestones
Commitments and Contingencies Disclosure [Line Items]
Milestone payment											$ 256,000
Novella Clinical, Inc. \| Upon two database related milestones
Commitments and Contingencies Disclosure [Line Items]
Milestone payment									$ 126,000

Number of Warrants Outstanding (Detail) - shares	Jun. 30, 2013	Dec. 31, 2012
Class of Warrant or Right [Line Items]
Classified warrants	10,441,431	11,197,454
Liabilities
Class of Warrant or Right [Line Items]
Classified warrants	8,050,709	8,050,709
Equity
Class of Warrant or Right [Line Items]
Classified warrants	2,390,722	3,146,745

Warrants - Additional Information (Detail) $ / shares in Units, $ in Thousands	1 Months Ended				3 Months Ended		6 Months Ended		12 Months Ended	118 Months Ended
	May 31, 2012 shares	Feb. 23, 2007 $ / Right shares	May 03, 2006 $ / Right shares	May 31, 2005 USD ($) $ / shares $ / Right shares	Jun. 30, 2013 USD ($) shares	Jun. 30, 2012 USD ($)	Jun. 30, 2013 USD ($) shares	Jun. 30, 2012 USD ($)	Dec. 31, 2009 USD ($) yr $ / shares shares	Jun. 30, 2013 USD ($) shares	Dec. 31, 2012 shares	Dec. 31, 2006 $ / shares
Class of Warrant or Right [Line Items]
Warrant issued		1,359,317	706,708	579
Warrant outstanding					10,441,431		10,441,431			10,441,431	11,197,454
Warrants to purchase an aggregate of shares of common stock									8,206,520
Warrant term									5 years
Estimated fair value of warrant \| $									$ 22,900
Expected volatility									105.00%
Risk free interest									2.14%
Expected life \| yr									5
Expected dividend yield									0.00%
Other income (expense) \| $					$ 7	$ 3	$ 3	$ (23)		$ 4,704
Warrants expiration date		Feb. 23, 2012	May 03, 2013	May 31, 2012
Warrant exercise price \| $ / Right		5.75	5.09	3.93
Liability Warrants
Class of Warrant or Right [Line Items]
Other income (expense) \| $					$ (400)	$ (600)	$ 10,400	$ (6,400)
J. P. Morgan Securities LLC
Class of Warrant or Right [Line Items]
Warrants issued									464,520
Warrant exercise Price \| $ / shares									$ 4.02
Warrant exercisable Period									6 months
Private Placement
Class of Warrant or Right [Line Items]
Warrant issued				419,786
Warrant exercised	419,207			11,083
Warrant outstanding				408,703
Value of warrant issued \| $				$ 1,600
Sale of stock price per share \| $ / shares				$ 4.75					$ 1.825			$ 4.63
Revised price for warrants \| $ / shares				$ 4.69					4.25
Common stock warrants exercise price \| $ / shares									2.04
Warrant expired	579
Registered direct offering
Class of Warrant or Right [Line Items]
Revised price for warrants \| $ / shares									3.93
Issuable price for common stock \| $ / shares									$ 3.10

Assumptions Used In Binomial and Monte Carlo Valuation Model (Detail) - yr	Jun. 30, 2013	Jun. 30, 2012	Dec. 31, 2009
Class of Warrant or Right [Line Items]
Risk-free interest rate			2.14%
Expected volatility			105.00%
Expected dividend yield			0.00%
Expected life in years			5
Binomial/Monte Carlo Option Pricing Model
Class of Warrant or Right [Line Items]
Risk-free interest rate	0.26%	0.37%
Expected volatility	70.00%	70.00%
Expected dividend yield	0.00%	0.00%
Expected life in years	12	12
Binomial/Monte Carlo Option Pricing Model \| Minimum
Class of Warrant or Right [Line Items]
Expected life in years	1.44	2.44

Warrant Exercise (Detail) - USD ($) $ in Thousands	6 Months Ended		118 Months Ended
Warrant Exercise (Detail) - USD ($) $ in Thousands	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013
Class of Warrant or Right [Line Items]
Liability Reclassed to Equity		$ 412
Cash Received	$ 101	$ 210	$ 13,180
Equity Warrants
Class of Warrant or Right [Line Items]
Number Of Warrants Exercised	49,315	115,073
Liability Warrants
Class of Warrant or Right [Line Items]
Number Of Warrants Exercised		373,617
Common Stock Issued
Class of Warrant or Right [Line Items]
Number Of Warrants Exercised	49,315	192,603
Cash exercises
Class of Warrant or Right [Line Items]
Cash Received	$ 101	$ 210
Cash exercises \| Equity Warrants
Class of Warrant or Right [Line Items]
Number Of Warrants Exercised	49,315	102,744
Cash exercises \| Common Stock Issued
Class of Warrant or Right [Line Items]
Number Of Warrants Exercised	49,315	102,744
Cashless Exercise
Class of Warrant or Right [Line Items]
Liability Reclassed to Equity		$ 412
Cashless Exercise \| Equity Warrants
Class of Warrant or Right [Line Items]
Number Of Warrants Exercised		12,329
Cashless Exercise \| Liability Warrants
Class of Warrant or Right [Line Items]
Number Of Warrants Exercised		373,617
Cashless Exercise \| Common Stock Issued
Class of Warrant or Right [Line Items]
Number Of Warrants Exercised		89,859

Common Stock - Additional Information (Detail) - USD ($) $ / shares in Units, $ in Millions	1 Months Ended
	Nov. 07, 2012	Jan. 25, 2012	Jan. 20, 2012
Class of Stock [Line Items]
Common Stock Shares Sold			10,114,401
Common stock price per share			$ 5.20
Proceeds from issuance of common stock			$ 52.6
Intrexon Corporation
Class of Stock [Line Items]
Issuance of common stock	3,636,926	1,923,075

Stock-Based Compensation Expense on All Employee and Non-Employee Awards (Detail) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended		118 Months Ended
	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	$ 132	$ 1,078	$ 1,673	$ 2,290	$ 21,854
Research and Development Expense
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	(145)	426	392	942
General and Administrative Expense
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	$ 277	$ 652	$ 1,281	$ 1,348

Stock-Based Compensation - Additional Information (Detail) - USD ($) $ / shares in Units, $ in Millions	1 Months Ended		3 Months Ended		6 Months Ended
	May 31, 2013	Jul. 16, 2012	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options, granted			1,315,500	361,900	1,426,400	425,400
Weighted-average grant date fair value			$ 1.77	$ 3.51	$ 1.89	$ 3.48
Unrecognized compensation costs			$ 6.3		$ 6.3
Expected recognition period					1 year 8 months 27 days
Unvested Restricted Common Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected recognition period					1 year 5 months 9 days
Unrecognized compensation costs			$ 1.4		$ 1.4
Vested options held by 3 employees
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share Based Compensation Arrangement By Share Based Payment Award Option Fully Vested		829,488
Vested options held by 3 employees \| Minimum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Award Vesting Period		12 months
Vested options held by 3 employees \| Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Award Vesting Period		18 months
Unvested options held by 2 employees
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share Based Compensation Arrangement By Share Based Payment Award Unvested Options		200,000
Share Based Compensation Arrangement By Share Based Payment Award Unvested Shares Of Restricted Stocks		147,427
Unvested options held by 2 employees \| Minimum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Award Vesting Period		6 months
Unvested options held by 2 employees \| Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Award Vesting Period		12 months
Vested options held by 1 employees
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share Based Compensation Arrangement By Share Based Payment Award Option Fully Vested	66,667
Vested options held by 1 employees \| Minimum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Award Vesting Period	3 months
Vested options held by 1 employees \| Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Award Vesting Period	12 months

Fair Value of Stock Options Assumptions Using Black-Scholes Option Valuation Model (Detail)	3 Months Ended
	Jun. 30, 2013	Jun. 30, 2012
Share based Compensation Arrangement by Share based Payment Award, Fair Value Assumptions, Method Used [Line Items]
Risk-free interest rate	1.65%
Risk-free interest rate, Minimum		0.93%
Risk-free interest rate, Maximum		1.10%
Expected life in years	6 years	6 years
Expected volatility	95.45%
Expected volatility, Minimum		83.36%
Expected volatility,Maximum		83.52%
Expected dividend yield	0.00%	0.00%

Stock Option Activity Under Stock Option Plan (Detail) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012	Dec. 31, 2012
Number of Shares
Beginning Balance			7,147,303
Granted	1,315,500	361,900	1,426,400	425,400
Exercised			(455,168)
Cancelled			(1,580,116)
Ending Balance	6,538,419		6,538,419		7,147,303
Vested and unvested expected to vest at end of period	6,481,884		6,481,884
Options exercisable, at end of period	3,406,985		3,406,985		3,683,786
Options available for future grant	1,430,403		1,430,403
Weighted Average Exercise Price
Beginning Balance			$ 4.11
Granted			2.49
Exercised			1.87
Cancelled			4.73
Ending Balance	$ 3.76		3.76		$ 4.11
Vested and unvested expected to vest at end of period	3.85		3.85
Options exercisable, at end of period	$ 3.85		$ 3.85		$ 3.56
Weighted Average Contractual Term (Years)
Outstanding, at end of period			7 years 1 month 10 days
Vested and unvested expected to vest at end of period			5 years 11 days
Options exercisable, at end of period			5 years 11 days		5 years 3 months 11 days
Aggregate Intrinsic Value
Outstanding, at end of period	$ 956		$ 956
Vested and unvested expected to vest at end of period	948		948
Options exercisable, at end of period	$ 956		$ 956		$ 3,972

Summary of Unvested Restricted Stock (Detail) - Unvested Restricted Common Stock	6 Months Ended
	Jun. 30, 2013 $ / shares shares
Number of Shares
Beginning Balance \| shares	733,739
Granted \| shares
Vested \| shares	(138,814)
Cancelled \| shares	(140,600)
Ending Balance \| shares	454,325
Weighted Average Grant Date Fair Value
Beginning Balance \| $ / shares	$ 4.37
Granted \| $ / shares
Vested \| $ / shares	4.26
Cancelled \| $ / shares	4.42
Ending Balance \| $ / shares	$ 4.38