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Document and Entity Information - USD ($)	12 Months Ended
Document and Entity Information - USD ($)	Dec. 31, 2013	Feb. 10, 2014	Jun. 30, 2013
Document Information [Line Items]
Document Type	10-K
Amendment Flag	false
Document Period End Date	Dec. 31, 2013
Document Fiscal Year Focus	2013
Document Fiscal Period Focus	FY
Trading Symbol	ZIOP
Entity Registrant Name	ZIOPHARM ONCOLOGY INC
Entity Central Index Key	0001107421
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	No
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		100,556,625
Entity Public Float			$ 141,663,241

Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Current assets:
Cash and cash equivalents	$ 68,204	$ 73,306
Receivables	145	58
Prepaid expenses and other current assets	1,948	6,912
Total current assets	70,297	80,276
Property and equipment, net	801	1,994
Deposits	128	133
Other non current assets	528	1,001
Total assets	71,754	83,404
Current liabilities:
Accounts payable	422	1,509
Accrued expenses	6,357	16,516
Deferred revenue-current portion	800	800
Deferred rent-current portion	212	39
Total current liabilities	7,791	18,864
Deferred revenue	1,933	2,733
Deferred rent	851	400
Warrant liabilities	11,776	12,962
Other long term liabilities	20	0
Total liabilities	22,371	34,959
Commitments and contingencies (note 8)
Stockholders' equity:
Preferred stock, $0.001 par value; 30,000,000 shares authorized and no shares issued and outstanding	0	0
Common stock, $0.001 par value; 250,000,000 shares authorized; 100,159,618 and 83,236,840 shares issued and outstanding at December 31, 2013 and 2012, respectively	100	83
Additional paid-in capital-common stock	386,511	325,177
Additional paid-in capital-warrants issued	3,603	6,909
Deficit accumulated during the development stage	(340,831)	(283,724)
Total stockholders' equity	49,383	48,445
Total liabilities and stockholders' equity	$ 71,754	$ 83,404

Statements of Operations - USD ($) $ in Thousands	12 Months Ended			124 Months Ended
Statements of Operations - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2013
Revenue	$ 800	$ 800	$ 667	$ 2,267
Operating expenses:
Research and development	42,852	83,446	57,083	255,197
General and administrative	15,661	19,523	14,984	103,979
Total operating expenses	58,513	102,969	72,067	359,176
Loss from operations	(57,713)	(102,169)	(71,400)	(356,909)
Other income (expense), net	(579)	(13)	39	4,122
Change in fair value of warrants	1,185	6,050	7,583	11,956
Net loss	$ (57,107)	$ (96,132)	$ (63,778)	$ (340,831)
Basic and diluted net loss per share	$ (0.66)	$ (1.22)	$ (0.97)
Weighted average common shares outstanding used to compute basic and diluted net loss per share	85,943,175	78,546,112	66,003,789

Statement of Stockholders' Equity - USD ($) $ in Thousands	Total	Series A Preferred Stock	Warrants	Common Stock	Additional Paid in Capital, Common Stock	Other Additional Capital	Accumulated Deficit during Development Stage
Beginning Balance (in shares) at Sep. 09, 2003				250,487
Beginning Balance at Sep. 09, 2003	$ 500				$ 500
Net Loss	(160)						$ (160)
Ending Balance (in shares) at Dec. 31, 2003				250,487
Ending Balance at Dec. 31, 2003	340				500		(160)
Beginning Balance (in shares) at Sep. 09, 2003				250,487
Beginning Balance at Sep. 09, 2003	500				500
Net Loss	(15,364)
Ending Balance (in shares) at Dec. 31, 2005				7,247,992
Ending Balance at Dec. 31, 2005	7,202			$ 7	20,580	$ 1,979	(15,364)
Beginning Balance (in shares) at Sep. 09, 2003				250,487
Beginning Balance at Sep. 09, 2003	500				500
Net Loss	(340,831)
Ending Balance (in shares) at Dec. 31, 2013				100,159,618
Ending Balance at Dec. 31, 2013	49,383			$ 100	386,511	3,603	(340,831)
Beginning Balance (in shares) at Dec. 31, 2003				250,487
Beginning Balance at Dec. 31, 2003	340				500		(160)
Fair value of options/warrants issued \| Non-employee services	264				13	251
Issuance of common stock (in shares) \| All Other				2,254,389
Issuance of common stock (in shares) \| Services				256,749
Issuance of common stock \| All Other	4,500			$ 2	4,498
Issuance of common stock \| Services	439			$ 1	438
Net Loss	(5,687)						(5,687)
Ending Balance (in shares) at Dec. 31, 2004				2,761,625
Ending Balance at Dec. 31, 2004	(144)			$ 3	5,449	251	(5,847)
Issuance of Series A convertible preferred stock (net of expenses of $1,340 and warrant cost of $1,683) (in shares)		4,197,946
Issuance of Series A convertible preferred stock (net of expenses of $1,340 and warrant cost of $1,683)	15,077	$ 15,077
Fair value of options/warrants issued \| Non-employee services	99				54	45
Fair value of options/warrants issued	1,683		$ 1,683
Issuance of common stock to EasyWeb Stockholders				189,922
Conversion of Series A convertible preferred stock @ $0.001 into $0.001 common stock on September 13, 2005 at an exchange ratio of .500974 (in shares)		(4,197,946)		4,197,823
Conversion of Series A convertible preferred stock @ $0.001 into $0.001 common stock on September 13, 2005 at an exchange ratio of .500974		$ (15,077)	$ (1,683)	$ 4	15,073	1,683
Exercise of stock options				98,622
Exercise of stock options	4				4
Net Loss	(9,517)						(9,517)
Ending Balance (in shares) at Dec. 31, 2005				7,247,992
Ending Balance at Dec. 31, 2005	7,202			$ 7	20,580	1,979	(15,364)
Fair value of options/warrants issued	13,092					13,092
Stock-based compensation	2,777				2,777
Issuance of common stock (in shares) \| Services				25,000
Issuance of common stock (in shares) \| Private Placement				7,991,256
Issuance of common stock \| Services	106				106
Issuance of common stock \| Private Placement	21,188			$ 8	21,180
Exercise of warrants to purchase common stock (in shares)				2,806
Exercise of stock options				5,845
Exercise of stock options	25				25
Net Loss	(17,857)						(17,857)
Ending Balance (in shares) at Dec. 31, 2006				15,272,899
Ending Balance at Dec. 31, 2006	26,533			$ 15	44,668	15,071	(33,221)
Fair value of options/warrants issued	5,433					5,433
Stock-based compensation \| Employees	1,318				1,318
Stock-based compensation \| Non-employee services	120				120
Issuance of common stock (in shares) \| Private Placement				5,910,049
Issuance of common stock \| Private Placement	23,538			$ 6	23,532
Exercise of stock options				46,016
Exercise of stock options	36				36
Issuance of restricted common stock				70,000
Net Loss	(26,608)						(26,608)
Ending Balance (in shares) at Dec. 31, 2007				21,298,964
Ending Balance at Dec. 31, 2007	30,370			$ 21	69,674	20,504	(59,829)
Stock-based compensation	1,600				1,600
Issuance of restricted common stock				586,500
Issuance of restricted common stock				$ 1	(1)
Cancelled/ Forfeiture of unvested restricted common stock				(25,000)
Other					1		(1)
Net Loss	(25,231)						(25,231)
Ending Balance (in shares) at Dec. 31, 2008				21,860,464
Ending Balance at Dec. 31, 2008	6,739			$ 22	71,274	20,504	(85,061)
Stock-based compensation	2,181				2,181
Exercise of warrants to purchase common stock (in shares)				136,986
Exercise of warrants to purchase common stock	279				279
Exercise of stock options \| Employee Stock Option				102,564
Exercise of stock options \| Employee Stock Option	73				73
Issuance of restricted common stock				1,400,500
Issuance of restricted common stock				$ 2	(2)
Repurchase of shares of restricted common stock (in shares)				(103,823)
Repurchase of shares of restricted common stock	(380)				(380)
Cancelled/ Forfeiture of unvested restricted common stock				(69,500)
Issuance of common stock and warrants (in shares) \| Registered direct offering				15,484,000
Issuance of common stock and warrants (in shares) \| Private Placement				2,772,337
Issuance of common stock and warrants \| Registered direct offering	22,338			$ 15	22,323
Issuance of common stock and warrants \| Private Placement	4,595			$ 3	385	4,207
Net Loss	(7,649)						(7,649)
Ending Balance (in shares) at Dec. 31, 2009				41,583,528
Ending Balance at Dec. 31, 2009	28,104			$ 42	96,133	23,073	(91,144)
Cumulative effect of a change in accounting principle-January 1, 2009 reclassification of warrants to warrant liabilities	(72)					(1,638)	1,566
Stock-based compensation	3,637				3,637
Issuance of common stock (in shares) \| Registered direct offering				7,000,000
Issuance of common stock \| Registered direct offering	$ 32,804			$ 7	32,797
Exercise of warrants to purchase common stock (in shares)	39,225			39,225
Exercise of warrants to purchase common stock	$ 121				360	(239)
Exercise of stock options \| Employee Stock Option				196,167
Exercise of stock options \| Employee Stock Option	225				225
Issuance of restricted common stock				115,000
Repurchase of shares of restricted common stock (in shares)				(416,108)
Repurchase of shares of restricted common stock	(1,668)			$ (1)	(1,667)
Cancelled/ Forfeiture of unvested restricted common stock				(51,250)
Expired warrants					45	(45)
Net Loss	(32,670)						(32,670)
Ending Balance (in shares) at Dec. 31, 2010				48,466,562
Ending Balance at Dec. 31, 2010	30,553			$ 48	131,530	22,789	(123,814)
Stock-based compensation	2,759				2,759
Issuance of common stock (in shares) \| Securities Offering				11,040,000
Issuance of common stock (in shares) \| Collaboration Agreement				6,063,161
Issuance of common stock \| Securities Offering	59,806			$ 11	59,795
Issuance of common stock \| Collaboration Agreement	$ 28,858			$ 6	28,852
Exercise of warrants to purchase common stock (in shares)	2,377,571			2,377,571
Exercise of warrants to purchase common stock	$ 12,701			$ 2	21,766	(9,067)
Exercise of stock options \| Employee Stock Option				479,666
Exercise of stock options \| Non Employee Stock Options				6,904
Exercise of stock options	479,666
Exercise of stock options \| Employee Stock Option	$ 981			$ 1	980
Issuance of restricted common stock				848,406
Issuance of restricted common stock				$ 1	(1)
Repurchase of shares of restricted common stock (in shares)				(59,559)
Repurchase of shares of restricted common stock	(273)				(273)
Cancelled/ Forfeiture of unvested restricted common stock				(16,667)
Expired warrants					1,111	(1,111)
Net Loss	(63,778)						(63,778)
Ending Balance (in shares) at Dec. 31, 2011				69,206,044
Ending Balance at Dec. 31, 2011	71,607			$ 69	246,519	12,611	(187,592)
Stock-based compensation	4,880				4,880
Issuance of common stock (in shares) \| Registered direct offering				10,114,401
Issuance of common stock (in shares) \| Collaboration Agreement				3,636,926
Issuance of common stock \| Registered direct offering	49,170			$ 11	49,159
Issuance of common stock \| Collaboration Agreement	$ 18,694			$ 3	18,691
Exercise of warrants to purchase common stock (in shares)	259,660			259,660
Exercise of warrants to purchase common stock	$ 742				1,011	(269)
Exercise of stock options \| Employee Stock Option				8,300
Exercise of stock options	8,300
Exercise of stock options \| Employee Stock Option	$ 30				30
Issuance of restricted common stock				258,032
Repurchase of shares of restricted common stock (in shares)				(123,153)
Repurchase of shares of restricted common stock	(546)				(546)
Cancelled/ Forfeiture of unvested restricted common stock				(123,370)
Expired warrants					5,433	(5,433)
Net Loss	(96,132)						(96,132)
Ending Balance (in shares) at Dec. 31, 2012				83,236,840
Ending Balance at Dec. 31, 2012	48,445			$ 83	325,177	6,909	(283,724)
Stock-based compensation	3,507				3,507
Issuance of common stock (in shares) \| Registered direct offering				16,445,000
Issuance of common stock \| Registered direct offering	$ 53,880			$ 16	53,864
Exercise of warrants to purchase common stock (in shares)	112,808			112,808
Exercise of warrants to purchase common stock	$ 200				396	(196)
Exercise of stock options	570,168			570,168
Exercise of stock options	$ 956			$ 1	955
Issuance of restricted common stock				75,272
Repurchase of shares of restricted common stock (in shares)				(116,723)
Repurchase of shares of restricted common stock	(498)				(498)
Cancelled/ Forfeiture of unvested restricted common stock				(163,747)
Expired warrants					3,110	(3,110)
Net Loss	(57,107)						(57,107)
Ending Balance (in shares) at Dec. 31, 2013				100,159,618
Ending Balance at Dec. 31, 2013	$ 49,383			$ 100	$ 386,511	$ 3,603	$ (340,831)

Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended			124 Months Ended
Statements of Cash Flows - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2013
Cash flows from operating activities:
Net Loss	$ (57,107)	$ (96,132)	$ (63,778)	$ (340,831)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	738	658	268	3,313
Stock-based compensation	3,507	4,880	2,759	23,688
Change in fair value of warrants	(1,185)	(6,050)	(7,583)	(11,956)
Loss on disposal of fixed assets	585	48	0	641
Common stock issued in exchange for in-process research and development	0	18,694	17,457	36,151
(Increase) decrease in:
Receivables	(87)	21	(79)	(145)
Prepaid expenses and other current assets	4,964	(5,599)	(889)	(1,948)
Other noncurrent assets	473	(230)	(407)	(528)
Deposits	4	(43)	(4)	(128)
Increase (decrease) in:
Accounts payable	(1,087)	(218)	696	422
Accrued expenses	(10,159)	5,695	8,283	6,357
Deferred revenue	(800)	(800)	4,333	2,733
Deferred rent	625	244	109	1,063
Other noncurrent liabilities	20	0	0	20
Net cash used in operating activities	(59,509)	(78,832)	(38,835)	(281,148)
Cash flows from investing activities:
Purchases of property and equipment	(132)	(1,559)	(1,156)	(4,758)
Proceeds from sale of property and equipment	1	0	0	2
Net cash used in investing activities	(131)	(1,559)	(1,156)	(4,756)
Cash flows from financing activities:
Stockholders' capital contribution	0	0	0	500
Proceeds from exercise of stock options	956	30	980	2,329
Payments to employees for repurchase of restricted common stock	(498)	(546)	(274)	(3,364)
Proceeds from exercise of warrants	200	330	12,399	13,278
Proceeds from issuance of common stock and warrants, net	53,880	49,170	71,207	324,605
Proceeds from issuance of preferred stock, net	0	0	0	16,760
Net cash provided by financing activities	54,538	48,984	84,312	354,108
Net increase (decrease) in cash and cash equivalents	(5,102)	(31,407)	44,321	68,204
Cash and cash equivalents, beginning of period	73,306	104,713	60,392	0
Cash and cash equivalents, end of period	68,204	73,306	104,713	68,204
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	0	0	0	47,276
Exercise of liability-classified warrants to common shares	0	412	303	764
Convertible Preferred Stock
Supplementary disclosure of noncash investing and financing activities:
Preferred stock conversion/exercise of equity-classified warrants to common stock	0	0	0	16,760
Warrants
Supplementary disclosure of noncash investing and financing activities:
Preferred stock conversion/exercise of equity-classified warrants to common stock	$ 196	$ 269	$ 9,067	$ 9,789

Financings

12 Months Ended

Dec. 31, 2013

Financings

Financings

On October 23, 2013, the Company entered into an underwriting agreement with J. P. Morgan Securities LLC, as representative of the several underwriters named therein, relating to the issuance and sale of 14,300,000 shares of our common stock. The price to the public in the offering was $3.50 per share, and the underwriters agreed to purchase the shares from the Company pursuant to the underwriting agreement at a purchase price of $3.29 per share. Under the terms of the underwriting agreement, the Company also granted the underwriters an option, exercisable for 30 days, to purchase up to an additional 2,145,000 shares of common stock at a purchase price of $3.29 per share, and the underwriters elected to exercise such option in full. The offering was made pursuant to the Company’s effective registration statement on Form S-3 (Registration Statement No. 333-177793) previously filed with the SEC, and a prospectus supplement thereunder. The underwriters purchased the 14,300,000 shares and the additional 2,145,000 shares on October 29, 2013. The net proceeds from the offering were approximately $53.9 million after deducting underwriting discounts and estimated offering expenses payable by the Company.

On January 20, 2012, the Company entered into an underwriting agreement with J. P. Morgan Securities LLC, as representative of the several underwriters named therein, relating to the issuance and sale of 9,650,000 shares of our common stock. The price to the public in the offering was $5.20 per share, and the underwriters agreed to purchase the shares from the Company pursuant to the underwriting agreement at a purchase price of $4.888 per share. Under the terms of the underwriting agreement, the Company also granted the underwriters an option, exercisable for 30 days, to purchase up to an additional 1,447,500 shares of common stock at a purchase price of $4.888 per share. The offering was made pursuant to the Company’s effective registration statement on Form S-3 (Registration Statement No. 333-177793) previously filed with the SEC, and a prospectus supplement thereunder. The underwriters purchased the 9,650,000 shares on January 25, 2012 and purchased an additional 464,401 shares on January 31, 2012 pursuant to the partial exercise of their option to purchase additional shares, resulting in our issuing a total of 10,114,401 shares. The net proceeds from the offering were approximately $49.2 million after deducting underwriting discounts and estimated offering expenses payable by the Company.

On February 3, 2011, the Company entered into an underwriting agreement with Barclays Capital Inc., or Barclays, relating to the issuance and sale of 9,600,000 shares of the Company’s common stock in a public offering. The price to the public in the offering was $5.75 per share, and Barclays, as the sole underwriter for the offering, agreed to purchase the shares from the Company pursuant to the underwriting agreement at a purchase price of $5.425 per share. Under the terms of the underwriting agreement, the Company also granted Barclays an option, exercisable for 30 days, to purchase up to an additional 1,440,000 shares of the Company’s common stock at a purchase price of $5.425 per share. On February 8, 2011, the transactions contemplated by the underwriting agreement were completed. In connection with the closing, Barclays exercised in full its option to purchase the additional 1,440,000 shares, resulting in the Company issuing a total of 11,040,000 shares at the closing. The net proceeds from the offering were approximately $59.8 million after deducting underwriting discounts and offering expenses.

On January 6, 2011, and in conjunction with the Company’s execution and delivery of the Channel Agreement with Intrexon Corporation, or Intrexon, the Company entered into a Stock Purchase Agreement and Registration Rights Agreement with Intrexon. On January 12, 2011, and pursuant to that Stock Purchase Agreement, Intrexon purchased 2,426,235 shares of the Company’s common stock in a private placement for a total purchase price of $11.6 million, or $4.80 per share. The Company simultaneously issued to Intrexon an additional 3,636,926 shares of its common stock for a cash purchase price equal to the $0.001 par value of such shares, which price was deemed paid in partial consideration for the execution and delivery of the Channel Agreement. This resulted in a non-cash expense of approximately $17.5 million for the in process research and development. Under the terms of the Stock Purchase Agreement, the Company agreed to issue to Intrexon an additional 3,636,926 shares of its common stock 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. These shares were issued on November 7, 2012 (See Note 11 to the financial statements, Preferred Stock and Stockholders’ Equity), and when issued, the purchase price for such shares was equal to the $0.001 par value of such shares, which price was deemed paid in partial consideration for the execution and delivery of the Channel Agreement, in accordance with the terms of the Stock Purchase Agreement. Pursuant to the Registration Rights Agreement, the Company has filed a registration statement with the SEC registering the resale of the shares that we have issued or may issue to Intrexon under the Stock Purchase Agreement.

Also under the Stock Purchase Agreement, if requested by the Company and subject to certain conditions, restrictions and limitations, Intrexon has agreed to purchase the Company’s securities in conjunction with “qualified” securities offerings that are conducted by the Company while the Channel Agreement remains in effect. In conjunction with a qualified offering, Intrexon has committed to purchase up to 19.99% of the securities offered and sold therein (exclusive of Intrexon’s purchase) if requested to do so by the Company. Intrexon will not be obligated to purchase securities in a “qualified” securities offering unless the Company is then in substantial compliance with its obligations under the Channel Agreement and, with respect to a “qualified” offering that is completed following January 6, 2012, the Company confirms its intent that 40% of the offering’s net proceeds shall have been spent, or in the next year will be spent, by the Company under the Channel Agreement. In the case of a “qualified” offering that is completed after January 6, 2013, Intrexon’s purchase commitment was limited to an amount equal to one-half of the proceeds spent or to be spent by the Company under the Channel Agreement. Intrexon’s aggregate purchase commitment for all future qualified offerings is capped at $50.0 million. The Company and Intrexon subsequently amended the Stock Purchase Agreement to clarify that gross proceeds from the sale of Company securities to Intrexon in a qualified offering will apply against Intrexon’s $50.0 million purchase commitment regardless of whether Intrexon participates voluntarily or at the request of the Company. As a result of Intrexon’s purchase of securities in our February 2012 and October 2013 public offerings, the remaining maximum amount of Intrexon’s equity purchase commitment is approximately $19.0 million.

On May 27, 2010, the Company entered into an underwriting agreement with Jefferies & Company, Inc. (the “Representative”) relating to the issuance and sale of 7,000,000 shares of the Company’s common stock, par value $0.001 per share. The Representative, on behalf of itself and JMP Securities LLC, as underwriters for the offering, purchased 7,000,000 shares from the Company pursuant to the underwriting agreement and offered the shares to the public at a price of $5.00, and to certain dealers at that price less a concession not in excess of $0.18 per share of common stock. The net proceeds to the Company from this offering were $32.8 million, after deducting underwriting discounts, commissions and other offering expenses of $2.2 million. The offering was completed on June 2, 2010. Under the terms of the underwriting agreement, the Company granted the Representative an option, exercisable for 30 days, to purchase up to an additional 1,050,000 shares of common stock to cover over-allotments, if any. The overallotment expired on July 2, 2010, without being exercised.

On December 4, 2009, the Company entered into an underwriting agreement in which JMP Securities LLC and Rodman & Renshaw, LLC agreed to serve as co-lead managers (together, the “Underwriters”) in connection with a public offering and sale by the Company of 15,484,000 units at a price to the public of $3.10 per unit for gross proceeds of $48.0 million. The Company paid $2.8 million in commissions and offering expenses and expects to use the remaining net proceeds of $45.2 million for general corporate purposes, which include ongoing research and development activities. Each unit sold in the offering consisted of one share of our common stock and an investor warrant to purchase 0.5 of a share of common stock. The shares of common stock and investor warrants were immediately separable. The closing of the transaction occurred on December 9, 2009.

In connection with a 2009 underwritten public 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). The investor warrants are exercisable immediately and the underwriter warrants exercisable six months after the date of issuance. The warrants have an exercise price of $4.02 per share and have a five year term. The fair value of the 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 warrants require accounting as derivatives. The Company determined that the warrants were not indexed to the Company’s own stock in accordance with Financial Accounting Standards Board, or FASB, Accounting Standards Codification, or ASC, Topic 815, Derivatives and Hedging. As such, the Company has concluded the warrants did not meet the scope exception for determining whether the instruments require accounting as derivatives and should be classified as liabilities (see Note 9 to the financial statements, Warrants).

On September 9, 2009, the Company entered into a securities purchase agreement with certain investors pursuant to which it sold a total of 2,772,337 units (the “2009 Private Placement”), each unit consisting of one share of common stock and a warrant to purchase one share of common stock for a purchase price of $1.825 per unit. The closing of the transaction occurred on September 15, 2009. In connection with the 2009 Private Placement, the Company raised approximately $5.1 million in gross proceeds. After paying $455 thousand in placement agent fees and offering expenses, the net proceeds were $4.6 million.

In connection with a 2009 private placement, the Company issued warrants to purchase an aggregate of 2,910,954 shares of common stock (including 138,617 warrants issued to the placement agents) which are exercisable immediately. The warrants have an exercise price of $2.04 per share and have a five year term. The fair value of the warrants was estimated at $4.2 million using a Black-Scholes model with the following assumptions: expected volatility of 105%, risk free interest rate of 2.41%, expected life of five years and no dividends. The fair value of the warrants was recorded in the equity section of the balance sheet.

The Company assessed whether the warrants require accounting as derivatives. The Company determined that the warrants were indexed to the Company’s own stock in accordance with FASB ASC Topic 815, Derivatives and Hedging. As such, the Company has concluded the warrants meet the scope exception for determining whether the instruments require accounting as derivatives and should be classified in stockholders’ equity.

In connection with the 2009 Private Placement, the Company entered into a registration rights agreement with each of the investors. The registration rights agreement requires that the Company file a “resale” registration statement covering all of the shares issued in the 2009 Private Placement and the shares issuable upon exercise of the warrants issued in the 2009 Private Placement, up to the maximum number of shares able to be registered pursuant to applicable Securities and Exchange Commission (“SEC”) regulations, within 30 days of the closing of the 2009 Private Placement. The Company filed the registration statement with the SEC on September 28, 2009 (File No. 333-162160). Under the terms of the registration rights agreement, the Company is obligated to maintain the effectiveness of the “resale” registration statement until all securities therein are sold or are otherwise can be sold pursuant to Rule 144, without any restrictions. A cash penalty at the rate of 1% of the purchase price per month, capped at a maximum of 10% of the purchase price (or $506 thousand), will be triggered for any filing or effectiveness failures or if, at any time after six months following the closing of the 2009 Private Placement, the Company ceases to be current in periodic reports with the SEC.

In December 2006, the FASB issued an accounting standard, which addresses an issuer’s accounting for registration payment arrangements. The accounting standard specifies that the contingent obligation to make future payments or otherwise transfer consideration under a registration payment arrangement, whether issued as a separate agreement or included as a provision of a financial instrument or other agreement, should be separately recognized and measured in accordance with FASB guidance in Accounting for Contingencies. The accounting standard further clarifies that a financial instrument subject to a registration payment arrangement should be accounted for in accordance with US GAAP without regard to the contingent obligation to transfer consideration pursuant to the registration payment arrangement. The Company applied the recognition and measurement provisions of the accounting standard to the registration rights associated with the registration rights agreement. As result, the Company believes that the contingent obligation to make future payments is not probable and as such has recorded no liability associated with these registration rights.

On February 23, 2007, pursuant to subscription agreements between the Company and certain institutional and other accredited investors, the Company completed the sale of an aggregate of 5,910,049 shares of the Company’s common stock at a price of $5.225 per share in a private placement (the “2007 Offering”). In addition to these shares sold in the 2007 Offering, the Company also issued to each investor a five-year warrant to purchase, at an exercise price of $5.75 per share, an additional number of shares of common stock equal to 20 percent of the shares purchased by such investor in the 2007 Offering. In the aggregate, these warrants entitle investors to purchase an additional 1,182,015 shares of common stock. The Company estimated the fair value of these warrants at $4.7 million using the Black-Scholes model, using an assumed risk-free rate of 4.71% and an expected life of 5 years, volatility of 93%, and a dividend yield of 0%. The total gross proceeds resulting from the 2007 Offering was approximately $30.9 million, before deducting selling commissions and expenses.

The Company assessed whether the warrants require accounting as derivatives. The Company determined that the warrants were indexed to the Company’s own stock in accordance with ASC Topic 815, Derivatives and Hedging. As such, the Company has concluded the warrants meet the scope exception for determining whether the instruments require accounting as derivatives and should be classified in stockholders’ equity.

The Company engaged Paramount BioCapital, Inc. (“Paramount”), Oppenheimer & Co. Inc., and Griffin Securities, Inc. (together, the “2007 Placement Agents”) as placement agents in connection with the 2007 Offering. In consideration for their services, the Company paid the 2007 Placement Agents aggregate cash commissions of $1.6 million (of which $1.0 million was paid to Paramount; see Note 7 to the financial statements, Related Party Transactions) and issued 5-year warrants to the 2007 Placement Agents and their designees to purchase an aggregate of 156,058 shares of the Company’s common stock at an exercise price of $5.75 per share. In connection with the 2007 Offering, the Company also made cash payments of $222 thousand and issued 5-year warrants to purchase 21,244 shares of the Company’s common stock, at an exercise price of $5.75 per share, to a financial consultant pursuant to the non-circumvention provision of a prior agency agreement. The Company estimated the fair value of these 177,302 warrants at $709 thousand using the Black-Scholes model, using an assumed risk-free rate of 4.71% and an expected life of 5 years, volatility of 93%, and a dividend yield of 0%.

The Company assessed whether the warrants require accounting as derivatives. The Company determined that the warrants were indexed to the Company’s own stock in accordance with ASC Topic 815, Derivatives and Hedging. As such, the Company has concluded the warrants meet the scope exception for determining whether the instruments require accounting as derivatives and should be classified in stockholders’ equity.

Pursuant to the 2007 Offering, the Company agreed to use its best efforts to (i) file a registration statement covering the resale of the shares sold in the 2007 Offering and the common stock issuable upon exercise of the investor warrants and placement agent warrants issued in the 2007 Offering within 45 days following the closing date of the 2007 Offering, and (ii) use reasonable commercial efforts to cause the registration statement to be effective within 120 days after such final closing date.

With respect to each investor in the 2007 Offering, the Company also agreed to use reasonable commercial efforts to cause the registration statement to remain effective until the earliest of (i) the date on which the investor may sell all of the shares and shares issuable upon exercise of the warrants then held by the investor pursuant to then-Rule 144 of the Securities Act of 1933 without regard to volume restrictions; and (ii) such time as all of the securities held by the investor and registered under the registration statement have been sold pursuant to a registration statement, or in a transaction exempt from the registration and prospectus delivery requirements of the Securities Act of 1933 under Section 4(1) thereof so that all transfer restrictions and restrictive legends are removed upon the consummation of such sale. The 2007 Placement Agents have been afforded equivalent registration rights as the investors in the 2007 Offering with respect to the shares issuable upon exercise of the placement agent warrants. Effective January 1, 2007, the Company adopted a new accounting standard which requires that instruments subject to registration payments are accounted for without regard to the contingent obligation to make registration payments. As a result, the Company has determined that no contingent loss exists based on its history of timely annual, quarterly and registration filings. The Company intends to continue the timely compliance with all SEC filing requirements, which will keep the Company current and the shares registered. On March 1, 2007, the Company filed a registration statement on Form S-3 with the Securities and Exchange Commission. The registration statement was declared effective on March 26, 2007, rendering the resale of the shares issued in the 2007 Offering registered under the Securities Exchange Act of 1933 and no penalty was recorded.

On May 3, 2006, pursuant to subscription agreements, the Company and certain institutional and other accredited investors, the Company completed the sale of an aggregate of 7,991,256 shares of the Company’s common stock at a price of $4.63 per share in a private placement (the “2006 Offering”). In addition to the shares, the Company also issued to each investor a five-year warrant to purchase, at an exercise price of $5.56 per share, an additional number of shares of common stock equal to 30 percent of the shares purchased by such investor in the 2006 Offering. In the aggregate, these Warrants entitle investors to purchase an additional 2,397,392 shares of common stock. The Company estimated the fair value of these warrants at $9.6 million using the Black-Scholes model, using an assumed risk-free rate of 5.01% and an expected life of 5 years, volatility of 100%, and a dividend yield of 0%. The total gross proceeds resulting from the 2006 Offering was approximately $37 million, before deducting selling commissions and expenses.

The Company assessed whether the warrants require accounting as derivatives. The Company determined that the warrants were both (1) indexed to the Company’s own stock and (2) classified in stockholders’ equity in accordance with ASC Topic 815, Derivatives and Hedging. As such, the Company has concluded the warrants meet the scope exception for determining whether the instruments require accounting as derivatives and should be classified in stockholders’ equity.

The Company engaged Paramount BioCapital, Inc. and Griffin Securities, Inc. (together, the “2006 Placement Agents”) as co-placement agents in connection with the 2006 Offering. In consideration for their services, the Company paid the 2006 Placement Agents and certain selected dealers engaged by the 2006 Placement Agents and their designees aggregate cash commissions of $2.6 million (of which $1.7 million was paid to Paramount; see Note 7 to the financial statements, Related Party Transactions) and issued 7-year warrants to the 2006 Placement Agents and their designees to purchase an aggregate of 799,126 shares of the Company’s common stock (10 percent of the shares sold in the 2006 Offering) at an exercise price of $5.09 per share. The Company estimated the fair value of these warrants at $3.5 million using the Black-Scholes model, using an assumed risk-free rate of 5.01% and an expected life of 7 years, volatility of 100% and a dividend yield of 0%. The Company made reimbursements of $100 thousand to the 2006 Placement Agents for their expenses incurred in connection with the 2006 Offering.

Pursuant to the 2006 Offering, the Company agreed to use its best efforts to (i) file a registration statement covering the resale of the shares issued in the 2006 Offering and the common stock issuable upon exercise of the warrants issued in the 2006 Offering (including the placement agent warrants) within 30 days following the closing date of the 2006 Offering, and (ii) use its reasonable commercial efforts to cause the registration statement to be effective within 120 days after such final closing date.

With respect to each investor in the 2006 Offering, the Company also agreed to use its reasonable commercial efforts to cause the registration statement to remain effective until the earliest of (i) the date on which the investor may sell all of the shares issued in the 2006 Offering and shares issuable upon exercise of the warrants then held by the investor pursuant to then-Rule 144 of the Securities Act of 1933 without regard to volume restrictions; and (ii) such time as all of the securities held by the investor and registered under the registration statement have been sold pursuant to a registration statement, or in a transaction exempt from the registration and prospectus delivery requirements of the Securities Act of 1933 under Section 4(1) thereof so that all transfer restrictions and restrictive legends are removed upon the consummation of such sale. The 2006 Placement Agents have been afforded equivalent registration rights as the investors in the 2006 Offering with respect to the shares issuable upon exercise of the placement agent warrants. Warrants issued in the 2006 Offering are classified as equity. On May 19, 2006, the Company filed a registration statement on Form S-3 with the Securities and Exchange Commission. The registration statement was declared effective on May 30, 2006, rendering the resale of the shares issued in the 2006 Offering registered under the Securities Exchange Act of 1933 and no penalties were recorded.

On August, 3, 2005, the Company entered into an Agreement and Plan of Merger dated as of August 3, 2005 (the “Merger Agreement”) with EasyWeb, Inc., a Delaware corporation (“EasyWeb”), and ZIO Acquisition Corp., a Delaware corporation and wholly-owned subsidiary of EasyWeb (“ZIO Acquisition”). EasyWeb was a company that was incorporated in September 1998 and had been in the business of designing, marketing, selling and maintaining customized and template turnkey sites on the Internet that are hosted by third parties. At the time of the Merger (as defined below), however, EasyWeb had no operating business and had limited assets and liabilities. Pursuant to the Merger Agreement, ZIO Acquisition merged with and into ZIOPHARM, with ZIOPHARM remaining as the surviving company and a wholly-owned subsidiary of EasyWeb (the “Merger”). In connection with the Merger, which was effective as of September 13, 2005, ZIO Acquisition ceased to exist and the surviving company changed its corporate name to ZIOPHARM, Inc. Based upon an Exchange Ratio, as defined in the Merger Agreement, in exchange for all of their shares of capital stock in ZIOPHARM, the ZIOPHARM stockholders received a number of shares of common stock of EasyWeb such that, upon completion of the Merger, the then-current ZIOPHARM stockholders held approximately 96.8% of the outstanding shares of common stock of EasyWeb on a fully-diluted basis. Upon completion of the Merger, EasyWeb ceased all of its remaining operations and adopted and continued implementing the business plan of ZIOPHARM. Further, effective upon the Merger, the then current officers and directors of EasyWeb resigned, and the then current officers and directors of ZIOPHARM were appointed officers and directors of EasyWeb. In conjunction with the Merger, ZIOPHARM made payments of approximately $425,000 to certain affiliates of EasyWeb in the third quarter of 2005. Subsequently, on September 14, 2005, ZIOPHARM merged into EasyWeb, and EasyWeb changed its name to ZIOPHARM Oncology, Inc.

Although EasyWeb was the legal acquirer in the transaction, ZIOPHARM became the registrant with the Securities and Exchange Commission. Under generally accepted accounting principles, the transaction was accounted for as a reverse acquisition, whereby ZIOPHARM was considered the acquirer of EasyWeb for financial reporting purposes because ZIOPHARM’s stockholders controlled more than 50% of the post-transaction combined entity, the management and the board were that of ZIOPHARM after the transaction, EasyWeb had no operating activity and limited assets and liabilities as of the transaction date, and the continuing operations of the entity are those of ZIOPHARM.

Accordingly, the equity of EasyWeb was adjusted to reflect a recapitalization of the stock and the equity of ZIOPHARM was adjusted to reflect a financing transaction with the proceeds equal to the net asset value of EasyWeb immediately prior to the Merger. The historical financial statements of ZIOPHARM became the historical financial statements of the Company. The historical stockholders’ equity was retroactively restated to adjust for the exchange of shares pursuant to the Merger Agreement. All share and per share information included in the accompanying financial statements and notes give effect to the exchange, except as otherwise stated.

On June 6, 2005, the Company completed an offering (the “2005 Offering”) of Series A Convertible Preferred Stock (“Series A Preferred Stock”). The Company issued 4,197,946 shares at $4.31 for gross proceeds of approximately $18.1 million. In connection with the 2005 Offering, the Company compensated Paramount, placement agent for the 2005 Offering, or its affiliates for its services through the payment of (a) cash commissions equal to 7% of the gross proceeds from the sale of the shares of Series A Preferred Stock, and (b) placement warrants to acquire 419,794 shares of Series A Preferred Stock (the “Series A Stock Warrants”), exercisable for a period of 7 years from the closing date at a per-share exercise price equal to 110% of the price per share sold in the 2005 Offering. These commissions are also payable on additional sales by the Company of securities (other than in a public offering) to investors introduced to the Company by Paramount during the twelve (12) month period subsequent to the final closing of the Offering. The Company also paid Paramount an expense allowance of $50 thousand to reimburse Paramount for its out-of-pocket expenses. Also, for a period of 36 months from the final Closing, Paramount has the right of first refusal to act as the placement agent for any private sale of the Company’s securities. On September 13, 2005, the Series A Preferred Stock was converted to 4,197,946 of the Company’s common stock. Lastly, the Company has agreed to indemnify Paramount against certain liabilities, including liabilities under the Securities Act (see Note 7 to the financial statements, Related Party Transactions).

The Company valued the Series A Stock Warrants using the Black-Scholes model and recorded a charge of $1.7 million against additional paid-in capital. The Company has estimated the fair value of such warrants using the Black-Scholes model, using an assumed risk-free rate of 3.93% and expected life of 7 years, volatility of 134% and dividend yield of 0%. The net proceeds from the 2005 Offering were used for research and development, licensing fees and expenses, and for working capital and general corporate purposes.

Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2013

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

Basis of Presentation

The accompanying financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”).

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America 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 our 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 identify any material events that require accounting or disclosure in these financial statements.

Cash and Cash Equivalents

Cash equivalents consist primarily of demand deposit accounts and deposits in short-term U.S. treasury money market mutual funds. Cash equivalents are stated at cost, which approximates fair market value.

Concentrations of Credit Risk

Financial instruments which potentially subject the Company to concentrations of credit risk consist principally of cash and cash equivalents. The Company maintains cash accounts in commercial banks, which may, at times, exceed federally insured limits. The Company has not experienced any losses in such accounts. The Company believes it is not exposed to any significant credit risk on cash and cash equivalents.

Property and Equipment

Property and equipment are recorded at cost. Expenditures for maintenance and repairs are charged to expense while the costs of significant improvements are capitalized. Depreciation is provided using the straight-line method over the following estimated useful lives of the related assets, which is between three and five years. Upon retirement or sale, the cost of the assets disposed of and the related accumulated depreciation are eliminated from the balance sheets and related gains or losses are reflected in the statements of operations.

Restricted Cash

Current assets include $200 thousand that is restricted for the Company’s former line of credit. Other non-current assets include cash of $409 thousand that is restricted as collateral for the Company’s facility leases and subleases and $103 thousand that is restricted as collateral for a line of credit.

Long-Lived Assets

The Company reviews the carrying values of its long-lived assets for possible impairment whenever events or changes in circumstances indicate that the carrying amounts of the assets may not be recoverable. Any long-lived assets held for disposal are reported at the lower of their carrying amounts or fair values less costs to sell.

Warrants

The Company applies the accounting standard which provides guidance in assessing whether an equity-based financial instrument is indexed to an entity’s own stock for purposes of determining whether a financial instrument should be treated as a derivative. In applying the methodology the Company concluded that certain warrants issued by the Company have terms that do not meet the criteria to be considered indexed to the Company’s own stock and therefore are classified as liabilities in the Company’s balance sheet. The liability classified warrants are subject to re-measurement at each balance sheet date and any change in fair value is recognized as a component of “Other income, net” in the accompanying Statement of Operations. Fair value is measured using the binomial valuation model. In December 2011, the Company switched from the Black-Scholes valuation model to the binomial valuation model as it provides a better evaluation of the fair market value of the Company’s liability-classified warrants.

Fair Value Measurements

We have certain financial assets and liabilities recorded at fair value which have been classified as Level 1, 2 or 3 within the fair value hierarchy as described in the accounting standards for fair value measurements.

•

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 December 31, 2013 and 2012 are as follows:


($ in thousands)			Fair Value Measurements at Reporting Date Using
Description	Balance as of December 31, 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	$	66,794	$	66,794	$	—	$	—

Warrant liability	$	11,776	$	—	$	11,776	$	—


($ 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 consist primarily of short term U.S. treasury money market mutual funds which are actively traded. The warrants were valued using a binomial valuation model. See Note 9 to the financial statements, Warrants, for additional disclosure on the valuation methodology and significant assumptions.

Revenue Recognition

The Company receives revenue from a collaboration agreement (see Note 8 to the financial statements, Commitments and Contingencies). Collaboration arrangements typically include payments for one or more of the following: non-refundable, upfront license fees, funding of research and development efforts, milestone payments if specified objectives are achieved and/or profit-sharing or royalties on product sales. Arrangements containing multiple elements are divided into separate units of accounting if certain criteria are met, including whether the delivered element has stand-alone value to the collaborative partner. The consideration received is then allocated among the separate units based on their respective fair values and the applicable revenue recognition criteria are applied to each of the separate units.

Revenue from non-refundable, upfront research and development fees is reported as research and development revenue and is recognized on a straight-line basis over the contracted or estimated period of performance, which is typically the development term. Research and development funding is earned over the period of effort.

Milestone payments are recognized as research and development revenue upon achievement of the milestone only if (1) the milestone payment is non-refundable, (2) substantive effort is involved in achieving the milestone and (3) the amount of the milestone is reasonable in relation to the effort expended or the risk associated with achievement of the milestone. If any of these conditions are not met, the milestone payment is deferred and recognized as revenue over the estimated remaining period of performance under the contract as the Company completes its performance obligations.

Research and Development Costs

Research and development expenditures are charged to the statement of operations as incurred. Such costs include proprietary research and development activities, purchased research and development, and expenses associated with research and development contracts, whether performed by the Company or contracted with independent third parties.

Income Taxes

Income taxes are accounted for under the liability method. Deferred tax assets and liabilities are recognized for the estimated future tax consequences of temporary differences between the financial statement carrying amounts and their respective tax bases. Deferred tax assets and liabilities are measured using enacted tax rates expected to apply to taxable income in the year in which the temporary differences are expected to be recovered or settled. The Company evaluates the realizability of our deferred tax assets and establishes a valuation allowance when it is more likely than not that all or a portion of deferred tax assets will not be realized.

The Company accounts for uncertain tax positions using a “more-likely-than-not” threshold for recognizing and resolving uncertain tax positions. The evaluation of uncertain tax positions is based on factors including, but not limited to, changes in tax law, the measurement of tax positions taken or expected to be taken in tax returns, the effective settlement of matters subject to audit, new audit activity and changes in facts or circumstances related to a tax position. The Company evaluates this tax position on an annual basis. The Company also accrues for potential interest and penalties, related to unrecognized tax benefits in income tax expense (see Note 10 to the financial statements, Income Taxes).

Accounting for Stock-Based Compensation

Stock-based compensation cost is measured at the grant date, based on the estimated fair value of the award, and is recognized as expense over the employee’s requisite service period. Stock-based compensation expense is based on the number of awards ultimately expected to vest and is therefore reduced for an estimate of the awards that are expected to be forfeited prior to vesting. Consistent with prior years, the Company uses the Black-Scholes option pricing model which requires estimates of the expected term option holders will retain their options before exercising them and the estimated volatility of the Company’s common stock price over the expected term.

The Company recognizes the full impact of its share-based employee payment plans in the statements of operations for each of the years ended December 31, 2013, 2012, and 2011 and did not capitalize any such costs on the balance sheets. The Company recognized $2.3 million, $3.1 million, and $2.1 million of compensation expense related to vesting of employee stock options during the years ended December 31, 2013, 2012, and 2011, respectively. In the years ended December 31, 2013, 2012, and 2011, the Company recognized $1.2 million, $1.7 million, and $635 thousand of compensation expense, respectively, related to vesting of restricted stock (see Note 12 to the financial statements, Stock Option Plan). In the years ended December 31, 2013, 2012, and 2011, the Company recognized $3.5 million, $4.9 million, and $2.8 million of compensation expense, respectively, related to vesting of all employee and director awards. The following table presents share-based compensation expense included in the Company’s Statements of Operations:


	Year ended December 31,
(in thousands)	2013		2012		2011
Research and development	$	792	$	1,917	$	890
General and administrative		2,715		2,963		1,869

Share based employee compensation expense before tax		3,507		4,880		2,759
Income tax benefit		—		—		—

Net share based employee compensation expense	$	3,507	$	4,880	$	2,759

Prior to the adoption of the current accounting standards in 2006, the Company previously accounted for stock-based awards to employees using the intrinsic value method and had elected the disclosure-only alternative. All stock-based awards to nonemployees were accounted for at their fair value. The Company had recorded the fair value of each stock option issued to non-employees as determined at the date of grant using the Black-Scholes option pricing model.

The following table illustrates the effect on net loss and earnings per share if the Company had applied the fair value recognition provisions of current accounting standards to stock-based awards from September 9, 2003 (date of inception) to December 31, 2005:


(in thousands, except per share data)	September 9, 2003 (date of inception) to December 31, 2005
Net loss:
As reported	$	(15,364	)

Stock-based compensation expense included in reported net loss		802
Stock-based compensation expense under the fair-value based method		(1,756	)

Pro forma net loss	$	(16,318	)

Basic and diluted net loss per share:
As reported	$	(3.75	)
Pro forma	$	(3.98	)

The fair value of each stock option is estimated at the date of grant using the Black-Scholes option pricing model. The estimated weighted-average fair value of stock options granted to employees in 2013, 2012, and 2011 was approximately $2.51, $3.06, and $4.04 per share, respectively. Assumptions regarding volatility, expected term, dividend yield and risk-free interest rate are required for the Black-Scholes model. The volatility assumption is based on the Company’s historical experience. The risk-free interest rate is based on a U.S. treasury note with a maturity similar to the option award’s expected life. The expected life represents the average period of time that options granted are expected to be outstanding. The Company calculated expected term using the simplified method described in SEC Staff Accounting Bulletin, or SAB, No. 107 and No. 110. The assumptions for volatility, expected life, dividend yield and risk-free interest rate are presented in the table below:


	2013	2012	2011
Weighted average risk-free interest rate	1.00 - 2.10%	0.79 - 1.13%	1.09 - 2.69%
Expected life in years	6	6	6
Expected volatility	83.40 - 95.96%	83.36 - 83.53%	83.26 - 87.29%
Expected dividend yield	0	0	0

Net Loss Per Share

Basic net loss per share is computed by dividing net loss by the weighted average number of common shares 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 antidilutive. Such potential common shares at December 31, 2013, 2012, and 2011 consist of the following:


	December 31,
	2013		2012		2011
Stock options		6,747,303		7,147,303		5,138,486
Unvested restricted stock		352,865		733,739		950,906
Warrants		10,539,767		11,197,454		13,117,264

		17,639,935		19,078,496		19,206,656

New Accounting Pronouncements

In January 2013, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update, or ASU, No. 2013-01, Balance Sheet (Topic 210): Clarifying the Scoping of Disclosures about Offsetting Assets and Liabilities (ASU 2013-01) which clarifies the scope of ASU No. 2011-11 requiring an entity to disclose information about offsetting and related arrangements to enable users of its financial statements to understand the effect of those arrangements on its financial position. This ASU was effective for fiscal years beginning on or after January 1, 2013 and interim periods within those annual periods. The adoption of this standard did not have an impact on our financial position or results of operations.

In February 2013, the FASB issued ASU No. 2013-02, Comprehensive Income (Topic 220): Reporting of Amounts Reclassified Out of Accumulated Other Comprehensive Income (ASU 2013-02) which requires an entity to provide information about the amounts reclassified out of accumulated other comprehensive income by component. In addition, an entity is required to present, either on the face of the statement where net income is presented or in the notes, significant amounts reclassified out of accumulated other comprehensive income by the respective line items of net income but only if the amount reclassified is required under U.S. GAAP to be reclassified to net income in its entirety in the same reporting period. For other amounts that are not required under U.S. GAAP to be reclassified in their entirety to net income, an entity is required to cross-reference to other disclosures required under U.S. GAAP that provide additional detail about those amounts. This ASU was effective for reporting periods beginning after December 15, 2012 and did not have an impact on our financial position or results of operations.

Related Party Transactions

12 Months Ended

Dec. 31, 2013

Related Party Transactions

Related Party Transactions

During 2005, the Company engaged Paramount to assist in placing shares of Series A Preferred Stock on a “best efforts” basis. Lindsay A. Rosenwald, M.D. is Chairman and Chief Executive Officer of Paramount. Dr. Rosenwald is also a managing member of Horizon BioMedical Ventures, LLC, or Horizon. On December 30, 2004, Horizon authorized the distribution of 2,428,911 (4,848,376 pre-Merger) shares of the Company’s common stock (such shares, the “Horizon Distributed Shares”), in equal installments of 1,214,456 (2,424,188 pre-Merger) shares of common stock to Mibars, LLC, or Mibars, and to Dr. Rosenwald and his designees, which we refer to as the “Designated Shares”. The disposition of the Designated Shares will be subject to certain restrictions as agreed to among Dr. Rosenwald and Dr. Rosenwald’s designees. Among other things, under certain circumstances set forth in pledge agreements between Dr. Rosenwald and his designees, Dr. Rosenwald has the right to re-acquire the Designated Shares from his designees. As a result of those rights, Dr. Rosenwald may be deemed to be an affiliate of the Company.

In connection with the December 22, 2004 Option Agreement with Southern Research Institute, or SRI, the Company entered into a Finders Agreement, dated December 23, 2004, with Paramount pursuant to which the Company has agreed to compensate Paramount, for services in connection with the Company’s introduction to SRI through the payment of (a) a cash fee of $60 thousand and (b) warrants to purchase 62,621 (125,000 pre-Merger) shares of the Company’s common stock at a price equal to $4.75 ($2.38 pre-Merger) per share. The Company has estimated the fair value of such warrants using the Black-Scholes model, using an assumed risk-free rate of 3.93%, and expected life of 7 years, volatility of 134% and dividend yield of 0%. In December 2004, the Company expensed the $60 thousand that was payable to Paramount and recognized compensation expense in the amount of $251 thousand for the issuance of the warrants. These warrants expired on December 23, 2011.

In connection with the Series A Preferred Stock Offering, the Company and Paramount entered into an Introduction Agreement in January 2005, pursuant to which the Company had agreed to compensate Paramount for its services in connection with the Offering through the payment of (a) cash commissions equal to 7% of the gross proceeds from the sale of the shares of Series A Preferred Stock, and (b) placement warrants to acquire a number of shares of Series A Preferred Stock equal to 10% of the number of shares of Series A Preferred Stock issued in the Offering, exercisable for a period of 7 years from the Closing Date at a per Share exercise price equal to 110% of the price per Share sold in the Offering. These commissions are also payable on additional sales by the Company of securities (other than in a public offering) to investors introduced to the Company by Paramount during the 12 month period subsequent to the final closing of the Offering. The Company also agreed to pay to Paramount a non-accountable expense allowance of $50 thousand to reimburse Paramount for its out-of-pocket expenses. Also, for a period of 36 months from the final Closing, Paramount has the right of first refusal to act as the placement agent for the private sale of the Company’s securities. Lastly, the Company has agreed to indemnify Paramount against certain liabilities, including liabilities under the Securities Act.

In connection with the 2006 Offering, on May 3, 2006, the Company paid Paramount a cash commission equal to 7% of the gross proceeds from the sale of the Shares sold by Paramount in the 2006 Offering, resulting in a cash payment of approximately $1.7 million. In addition, the Company issued 7-year warrants to the 2006 Placement Agents and their designees to purchase an aggregate of 799,126 shares (10% of the Shares sold in the Offering) of the Company’s common stock, of which 532,750 were issued to Paramount at an exercise price of $5.09 per share.

On December 18, 2006 the Company paid Paramount a cash settlement of $180 thousand in exchange for Paramount’s agreement to terminate certain of its rights under the 2005 and 2004 agreements. This amount was expensed in the year ended December 31, 2006.

Mr. Timothy McInerney, who is a member of the Board of Directors of the Company, was a full-time employee of Paramount from 1992 through March 2007. In addition, Michael Weiser, a current member of the Board of Directors of the Company, and David M. Tanen, who was a member of the Board of Directors of the Company, were full-time employees of Paramount from July 1998 through November 2006, and July 1996 through August 2004, respectively. Mr. John Knox, our former Treasurer, was also a full-time Paramount employee.

In connection with the 2007 Offering, on February 23, 2007, the Company paid Paramount cash commissions equal to 6% of the gross proceeds from the sale of the shares sold by Paramount in the 2007 Offering, resulting in a cash payment of approximately $1.0 million. In addition, the Company issued 5-year warrants to the placement agents in the 2007 Offering and their designees to purchase an aggregate of 177,302 shares (3% of the shares sold in the 2007 Offering) of the Company’s common stock at an exercise price of $5.75 per share, of which 97,536 were issued to Paramount.

During the year ended December 31, 2008, there were no related party transactions.

Mr. Timothy McInerney, who is a member of the Board of Directors of the Company, has been a Partner at Riverbank Capital Securities, Inc. since June 2007. In connection with the 2009 Private Placement, on September 15, 2009, the Company paid Riverbank Capital Securities, Inc. cash commissions equal to 3.325% of the gross proceeds from the sale of the shares sold by Riverbank Capital Securities, Inc. in the 2009 Private Placement, resulting in a payment of approximately $168 thousand. In addition, the Company issued 5-year warrants to the placement agents in the 2009 Private Placement and their designees to purchase an aggregate of 138,617 shares of the Company’s common stock (5% of the shares sold in the September 2009 Offering) at an exercise price of $2.04 per share, of which 65,843 were issued to Riverbank Capital Securities, Inc.

On January 6, 2011, the Company entered into an Exclusive Channel Partner Agreement, or Channel Agreement, with Intrexon Corporation, or Intrexon (see Note 8 to the financial statements, Commitments and Contingencies, 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 year ended December 31, 2012, the Company paid Intrexon approximately $11.4 million, of which $6.6 million was for services already incurred and the remaining $4.8 million was for services expected to be incurred within a year. This amount was included as part of prepaid expenses and other current assets on the balance sheet as of December 31, 2012. During the year ended December 31, 2013, the Company expensed $7.8 million for services performed by Intrexon, of which $4.8 million was applied to the prepaid balance in other current assets, $2.4 million was paid to Intrexon and $0.6 million was recorded in accrued expenses. As of December 31, 2013, the prepaid balance in other current assets on the accompanying balance sheet has been reduced to $0.

On January 25, 2012, Intrexon purchased 1,923,075 shares of common stock in the Company’s public offering (see Note 2 to the financial statements, Financings).

On November 7, 2012, the Company issued 3,636,926 shares of common stock to Intrexon (see Note 11 to the financial statements, Preferred Stock and Stockholders’ Equity).

On October 29, 2013, Intrexon purchased 2,857,143 shares of common stock in the Company’s public offering (see Note 2 to the financial statements, Financings).

- 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

12 Months Ended

Dec. 31, 2013

Commitments and Contingencies

Commitments and Contingencies

Operating Leases

Prior to December 31, 2012, the Company entered into an operating lease in New York, NY, consisting of 6,251 square feet of office space. In accordance with this agreement, the Company entered into a letter of credit in the amount of $388 thousand, naming the Company’s landlord as beneficiary. In January 2012, the Company amended the lease agreement, adding 1,008 square feet of office space. As of December 31, 2012, the Company occupied 7,259 square feet of space in New York, NY, and maintained a $388 thousand letter of credit. The collateral for the letter of credit is recorded in other non-current assets on the balance sheet as of December 31, 2012. The lease for office space in New York, NY expires in October 2018.

On October 17, 2013, the Company entered into a sublease agreement to lease 7,259 square feet in our New York office to a subtenant. The Company remains primarily liable to pay rent on the original lease. We recorded a loss on the sublease in the amount of $729 thousand for the year ended December 31, 2013, representing the remaining contractual obligation of $2.3 million, less $1.6 million in payments from our subtenant. We retired assets in this subleased area as a result of this sublease with a net book value of $392 thousand, and recorded a loss on disposal of fixed assets for the same amount for the year ended December 31, 2013. The Company continues to maintain a $388 thousand letter of credit. The collateral for the letter of credit is recorded in other non-current assets on the balance sheet as of December 31, 2013. The lease for office space in New York, NY expires in October 2018.

Prior to December 31, 2012, the Company entered into separate operating lease agreements for various spaces in a building in Boston, MA. That space consisted of 5,249 square feet on the first floor, 8,538 square feet on the second floor, and 6,959 square feet on the third floor. In June 2012, the Company re-negotiated a master lease for the entire Boston office space, added 9,800 square feet of office space on the fourth floor, surrendered 4,113 square feet from the second floor, and incorporated all floors’ lease agreements under the same master agreement expiring in August 2016. The Company provided an additional $41 thousand security deposit for the additional space on the fourth floor. As of December 31, 2012, a total security deposit of $127 thousand was paid to its landlord for security deposits for these agreements.

On August 30, 2013, the Company entered into a sublease agreement to lease 5,249 square feet in our Boston office to a subtenant. The Company remains primarily liable to pay rent on the original lease. We recorded a loss on the sublease in the amount of $42 thousand for the year ended December 31, 2013, representing the remaining contractual obligation of $367 thousand, less $325 thousand in payments from our subtenant. We retired assets in this subleased area as a result of this sublease with a net book value of $194 thousand, and recorded a loss on disposal of fixed assets. In accordance with the sublease agreement, the subtenant provided the Company with a security deposit of $20 thousand, which is recorded in other non-current assets and other liabilities on the balance sheet for the year ended December 31, 2013.

As of December 31, 2013, the Company occupies 21,184 square feet of space in its Boston, MA office and has paid a total of $127 thousand for security deposits, which are recorded in other non-current assets on the balance sheet.

In April 2011, the Company entered into an operating lease for office space in Germantown, MD, consisting of 2,227 square feet. As of December 31, 2011, the Company recorded the $4 thousand security deposit in other non-current assets on the balance sheet. The lease would have expired in March 2014; however, on July 16, 2012, the Germantown, Maryland office was closed. In June 2013, we paid off the remainder of the Germantown, Maryland lease obligation.

Future net minimum lease payments under operating leases as of December 31, 2013 are as follows (in thousands):


2014	$	1,196
2015		1,236
2016		997
2017		501
2018		424

		4,354
Less: contractual sublease income		(1,883	)

Future minimum lease payments, net	$	2,471

Total rent expense was approximately $1.0 million, $1.1 million, $647 thousand, and $5.2 million for the years ended December 31, 2013, 2012, 2011 and from September 9, 2003 (date of inception) to December 31, 2013, respectively.

The Company records rent expense on a straight-line basis over the term of the lease. Accordingly, the Company has recorded a liability for deferred rent at December 31, 2013 and 2012 of $1.1 million ($212 thousand current and $851 long-term) and $439 thousand ($39 thousand current and $400 thousand long-term), respectively, which is recorded in deferred rent on the balance sheet.

License Agreements

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, which the Company refers to, collectively, as 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, or 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, or 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 Registrant-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. In addition, the Company also paid the Licensors $100 thousand in 2006 and 2007 to conduct scientific research with the Company obtaining exclusive right to all resulting intellectual property rights. The sponsored research agreements governing this research and any related extensions expired in February 2008 with no payments being made subsequent to that date.

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 during the years ended December 31, 2013, 2012 or 2011.

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. There were no payments made during 2009. 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 have been reached or expensed since 2010.

License Agreement with Southern Research Institute

On December 22, 2004, the Company entered into an Option Agreement with the Southern Research Institute, or SRI, 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, 2013, 2012, 2011, 2010, 2009 and 2008. 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 $775,000. 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. No milestones under the license agreement were reached or expensed during the years ended December 31, 2011 or 2010. During each of the years ended December 31, 2013 and 2012, milestones of $250 thousand were reached and expensed.

Exclusive Channel Partner Agreement with Intrexon Corporation

On January 6, 2011, we entered into an Exclusive Channel Partner Agreement, or 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 Ad-RTS-IL-12 + veledimex and DC-RTS-IL-12 + veledimex 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, which we collectively refer to as 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 (see Note 2 to the financial statements, Financings).

Following the first 24 months of the agreement, Intrexon had the option to terminate the Channel Agreement, if we failed to use diligent efforts to develop and commercialize ZIOPHARM Products or if we elected not to pursue the development of a Cancer Program identified by Intrexon that is a “Superior Therapy” as defined in the Channel Agreement. Also following the first 24 months of the agreement, we had the option to voluntarily terminate the Channel Agreement, upon 90 days written notice to Intrexon. The 24 month termination period expired during the year ended December 31, 2013.

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.

Collaboration Agreement with Harmon Hill, LLC

On April 8, 2008, the Company signed a collaboration agreement for Harmon Hill, LLC, or 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, as defined in the collaboration agreement, 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, during 2010, the agreement was formally extended through April 8, 2011 and again through April 8, 2012. The agreement was extended through November 8, 2012 and has now expired. The Company expensed $240 thousand during the years ended December 31, 2011 and 2010 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 during the years ended December 31, 2013, 2012, 2011 or 2010.

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, effective April 1, 2013. 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. The Company expensed $135 thousand for the year ended December 31, 2013.

Collaboration Agreement with Solasia Pharma K.K.

On March 7, 2011, the Company entered into a License and Collaboration Agreement with Solasia Pharma K.K., or Solasia.

Pursuant to the License and Collaboration Agreement, the Company 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, the Company 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. The Company 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. The Company currently estimates this period to be 75 months, which could be adjusted in the future.

Under the License and Collaboration Agreement, the Company provides 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.

The Company is 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 the Company’s clinical trials. PPD is entitled to cumulative payments of up to $20.0 million under these arrangements, which is payable by the Company in varying amounts upon PPD achieving specified milestones. During the year ended December 31, 2010, the Company 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 the Company 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 year ended December 31, 2013, patient progression and data based milestones totaling $9.2 million were met and expensed.

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 year ended December 31, 2013, contract modification and patient enrollment based milestones totaling $2.2 million were met and expensed.

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 newest 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 year ended December 31, 2013, two database related milestones and one site activation related milestone were met and expensed totaling $136 thousand.

Warrants

12 Months Ended

Dec. 31, 2013

Warrants

Warrants

The Company has issued both warrants that are accounted for as liabilities and warrants that are accounted for as equity instruments.

The Company follows accounting standards that provide guidance in assessing whether an equity-issued financial instrument is indexed to an entity’s own stock for purposes of determining whether a financial instrument should be treated as a derivative and classified as a liability. Accounting standards require that liability classified warrants be recorded at their fair value at each financial reporting period and the resulting gain or loss be recorded as other income (expense) in the Statements of Operations. Fair value is measured using the binomial valuation model.

In May 2005, the Company issued 419,786 warrants to placement agents for services performed in connection with the 2005 Offering, 11,083 of which were subsequently exercised. The remaining 408,703 warrants were originally valued at $1.6 million. Subject to certain exceptions, these 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 warrants then in effect, which was initially $4.75 per share. This provision was triggered in 2006 when stock was sold at $4.63 per share in the 2006 Offering. Accordingly, the warrants were re-priced at $4.69. The provision was triggered a second time with 2009 Private Placement when stock was sold at $1.825 per share and the warrants were subsequently re-priced at $4.25. The provision was triggered again with the Company’s December 2009 public offering when stock was sold at $3.10 per share and the warrants were subsequently re-priced at $3.93. Using a Black-Scholes model, the warrants were valued at $72 thousand on January 1, 2009, when the accounting standard was adopted. The reclassification attributed to adoption of the standard had the following cumulative effect on the Balance Sheets:


(in thousands)	Liabilities		Stockholders’ Equity
	Warrants		Warrants			Deficit Accumulated During the Development Stage
As reported on December 31, 2008	$	—	$	20,504		$	(85,061	)
Re-classification		72		(1,638	)		1,566

Balance on January 1, 2009	$	72	$	18,866		$	(83,495	)

The following Black-Scholes pricing assumptions were used at January 1, 2009:


	January 1, 2009
Risk-free interest rate		1.55	%
Expected life in years		3.42
Expected volatility		102	%
Expected dividend yield		0

Also, in connection with the December 2009 public 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). The investor warrants are exercisable immediately and the underwriter warrants exercisable six months after the date of issuance. The warrants have an exercise price of $4.02 per share and have a 5 year term. The fair value of the 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 5 years and no dividends.

Subject to certain exceptions, these 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 warrants then in effect, which was initially $4.02 per share. This provision was triggered in 2013 when stock was sold at $3.50 per share in our 2013 public offering. Accordingly, the outstanding warrants were increased by 184,367 warrants to 8,235,076 warrants.

The Company assessed whether the 2005 Warrants and the 2009 Warrants require accounting as derivatives. The Company determined that the 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 the warrants did not meet the scope exception for determining whether the instruments require accounting as derivatives and should be classified in liabilities.

On December 31, 2013, the liability-classified warrants were valued at $11.8 million using a Binomial/Monte Carlo valuation model. The decrease in the fair value of the warrant liabilities of $1.2 million for the year ended December 31, 2013 was charged to Other income, net in the Statements of Operations.

On December 31, 2012, the liability-classified warrants were valued at $13.0 million using a Binomial/Monte Carlo valuation model. The decrease in the fair value of the warrant liabilities of $6.1 million for the year ended December 31, 2012 was charged to Other income, net in the Statements of Operations.

On December 31, 2011, the liability-classified warrants were valued at $19.4 million using a Binomial/Monte Carlo valuation model. The decrease in the fair value of the warrant liabilities of $7.6 million for the year ended December 31, 2011 was charged to Other income, net in the Statements of Operations. Additionally, $0.3 million of the decrease resulted from the exercise of warrants.

The following pricing assumptions were used in the Binomial/Monte Carlo valuation model at December 31, 2013, 2012 and 2011:


	December 31, 2013	December 31, 2012	December 31, 2011
Risk-free interest rate	0.13%	0.25%	0.05 - 0.35%
Expected life in years	0.94	1.94	0.42 - 2.92
Expected volatility	80%	70%	64 - 80%
Expected dividend yield	0	0	0

Warrants accounted for as equity instruments include the following issuances:

During 2004, the Company issued warrants to purchase 62,621 shares of the Company’s common stock to Paramount as compensation for services rendered in connection with our entering into an option agreement with Southern Research Institute. In connection with the warrants issued, the Company recorded a charge of $251 thousand to general and administrative expense. The Company has estimated the fair value of such options using the Black-Scholes model, using an assumed risk-free rate of 3.93%, and expected life of 7 years, volatility of 134% and dividend yield of 0%.

In 2005, the Company issued performance warrants to purchase 50,000 shares of the Company’s common stock for services to be rendered to its investor relations consultant as compensation. In connection with the warrant issuance, 12,500 shares were exercisable immediately and the Company recorded a charge of $45 thousand to general and administrative expense in the year ended December 31, 2005. The Company has estimated the fair value of such options using the Black-Scholes model, using an assumed risk-free rate of 4.39%, an expected life of 5 years, volatility of 109%, and dividend yield of 0%. The remaining 37,500 warrants were cancelled in the year ended December 31, 2006 due to performance objectives not being obtained at the expiration of agreement.

In connection with the 2006 Offering completed on May 3, 2006, the Company issued warrants to purchase 2,397,392 shares of common stock to investors and 799,126 warrants to purchase common stock to the 2006 Placement Agents and their designees. The Company estimated the fair value of the warrants at $9.6 million and $3.5 million, respectively, using the Black-Scholes model, using an assumed risk-free rate of 5.01% and an expected life of 5 and 7 years, volatility of 100% and a dividend yield of 0%.

On February 23, 2007, as part of the 2007 Offering, the Company issued warrants to purchase 1,182,015 shares of common stock to investors and 177,302 warrants to purchase common stock to the placement agents in connection with the Company’s 2007 private placement, their designees and a previously-engaged financial consultant. The Company estimated the fair value of the warrants at $4.7 million and $709 thousand respectively, using the Black-Scholes model, using an assumed risk-free rate of 4.71% and an expected life of 5 years, volatility of 93% and a dividend yield of 0%.

In connection with its 2009 private placement, the Company issued warrants to purchase an aggregate of 2,910,954 shares of common stock (including 138,617 warrants issued to the placement agents) which were exercisable immediately. The warrants have an exercise price of $2.04 per share and have a 5 year term. The fair value of the warrants was estimated at $4,207 thousand using a Black-Scholes model with the following assumptions: expected volatility of 105%, risk free interest rate of 2.41%, expected life of 5 years and no dividends. The fair value of the warrants was recorded in the equity section of the balance sheet. In October 2009, 136,986 of these warrants were exercised.

During 2010, no new warrants were issued. However, 95,505 warrants were exercised for 39,225 shares of common stock. Of these warrants, 70,738 were equity-classified and 24,767 were liability-classified. Additionally, 12,500 equity-classified warrants expired without being exercised.

During 2011, no new warrants were issued. However, 2,516,968 warrants were exercised for 2,377,571 shares of common stock. Of these warrants, 2,351,417 were equity-classified and 165,551 were liability-classified. Additionally, 277,910 equity-classified warrants expired without being exercised.

During 2012, no new warrants were issued. However, 553,914 warrants were exercised for 259,660 shares of common stock. Of these warrants, 186,297 were equity-classified and 373,617 were liability-classified. Additionally, 1,359,317 equity-classified warrants and 579 liability-classified warrants expired without being exercised.

During 2013, no new warrants were issued. However 135,346 warrants were exercised for 112,808 shares of common stock. Of these warrants, all 135,346 were equity-classified; there were no liability-classified warrants exercised. Additionally, 706,708 equity-classified warrants expired without being exercised. All warrants will expire during the year ending December 31, 2014.

The following is a summary of warrants outstanding as of December 31, 2013.


Number of Warrants		Issued in Connection With	Exercise Price		Expiration Date
	2,264,393	Investor warrants	$	2.04	September 15, 2014
	40,298	Placement warrants for services performed		2.04	September 15, 2014
	8,235,076	Investor warrants		4.02	December 9, 2014

	10,539,767

Income Taxes

12 Months Ended

Dec. 31, 2013

Income Taxes

10.

Income Taxes

There is no provision for income taxes because the Company has incurred operating losses since inception. The reported amount of income tax expense for the years differs from the amount that would result from applying domestic federal statutory tax rates to pretax losses primarily because of the changes in the valuation allowance. Significant components of the Company’s deferred tax assets at December 31, 2013 and 2012 are as follows:


	December 31,
(in thousands)	2013			2012
Net operating loss carryforwards	$	66,209		$	42,715
Start-up and organizational costs		41,529			44,262
Research and development credit carryforwards		25,058			18,388
Stock compensation		1,028			991
Capitalized acquisition costs		12,323			13,270
Deferred revenue		1,074			1,388
Depreciation		129			331
Other		1,254			998

		148,604			122,343
Less valuation allowance		(148,604	)		(122,343	)

Net deferred tax assets	$	—		$	—

Deferred income taxes reflect the net tax effects of temporary differences between the carrying amount of assets and liabilities for financial reporting purposes and the amounts used for income tax purposes. At December 31, 2013, the Company has aggregate net operating loss carryforwards for federal tax purposes of approximately $197.0 million available to offset future federal taxable income to the extent permitted under the Internal Revenue Code of 1986, as amended, or IRC, expiring in varying amounts through 2032. Additionally, the Company has approximately $25.0 million of research and development credits at December 31, 2013, expiring in varying amounts through 2032, which may be available to reduce future taxes.

Under the IRC Section 382, certain substantial changes in the Company’s ownership may limit the amount of net operating loss carryforwards that can be utilized in any one year to offset future taxable income. The net operating loss carryforwards for the year ended December 31, 2013 includes approximately $4.2 million resulting from excess tax deductions from stock options. Pursuant to ASC 740, the deferred tax asset relating to excess tax benefits generated from exercises of stock options was not recognized for financial statement purposes.

Section 382 of the IRC provides limits to which a corporation that has undergone a change in ownership (as defined) can utilize any net operating loss, or NOL, and general business tax credit carryforwards it may have. The Company commissioned an analysis to determine whether Section 382 could limit the use of its carryforwards in this manner. After completing the analysis, it was determined an ownership change had occurred in February 2007. As a result of this change, the Company’s NOL’s and general business tax credits from February 23, 2007 and prior would be completely limited under IRC Section 382. The deferred tax assets related to NOL’s and general business credits have been reduced by $11.2 million and $636 thousand, respectively, as a result of the change. The Company updated the IRC Section 382 analysis through December 31, 2013. It was determined a change of ownership occurred on February 28, 2011. The Company’s NOL’s were not further limited as a result of the change.

The Company has provided a valuation allowance for the full amount of these net deferred tax assets, since it is more likely than not that these future benefits will not be realized. However, these deferred tax assets may be available to offset future income tax liabilities and expenses. The valuation allowance increased by $26.3 million primarily due to net operating loss carryforwards, start-up and organizational costs, and the increase in research and development credits.

A reconciliation of income tax expense (benefit) at the statutory federal income tax rate and income taxes as reflected in the financial statements is as follows:


	Year Ended December 31,
(in thousands)	2013			2012			2011
Federal income tax at statutory rates		34	%		34	%		34	%
State income tax, net of federal tax benefit		4	%		5	%		6	%
Research and development credits		9	%		10	%		11	%
Stock compensation		-2	%		-1	%		-1	%
Uncertain tax position adjustment		0	%		0	%		0	%
Change in warrant value		1	%		2	%		4	%
Federal R&D tax grant		0	%		0	%		0	%
Other		0	%		0	%		0	%
Increase in valuation allowance		-46	%		-49	%		-54	%

Effective tax rate		0	%		0	%		0	%

The Company adopted ASC740, “Accounting for Uncertain Tax Positions” on January 1, 2007. ASC740 clarifies the accounting for uncertainty in income taxes recognized in an enterprise’s financial statements in accordance with FASB Statement No. 109, “Accounting for Income Taxes.” ASC 740 prescribes a recognition threshold and measurement of a tax position taken or expected to be taken in a tax return. The Company did not establish any additional reserves for uncertain tax liabilities upon adoption of ASC 740. A summary of the company’s adjustments to its uncertain tax positions in the years ended December 31, 2013, 2012, and 2011 are as follows:


(in thousands)
Balance at December 31, 2010	$	275
Increase/Decrease for tax positions related to the current year		—
Increase/Decrease for tax positions related to prior years		—
Decreases for settlements with applicable taxing authorities		—
Decreases for lapses of statute of limitations		—

Balance at December 31, 2011	$	275
Increase/Decrease for tax positions related to the current year		—
Increase/Decrease for tax positions related to prior years		—
Decreases for settlements with applicable taxing authorities		—
Decreases for lapses of statute of limitations		—

Balance at December 31, 2012	$	275
Increase/Decrease for tax positions related to the current year		—
Increase/Decrease for tax positions related to prior years		(37	)
Decreases for settlements with applicable taxing authorities		—
Decreases for lapses of statute of limitations		—

Balance at December 31, 2013	$	238

The Company has not recognized any interest and penalties in the statement of operations because of the Company’s net operating losses and tax credits that are available to be carried forward. When necessary, the Company will account for interest and penalties related to uncertain tax positions as part of its provision for federal and state income taxes. The Company does not expect the amounts of unrecognized benefits will change significantly within the next twelve months.

The Company is currently open to audit under the statute of limitations by the Internal Revenue Service and state jurisdictions for the years ended December 31, 1999 through 2013.

Preferred Stock and Stockholders' Equity

12 Months Ended

Dec. 31, 2013

Preferred Stock and Stockholders' Equity

11.

Preferred Stock and Stockholders’ Equity

On April 26, 2006, the date of the Company’s annual stockholders meeting that year, the shareholders approved the adoption of an Amended and Restated Certificate of Incorporation pursuant to which the Company has 280,000,000 shares of authorized capital stock, of which 250,000,000 shares are designated as common stock (par value $.001 per share), and 30,000,000 shares are designated as preferred stock (par value $.001 per share), which the Company refers to as the Preferred Stock.

Common Stock

In September 2003, the Company issued 1,001,949 shares of common stock at $0.50 per share for gross proceeds of $500 thousand.

In January 2004, the Company issued 9,017,538 shares of common stock at $0.50 per share for gross proceeds of $4.5 million.

In February 2004, the Company amended its articles of incorporation to provide for the combination of the Company’s common stock, par value $0.001 per share on a 1-for-4 basis.

On June 6, 2005, the Company completed the 2005 Offering (see Note 2 to the financial statements, Financings). As a result of the Merger, all shares of the Series A Preferred Stock were automatically converted into the number of shares of common stock that the holders of Series A Preferred Stock would have received if their shares of Series A Preferred Stock had been converted into common stock immediately prior to the Merger.

On May 3, 2006, pursuant to subscription agreements between the Company and certain institutional and other accredited investors, the Company completed the sale of an aggregate of 7,991,256 shares of the Company’s common stock at a price of $4.63 per share in the 2006 Offering. The total gross proceeds resulting from the 2006 Offering was approximately $37 million, before deducting selling commissions and expenses.

On September 15, 2009, pursuant to subscription agreements between the Company and certain institutional and other accredited investors, the Company completed the sale of an aggregate of 2,772,337 shares of the Company’s common stock at a price of $1.825 per share in a private placement. The total gross proceeds resulting from the September 2009 Offering was approximately $5.1 million, before deducting selling commissions and expenses (see Note 2 to the financial statements, Financings).

On December 9, 2009, pursuant to underwriting agreement between the Company and certain brokers, the Company completed the sale of an aggregate of 15,484,000 shares of the Company’s common stock at a price of $3.10 per share in a private placement. The total gross proceeds resulting from the 2009 public offering was approximately $48.0 million, before deducting selling commissions and expenses (see Note 2 to the financial statements, Financings).

On June 2, 2010, pursuant to underwriting agreement between the Company and certain brokers, the Company completed the sale of an aggregate of 7,000,000 shares of the Company’s common stock at a price of $5.00 per share in a public offering. The total gross proceeds resulting from the 2010 public offering were approximately $35.0 million, before deducting selling commissions and expenses (see Note 2 to the financial statements, Financings).

On January 6, 2011, and in conjunction with the Company’s execution and delivery of a Channel Agreement, the Company entered into a Stock Purchase Agreement and Registration Rights Agreement. On January 12, 2011, and pursuant to that Stock Purchase Agreement, the Company sold 2,426,235 shares of the Company’s common stock in a private placement for a total purchase price of $11.6 million, or $4.80 per share. The Company simultaneously issued an additional 3,636,926 shares of its common stock for a cash purchase price equal to the $0.001 par value of such shares, which price was deemed paid in partial consideration for the execution and delivery of the Channel Agreement (see Note 2, Financings).

On February 3, 2011, pursuant to underwriting agreement between the Company and certain brokers, the Company completed the sale of an aggregate of 11,040,000 shares of the Company’s common stock at a price of $5.75 per share in a public offering. The total gross proceeds resulting from the 2011 public offering were approximately $63.5 million, before deducting selling commissions and expenses (see Note 2 to the financial statements, Financings).

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 (see Note 2 to the financial statements, Financings).

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 + veledimex for unresectable Stage III or IV melanoma, triggering the issuance of the Milestone Shares.

On October 29, 2013, 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 16,445,000 shares of the Company’s common stock at a price of $3.50 per share in a public offering. The total gross proceeds resulting from this public offering were approximately $57.6 million, before deducting selling commissions and expenses (see Note 2 to the financial statements, Financings).

As of December 31, 2013, the Company had 100,159,618 shares of common stock issued and outstanding and no shares of Preferred Stock issued and outstanding.

Series A Preferred Stock

All shares of Series A Preferred Stock have been converted into shares of common stock of the Company.

Preferred Stock

The Company’s Board of Directors are authorized to designate any series of Preferred Stock, to fix and determine the variations in relative rights, preferences, privileges and restrictions as between and among such series.

- Definition

The entire disclosure for shareholders' equity comprised of portions attributable to the parent entity and noncontrolling interest, including other comprehensive income. Includes, but is not limited to, balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings, accumulated balance for each classification of other comprehensive income and amount of comprehensive income.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08.(d),(e))
-URI http://asc.fasb.org/extlink&oid=26873400&loc=d3e23780-122690

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21484-112644

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 310
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SAB TOPIC 4.E)
-URI http://asc.fasb.org/extlink&oid=27010918&loc=d3e74512-122707

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21488-112644

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02.29-31)
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
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-Paragraph 4
-Subparagraph (SAB TOPIC 4.C)
-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187143-122770

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
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-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21506-112644

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.3-04)
-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187085-122770

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 30
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6405834&loc=d3e23285-112656

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

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Preferred Stock
-URI http://asc.fasb.org/extlink&oid=6521494

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21463-112644

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21564-112644

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 08
-Paragraph d
-Article 4

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 02
-Paragraph 29, 30, 31
-Article 5

Reference 16: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 4
-Section E

Reference 17: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 08
-Article 4

Reference 18: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
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Reference 19: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Article 3

+ Details

Stock Option Plan

12 Months Ended

Dec. 31, 2013

Stock Option Plan

12.

Stock Option Plan

The Company adopted the 2003 Stock Option Plan, or the 2003 Plan, in 2003, under which the Company initially reserved for the issuance of 1,252,436 shares of its common stock. The 2003 Plan was approved by the Company’s stockholders on December 21, 2004. On June 23, 2010, June 4, 2009, April 25, 2007 and April 26, 2006, the dates of the Company’s annual stockholders meetings during such years, the Company’s stockholders approved amendments to the 2003 Plan increasing the total shares reserved by 3,000,000, 2,000,000, 2,000,000 and 750,000 shares, respectively, for a total of 9,002,436 shares. Upon approval of the 2012 Equity Incentive Plan, no additional stock awards may be granted under the 2003 Plan.

The Company adopted the 2012 Equity Incentive Plan, or the 2012 Plan, in May 2012, under which the Company initially reserved for the issuance of 4,000,000 shares of its common stock. The 2012 Plan was approved by the Company’s stockholders on June 20, 2012.

As of December 31, 2013, the Company had outstanding options issued to its employees to purchase up to 5,834,408 shares of the Company’s common stock, to its directors to purchase up to 912,645 shares of the Company’s common stock, as well as options to consultants in connection with services rendered to purchase up to 250 shares of the Company’s common stock.

Stock options to employees generally vest ratably over three years and have contractual terms of ten years. Stock options to directors generally vest ratably over two or three years and have contractual terms of ten years. Stock options are valued using the Black-Scholes option pricing model and compensation is recognized based on such fair value over the period of vesting on a straight-line basis. The Company has also reserved an aggregate of 45,823 additional shares for issuance under options granted outside of the 2003 Stock Option Plan. The options were granted to The University of Texas M. D. Anderson Cancer Center and DEKK-Tec, Inc. (see Note 8 to the financial statements, Commitments and Contingencies). During the year ended December 31, 2007, the Company recorded a $120 thousand stock compensation expense in connection with the Company achieving a predetermined development milestone, which triggered the vesting of 25,111 of the options granted outside of the 2003 Stock Option Plan. The 25,111 options were exercised on August 13, 2007. Proceeds from this exercise amounted to $50 thousand and the intrinsic value of these options amounted to $104 thousand. During 2010, the Company recorded an expense of $27 thousand when 6,904 DEKK-Tec stock options vested upon achieving Phase 3 milestones.

Proceeds from the 2013, 2012, and 2011 exercises amounted to $956 thousand, $30 thousand, and $980 thousand, respectively. The intrinsic value of these options amounted to $1.4 million, $11 thousand and $2.5 million for years ended December 31, 2013, 2012 and 2011, respectively.

Transactions under the Plan for the years ending December 31, 2013, 2012, and 2011 were 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, 2010		4,566,935		$	2.82
Granted		1,894,300			5.65
Exercised		(479,666	)		2.04
Cancelled		(843,083	)		5.01

Outstanding, December 31, 2011		5,138,486			4.08
Granted		2,309,650			4.36
Exercised		(8,300	)		3.61
Cancelled		(292,533	)		5.70

Outstanding, December 31, 2012		7,147,303			4.11
Granted		2,649,900			3.28
Exercised		(570,168	)		1.68
Cancelled		(2,479,732	)		4.58

Outstanding, December 31, 2013		6,747,303		$	3.81		7.17	$	5,339

Vested and unvested expected to vest at December 31, 2013		6,711,969		$	4.01		5.03	$	5,311

Options exercisable, December 31, 2013		3,471,935		$	4.01		5.03	$	2,654

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

Options available for future grant		416,964

At December 31, 2013, total unrecognized compensation costs related to non-vested stock options outstanding amounted to $8.5 million. The cost is expected to be recognized over a weighted-average period of 1.84 years.

Restricted Stock

In December 2013, the Company issued 75,272 shares of restricted stock to its non-employee directors, which vested in their entirety on the one year anniversary of the grant date. In January, February and May 2012, the Company issued 101,500, 43,802 and 25,000 shares of restricted stock to employees, which vested ratably in annual installments over three years, respectively, commencing on the first anniversary of the grant date. In December 2012, the Company also issued 87,730 shares of restricted stock to its non-employee directors, which vested ratably in annual installments over three years, commencing on the first anniversary of the grant date. In July and December 2011, the Company issued 50,000 and 720,675 shares of restricted stock to employees, which vested ratably in annual installments over three years, respectively, commencing on the first anniversary of the grant date. In January and December 2011, the Company also issued 25,000 and 52,731 shares of restricted stock to its non-employee directors, which vested in their entirety on the one year anniversary of the grant date and ratably in annual installments over three years, respectively, commencing on the first anniversary of the grant date. In March and April 2010, the Company issued 90,000 and 25,000 shares of restricted stock to its non-employee directors, respectively, all of which vested in their entirety on the one year anniversary of the grant date. In December 2009, the Company issued 347,500 shares of restricted stock to employees and 45,000 shares of restricted stock to its non-employee directors, which vested ratably in annual installments over three and two years, respectively, commencing on the first anniversary of the grant date. In September 2009, the Company issued 828,000 shares of restricted stock to employees and 180,000 shares of restricted stock to its board of directors, all of which vested in their entireties on the one year anniversary of the grant date. In December 2008, the Company issued 396,500 shares of restricted stock to employees and 90,000 shares of restricted stock to its board of directors, all of which vested in December 2009. Also, in January 2008, the Company issued 100,000 shares of restricted stock to one employee which vested ratably over a three-year period. In 2007, the Company issued 70,000 shares of restricted stock to several employees which vested in December 2008. During the years ended December 31, 2013, 2012 and 2011, $1.2 million, $1.7 million, and $635 thousand of compensation expense was recognized, respectively.

In January, March, May and December 2013, the Company repurchased 52,018, 5,400, 2,623, and 56,683 shares at average prices of $4.28, $4.50, $1.65 and $4.37 per share, respectively, to cover payroll taxes. In July and December 2012, the Company repurchased 15,740 and 107,413 shares at $6.06 and $4.19 per share, respectively, to cover payroll taxes. In January and December 2011, the Company repurchased 15,190 shares and 44,369 shares at $5.14 and $4.41 per share, respectively, to cover payroll taxes. In January, September and December 2010, the Company repurchased 15,283 shares, 349,710 shares and 51,116 shares at $3.10, $3.95 and $4.66 per share, respectively, to cover payroll taxes. In December 2009, the Company repurchased 103,823 shares of vested restricted stock from employees at $3.66 per share to cover payroll taxes. A summary of the status of non-vested restricted stock as of December 31, 2013, 2012 and 2011 is as follows:


	Number of Shares			Weighted-Average Grant Date Fair Value
Non-vested, December 31, 2010		348,753		$	2.30
Granted		848,406			4.52
Vested		(229,586	)		3.56
Cancelled		(16,667	)		2.85

Non-vested, December 31, 2011		950,906			4.34
Granted		258,032			4.39
Vested		(351,829	)		4.32
Cancelled		(123,370	)		4.34

Non-vested, December 31, 2012		733,739			4.37
Granted		75,272			4.34
Vested		(292,399	)		4.31
Cancelled		(163,747	)		4.42

Non-vested, December 31, 2013		352,865		$	4.38

As of December 31, 2013, there was $1.3 million of total unrecognized stock-based compensation expense related to non-vested restricted stock arrangements. The expense is expected to be recognized over a weighted-average period of 1.45 years.

Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2013

Basis of Presentation

Basis of Presentation

The accompanying financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”).

Use of Estimates

Use of Estimates

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

•

Clinical trial expenses;

•

Fair value measurements for stock based compensation and warrants; and

•

Income taxes.

Subsequent Events

Subsequent Events

Cash and Cash Equivalents

Cash and Cash Equivalents

Concentrations of Credit Risk

Concentrations of Credit Risk

Property and Equipment

Property and Equipment

Restricted Cash

Restricted Cash

Long-Lived Assets

Long-Lived Assets

Warrants

Warrants

Fair Value Measurements

Fair Value Measurements

•

Level 1—Quoted prices in active markets for identical 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 December 31, 2013 and 2012 are as follows:


($ in thousands)			Fair Value Measurements at Reporting Date Using
Description	Balance as of December 31, 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	$	66,794	$	66,794	$	—	$	—

Warrant liability	$	11,776	$	—	$	11,776	$	—


($ 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	$	—

Revenue Recognition

Revenue Recognition

Research and Development Costs

Research and Development Costs

Income Taxes

Income Taxes

Accounting for Stock-Based Compensation

Accounting for Stock-Based Compensation


	Year ended December 31,
(in thousands)	2013		2012		2011
Research and development	$	792	$	1,917	$	890
General and administrative		2,715		2,963		1,869

Share based employee compensation expense before tax		3,507		4,880		2,759
Income tax benefit		—		—		—

Net share based employee compensation expense	$	3,507	$	4,880	$	2,759


(in thousands, except per share data)	September 9, 2003 (date of inception) to December 31, 2005
Net loss:
As reported	$	(15,364	)

Stock-based compensation expense included in reported net loss		802
Stock-based compensation expense under the fair-value based method		(1,756	)

Pro forma net loss	$	(16,318	)

Basic and diluted net loss per share:
As reported	$	(3.75	)
Pro forma	$	(3.98	)


	2013	2012	2011
Weighted average risk-free interest rate	1.00 - 2.10%	0.79 - 1.13%	1.09 - 2.69%
Expected life in years	6	6	6
Expected volatility	83.40 - 95.96%	83.36 - 83.53%	83.26 - 87.29%
Expected dividend yield	0	0	0

Net Loss Per Share

Net Loss Per Share


	December 31,
	2013		2012		2011
Stock options		6,747,303		7,147,303		5,138,486
Unvested restricted stock		352,865		733,739		950,906
Warrants		10,539,767		11,197,454		13,117,264

		17,639,935		19,078,496		19,206,656

New Accounting Pronouncements

New Accounting Pronouncements

Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2013

Assets and Liabilities Measured at Fair Value on Recurring Basis

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


($ in thousands)			Fair Value Measurements at Reporting Date Using
Description	Balance as of December 31, 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	$	66,794	$	66,794	$	—	$	—

Warrant liability	$	11,776	$	—	$	11,776	$	—


($ 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	$	—

Share-Based Compensation Expense Included in Statements of Operations

The following table presents share-based compensation expense included in the Company’s Statements of Operations:


	Year ended December 31,
(in thousands)	2013		2012		2011
Research and development	$	792	$	1,917	$	890
General and administrative		2,715		2,963		1,869

Share based employee compensation expense before tax		3,507		4,880		2,759
Income tax benefit		—		—		—

Net share based employee compensation expense	$	3,507	$	4,880	$	2,759

Effect on Net Loss and Earnings Per Share if Applied Fair Value Recognition Provisions to Stock-Based Awards


(in thousands, except per share data)	September 9, 2003 (date of inception) to December 31, 2005
Net loss:
As reported	$	(15,364	)

Stock-based compensation expense included in reported net loss		802
Stock-based compensation expense under the fair-value based method		(1,756	)

Pro forma net loss	$	(16,318	)

Basic and diluted net loss per share:
As reported	$	(3.75	)
Pro forma	$	(3.98	)

Assumptions for Volatility, Expected life, Dividend Yield and Risk-free Interest Rate

and No. 110. The assumptions for volatility, expected life, dividend yield and risk-free interest rate are presented in the table below:


	2013	2012	2011
Weighted average risk-free interest rate	1.00 - 2.10%	0.79 - 1.13%	1.09 - 2.69%
Expected life in years	6	6	6
Expected volatility	83.40 - 95.96%	83.36 - 83.53%	83.26 - 87.29%
Expected dividend yield	0	0	0

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 antidilutive. Such potential common shares at December 31, 2013, 2012, and 2011 consist of the following:


	December 31,
	2013		2012		2011
Stock options		6,747,303		7,147,303		5,138,486
Unvested restricted stock		352,865		733,739		950,906
Warrants		10,539,767		11,197,454		13,117,264

		17,639,935		19,078,496		19,206,656

Financings - Additional Information (Detail)	1 Months Ended																					12 Months Ended						124 Months Ended
Financings - Additional Information (Detail)	Oct. 29, 2013 USD ($) $ / shares shares	Oct. 23, 2013 $ / shares shares	Jan. 31, 2012 USD ($) shares	Jan. 25, 2012 shares	Jan. 20, 2012 USD ($) $ / shares shares	Feb. 08, 2011 USD ($) shares	Feb. 03, 2011 USD ($) $ / shares shares	Jan. 12, 2011 USD ($) $ / shares shares	Jun. 02, 2010 USD ($) $ / shares shares	May 27, 2010 USD ($) $ / shares shares	Dec. 09, 2009 USD ($) $ / shares shares	Dec. 04, 2009 USD ($) $ / shares shares	Sep. 15, 2009 USD ($) $ / shares shares	Feb. 23, 2007 USD ($) yr $ / shares shares	May 03, 2006 USD ($) yr $ / shares shares	Sep. 13, 2005 USD ($) shares	Jun. 06, 2005 USD ($) $ / shares shares	Jan. 31, 2005	Dec. 22, 2004 yr $ / shares shares	Jan. 31, 2004 USD ($) shares	Sep. 30, 2003 USD ($) shares	Dec. 31, 2013 USD ($) yr $ / shares shares	Dec. 31, 2012 USD ($) $ / shares shares	Dec. 31, 2011 USD ($)	Dec. 31, 2009 USD ($) yr $ / shares shares	Dec. 31, 2005 USD ($) yr $ / shares shares	Dec. 31, 2004 yr shares	Dec. 31, 2013 USD ($) yr $ / shares shares	Sep. 09, 2009 USD ($)	Dec. 31, 2006 $ / shares	Apr. 26, 2006 $ / shares	May 31, 2005 $ / shares	Feb. 29, 2004 $ / shares
Long Term Debt And Equity Financings [Line Items]
Common stock, shares issued										30 days
Option to purchase common stock \| shares										1,050,000
Net proceeds from issuance of common stock										$ 32,800,000		$ 45,200,000	$ 4,600,000
Common Stock Shares Sold \| shares	16,445,000				10,114,401		11,040,000	2,426,235	7,000,000	7,000,000	15,484,000	15,484,000	2,772,337	5,910,049	7,991,256
Proceeds from issuance of common stock	$ 57,600,000				$ 52,600,000		$ 63,500,000	$ 11,600,000	$ 35,000,000		$ 48,000,000		$ 5,100,000	$ 30,900,000	$ 37,000,000		$ 18,100,000			$ 4,500,000	$ 500,000
Common stock price per share \| $ / shares	$ 3.50				$ 5.20		$ 5.75	$ 4.80	$ 5.00		$ 3.10	$ 3.10	$ 1.825	$ 5.225	$ 4.63
Common stock sdditional shares issued \| shares								3,636,926												9,017,538	1,001,949	100,159,618	83,236,840					100,159,618
Common stock par value per share \| $ / shares								$ 0.001		$ 0.001												$ 0.001	$ 0.001			$ 0.001		$ 0.001			$ 0.001		$ 0.001
Research and development expense								$ 17,500,000														$ 42,852,000	$ 83,446,000	$ 57,083,000				$ 255,197,000
Percentage of purchase commitment of securities offered																						19.99%
Percentage of net proceed offering																						40.00%
Aggregate purchase commitment amount																						$ 50,000,000
Remaining maximum purchase commitment amount																						$ 19,000,000						19,000,000
Underwriting discounts, commissions and other offering expenses										$ 2,200,000
Gross proceeds from the offering												$ 48,000,000
Payment of commissions and offering expenses												$ 2,800,000
Warrants to purchase shares \| shares												0.5
Warrants to purchase an aggregate of shares of common stock \| shares															799,126				62,621			799,126			8,206,520	50,000	62,621
Exercise price per share \| $ / shares														$ 5.75					$ 4.75			$ 5.09
Exercisable period of warrants																	7 years
Warrant term														5 years											5 years
Estimated fair value of warrant																						$ 3,500,000			$ 22,900,000			$ 3,500,000
Expected volatility														93.00%	100.00%				134.00%			134.00%			105.00%	109.00%	134.00%	134.00%
Risk free interest														4.71%	5.01%				3.93%			3.93%			2.14%	4.39%	3.93%	3.93%
Expected life \| yr														5					7			7			5	5	7	7
Expected dividend yield														0.00%	0.00%				0.00%			0.00%			0.00%	0.00%	0.00%	0.00%
Payment of placement agent fees													$ 455,000
Term of warrant														5 years	5 years
Exercise price per share \| $ / shares														$ 5.75
Percentage of additional shares issued by company														20.00%	30.00%
Cash commission paid														$ 1,000,000	$ 1,700,000							$ 1,700,000
Term of warrant														5 years								7 years
Purchase of common stock \| shares														21,244
Exercise price per share \| $ / shares															$ 5.56
Warrants issuable as a percentage of shares													5.00%									10.00%
Risk free interest rate of warrants																						5.01%
Reimbursements made by company																						$ 100,000
Percentage of common stock outstanding on fully diluted basis																96.80%
Payment made to affiliate																$ 425,000
Issuance of series A convertible preferred stock																										$ 15,077,000
Cash commission paid																	7.00%
Warrant exercise price as percent of market value																	110.00%
Expenses to reimburse																	$ 50,000
Right of first refusal to act as the placement agent																	3 years
Additional paid-in capital recorded using Black- Scholes model																						$ 1,700,000
J. P. Morgan Securities LLC
Long Term Debt And Equity Financings [Line Items]
Warrants issued \| shares																									464,520
Exercise price per share \| $ / shares																									$ 4.02
Exercisable period of warrants																									6 months
Placement Agents
Long Term Debt And Equity Financings [Line Items]
Cash commission paid														$ 1,600,000
Term of warrant														5 years
Purchase of common stock \| shares														156,058
Exercise price per share \| $ / shares														$ 5.75
Paramount
Long Term Debt And Equity Financings [Line Items]
Warrants to purchase an aggregate of shares of common stock \| shares															532,750
Exercise price per share \| $ / shares															$ 5.09
Warrant term															7 years			7 years
Cash commission paid														$ 1,000,000
Warrants issuable as a percentage of shares															10.00%			10.00%
Series A Preferred Stock
Long Term Debt And Equity Financings [Line Items]
Issuance of series A convertible preferred stock																	$ 4,197,946									$ 15,077,000
Underwritten Public Offering
Long Term Debt And Equity Financings [Line Items]
Common stock price per share \| $ / shares										$ 5.00
Issuance and sale of our common stock \| shares										7,000,000
Private Placement
Long Term Debt And Equity Financings [Line Items]
Common stock price per share \| $ / shares																	$ 4.31								$ 1.825					$ 4.63		$ 4.75
Common Stock Shares Sold \| shares															7,991,256
Common stock price per share \| $ / shares															$ 4.63
Warrants to purchase an aggregate of shares of common stock \| shares														177,302	799,126										2,910,954
Exercise price per share \| $ / shares														$ 5.75											$ 2.04
Exercisable period of warrants																									5 years
Estimated fair value of warrant														$ 709,000	$ 3,500,000										$ 4,207,000
Expected volatility																						100.00%			105.00%			100.00%
Risk free interest																									2.41%
Expected life \| yr															7							7			5			7
Expected dividend yield																						0.00%			0.00%			0.00%
Cash commission paid																						$ 2,600,000
Warrants issuable as a percentage of shares														3.00%
Private Placement \| Placement Agents
Long Term Debt And Equity Financings [Line Items]
Warrants to purchase an aggregate of shares of common stock \| shares													138,617												138,617
Exercise price per share \| $ / shares													$ 2.04
Investor
Long Term Debt And Equity Financings [Line Items]
Warrants to purchase an aggregate of shares of common stock \| shares														1,182,015	2,397,392
Estimated fair value of warrant														$ 4,700,000	$ 9,600,000
Expected life \| yr															5
Securities Offering
Long Term Debt And Equity Financings [Line Items]
Cash commission paid														$ 222,000
Convertible Preferred Stock
Long Term Debt And Equity Financings [Line Items]
Warrant to purchase additional shares \| shares																	419,794
Series A preferred stock was converted to common stock \| shares																4,197,946
Maximum \| Underwritten Public Offering
Long Term Debt And Equity Financings [Line Items]
Initial public offering price per share \| $ / shares										$ 0.18
Maximum \| Private Placement
Long Term Debt And Equity Financings [Line Items]
Cash penalty																													10.00%
Total purchase price																													$ 506,000
Minimum \| Private Placement
Long Term Debt And Equity Financings [Line Items]
Cash penalty																													1.00%
J.P. Morgan Securities Inc.
Long Term Debt And Equity Financings [Line Items]
Stock issued during period \| shares	2,145,000	14,300,000	464,401	9,650,000
Issuance & sale of common stock in public offering price per share \| $ / shares		$ 3.50			$ 5.20
Common stock, shares issued		30 days			30 days
Option to purchase common stock \| shares		2,145,000			1,447,500
Common stock price per share \| $ / shares		$ 3.29			$ 4.888
Net proceeds from issuance of common stock	$ 53,900,000		$ 49,200,000
Issuance & sale of common stock in public offering \| shares					9,650,000
J.P. Morgan Securities Inc. \| Total
Long Term Debt And Equity Financings [Line Items]
Stock issued during period \| shares			10,114,401
Barclays Capital Inc.
Long Term Debt And Equity Financings [Line Items]
Issuance & sale of common stock in public offering price per share \| $ / shares							$ 5.75
Common stock, shares issued							30 days
Option to purchase common stock \| shares							1,440,000
Common stock price per share \| $ / shares							$ 5.425
Net proceeds from issuance of common stock						$ 59,800,000
Issuance & sale of common stock in public offering \| shares							9,600,000
Barclays Capital Inc. \| Total
Long Term Debt And Equity Financings [Line Items]
Stock issued during period \| shares						11,040,000

Component of Accrued Expenses (Detail) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Accrued Liabilities [Line Items]
Professional services	$ 582	$ 835
Clinical consulting services	3,751	9,628
Preclinical services	513	411
Manufacturing services	547	3,217
Accrued vacation	227	452
Other consulting services	230	903
Payroll taxes and benefits	255	585
Severance		474
Employee compensation	252	11
Accrued expenses	$ 6,357	$ 16,516

Related Party Transactions - Additional Information (Detail) $ / shares in Units, $ in Thousands	1 Months Ended									12 Months Ended						124 Months Ended
	Oct. 29, 2013 shares	Nov. 07, 2012 shares	Jan. 25, 2012 shares	Sep. 15, 2009 USD ($) $ / shares shares	Feb. 23, 2007 USD ($) yr $ / shares shares	Dec. 18, 2006 USD ($)	May 03, 2006 USD ($) yr $ / shares shares	Jan. 31, 2005 USD ($)	Dec. 22, 2004 USD ($) yr $ / shares shares	Dec. 31, 2013 USD ($) yr $ / shares shares	Dec. 31, 2012 USD ($) shares	Dec. 31, 2011 USD ($)	Dec. 31, 2009 yr $ / shares shares	Dec. 31, 2005 USD ($) yr shares	Dec. 31, 2004 USD ($) yr shares	Dec. 31, 2013 USD ($) yr shares	Apr. 26, 2006 shares	Dec. 30, 2004 shares
Related Party Transaction [Line Items]
Common stock, shares authorized										250,000,000	250,000,000					250,000,000	250,000,000
Payable to related parties \| $									$ 60
Warrants to purchase an aggregate of shares of common stock							799,126		62,621	799,126			8,206,520	50,000	62,621
Warrant exercise price \| $ / shares					$ 5.75				$ 4.75	$ 5.09
Risk free interest					4.71%		5.01%		3.93%	3.93%			2.14%	4.39%	3.93%	3.93%
Expected life \| yr					5				7	7			5	5	7	7
Expected volatility					93.00%		100.00%		134.00%	134.00%			105.00%	109.00%	134.00%	134.00%
Expected dividend yield					0.00%		0.00%		0.00%	0.00%			0.00%	0.00%	0.00%	0.00%
General administrative expenses \| $									$ 251	$ 15,661	$ 19,523	$ 14,984		$ 45	$ 251	$ 103,979
Warrants issuable as a percentage of shares				5.00%						10.00%
Warrant term					5 years								5 years
Cash commission paid \| $					$ 1,000		$ 1,700			$ 1,700
Payment to related parties \| $						$ 180
Remaining service expenses expected to be incurred \| $										$ 1,948	6,912					$ 1,948
Placement Agents
Related Party Transaction [Line Items]
Cash commission paid \| $					$ 1,600
Private Placement
Related Party Transaction [Line Items]
Warrants to purchase an aggregate of shares of common stock					177,302		799,126						2,910,954
Warrant exercise price \| $ / shares					$ 5.75								$ 2.04
Risk free interest													2.41%
Expected life \| yr							7			7			5			7
Expected volatility										100.00%			105.00%			100.00%
Expected dividend yield										0.00%			0.00%			0.00%
Warrants issuable as a percentage of shares					3.00%
Cash commission paid \| $										$ 2,600
Private Placement \| Placement Agents
Related Party Transaction [Line Items]
Warrants to purchase an aggregate of shares of common stock				138,617									138,617
Warrant exercise price \| $ / shares				$ 2.04
Pre-Merger
Related Party Transaction [Line Items]
Warrants to purchase an aggregate of shares of common stock									125,000
Warrant exercise price \| $ / shares									$ 2.38
Paramount
Related Party Transaction [Line Items]
Common stock, shares authorized																		2,428,911
Warrants to purchase an aggregate of shares of common stock							532,750
Warrant exercise price \| $ / shares							$ 5.09
Cash commission Percentage							7.00%	7.00%
Warrants issuable as a percentage of shares							10.00%	10.00%
Warrant term							7 years	7 years
Percentage of per share exercise price								110.00%
Payable to related parties \| $								$ 50
Cash commission paid \| $					$ 1,000
Paramount \| Installment One
Related Party Transaction [Line Items]
Common stock, shares authorized																		1,214,456
Paramount \| Installment Two
Related Party Transaction [Line Items]
Common stock, shares authorized																		1,214,456
Paramount \| Pre-Merger
Related Party Transaction [Line Items]
Common stock, shares authorized																		4,848,376
Paramount \| Pre-Merger \| Installment One
Related Party Transaction [Line Items]
Common stock, shares authorized																		2,424,188
Paramount \| Pre-Merger \| Installment Two
Related Party Transaction [Line Items]
Common stock, shares authorized																		2,424,188
Related Parties
Related Party Transaction [Line Items]
Warrants to purchase an aggregate of shares of common stock					97,536
Cash commission Percentage				3.325%	6.00%
Warrant term				5 years
Cash commission paid \| $				$ 168
Related Parties \| Private Placement
Related Party Transaction [Line Items]
Warrants to purchase an aggregate of shares of common stock				65,843
Intrexon Corporation
Related Party Transaction [Line Items]
Payments for services \| $										2,400	11,400
Amounts paid for services incurred \| $										7,800	6,600
Remaining service expenses expected to be incurred \| $										0	$ 4,800					$ 0
Accrued expense \| $										$ 600						$ 600
Issuance of common stock	2,857,143	3,636,926	1,923,075

Commitments and Contingencies - Additional Information (Detail)	1 Months Ended												12 Months Ended										24 Months Ended	124 Months Ended
	Oct. 17, 2013 ft²	Aug. 30, 2013 USD ($) ft²	Jun. 27, 2013 USD ($)	Mar. 07, 2011 USD ($)	Jan. 12, 2011 USD ($)	Jan. 06, 2011	May 27, 2010 shares	Mar. 16, 2010 USD ($)	Apr. 08, 2008 USD ($)	Nov. 03, 2006 USD ($)	Oct. 15, 2004 USD ($)	Aug. 24, 2004 Patent	Dec. 31, 2013 USD ($) ft² shares	Dec. 31, 2012 USD ($) ft² shares	Dec. 31, 2011 USD ($) ft² shares	Dec. 31, 2010 USD ($) shares	Dec. 31, 2009 USD ($)	Dec. 31, 2008 USD ($)	Dec. 31, 2007 USD ($) shares	Dec. 31, 2006 USD ($)	Dec. 31, 2005 USD ($)	Dec. 31, 2004 USD ($) $ / shares shares	Dec. 22, 2006 USD ($)	Dec. 31, 2013 USD ($) ft² shares	Nov. 02, 2012 USD ($)	Jun. 30, 2012 USD ($) ft²	Jan. 31, 2012 ft²	Apr. 30, 2011 ft²	Jan. 29, 2010 USD ($)
Commitments and Contingencies Disclosure [Line Items]
Loss on disposal of fixed assets													$ (585,000)	$ (48,000)	$ 0									$ (641,000)
Total rent Expense													1,000,000	1,100,000	$ 647,000									5,200,000
Deferred rent liability - current													212,000	39,000										212,000
Deferred rent liability - long term													851,000	400,000										851,000
Deferred rent liability net													$ 1,100,000	$ 439,000										1,100,000
Shares of common stock granted \| shares													2,649,900	2,309,650	1,894,300
Option to purchase common stock \| shares							1,050,000
Stock based compensation expenses													$ 3,507,000	$ 4,880,000	$ 2,759,000									23,688,000
Shares vested \| shares																6,904			25,111
Research expenses					$ 17,500,000								42,852,000	83,446,000	57,083,000									255,197,000
Milestones under the license agreement expense													$ 250,000	250,000	0	$ 0
Harmon Hill LLC \| Collaboration Agreement
Commitments and Contingencies Disclosure [Line Items]
Percent of company net profit													1.00%
Other expense													$ 135,000	200,000	240,000	240,000
Agreement term			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 \| shares																						27,616
Sale of stock ,price per share \| $ / shares																						$ 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]
Milestone payment																$ 300,000
Shares vested \| shares																6,904
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%
The University of Texas M.D. Anderson Cancer Center and The Texas A & M University System
Commitments and Contingencies Disclosure [Line Items]
Number of products \| Patent												2
Shares of common stock granted \| shares																						250,487
Option to purchase common stock \| shares																						50,222
Sale of stock ,price per share \| $ / shares																						$ 0.002
Stock based compensation expenses																			$ 120,000
Milestone maximum payment													$ 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 \| Intellectual Property Rights
Commitments and Contingencies Disclosure [Line Items]
Milestone payment																			100,000	$ 100,000
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 \| shares													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
Southern Research Institute
Commitments and Contingencies Disclosure [Line Items]
Milestone maximum payment													$ 775,000											$ 775,000
Royalty payment													25,000	25,000	25,000	$ 25,000	$ 25,000	$ 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
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																													$ 20,000,000
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 contract execution
Commitments and Contingencies Disclosure [Line Items]
Milestone payment															4,000,000	$ 1,800,000
PPD Development L. P. \| Upon initial clinical study enrollment
Commitments and Contingencies Disclosure [Line Items]
Milestone payment														3,800,000
PPD Development L. P. \| Upon the achievement of various milestones
Commitments and Contingencies Disclosure [Line Items]
Milestone payment													9,200,000
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													136,000
NEW YORK
Commitments and Contingencies Disclosure [Line Items]
Office space under operating lease \| ft²														7,259	6,251
Letter of credit													$ 388,000	$ 388,000	$ 388,000									388,000
Additional office space under operating lease \| ft²																											1,008
Operating lease expiration month and year													2018-10	2018-10
Area under sublease agreement \| ft²	7,259
Loss on sublease													$ 729,000
Remaining contractual obligation													2,300,000											$ 2,300,000
Sublease revenue from subtenant													1,600,000
Loss on disposal of fixed assets													$ (392,000)
Boston, MA
Commitments and Contingencies Disclosure [Line Items]
Operating lease expiration month and year															2016-08
Security deposits														$ 127,000
Boston, MA \| The first floor
Commitments and Contingencies Disclosure [Line Items]
Operating lease space \| ft²															5,249
Boston, MA \| The second floor
Commitments and Contingencies Disclosure [Line Items]
Office space under operating lease \| ft²																										4,113
Operating lease space \| ft²															8,538
Boston, MA \| The third floor
Commitments and Contingencies Disclosure [Line Items]
Operating lease space \| ft²															6,959
Boston, MA \| The four floor
Commitments and Contingencies Disclosure [Line Items]
Office space under operating lease \| ft²																										9,800
Security deposits																										$ 41,000
Germantown, MD
Commitments and Contingencies Disclosure [Line Items]
Office space under operating lease \| ft²																												2,227
Operating lease expiration month and year															2014-03
Security deposits															$ 4,000
Office closing date														Jul. 16, 2012
Boston MA Office
Commitments and Contingencies Disclosure [Line Items]
Office space under operating lease \| ft²													21,184											21,184
Area under sublease agreement \| ft²		5,249
Loss on sublease													$ 42,000
Remaining contractual obligation													367,000											$ 367,000
Sublease revenue from subtenant													325,000
Loss on disposal of fixed assets													(194,000)
Security deposits		$ 20,000											127,000											127,000
Security deposit from subtenant													$ 20,000											$ 20,000

Warrants - Additional Information (Detail) $ / shares in Units, $ in Thousands	1 Months Ended							12 Months Ended								124 Months Ended
	Oct. 31, 2009 shares	Sep. 15, 2009 $ / shares shares	Feb. 23, 2007 USD ($) yr $ / shares shares	May 03, 2006 USD ($) yr shares	Jun. 06, 2005 $ / shares	May 31, 2005 USD ($) $ / shares shares	Dec. 22, 2004 USD ($) yr $ / shares shares	Dec. 31, 2013 USD ($) yr $ / shares shares	Dec. 31, 2012 USD ($) shares	Dec. 31, 2011 USD ($) shares	Dec. 31, 2010 shares	Dec. 31, 2009 USD ($) yr $ / shares shares	Dec. 31, 2006 $ / shares shares	Dec. 31, 2005 USD ($) yr shares	Dec. 31, 2004 USD ($) yr shares	Dec. 31, 2013 USD ($) yr $ / shares shares	Dec. 31, 2008 USD ($)	Jan. 31, 2004 $ / shares	Sep. 30, 2003 $ / shares
Class of Warrant or Right [Line Items]
Warrant issued								184,367
Warrant exercised								135,346	553,914	2,516,968	95,505			12,500
Warrant outstanding								10,539,767								10,539,767
Warrants liabilities \| $								$ 11,776	$ 12,962							$ 11,776	$ 72
Warrants to purchase an aggregate of shares of common stock				799,126			62,621	799,126				8,206,520		50,000	62,621
Warrant exercise price \| $ / shares			$ 5.75				$ 4.75	$ 5.09
Warrant exercisable Period					7 years
Warrant term			5 years									5 years
Estimated fair value of warrant \| $								$ 3,500				$ 22,900				$ 3,500
Expected volatility			93.00%	100.00%			134.00%	134.00%				105.00%		109.00%	134.00%	134.00%
Risk free interest			4.71%	5.01%			3.93%	3.93%				2.14%		4.39%	3.93%	3.93%
Expected life \| yr			5				7	7				5		5	7	7
Expected dividend yield			0.00%	0.00%			0.00%	0.00%				0.00%		0.00%	0.00%	0.00%
Common stock price per share in public offering \| $ / shares								$ 3.50								$ 3.50		$ 0.50	$ 0.50
Classified warrants \| $																	$ 18,866
Other income (expense) \| $								$ (579)	(13)	$ 39						$ 4,122
General administrative expenses \| $							$ 251	$ 15,661	$ 19,523	$ 14,984				$ 45	$ 251	$ 103,979
Warrants cancelled													37,500
Conversion of Warrants to Common Stock								112,808	259,660	2,377,571	39,225
Equity
Class of Warrant or Right [Line Items]
Warrant outstanding								135,346	186,297	2,351,417	70,738					135,346
Warrants expired								706,708	1,359,317	277,910	12,500
Liability Reclassed To Equity
Class of Warrant or Right [Line Items]
Warrant outstanding								0	373,617	165,551	24,767					0
Warrants expired									579
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
Placement warrants for services performed, expiration date September 15, 2014
Class of Warrant or Right [Line Items]
Warrant outstanding								8,235,076								8,235,076
Liability
Class of Warrant or Right [Line Items]
Classified warrants \| $								$ 11,800	$ 13,000	$ 19,400						$ 11,800
Liability Warrants
Class of Warrant or Right [Line Items]
Other income (expense) \| $								$ (1,200)	$ (6,100)	(7,600)
Exercise of Warrants
Class of Warrant or Right [Line Items]
Other income (expense) \| $										$ (300)
Private Placement
Class of Warrant or Right [Line Items]
Warrant issued						419,786
Warrant exercised	136,986					11,083
Warrant outstanding						408,703
Value of warrant issued \| $						$ 1,600
Sale of stock price per share \| $ / shares					$ 4.31	$ 4.75						$ 1.825	$ 4.63
Revised price for warrants \| $ / shares						$ 4.69						$ 4.25
Warrants to purchase an aggregate of shares of common stock			177,302	799,126								2,910,954
Warrant exercise price \| $ / shares			$ 5.75									$ 2.04
Warrant exercisable Period												5 years
Estimated fair value of warrant \| $			$ 709	$ 3,500								$ 4,207
Expected volatility								100.00%				105.00%				100.00%
Risk free interest												2.41%
Expected life \| yr				7				7				5				7
Expected dividend yield								0.00%				0.00%				0.00%
Private Placement \| Placement Agents
Class of Warrant or Right [Line Items]
Warrants to purchase an aggregate of shares of common stock		138,617										138,617
Warrant exercise price \| $ / shares		$ 2.04
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
Investor
Class of Warrant or Right [Line Items]
Warrants to purchase an aggregate of shares of common stock			1,182,015	2,397,392
Estimated fair value of warrant \| $			$ 4,700	$ 9,600
Expected life \| yr				5

Significant Component of Deferred Tax Assets (Detail) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Deferred Tax Assets [Line Items]
Net operating loss carryforwards	$ 66,209	$ 42,715
Start-up and organizational costs	41,529	44,262
Research and development credit carryforwards	25,058	18,388
Stock compensation	1,028	991
Capitalized acquisition costs	12,323	13,270
Deferred revenue	1,074	1,388
Depreciation	129	331
Other	1,254	998
Deferred Tax Assets Gross	148,604	122,343
Less valuation allowance	(148,604)	(122,343)
Net deferred tax assets

Reconciliation of Income Tax Expense (Benefit) (Detail)	12 Months Ended
Reconciliation of Income Tax Expense (Benefit) (Detail)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Reconciliation of Effective Tax Rate [Line Items]
Federal income tax at statutory rates	34.00%	34.00%	34.00%
State income tax, net of federal tax benefit	4.00%	5.00%	6.00%
Research and development credits	9.00%	10.00%	11.00%
Stock compensation	(2.00%)	(1.00%)	(1.00%)
Uncertain tax position adjustment	0.00%	0.00%	0.00%
Change in warrant value	1.00%	2.00%	4.00%
Federal R&D tax grant	0.00%	0.00%	0.00%
Other	0.00%	0.00%	0.00%
Increase in valuation allowance	(46.00%)	(49.00%)	(54.00%)
Effective tax rate	0.00%	0.00%	0.00%

Preferred Stock and Stockholders' Equity - Additional Information (Detail) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended
	Oct. 29, 2013	Nov. 07, 2012	Jan. 25, 2012	Jan. 20, 2012	Feb. 03, 2011	Jan. 12, 2011	Jun. 02, 2010	May 27, 2010	Dec. 09, 2009	Dec. 04, 2009	Sep. 15, 2009	Feb. 23, 2007	May 03, 2006	Jun. 06, 2005	Jan. 31, 2004	Sep. 30, 2003	Dec. 31, 2013	Dec. 31, 2012	Apr. 26, 2006	Dec. 31, 2005	Feb. 29, 2004
Equity [Line Items]
Shares of authorized capital stock																			280,000,000
Common stock, shares authorized																	250,000,000	250,000,000	250,000,000
Common stock par value per share						$ 0.001		$ 0.001									$ 0.001	$ 0.001	$ 0.001	$ 0.001	$ 0.001
Preferred stock, shares authorized																	30,000,000	30,000,000	30,000,000
Preferred stock par value																	$ 0.001	$ 0.001	$ 0.001	$ 0.001
Common Stock Additional Shares Issued						3,636,926									9,017,538	1,001,949	100,159,618	83,236,840
Price per share															$ 0.50	$ 0.50	$ 3.50
Proceeds from issuance of common stock	$ 57,600			$ 52,600	$ 63,500	$ 11,600	$ 35,000		$ 48,000		$ 5,100	$ 30,900	$ 37,000	$ 18,100	$ 4,500	$ 500
Common Stock Shares Sold	16,445,000			10,114,401	11,040,000	2,426,235	7,000,000	7,000,000	15,484,000	15,484,000	2,772,337	5,910,049	7,991,256
Common stock price per share	$ 3.50			$ 5.20	$ 5.75	$ 4.80	$ 5.00		$ 3.10	$ 3.10	$ 1.825	$ 5.225	$ 4.63
Common stock, shares outstanding																	100,159,618	83,236,840
Preferred stock, shares issued																	0	0
Preferred stock, shares outstanding																	0	0
Intrexon Corporation
Equity [Line Items]
Issuance of common stock	2,857,143	3,636,926	1,923,075

Stock Option Plan - Additional information (Detail) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended																					12 Months Ended						124 Months Ended
	Dec. 31, 2013	May 31, 2013	Mar. 31, 2013	Jan. 31, 2013	Dec. 31, 2012	Jul. 31, 2012	May 31, 2012	Feb. 29, 2012	Jan. 31, 2012	Dec. 31, 2011	Jul. 31, 2011	Jan. 31, 2011	Dec. 31, 2010	Sep. 30, 2010	Apr. 30, 2010	Mar. 31, 2010	Jan. 31, 2010	Dec. 31, 2009	Sep. 30, 2009	Dec. 31, 2008	Aug. 31, 2007	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Jan. 31, 2008	Dec. 31, 2007	Dec. 31, 2013	Jun. 23, 2010	Jun. 04, 2009	Apr. 25, 2007	Apr. 26, 2006	Dec. 21, 2004
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Common stock reserved for future issuance	45,823																					45,823						45,823
Outstanding options issued	6,747,303				7,147,303					5,138,486			4,566,935									6,747,303	7,147,303	5,138,486	4,566,935			6,747,303
Compensation expenses																						$ 3,507	$ 4,880	$ 2,759	$ 27		$ 120
Options vested in period																									6,904		25,111
Options exercised																					25,111	570,168	8,300	479,666
Proceeds from stock options exercised																					$ 50	$ 956	$ 30	$ 980				$ 2,329
Total intrinsic value of options																					$ 104	1,400	$ 11	$ 2,500
Unrecognized compensation costs	$ 8,500																					$ 8,500						8,500
Expected recognition period																						1 year 10 months 2 days
Share-based payment award granted																						75,272	258,032	848,406
Employees
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period																							3 years
Contractual terms																							10 years
Director
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Contractual terms																							10 years
Director \| Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period																							3 years
Director \| Minimum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period																							2 years
Restricted Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Compensation expenses	$ 1,200				$ 1,700					$ 635													$ 1,700	$ 635
Repurchase of shares of restricted common stock	56,683	2,623	5,400	52,018	107,413	15,740				44,369		15,190	51,116	349,710			15,283	103,823
Repurchase of shares of restricted common stock, price per share	$ 4.37	$ 1.65	$ 4.50	$ 4.28	$ 4.19	$ 6.06				$ 4.41		$ 5.14	$ 4.66	$ 3.95			$ 3.10	$ 3.66
Restricted Stock \| Employees
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period							3 years	3 years	3 years	3 years	3 years							3 years	1 year							3 years
Share-based payment award granted							25,000	43,802	101,500	720,675	50,000							347,500	828,000	396,500						100,000	70,000
Restricted Stock \| Non Employee Directors
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period	1 year				3 years					3 years		3 years			1 year	1 year		2 years
Share-based payment award granted	75,272				87,730			43,802		52,731		25,000			25,000	90,000		45,000
Restricted Stock \| Board of Directors
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period																			1 year
Share-based payment award granted																			180,000	90,000
Unvested Restricted Common Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized compensation costs	$ 1,300																					$ 1,300						$ 1,300
Expected recognition period																						1 year 5 months 12 days
the "2003" plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Common stock reserved for future issuance	9,002,436																					9,002,436						9,002,436	3,000,000	2,000,000	2,000,000	750,000	1,252,436
the "2012 Plan"
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Common stock reserved for future issuance							4,000,000
the "2012 Plan" \| Employees \| Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Outstanding options issued	5,834,408																					5,834,408						5,834,408
the "2012 Plan" \| Director \| Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Outstanding options issued	912,645																					912,645						912,645
the "2012 Plan" \| Consultants \| Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Outstanding options issued	250																					250						250

Stock Option Activity Under Stock Option Plan (Detail) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	12 Months Ended
	Aug. 31, 2007	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Number of Shares
Beginning Balance		7,147,303	5,138,486	4,566,935
Granted		2,649,900	2,309,650	1,894,300
Exercised	(25,111)	(570,168)	(8,300)	(479,666)
Cancelled		(2,479,732)	(292,533)	(843,083)
Ending Balance		6,747,303	7,147,303	5,138,486
Vested and unvested expected to vest at end of period		6,711,969
Options exercisable, at end of period		3,471,935	3,683,786
Options available for future grant		416,964
Weighted Average Exercise Price
Beginning Balance		$ 4.11	$ 4.08	$ 2.82
Granted		3.28	4.36	5.65
Exercised		1.68	3.61	2.04
Cancelled		4.58	5.70	5.01
Ending Balance		3.81	4.11	$ 4.08
Vested and unvested expected to vest at end of period		4.01
Options exercisable, at end of period		$ 4.01	$ 3.56
Weighted Average Contractual Term (Years)
Outstanding, at end of period		7 years 2 months 1 day
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		$ 5,339
Vested and unvested expected to vest at end of period		5,311
Options exercisable, at end of period		$ 2,654	$ 3,972

Statement of Stockholders' Equity (Parenthetical) $ in Thousands	4 Months Ended	12 Months Ended
	Dec. 31, 2003	Dec. 31, 2013 USD ($) $ / shares	Dec. 31, 2012 USD ($) $ / shares	Dec. 31, 2011 USD ($)	Dec. 31, 2010 USD ($)	Dec. 31, 2009 USD ($)	Dec. 31, 2007 USD ($)	Dec. 31, 2006 USD ($)	Dec. 31, 2005 USD ($) $ / shares
Stockholders' contribution, date	Sep. 09, 2003
Issuance of Series A convertible preferred stock, expenses									$ 1,340
Issuance of Series A convertible preferred stock, warrant cost									$ 1,683
Series A convertible preferred stock, par value \| $ / shares		$ 0.001	$ 0.001						$ 0.001
Common stock, par value \| $ / shares		$ 0.001	$ 0.001						$ 0.001
Conversion of Series A convertible preferred stock into common stock, conversion date									Sep. 13, 2005
Conversion of Series A convertible preferred stock into common stock, exchange ratio									0.500974
Private Placement
Issuance of common stock, issuance expenses						$ 465	$ 1,909	$ 2,719
Registered direct offering
Issuance of common stock, issuance expenses		$ 3,678	$ 3,426		$ 2,203	2,802
Issuance of common stock and warrants in a registered direct offering, warrants						$ 22,860
Securities Offering
Issuance of common stock, issuance expenses				$ 245
Collaboration Agreement
Issuance of common stock, issuance expenses				$ 86

Organization - Additional Information (Detail) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2008
Nature Of Operations [Line Items]
Accumulated deficit	$ 340,831	$ 283,724	$ (83,495)

Effect on Net Loss and Earnings per Share if Applied Fair Value Recognition Provisions to Stock-Based Awards (Detail) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								4 Months Ended	12 Months Ended										28 Months Ended	124 Months Ended
	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2003	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2009	Dec. 31, 2008	Dec. 31, 2007	Dec. 31, 2006	Dec. 31, 2005	Dec. 31, 2004	Dec. 31, 2005	Dec. 31, 2013
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Net Loss	$ (8,903)	$ (16,713)	$ (18,692)	$ (12,799)	$ (30,225)	$ (17,824)	$ (23,613)	$ (24,470)	$ (160)	$ (57,107)	$ (96,132)	$ (63,778)	$ (32,670)	$ (7,649)	$ (25,231)	$ (26,608)	$ (17,857)	$ (9,517)	$ (5,687)	$ (15,364)	$ (340,831)
Stock-based compensation expense										$ (3,507)	$ (4,880)	$ (2,759)									$ (23,688)
Basic and diluted net loss per share:
Basic and diluted net loss per share	$ (0.09)	$ (0.20)	$ (0.22)	$ (0.15)	$ (0.37)	$ (0.23)	$ (0.30)	$ (0.32)		$ (0.66)	$ (1.22)	$ (0.97)								$ (3.75)
Included in reported net loss
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation expense																				$ 802
Under the fair-value based method
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation expense																				(1,756)
Pro Forma
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Net Loss																				$ (16,318)
Basic and diluted net loss per share:
Basic and diluted net loss per share																				$ (3.98)

Component of Property and Equipment, Net (Detail) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Property, Plant and Equipment [Line Items]
Office and computer equipment	$ 1,076	$ 1,552
Software	884	856
Leasehold improvements	841	1,357
Manufacturing equipment	153	153
Property and equipment, Gross	2,954	3,918
Less: accumulated depreciation	(2,153)	(1,924)
Property and equipment, net	$ 801	$ 1,994

Income Taxes - Additional Information (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
Income Taxes [Line Items]
Net operating loss carryforwards	$ 66,209	$ 42,715
Research and development credit carryforwards	25,058	$ 18,388
Net Operating loss Carryforwards resulting from excess tax deduction	4,200
Increase (decrease) in valuation allowance	26,300
Federal
Income Taxes [Line Items]
Net operating loss carryforwards	$ 197,000
Net operating loss carryforwards, expiration date	2032
Research and Development Credit
Income Taxes [Line Items]
Net operating loss carryforwards, expiration date	2032
Research and development credit carryforwards	$ 25,000
Net Operating Loss Carryforwards
Income Taxes [Line Items]
Increase (decrease) in deferred tax assets	(11,200)
General Business Credits
Income Taxes [Line Items]
Increase (decrease) in deferred tax assets	$ (636)

Balance Sheets (Parenthetical) - $ / shares	Dec. 31, 2013	Dec. 31, 2012	Jan. 12, 2011	May 27, 2010	Apr. 26, 2006	Dec. 31, 2005	Feb. 29, 2004	Jan. 31, 2004	Sep. 30, 2003
Preferred stock, par value	$ 0.001	$ 0.001			$ 0.001	$ 0.001
Preferred stock, shares authorized	30,000,000	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	$ 0.001	$ 0.001	$ 0.001	$ 0.001	$ 0.001
Common stock, shares authorized	250,000,000	250,000,000			250,000,000
Common stock, shares issued	100,159,618	83,236,840	3,636,926					9,017,538	1,001,949
Common stock, shares outstanding	100,159,618	83,236,840

Assets and Liabilities Measured at Fair Value on Recurring Basis (Detail) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Cash equivalents	$ 66,794	$ 72,002
Warrant liability	11,776	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	66,794	72,002
Significant Other Observable Inputs (Level 2)
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Warrant liability	$ 11,776	$ 12,962

Restructuring - Additional Information (Detail) $ in Thousands	1 Months Ended		12 Months Ended			124 Months Ended
	Oct. 17, 2013 ft²	Aug. 30, 2013 USD ($) ft²	Dec. 31, 2013 USD ($)	Dec. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)	Dec. 31, 2013 USD ($)
Restructuring Cost and Reserve [Line Items]
Restructuring charges			$ 1,700
Loss on disposition of business			800
Loss on disposal of fixed assets			600
Loss on disposal of fixed assets			(585)	$ (48)	$ 0	$ (641)
Severance and Health Benefit Continuation Costs
Restructuring Cost and Reserve [Line Items]
Restructuring charges				$ 1,300		1,300
NEW YORK
Restructuring Cost and Reserve [Line Items]
Area given for sublease \| ft²	7,259
Loss on sublease			729
Remaining contractual obligation			2,300			2,300
Expected sublease revenue from subtenant			1,600
Loss on disposal of fixed assets			(392)
Boston MA Office
Restructuring Cost and Reserve [Line Items]
Area given for sublease \| ft²		5,249
Loss on sublease			42
Remaining contractual obligation			367			367
Expected sublease revenue from subtenant			325
Loss on disposal of fixed assets			(194)
Security deposit		$ 20	127			$ 127
General and Administrative Expense
Restructuring Cost and Reserve [Line Items]
Restructuring charges			600
Research and Development Expense
Restructuring Cost and Reserve [Line Items]
Restructuring charges			$ 1,100

Future Minimum Lease Payments under Operating Leases (Detail) $ in Thousands	Dec. 31, 2013 USD ($)
Operating Leased Assets [Line Items]
2014	$ 1,196
2015	1,236
2016	997
2017	501
2018	424
Operating Leases, Future Minimum Payments Due, Total	4,354
Less: contractual sublease income	(1,883)
Future minimum lease payments, net	$ 2,471

Cumulative Effect on Balance Sheets of Reclassification Attributed to Adoption of Standard (Detail) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2008
Class of Warrant or Right [Line Items]
Liabilities Warrants	$ 11,776	$ 12,962	$ 72
Stockholders' Equity, Warrants			18,866
Stockholders' Equity, Deficit Accumulated During the Development Stage	$ 340,831	$ 283,724	(83,495)
As reported
Class of Warrant or Right [Line Items]
Stockholders' Equity, Warrants			20,504
Stockholders' Equity, Deficit Accumulated During the Development Stage			(85,061)
Restatement Adjustment
Class of Warrant or Right [Line Items]
Liabilities Warrants			72
Stockholders' Equity, Warrants			(1,638)
Stockholders' Equity, Deficit Accumulated During the Development Stage			$ 1,566

Summary of Warrants Outstanding (Detail)	12 Months Ended
Summary of Warrants Outstanding (Detail)	Dec. 31, 2013 $ / Warrants shares
Class of Warrant or Right [Line Items]
Warrants outstanding	10,539,767
Placement warrants for services performed, expiration date May 3, 2013
Class of Warrant or Right [Line Items]
Warrants outstanding	2,264,393
Exercise Price \| $ / Warrants	2.04
Expiration Date	Sep. 15, 2014
Investor warrants, expiration date September 15, 2014
Class of Warrant or Right [Line Items]
Warrants outstanding	40,298
Exercise Price \| $ / Warrants	2.04
Expiration Date	Sep. 15, 2014
Placement warrants for services performed, expiration date September 15, 2014
Class of Warrant or Right [Line Items]
Warrants outstanding	8,235,076
Exercise Price \| $ / Warrants	4.02
Expiration Date	Dec. 09, 2014