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CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $)
In Thousands, unless otherwise specified
 12 Months Ended
Dec. 31, 2013
Dec. 31, 2012
Dec. 31, 2011
Cash flows from operating activities:      
Net loss $ (38,379) $ (68,881) $ (96,853)
Adjustments to reconcile net loss to net cash used in operating activities:      
Depreciation and amortization 320 830 1,580
Accretion and amortization on investments, net 1,322 2,184 4,422
Accretion of discount on long-term debt     51
Loss on debt extinguishment     1,664
(Gain) loss on sale/retirement of property and equipment, net (831) (142) 5
Loss on write-downs of property and equipment 200 271 874
Loss on sale of marketable securities     2
Issuance of common stock in connection with acquired in-process research technology     594
Stock-based compensation for services by non-employees 252 183 744
Stock-based compensation for employees and directors 4,435 5,311 15,249
Amortization related to 401(k) contributions 458 726 709
Loss on equity method investment     503
Unrealized loss (gain) on derivatives 316 (13) (643)
Changes in assets and liabilities:      
Interest and other receivables 188 646 401
Prepaid assets 1,081 1,311 4,085
Deposits and other assets (4) 112 (658)
Accounts payable (2,032) 449 (482)
Accrued compensation and benefits (431) 3,548 944
Accrued restructuring charges (1,878) (1,758) 3,730
Accrued liabilities (1,697) (92) 1,038
Deferred revenue     (350)
Translation adjustment   169 (1)
Net cash used in operating activities (36,680) (55,146) (62,392)
Cash flows from investing activities:      
Restricted cash transfer (1) (1) (1)
Purchases of property and equipment (3) (862) (612)
Proceeds from sales of property and equipment 1,196 170  
Purchases of marketable securities (88,977) (79,369) (144,890)
Proceeds from sales of marketable securities     809
Proceeds from maturities of marketable securities 108,839 141,016 176,832
Proceeds from sale of investment in licensees     1
Net cash provided by investing activities 21,054 60,954 32,139
Cash flows from financing activities:      
Proceeds from issuance of long-term debt     6,422
Repayment of long-term debt     (6,422)
Proceeds from issuance of common stock, net of issuance costs 6,553 150 386
Net cash provided by financing activities 6,553 150 386
Net (decrease) increase in cash and cash equivalents (9,073) 5,958 (29,867)
Cash and cash equivalents, at beginning of year 22,063 16,105 45,972
Cash and cash equivalents, at end of year 12,990 22,063 16,105
Supplemental disclosure of cash flow information:      
Cash paid for interest     $ 37