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	$ (162,013)	$ (171,855)	$ (133,978)
Adjustments to reconcile net loss to net cash used in operating activities:
Non-cash royalty revenue related to sale of future royalties	(22,055)	(10,791)
Non-cash interest expense on liability related to sale of future royalties	22,309	18,057
Stock-based compensation	17,708	16,199	18,885
Depreciation and amortization	14,275	14,508	14,951
Impairment of long-lived assets		1,675
Other non-cash transactions	664	845	1,359
Changes in assets and liabilities:
Accounts receivable, net	3,576	(867)	20,164
Inventory	4,817	(5,613)	(5,390)
Other assets	6,423	6,031	(12,267)
Accounts payable	6,199	(122)	(3,384)
Accrued compensation	5,481	(4,034)	3,555
Accrued expenses	(1,915)	1,495	1,013
Accrued clinical trial expenses	(595)	5,547	(191)
Deferred revenue	(12,399)	(9,384)	(17,516)
Interest payable	(166)	5,278
Liability related to receipt of refundable milestone payment	70,000
Other liabilities	9,164	3,275	(943)
Net cash used in operating activities	(38,527)	(129,756)	(113,742)
Cash flows from investing activities:
Maturities of investments	319,181	307,887	383,052
Purchases of investments	(268,068)	(164,662)	(695,371)
Sales of investments	2,887	5,378	210,089
Restricted cash		(25,000)
Purchases of property and equipment	(4,091)	(10,583)	(9,722)
Net cash provided by (used in) investing activities	49,909	113,020	(111,952)
Cash flows from financing activities:
Payment of capital lease obligations	(2,992)	(2,437)	(1,978)
(Repayment of) proceeds from sale of future royalties, net of $4.4 million of transaction costs in 2012	(3,000)	119,588
Proceeds from issuance of senior secured notes, net of $4.5 million of issuance costs		77,940
Repayment of convertible subordinated notes		(172,407)
Proceeds from shares issued under equity compensation plans	8,208	4,117	4,530
Issuance of common stock, net of issuance costs			219,783
Net cash provided by financing activities	2,216	26,801	222,335
Effect of exchange rates on cash and cash equivalents	32	60	916
Net increase (decrease) in cash and cash equivalents	13,630	10,125	(2,443)
Cash and cash equivalents at beginning of year	25,437	15,312	17,755
Cash and cash equivalents at end of year	39,067	25,437	15,312
Supplemental disclosure of cash flow information:
Cash paid for interest	17,590	9,620	10,277
Cash paid for income taxes	1,014	1,021	957
Supplemental schedule of non-cash investing and financing activities:
Retirement of convertible subordinated notes in exchange for senior secured notes		$ 42,548