CONDENSED CONSOLIDATED BALANCE SHEETS (USD $) In Thousands, unless otherwise specified	Sep. 30, 2012	Dec. 31, 2011
Current assets:
Cash and cash equivalents	$ 84,563	$ 65,477
Short-term investments	259,010	278,187
Contracts receivable	3,476	6,921
Inventories	6,737	4,139
Other current assets	7,800	5,415
Total current assets	361,586	360,139
Property, plant and equipment, net	92,598	96,615
Licenses, net	7,191	9,036
Patents, net	18,180	16,259
Deposits and other assets	6,126	2,845
Total assets	485,681	484,894
Current liabilities:
Accounts payable	5,256	8,300
Accrued compensation	5,836	9,183
Accrued liabilities	11,900	18,655
Current portion of long-term obligations	5,182	3,390
Current portion of deferred contract revenue	23,427	36,584
Total current liabilities	51,601	76,112
Long-term deferred contract revenue	36,961	17,474
2 3/4 percent convertible senior notes	142,500
2 5/8 percent convertible subordinated notes		141,448
Long-term obligations, less current portion	8,404	4,125
Long-term financing liability for leased facility	70,375	69,877
Investment in Regulus Therapeutics Inc.	5,563	4,424
Total liabilities	315,404	313,460
Stockholders' equity:
Common stock, $0.001 par value; 200,000,000 shares authorized, 101,193,132 and 100,042,976 shares issued and outstanding at September 30, 2012 and December 31, 2011, respectively	102	100
Additional paid-in capital	1,073,658	1,013,592
Accumulated other comprehensive gain (loss)	846	(770)
Accumulated deficit	(904,329)	(841,488)
Total stockholders' equity	170,277	171,434
Total liabilities and stockholders' equity	$ 485,681	$ 484,894