CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016		Sep. 30, 2015
Cash flows from operating activities
Net income (loss)	$ 34,065		$ (23,061)
Adjustments to reconcile net income (loss) to net cash provided by operating activities:
Depreciation and amortization	10,458		10,449
Stock-based compensation	6,423		5,223
Amortization of premium (discount) on short term investments	(8)		526
Interest added to the principal balance of the non-recourse term notes due 2029	855		18,449
Gain on repurchase of convertible subordinated notes due 2023	(1,752)		0
Amortization of debt issuance costs	2,138		2,296
Realized gain on sale of marketable securities, net	(1)		(1,204)
Amortization of lease guarantee	(108)		0
Other non-cash items	0		(2)
Changes in operating assets and liabilities:
Receivables from collaborative arrangements	(10,393)		(6,397)
Prepaid expenses and other current assets	280		519
Other assets	(22)		0
Accounts payable	(290)		154
Payable to Theravance Biopharma, Inc., net	0		(1,056)
Accrued personnel-related expenses and other accrued liabilities	220		(851)
Accrued interest payable	(1,305)		(1,161)
Other long-term liabilities	2		(5)
Deferred revenue	(664)		(665)
Net cash provided by operating activities	39,898		3,214
Cash flows from investing activities
Maturities of marketable securities	52,101		89,311
Purchases of marketable securities	(82,746)		(86,523)
Sales of marketable securities	2,995		57,098
Purchases of property and equipment	(250)		(6)
Net cash provided by (used in) investing activities	(27,900)		59,880
Cash flows from financing activities
Repurchase of common stock	(65,565)		0
Repurchase of convertible subordinated notes due 2023	(8,095)		0
Payment of principal on non-recourse notes due 2029	(3,277)		0
Payments of cash dividends to stockholders	(895)		(87,144)
Repurchase of shares to satisfy tax withholding	(884)		(2,121)
Proceeds from capped-call options	391		0
Proceeds from issuances of common stock, net	341		8,117
Net cash used in financing activities	(77,984)		(81,148)
Net decrease in cash and cash equivalents	(65,986)		(18,054)
Cash and cash equivalents at beginning of period	159,180	[1]	96,800
Cash and cash equivalents at end of period	93,194		78,746
Supplemental disclosure of cash flow information
Cash paid for interest	$ 37,729		$ 19,169

[1] Condensed consolidated balance sheet as of December 31, 2015 has been derived from audited consolidated financial statements.