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Isis Reports Financial Results and Highlights for Third Quarter 2011
Date:11/7/2011

nzyme Corporation.Isis Pharmaceuticals, Inc.Selected Financial InformationCondensed Consolidated Statements of Operations(In Thousands, Except Per Share Data)Three months ended,Nine months ended,September 30,September 30,2011201020112010Revenue:(unaudited)(unaudited)Research and development revenue under collaborative agreements$20,189$27,785$64,508$77,484Licensing and royalty revenue5248392,1754,569Total revenue20,71328,62466,68382,053Expenses:Research and development 39,92434,716110,178105,827General and administrative3,1052,8558,9898,724Total operating expenses43,02937,571119,167114,551Loss from operations(22,316)(8,947)(52,484)(32,498)Other income (expense):Equity in net loss of Regulus Therapeutics Inc.(386)(930)(2,275)(6,358)Investment income5757761,8962,590Interest expense(4,773)(3,338)(11,624)(9,835)Gain (loss) on investments, net18(15)(267)(1,162)Loss before income tax expense (26,882)(12,454)(64,754)(47,263)Income tax expense--(11)(2)Net loss $(26,882)$(12,454)$(64,765)$(47,265)Basic and diluted net loss per share$(0.27)$(0.13)$(0.65)$(0.48)Shares used in computing basic and diluted net loss per share99,68799,19699,62099,101Isis Pharmaceuticals, Inc.Reconciliation of GAAP to Pro Forma Basis:  Condensed Consolidated Operating Expenses and Loss From Operations (In Thousands)Three months ended,

September 30,Six months ended,

September 30, 2011201020112010(unaudited)(unaudited)As reported operating expenses according to GAAP$43,029$37,571$119,167$114,551Excluding compensation expense related to stock options(2,364)(2,960)(7,596)(9,448)Pro forma operating expenses$40,665$34,611$111,571$105,103As reported loss from operations according to GAAP$(22,316)$(8,947)$(52,484)$(32,498)Excluding compensation expense related to stock options (2,364)(2,960)(7,596)(9,448)Pro forma loss from operations$(19,952)$(5,987)$(44,888)$(23,050)Reconciliation of GAAP to Pro Forma BasisAs illustrated in the Selected Financial Information in this press release, pro f
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