JANA Partners 13F Shows New Stakes in Genentech (DNA), Sears (SHLD), Washington Mutual (WM); Adds to Positions in AK Steel (AKS), Focus Media (FMCN), Transocean (RIG); Sells Out of Apple (AAPL), Lehma

Barry Rosenstein's JANA Partners released its 13F for the quarter ended June 30, 2008. The firm showed new stakes in Genentech, Nokia, Peabody Energy, Sears, unitedhealth and Washington Mutual. JANA boosted its stakes in AK Steel, Focus Media, Microsoft and Transocean while lowering positions in Anadarko, Cisco, Oracle and Williams Companies. Notably, JANA also liquidated its stakes in Amazon, Apple, CSX Corp., Freeport-McMoRan, Garmin, Lehman Brothers, SLM and Wyeth.

Below is a full summary:

New Stakes:
Agilysys (Nasdaq: AGYS) 765,060 shares
Alpha Natural Resources (NYSE: ANR) 235,000 shares
Arena Resources (NYSE: ARD) 120,000 shares
Belden (NYSE: BDC) 750,000 shares
Century Aluminum (Nasdaq: CENX) 1,204,656 shares
Chubb Corp. (NYSE: CB) 1,517,799 shares
Colfax (NYSE: CFX) 450,000 shares
Columbus McKinnon (Nasdaq: CMCO) 142,755 shares
ConocoPhillips (NYSE: COP) 350,000 shares through puts
Devon Energy (NYSE: DVN) 445,000 shares
EchoStar (Nasdaq: SATS) 554,571 shares
Elizabeth Arden (Nasdaq: RDEN) 148,594 shares
EV3 (Nasdaq: EVVV) 1,126,424 shares
First American Corp. (NYSE: FAF) 2,870,686 shares
Genentech (NYSE: DNA) 1,012,800 shares
Graphic Packaging (NYSE: GPK) 4,370,000 shares
Hanover Insurance Group (NYSE: THG) 115,000 shares
Harris Corp. (NYSE: HRS) 149,783 shares
Hayes Lemmerz Int’l (Nasdaq: HAYZ) 4,509,248 shares
HCC Insurance Holdings (NYSE: HCC) 4,431,203 shares
International Paper (NYSE: IP) 750,000 shares
Invitrogen (Nasdaq: IVGN) 1,666,100 shares
Medicis Pharmaceutical (NYSE: MRX) 550,000 shares
Mercury General (NYSE: MCY) 200,000 shares
Nokia (NYSE: NOK) 1,750,000 shares
Peabody Energy (NYSE: BTU) 1,366,000 shares
Pre-Paid Legal Services (NYSE: PPD) 226,200 shares
Sandridge (NYSE: SD) 1,562,960 shares
Sears Holdings (Nasdaq: SHLD) 200,000 shares
Steel Dynamics (Nasdaq: STLD) 450,000 shares
Talisman Energy (NYSE: TLM) 8,714,300 shares and 900,000 shares through calls
Thinkorswim Group (Nasdaq: SWIM) 2,344,493 shares
Trimas (NYSE: TRS) 735,000 shares
Unitedhealth (NYSE: UNH) 1,600,000 shares
Walter Industries (NYSE: WLT) 35,000 shares
Washington Mutual (NYSE: WM) 500,000 shares through calls
Xerium Technologies (NYSE: XRM) 3,800,000 shares

Raised Stakes:
AK Steel (NYSE: AKS) from 806,261 shares to 4,132,661 shares
American Italian Pasta (Nasdaq: AITP) from 2,769,223 shares to 2,898,223 shares
Calpine (NYSE: CPN) from 10,204,327 shares to 11,300,798 shares
Commercial Metals (NYSE: CMC) from 2,890,314 shares to 4,511,248 shares
CONSOL Energy (NYSE: CNX) from 814,927 shares to 1,125,402 shares
Convergys (NYSE: CVG) from 6,336,192 shares to 10,505,575 shares
DineEquity (NYSE: DIN) from 464,100 shares to 467,600 shares
Focus Media (Nasdaq: FMCN) from 3,056,132 shares to 3,768,400 shares
GigaMedia (Nasdaq: GIGM) from 663,728 shares to 763,728 shares
Health Net (NYSE: HNT) from 2,123,262 shares to 5,299,433 shares
Hilltop Holdings (NYSE: HTH) from 460,000 shares to 599,100 shares
Idearc (NYSE: IAR) from 2,250,000 shares to 2,872,855 shares
Ingersoll-Rand (NYSE: IR) from 200,000 shares and 508,200 shares through calls to 255,800 shares and 508,200 shares
Inverness Medical Innovations (NYSE: IMA) from 500,000 shares to 753,757 shares
M&F Worldwide (NYSE: MFW) from 265,300 shares to 434,900 shares
MAXIMUS (NYSE: MMS) from 775,000 shares to 868,498 shares
MF Global (NYSE: MF) from 5,601,044 shares to 10,973,613 shares
Microsoft (Nasdaq: MSFT) from 3,140,200 shares to 3,725,900 shares
NBTY (NYSE: NTY) from 825,000 shares to 1,283,530 shares
Quicksilver Resources (NYSE: KWK) from 550,000 shares to 565,000 shares
Shire (Nasdaq: SHPGY) from 413,575 shares to 1,194,247 shares
Transocean (NYSE: RIG) from 330,000 shares to 704,600 shares
Uluru (NYSE: ULU) from 6,064,721 shares to 9,064,721 shares

Lowered Stakes:
Actuate (Nasdaq: ACTU) from 3,705,583 shares to 3,410,000 shares
Alcoa (NYSE: AA) from 300,000 shares to 0 shares
Amazon.com (Nasdaq: AMZN) from 250,000 shares to 0 shares
Anadarko Petroleum (NYSE: APC) from 4,005,265 shares to 2,097,690 shares and 430,00 shares through calls
Apple (Nasdaq: AAPL) from 350,000 shares through calls to 0 shares
Armstrong World Industries (NYSE: AWI) from 264,600 shares to 0 shares
ARRIS Group (Nasdaq: ARRS) from 1,900,000 shares to 0 shares
Arthrocare (Nasdaq: ARTC) from 494,979 shares to 0 shares
Cisco Systems (Nasdaq: CSCO) from 3,500,000 shares to 1,248,400 shares
CNET Networks (Nasdaq: CNET) from 16,595,492 shares to 15,595,492 shares
Citigroup (NYSE: C) from 1,000,000 shares through puts to 0 shares
CommScope (NYSE: CTV) from 4,860,288 shares to 2,154,065 shares
Compuware (Nasdaq: CPWR) from 12,986,626 shares to 0 shares
Comstock Resources (NYSE: CRK) from 850,000 shares to 325,000 shares
Equitable Resources (NYSE: EQT) from 2,109,833 sharse to 1,092,721 shares
Crocs (Nasdaq: CROX) from 780,156 shares to 0 shares
CSX Corp. (NYSE: CSX) from 827,657 shares to 0 shares
DaVita (NYSE: DVA) from 614,666 shares to 0 shares
Delta Air Lines (NYSE: DAL) from 1,112,466 shares to 0 shares
Diana Shipping (NYSE: DSX) from 200,000 shares to 0 shares
DryShips (Nasdaq: DRYS) from 194,415 shares to 0 shares
Forest Oil (NYSE: FST) from 1,747,641 shares to 570,908 shares
Forestar Real Estate Group (NYSE: FOR) from 673,317 shares to 393,225 shares
Freeport-McMoRan (NYSE: FCX) from 1,177,625 shares to 0 shares
Frontier Oil (NYSE: FTO) from 384,600 shares to 0 shares
Garmin (Nasdaq: GRMN) 300,000 shares to 0 shares
Goodyear Tire & Rubber (NYSE: GT) from 1,300,000 shares to 395,900 shares
Haynes International (Nasdaq: HAYN) from 224,063 shares to 0 shares
Hess Corp. (NYSE: HES) from 2,868,540 shares and 200,000 shares through calls and 200,000 shares through puts to 1,767,600 shares and 450,000 shares through calls
ICT Group (Nasdaq: ICTG) from 318,981 shares to 290,316 shares
I2 Technologies (Nasdaq: ITWO) from 639,422 shares to 0 shares
Interactive Brokers (Nasdaq: IBKR) from 135,100 shares to 0 shares
KBR Inc. (NYSE: KBR) from 13,600,634 shares and 150,000 shares through calls to 5,252,317 shares and 150,000 shares through calls
Kansas City Southern (NYSE: KSU) from 1,850,245 shares to 0 shares
KHD Humboldt Wedag International from 215,000 shares to 0 shares
LAM Research (Nasdaq: LRCX) from 400,000 shares to 0 shares
Lehman Brothers (NYSE: LEH) from 500,000 shares to 0 shares
National Oilwell Varco (NYSE: NOV) from 2,413,814 shares to 705,282 shares
MicroStrategy (Nasdaq: MSTR) from 38,417 shares to 0 shares
Northwest Airlines (NYSE: NWA) from 144,881 shares to 0 shares
NRG Energy (NYSE: NRG) from 2,598,200 shares to 0 shares
Nucor (NYSE: NUE) from 339,575 shares to 0 shares
Nutri Sytems (Nasdaq: NTRI) from 100,000 shares to 0 shares
Office Depot (NYSE: ODP) from 1,039,600 shares to 0 shares
Omnicare (NYSE: OCR) from 9,041,897 shares to 3,847,647 shares
ON Semiconductor (Nasdaq: ONNN) from 1,500,000 shares to 0 shares
Oracle (Nasdaq: ORCL) from 7,362,600 shares to 4,131,100 shares
Orion Marine Group (Nasdaq: OMGI) from 1,970,240 shares to 0 shares
Parker Drilling (NYSE: PKD) from 780,000 shares to 0 shares
PRG-Schultz (Nasdaq: PRGX) from 2,125,200 shares to 1,797,182 shares
Redwood Trust (NYSE: RWT) from 450,100 shares to 30,000 shares
RCN Corp. (Nasdaq: RCNI) from 585,409 shares
Research In Motion (Nasdaq: RIMM) from 1,000,000 shares to 0 shares
Reynolds American (NYSE: REI) from 1,145,167 shares to 0 shares
Rock-Tenn (NYSE: RKT) from 150,000 shares to 0 shares
SanDisk (Nasdaq: SNDK) from 950,000 shares to 0 shares
SLM Corp. (NYSE: SLM) from 1,600,000 shares to 0 shares
Temple Inland (NYSE: TIN) from 500,000 shares to 0 shares
Titanium Metals (NYSE: TIE) from 284,300 shares to 0 shares
Triple-S Management (NYSE: GTS) from 383,200 shares to 0 shares
Tyco Electronics (NYSE: TEL) from 1,852,930 shares to 0 shares
Union Pacific (NYSE: UNP) from 281,000 shares to 0 shares
URS Corp. (NYSE: URS) from 106,600 shares to 0 shares
US Airways (NYSE: LCC) from 500,000 shares to 0 shares
Valeant Pharmaceuticals (NYSE: VRX) from 1,817,300 shares to 1,200,000 shares
Valero Energy (NYSE: VLO) from 1,160,000 shares to 0 shares
Wells Fargo (NYSE: WFC) from 1,000,000 shares through puts to 0 shares
Williams Companies (NYSE: WMB) from 4,113,808 shares to 2,715,808 shares
Wyeth (NYSE: WYE) from 2,086,000 shares to 0 shares
Zimmer Holdings (NYSE: ZMH) from 1,537,930 shares to 0 shares

Maintained Stakes:
American International Group (NYSE: AIG) 200,000 shares through calls
Arcadia Resources (NYSE: KAD) 15,235,396 shares
Brocade Communications (Nasdaq: BRCD) 3,000,000 shares
Coleman Cable (Nasdaq: CCIX) 2,734,558 shares
Copart (Nasdaq: CPRT) 6,848,172 shares
Corel Corp. (Nasdaq: CREL) 1,255,274 shares
General Motors (NYSE: GM) 100,000 shares through calls
GSC Acquisition (NYSE: GGA) 500,000 shares
Liberty Acquisition (NYSE: LIA) 3,000,000 shares
JC Penney (NYSE: JCP) 47,800 shares
QLT Inc (Nasdaq: QLTI) 3,577,269 shares
Taiwan Semiconductor (NYSE: TSM) 3,000,000 shares
Transforma Acquisition (NYSE: TAQ) 2,000,000 shares
Yahoo! (Nasdaq: YHOO) 500,000 shares

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