In a move that raised some eyebrows on Wall Street, Exelixis CEO George Scangos is stepping down from his post effective July 15 to become chief executive officer of Biogen Idec. Scangos replaces Biogen CEO Jim Mullen, who retired on June 8. Scangos, a scientist by training, moves from the South San Francisco-based drug discovery company with a market cap of about $417 million and no commercial products to take the helm of Biogen, one of the biggest biotech companies with a market value of more than $13 billion.

Scangos will also serve as a member of Biogen’s board of directors, joining colleague Stelios Papadopoulos, co-founder and chairman of Exelixis and formerly vice chairman of investment bank Cowen & Co., who joined Biogen’s board in 2008.

Scangos’ move comes at a tumultuous time for both companies. In early 2010 Exelixis said it would reduce the number of new compounds in clinical development and cut 270 jobs, about 40 percent of its work force. Just last week the company announced that its partner Bristol-Myers Squibb had decided to return the rights to Exelixis’ cancer treatment XL 184 citing disagreement over an appropriate clinical program.

Biogen Idec only recently settled its long-running dispute with major shareholder Carl Icahn, which resulted in Mullen’s retirement and the election of four supportive members on Biogen’s board of directors.

Biogen’s MS drug Tysabri has faced serious safety issues, including a temporary recall, and has failed to attract significant numbers of new patients. The company also faces a serious challenge from Novartis’ new oral product Gilena, which received a favorable report in mid-June from a U.S. Food and Drug Administration expert review panel and is expected to be approved at the end of September.

News of Scangos appointment raised concern among Wall Street analysts that although Scangos had extensive experience managing research organizations, he had no commercial experience.

Biogen shares were down 2.6 percent at $47.45 on the Nasdaq market at the close of trading on the day of the news.

Scangos earned a bachelor’s degree in biology from Cornell University and a Ph.D. in microbiology from the University of Massachusetts. Before coming to Exelixis in 1996, he was president of biotechnology at Bayer.

He guided Exelixis through its IPO in 2000. During his tenure there, Exelixis developed a rich pipeline, especially in oncology, and Scangos forged licensing deals with several large pharmaceutical companies, including Sanofi-Aventis, GlaxoSmithKline, Roche, Bristol-Myers Squibb, and Pfizer, which helped Exelixis generate $151.8 million in revenue in 2009.

Michael Morrissey, currently head of R&D at Exelixis, will become its new CEO and take a seat on its board of directors.