Tim Cook, who earned his master’s in business at Duke University’s Fuqua School in 1988, is taking over day-to-day operations at Apple (Nasdaq: AAPL) now that Steve Jobs has given up the chief executive officer role.

Apple announced the changes Wednesday night. (Read details here.)

Cook, 50, has been Apple’s chief operating officer and is a former IBM executive.

Cook had been acting CEO since January. For years, he has been running Apple’s day-to-day operations, and has long been seen as the natural successor. He also served as Apple’s leader for two months in 2004 while Jobs battled cancer, and again for five-and-a-half months in 2009 when Jobs received a liver transplant.

“The Board has complete confidence that Tim is the right person to be our next CEO,” said Apple Chairman Art Levinson. “Tim’s 13 years of service to Apple have been marked by outstanding performance, and he has demonstrated remarkable talent and sound judgment in everything he does.”

Apple said Jobs “strongly recommended” that the board “implement its succession plan and name Tim Cook as CEO.”

“As far as my successor goes, I strongly recommend that we execute our succession plan and name Tim Cook as CEO of Apple,” Jobs said in his resignation. (Read the letter here.)

The company has thrived under Cook’s leadership, briefly becoming the most valuable company in America earlier this month.

“He’s a very competent corporate manager,” said Apple investor Peter Sorrentino, a senior portfolio manager at Huntington Asset Advisors in Cincinnati, in an interview with Bloomberg. “People are going to be looking for that crack of weakness, and they’ll be looking at him a lot closer than they look at Steve.”

Peter Misek, an analyst at Jefferies & Co., said Cook can do the job in January when Cook took over on an interim basis.

“He’s a star, just a different kind of star from Steve,” said Misek in an interview with Bloomberg news.

“He’s arguably one of the best supply chain managers in the world, if you look at working capital management, cash-flow management, cash conversion cycles — all those great metrics,” Misek added.

Cook graduated from Auburn with a degree in engineering.

A director at Nike, Cook joined Apple as senior vice president for worldwide operations. He also took over for Jobs in 2004 and 2009. He worked at IBM for 12 years.

Cook is not nearly as recognizable as Jobs, who after returning from a 12-year hiatus in 1997 became the very public face of Apple, clad in his signature blue jeans, black turtleneck and wire-rimmed glasses when trotting out the company’s iPhones, iPads, iPods at immensely popular and anticipated media events. Though Jobs has looked increasingly frail, he emerged from his leave twice this year to tout products at such events: First, he unveiled the second version of Apple’s iPad tablet computer in March. Then, in June, he resurfaced to show off Apple’s iCloud music synching service.

But while Jobs is the most recognized person at Apple, he is not the only one responsible for the company’s success. Many industry watchers believe that despite his importance, Apple will continue to innovate and not just survive, but thrive.

Says Cross Research analyst Shannon Cross: “Steve Jobs put in place at Apple a culture of innovation.”

And its innovation has translated to sales. With Cook running the company, Apple sold 9.25 million iPads during the most recent quarter, which ended in June, bringing sales to nearly 29 million iPads since they first began selling in April 2010. Apple also sold 20.3 million iPhones in the same period, which was millions more than analysts expected. The company’s stock has risen 8 percent since Jobs announced his most recent medical leave.

Tim Cook’s record

Cook’s track record at Apple is strong. The first time he was in charge back in 2004, things went so well that Apple promoted him from executive vice president to chief operating officer in 2005.

During the second time, which lasted from mid-January to the end of June 2009, Apple released a new version of the iPhone and updated laptop computers on schedule. The company also announced that its iTunes app store hit a major milestone: More than one billion apps were downloaded within the first nine months of its existence.

Apple’s stock rose 62 percent during that time, satisfying investors’ concerns over Jobs’ absence.

Cook, an Alabaman with short, gray hair and a broad, thin-lipped smile, has been an asset to Apple since his arrival in 1998. He is credited with tuning Apple’s manufacturing process to solve chronic product delays and supply problems. His inventory management skills helped Apple build up its $72.6 billion hoard of cash and marketable securities — funds that it can use to keep its lead in the portable electronics market.

Like IBM, McDonald’s or Ford, all of which lost visionary CEOs, Apple is not necessarily dependent on the immortality of the genius behind it, says Terry Connelly, dean of the Ageno School of Business at Golden Gate University in San Francisco.

“A company is dependent on its ability to institutionalize that genius in the corporate DNA,” he says. “Apple shows every sign of having done that. We will see that when we see how Cook responds to competitive pressure.”

And, as Cross points out, Cook won’t be leading Apple alone. His supporting team includes Jonathan Ive, who oversees the elegant, minimalist design of Apple’s products; Ron Johnson, who runs Apple’s stores; Philip Schiller, the marketing chief; and Scott Forstall, who supervises the iPhone software.

“The bench at Apple is extremely strong,” Cross says. “He has a good group of executives behind him.”

And consumers — the group Apple really depends on to make its products popular — may not be that affected by the change.

Apple customers don’t buy the company’s products because of Steve Jobs, Gartner Research analyst Michael Gartenberg says, they buy Apple products because they’re Apple products. Without Jobs, he believes the company’s challenge will be the same as it was with him: continuing to find ways to raise the bar with its consumer electronics.

“Yes, this is quite some transition at the end of Steve’s role and his time at Apple, but it doesn’t mean Apple itself will fundamentally change,” he says. “Certainly Apple’s competition would be foolish to think this is a situation they could somehow capitalize on.”

Cook’s bio from Apple:

“Tim Cook is Apple’s chief operating officer and reports to Apple’s CEO. He is responsible for all of the company’s worldwide sales and operations, including end-to-end management of Apple’s supply chain, sales activities, and service and support in all markets and countries. Cook also heads Apple’s Macintosh division and plays a key role in the continued development of strategic reseller and supplier relationships, ensuring flexibility in response to an increasingly demanding marketplace.

“Before joining Apple, Cook was vice president of Corporate Materials for Compaq and was responsible for procuring and managing all of Compaq’s product inventory. Previous to his work at Compaq, Cook was the chief operating officer of the Reseller Division at Intelligent Electronics.

“Cook also spent 12 years with IBM, most recently as director of North American Fulfillment where he led manufacturing and distribution functions for IBM’s Personal Computer Company in North and Latin America.”

“Cook serves on the board of directors for Nike, Inc. and the National Football Foundation.

“Cook earned an M.B.A. from Duke University, where he was a Fuqua Scholar, and a Bachelor of Science degree in Industrial Engineering from Auburn University.

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