SOUTH BEND | He got heckled. Air Force One flew into airspace where hours earlier a plane had trailed a banner showing an aborted fetus. But President Barack Obama appeared unruffled Sunday as he urged graduates of the University of Notre Dame to listen to those who disagree with them and work to right the wrongs in the world.

Obama's appearance at Sunday's commencement capped weeks of protests that have seen Notre Dame become the center of an abortion debate that threatened to overshadow the commencement ceremony. Protesters have criticized the university's decision to invite Obama, who supports abortion rights and embryonic stem-cell research. Some called for the resignation of the university's president, the Rev. John Jenkins, and dozens of bishops have questioned Jenkins' judgment and whether the university has strayed too far from its roots.

Jenkins and Obama acknowledged the controversy Sunday but said both Notre Dame and Obama share a willingness to talk to those with different viewpoints.

"President Obama has come to Notre Dame though he knows full well that we are fully supportive of the church's teaching on the sanctity of human life and that we oppose his policies on abortion and embryonic stem cell research," Jenkins said in introducing Obama. "Others might have avoided this venue for that reason, but President Obama is not someone who stops talking to those who differ with him.

"It is a principle we share," he said.

Obama told graduates he was honored to be at Notre Dame, where he received an honorary law degree.

"I know it has not been without controversy," Obama said, thanking graduates for the "maturity and responsibility" they showed in approaching the debate surrounding Sunday's ceremony.

Students opposing the Obama invitation had urged peaceful protests. Hundreds of people attended an outdoor Mass and rally Sunday, and some students who decided not to attend the commencement later went to the campus Grotto for prayer.

Bishop John D'Arcy, whose diocese includes Notre Dame, joined the rally on the south quadrangle and called students "heroes" for expressing their anger over the invitation to Obama.

"It's certainly the place for the bishop to be here. There's no doubt about that," said D'Arcy, who declined to attend the commencement because of Obama's attendance. "All of you here today are heroes, and I'm proud to stand with you."

Although student organizers urged those attending the rally not to bring signs on to campus, many did, with signs declaring "Shame on Notre Dame" and "Stop Abortion Now." Many wore anti-abortion T-shirts; one depicted a leprechaun dressed in green throwing a baby into a trash can and the words "May 17, 2009, The day the dome was forever tarnished," referring to the school's famed golden dome.

Police said at least 39 people were arrested on trespassing charges, including Norma McCorvey, the plaintiff identified as "Roe" in the Roe v. Wade Supreme Court decision that legalized abortion, was among those arrested. She now opposes abortion.

The protests extended into the Joyce Center, where university spokesman Dennis Brown said three people were ejected after shouting anti-abortion slogans during Obama's speech. Many students in the audience responded with chants of "Yes we can," a key Obama campaign slogan.

Obama said the views of the two camps on abortion issues are irreconcilable at some levels, which was apparent from those in attendance.

"This is our graduation and it's neither the time nor the place to stage something like that," said Graduate Kathleen Hession of Iowa City, Iowa,. "I respect their beliefs, but it's not the right platform."

Associated Press writer Mike Smith contributed to this story from Indianapolis.