Bioinformatics team wins half of NCI-DREAM challenge

Bionformatics Dream Team
Members of the Quantitative Biomedical Research Center team, including (from left) Dr. Jichen Yang, Dr. Yang Xie, Dr. Guanghua Xiao, and Dr. Hao Tang, placed first on one of two questions at a recent NCI-DREAM challenge. (David Gresham Photo)

By Deborah Wormser

A computational model devised by a UT Southwestern Medical Center team recently beat groups from around the world to place first on one of two questions in the National Cancer Institute-DREAM (NCI-DREAM) Drug Sensitivity Prediction Challenge.

The team’s win in the international crowdsourcing competition comes just two years after UT Southwestern created the university’s first research-oriented statistical and informatics group, said Dr. Yang Xie, Assistant Professor of Clinical Sciences, who was invited to present the team’s computation models to fight cancers at the DREAM7 conference in November in San Francisco.

“People were quite amazed to see our solution and praised the model as highly innovative,” Dr. Xie said, adding it was the first time her group had entered the challenge.

The team led by Dr. Xie and Dr. Guanghua “Andy” Xiao, Assistant Professor of Clinical Sciences, won the second part of the two-part NCI-DREAM challenge with a computation model the team developed using vast amounts of genomic information to predict the activity of pairs of compounds on a cancer cell line. Thirty-one teams competed in this part of the challenge.

The questions tackled in the NCI challenge represent common problems in cancer treatment today: How to predict the effectiveness of new drugs, and how different drugs will react if administered together, Dr. Xie explained.

All UT Southwestern team members came from the Department
of Clinical Sciences’ Quantitative Biomedical Research Center (QBRC), which also serves as the bioinformatics core for the Harold C. Simmons Comprehensive Cancer Center. Bioinformatics uses mathematics and computational science to analyze and interpret biological phenomena. Crowdsourcing is a problem-solving method that seeks creative ideas or solutions from large groups of people.

Other team members include postdoctoral researchers Dr. Jichen Yang, Dr. Hao Tang, and Dr. Beibei Chen; graduate students Rui Zhong and Tao Wang; and computational biologists Jeffrey Allen and Min Soo Kim.

The prize includes publication of the solution in an upcoming issue of Nature Biotechnology and NCI support for the subsequent experimental validation and development of the team’s model.

Dr. Xie said the QBRC was established with crucial support from Dr. Milton Packer, Chair of Clinical Sciences, and Dr. James Willson, Director of the Simmons Cancer Center, as well as Dr. David Russell, Vice Provost and Dean of Basic Research; Dr. David Mangelsdorf, Chair of Pharmacology; Dr. Michael White, Professor of Cell Biology; and Dr. John Minna, Director of the Nancy B. and Jake L. Hamon Center for Therapeutic Oncology Research and of the W.A. “Tex” and Deborah Moncrief Jr. Center for Cancer Genetics.

Dr. Mangelsdorf holds the Distinguished Chair in Pharmacology, and the Raymond and Ellen Willie Distinguished Chair in Molecular Neuropharmacology in Honor of Harold B. Crasilneck, Ph.D.

Dr. Minna holds the Sarah M. and Charles E. Seay Distinguished Chair in Cancer Research and the Max L. Thomas Distinguished Chair in Molecular Pulmonary Oncology.

Dr. Packer holds the Gayle and Paul Stoffel Distinguished Chair in Cardiology.

Dr. Russell holds the Eugene McDermott Distinguished Chair in Molecular Genetics.

Dr. White holds the Grant A. Dove Chair for Research in Oncology and the Sherry Wigley Crow Cancer Research Endowed Chair in Honor of Robert Lewis Kirby, M.D.

Dr. Willson holds The Lisa K. Simmons Distinguished Chair in Comprehensive Oncology.

 

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