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Using software to search for a HIV vaccine design
Posted on 24-Feb-2005 08:53 | Tags Filed under: News



During the 12th Conference on Retroviruses and Opportunistic Infections (CROI), Microsoft Research will show how medical researchers can use machine-learning, data-mining and other software techniques to comb through millions of strains of human immunodeficiency virus (HIV) to find the genetic patterns necessary to train a patient's immune system to fight the virus. The first of these vaccine designs are currently undergoing laboratory testing.

Microsoft Research says it has pioneered promising new ways to combat HIV with advanced software typically used to analyze large computer databases and complex digital images, or to separate spam from legitimate e-mail.

Microsoft Corp. researchers David Heckerman and Nebojsa Jojic are the first to use algorithms similar to those database and anti-spam software to uncover hidden patterns within the genetic mutations of the virus and the immune system of the patient. The researchers, in collaboration with doctors and scientists from the University of Washington (UW) in Seattle and Australia's Royal Perth Hospital, plan to exploit these patterns to create improved vaccine designs that pack more HIV-fighting genetic markers into vaccines. Microsoft researchers Christopher Meek and Carl Kadie and Jojic's brother (and former Microsoft Research intern), Vladimir, also contributed to the project.

"Microsoft Research's contributions enabled us to filter patient data 10 times faster than any previous research technique we've used and produced vital clues about the building blocks of a vaccine -- clues that were all but impossible to find in our growing stockpile of medical data" said Simon Mallal, professor and executive director of the Centre for Clinical Immunology and Biomedical Statistics at Royal Perth Hospital and Murdoch University.

The Microsoft Research-aided vaccine designs are currently undergoing laboratory testing at the University of Washington. The tests are being conducted on samples of immune cells taken from HIV-infected patients to determine how effectively the models uncover the appropriate genetic patterns. Similar tests are planned at the Royal Perth Hospital in Australia. Initial results should be available later this year.

Researchers plan to use the same techniques to analyze HIV strains from different parts of the world to gain a global understanding of vaccine components in a fraction of the time it would otherwise take. The new vaccine models may also help in the development of treatments for hepatitis C and other mutating viruses.

In addition to their work on HIV vaccine design, Microsoft researchers are working with colleagues in other fields of science to apply their know-how and resources to the toughest problems outside traditional computer science. Other collaborative efforts include bioinformatics: Microsoft Research is working with scientists to apply advanced technology in areas of biology other than HIV-vaccine development. The work includes unraveling gene-splicing mechanisms in higher-level organisms, creating an improved model of evolution, and analyzing associations between diseases and genetic variations in humans.






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