Adam Phillippy
University of Maryland at College Park

Abstract

Pathogenic microbes, both natural and weaponized, pose significant dangers to human health and safety. To defend against these threats, it is essential to rapidly detect and characterize pathogens in any environmental or clinical medium with high accuracy. Now that the genome sequences of hundreds of bacteria and viruses are known, it is possible to design biomolecular tests, such as real-time PCR, to rapidly detect and characterize pathogens based solely on their DNA. These tests can detect a pathogen in a complex mixture of organic material by recognizing short, distinguishing sequences (called DNA signatures) that occur in the pathogen and not in any other species. Possible applications of this technology are far-reaching and include real-time clinical diagnosis and biosurveillance.

I will present a novel computational method, called Insignia, for identifying DNA signatures, and show that these signatures can be used as the basis for biomolecular assays to detect and genotype pathogens in real-time and with high accuracy. Insignia utilizes highly efficient string algorithms and distributed computing to compare over 100 billion nucleotides of genomic DNA from bacteria, virus, plants, animals, and human. The results of this computation are stored in a unique data structure that compresses the data and permits rapid retrieval of genomic signatures for any set of target genomes. In addition, signature retrieval is made available through a web application, making it accessible to biologists who may lack high- throughput computing resources. To date, hundreds of Insignia designed TaqMan PCR assays have undergone rigorous laboratory validation for the detection of select pathogens, and results from these experiments indicate that Insignia signatures are both sensitive and specific for detection of pathogens at the species level.

Bio

Adam Phillippy is a PhD candidate in the Department of Computer Science at the University of Maryland, and holds positions at both the UMD Center for Bioinformatics and Computational Biology and the UMD Institute for Genome Sciences. His research focuses on computational genomics, genome assembly, genome alignment, and microbial diagnostics. Prior to starting his PhD, he worked as a bioinformatics engineer at the Institute for Genome Research, where he aided projects such as the FBI's investigation of the 2001 anthrax attacks. He received his BS Summa Cum Laude in Computer Science from Loyola College in 2002, and his MS in Computer Science from the University of Maryland in 2009. He is scheduled to complete his PhD in the Spring of 2010.