Kelly Westbrooks

Learn More
RNA viruses infecting a host usually exist as a set of closely related sequences, referred to as quasispecies. The genomic diversity of viral quasispecies is a subject of great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral(More)
In this paper, we introduce a new method of combined synthesis and inference of biological signal transduction networks. A main idea of our method lies in representing observed causal relationships as network paths and using techniques from combinatorial optimization to find the sparsest graph consistent with all experimental observations. Our contributions(More)
Constructing a complete human haplotype map is helpful when associating complex diseases with their related SNPs. Unfortunately, the number of SNPs is very large and it is costly to sequence many individuals. Therefore, it is desirable to reduce the number of SNPs that should be sequenced to a small number of informative representatives called tag SNPs. In(More)
Understanding how the genomes of viruses mutate and evolve within infected individuals is critically important in epidemiology. By exploiting knowledge of the forces that guide viral microevolution, researchers can design drugs and treatments that are effective against newly evolved strains. Therefore, it is critical to develop a method for typing the(More)
Like many RNA viruses, Hepatitis C virus (HCV) exists as a set of closely related sequences (quasispecies). The diversity of the quasispecies sequences can explain vaccines failures and virus resistance to existing therapies. Would the most virulent quasispecies are known in an infected host, the more effective treatment would be given to a patient. Since(More)
The search for genetic regions associated with complex diseases, such as cancer or Alzheimer's disease, is an important challenge that may lead to better diagnosis and treatment. The existence of millions of DNA variations, primarily single nucleotide polymorphisms (SNPs), may allow the fine dissection of such associations. However, studies seeking disease(More)
Many problems in bioinformatics are inference problems, that is, the problem objective is to infer something based upon a limited amount of information. In this work we explore two different inference problems in bioinformatics. The first problem is inferring the structure of signal transduction networks from interactions between pairs of cellular(More)
  • 1