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RNA viruses exist in their hosts as populations of different but related strains. The virus population, often called quasispecies, is shaped by a combination of genetic change and natural selection. Genetic change is due to both point mutations and recombination events. We present a jumping hidden Markov model that describes the generation of viral(More)
Virus populations can display high genetic diversity within individual hosts. The intra-host collection of viral haplotypes, called viral quasispecies, is an important determinant of virulence, pathogenesis, and treatment outcome. We present HaploClique, a computational approach to reconstruct the structure of a viral quasispecies from next-generation(More)
MOTIVATION The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used,(More)
Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations(More)
MOTIVATION Computer-assisted studies of structure, function and evolution of viruses remains a neglected area of research. The attention of bioinformaticians to this interesting and challenging field is far from commensurate with its medical and biotechnological importance. It is telling that out of >200 talks held at ISMB 2013, the largest international(More)
Viruses can display high intra-patient genetic diversity. A single infected individual hosts billions of virus particles that can be summarized as a set of genetically different strains, called haplotypes, with their respective frequencies. The haplotype distribution, also known as a viral quasispecies, is a key determinent of virulence, pathogenesis, and(More)
BACKGROUND In standard perimetry, subjects fixate so that saccades are reduced and testing precision is increased. However, because vision in daily life requires eye movements, it is appropriate to assess visual fields during eye movement. METHODS Perimetry was carried out in 8 healthy subjects and in 16 patients with visual field defects under conditions(More)
According to the resource base view, organisations and markets can be described as clusters of interdependent resources stocks and flows. The performance of organisations is influenced by strategic decisions to reallocate resources, such as investments to build up organisational capabilities. Both, the actual amount invested as well as the timing of(More)
The focus in clinical virology shifts from well-established identification of single nucleotide variants (SNV) to probing of individual viral RNA strains, called haplotypes. The success of antiretroviral treatment of HIV infection heavily depends on the knowledge of an intra-patient's viral population heterogeneity, because diversity and in particular, low(More)
Hepatitis C virus (HCV) is a rapidly evolving RNA virus that has been classified into seven genotypes. All HCV genotypes cause chronic hepatitis, which ultimately leads to liver diseases such as cirrhosis. The genotypes are unevenly distributed across the globe, with genotypes 1 and 3 being the most prevalent. Until recently, molecular epidemiological(More)
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