Armin Töpfer

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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)
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 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)
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)
Classical swine fever virus (CSFV) is a positive-sense RNA virus with a high degree of genetic variability among isolates. High diversity is also found in virulence, with strains covering the complete spectrum from avirulent to highly virulent. The underlying genetic determinants are far from being understood. Since RNA polymerases of RNA viruses lack any(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)
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)
UNLABELLED Chronic hepatitis B (CHB) is prevalent worldwide. The infectious agent, hepatitis B virus (HBV), replicates via an RNA intermediate and is error prone, leading to the rapid generation of closely related but not identical viral variants, including those that can escape host immune responses and antiviral treatments. The complexity of CHB can be(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)
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)