A5021595697- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- Plant Virus Research Studies
- HIV Research and Treatment
- Genetic diversity and population structure
- HIV/AIDS drug development and treatment
- HIV/AIDS Research and Interventions
- Gene expression and cancer classification
- Amphibian and Reptile Biology
- Wildlife Ecology and Conservation
- Bacteriophages and microbial interactions
- Mathematical and Theoretical Epidemiology and Ecology Models
- Fish Ecology and Management Studies
- Wildlife-Road Interactions and Conservation
- Bayesian Methods and Mixture Models
SIB Swiss Institute of Bioinformatics
2014-2022
ETH Zurich
2014-2022
Washington and Lee University
2007
High-throughput sequencing technologies are used increasingly not only in viral genomics research but also clinical surveillance and diagnostics. These facilitate the assessment of genetic diversity intra-host virus populations, which affects transmission, virulence pathogenesis infections. However, there two major challenges analysing diversity. First, amplification errors confound identification true biological variants, second, large data volumes represent computational limitations.To...
Abstract Fitness is a central quantity in evolutionary models of viruses. However, it remains difficult to determine viral fitness experimentally, and existing vitro assays can be poor predictors vivo populations within their hosts. Next-generation sequencing nowadays provide snapshots evolving virus populations, these data offer new opportunities for inferring fitness. Using the equilibrium distribution quasispecies model, an established model intrahost evolution, we linked parameters...
While many studies have examined the barrier effects of large rivers on animal dispersal and gene flow, few considered small streams. We used displacement experiments analyses genetic population structure to examine first-order second-order streams terrestrial red-backed salamanders, Plethodon cinereus (Green, 1818). marked salamanders from near edges one stream stream, experimentally displaced them either across or an equal distance farther into forest. A comparison return rates indicated...
Determining the composition of viral populations is becoming increasingly important in field medical virology. While recently developed computational tools for haplotype analysis allow correcting sequencing errors, they do not always removal errors occurring upstream experimental protocol, such as PCR errors. Primer IDs (pIDs) are one method to address this problem by harnessing redundant template resampling error correction. By using a reference mixture five HIV-1 strains, we show how pIDs...
Abstract High-throughput sequencing technologies are used increasingly, not only in viral genomics research but also clinical surveillance and diagnostics. These facilitate the assessment of genetic diversity intra-host virus populations, which affects transmission, virulence, pathogenesis infections. However, there two major challenges analysing diversity. First, amplification errors confound identification true biological variants, second, large data volumes represent computational...
Little is known about whether and how variation in the HIV-1 genome affects its transmissibility. Assessing which genomic features of are under positive or negative selection during transmission challenging, because very few virus particles typically transmitted, random genetic drift can dilute signals recipient population. We analyzed 30 transmitter-recipient pairs from Zurich Primary HIV Infection Study Swiss Cohort using near full-length genomes. developed a new statistical test to detect...
Advances in high-throughput sequencing (HTS) technologies have facilitated the assessment of genetic diversity heterogeneous virus populations at an unprecedented level detail. However, existence technical errors confounds identification truthful variants. Here, we present a comparative approach for patterns co-variation deep-sequenced populations. In addition to errors, account other unknown sources error by modeling occurrences mutations using Dirichlet distribution as prior multinomial...
M ea n qu as is pe ci es e nt ro py Entropy a measure of diversity: Frequency distribution entropy Mean position-wise weighted allel distributions The focus in clinical virology shifts from well-established identification single nucleotide variants to genome-wide probing full-length viral RNA strains, called haplotypes. success antiretroviral HIV treatment heavily depends on the knowledge an intra-patient's population heterogeneity, because diversity and particular, low frequency affect...