A5033444929- Parasites and Host Interactions
- HIV Research and Treatment
- Genomics and Phylogenetic Studies
- Genetics, Aging, and Longevity in Model Organisms
- Epigenetics and DNA Methylation
- HIV/AIDS Research and Interventions
- Stochastic processes and financial applications
- Mathematical and Theoretical Epidemiology and Ecology Models
- Bayesian Methods and Mixture Models
- Statistical Methods and Inference
- Markov Chains and Monte Carlo Methods
- Financial Markets and Investment Strategies
- RNA and protein synthesis mechanisms
- Helminth infection and control
- Complex Systems and Time Series Analysis
- Financial Risk and Volatility Modeling
- Parasite Biology and Host Interactions
- Monetary Policy and Economic Impact
- Geometric Analysis and Curvature Flows
- Marine Bivalve and Aquaculture Studies
- HIV, Drug Use, Sexual Risk
- Economic Policies and Impacts
- Influenza Virus Research Studies
- Homelessness and Social Issues
- HIV/AIDS drug development and treatment
ETH Zurich
2018-2022
Université de Perpignan
2018-2022
Universität Greifswald
2012-2022
Ifremer
2018-2022
Université de Montpellier
2018-2022
Centre National de la Recherche Scientifique
2011-2022
Board of the Swiss Federal Institutes of Technology
2021
Universitätsmedizin Greifswald
2015-2019
Los Alamos National Laboratory
2010-2017
University of Göttingen
2005-2015
Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints query sequence and assigns each position of the one major subtypes. Since incorrect subtype assignment or prediction may lead wrong conclusions epidemiological vaccine research, information about reliability predicted parental subtypes breakpoint positions is valuable. For this reason, extended output include such terms...
Inter-subtype recombinants dominate the HIV epidemics in three geographical regions. To better understand role of shaping current epidemic, we here present results a large-scale subtyping analysis 9435 HIV-1 sequences that involve subtypes A, B, C, G, F and epidemiologically important derived from continents. The circulating recombinant form CRF02_AG, common West Central Africa, appears to result recombination events occurred early divergence between A followed by additional recent...
Significance Phylogenetic inference of who infected whom has great value in epidemiological investigations because it should provide an objective test explicit hypothesis about how transmission(s) occurred. Until now, however, there not been a systematic evaluation which phylogeny to expect from different transmission histories, and thus the interpretation what observed actually means remained somewhat elusive. Here, we show that certain types phylogenies associate with may make possible...
Schistosomes cause schistosomiasis, the world’s second most important parasitic disease after malaria in terms of public health and social-economic impacts. A peculiar feature these dioecious parasites is their ability to produce viable fertile hybrid offspring. Originally only present tropics, schistosomiasis now also endemic southern Europe. Based on analysis two genetic markers European schistosomes had previously been identified as hybrids between livestock- human-infective species...
Abstract Background The interaction of organisms with their surrounding microbial communities influences many biological processes, a notable example which is the shaping immune system in early life. In Pacific oyster, Crassostrea gigas , role environmental community on maturation — and, importantly, protection from infectious disease still an open question. Results Here, we demonstrate that life exposure durably improves oyster survival when challenged pathogen causing mortality syndrome...
Pathogen phylogenies are often used to infer spread among hosts. There is, however, not an exact match between the pathogen phylogeny and host transmission history. Here, we examine in detail limitations of this relationship. First, all splits a more than 1 occur within hosts, at moment transmission, predating events as described by pretransmission interval. Second, order which nodes may be reflective within-host dynamics rather epidemiologic relationships. To investigate these phenomena,...
jpHMM is a very accurate and widely used tool for recombination detection in genomic sequences of HIV-1. Here, we present an extension to analyze recombinations viruses with circular genomes such as the hepatitis B virus (HBV). Sequence analysis usually performed on linearized using linear models. Since models are unable model dependencies between nucleotides at 5′- 3′-end sequence, this can result inaccurate predictions breakpoints thus incorrect classification genomes. The proposed takes...
Abstract Genetics and epigenetics are tightly linked heritable information classes. Question arises if provides just a set of environment dependent instructions, or whether it is integral part an inheritance system. We argued that in the latter case epigenetic code should share universality quality genetic code. focused on DNA methylation. Since availability methylation data biased towards model organisms we developed method uses kernel density estimations CpG observed/expected ratios to...
Background New insights have expanded the influence of vestibular system to regulation circadian rhythmicity. Indeed, hypergravity or bilateral loss (BVL) in rodents causes a disruption their daily rhythmicity for several days. The thus influences hypothalamic rhythms on Earth, which raises question whether might be altered due pathology humans. aim this study was evaluate human people presenting total comparison with control participants. Methodology and Principal Findings Nine patients...
Abstract Background Methods of determining whether or not any particular HIV-1 sequence stems - completely in part from some unknown subtype are important for the design vaccines and molecular detection systems, as well epidemiological monitoring. Nevertheless, a single algorithm only, Branching Index (BI), has been developed this task so far. Moving along genome query sliding window, BI computes ratio quantifying how closely clusters with clade. In its current version, however, does provide...
Abstract Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or dosage be compensated epigenetic mechanisms results into level equalization. Schistosoma mansoni has been previously described as ZW species (i.e., female heterogamety, opposition XY male heterogametic species) with partial compensation, but underlying still unexplored. Here, we...
This paper is about numerical control of HIV propagation. The contribution the threefold: first, a novel model propagation proposed; second, methods from optimal are successfully applied to developed compute profiles; finally, computed results real problem yielding important and practically relevant results.
Abstract Diversity of the founding population Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% sexual infections, there is clear evidence for multiple variants, which can influence efficacy putative prevention methods, reconstruction epidemiologic histories. To infer who-infected-whom, compute probability alternative transmission scenarios while explicitly taking phylogenetic uncertainty into...
Abstract Schistosomes cause schistosomiasis, the world’s second most important parasitic disease after malaria. A peculiar feature of schistosomes is their ability to produce viable and fertile hybrids. Originally only present in tropics, schistosomiasis now also endemic Europe. Based on two genetic markers European species had been identified as a hybrid between ruminant-infective Schistosoma bovis human-infective haematobium. Here we describe for first time genomic composition schistosome...
Accurate and rapid characterization of influenza A virus (IAV) hemagglutinin (HA) neuraminidase (NA) sequences with respect to subtype clade is at the basis extended diagnostic services implicit molecular epidemiologic studies. ClassyFlu a new tool web service for classification IAV HA NA gene into subtypes phylogenetic clades using discriminatively trained profile hidden Markov models (HMMs), one each or clade. merely requires as input unaligned, full-length partial DNA sequences. It...
DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with detection however have created a bias number studies towards model organisms. Consequently, it remains challenging to infer kingdom-wide general rules about functions evolutionary conservation methylation. Methylated cytosine is often found specific CpN dinucleotides, frequency distributions of, for instance, CpG...
Myxomatosis is a recurrent problem on rabbit farms throughout Europe despite the success of vaccines. To identify gene variations field and vaccine strains that may be responsible for changes in virulence, immunomodulation, immunoprotection, genomes 6 myxoma virus (MYXV) were sequenced: German isolates Munich-1, FLI-H, 2604, 3207; strain MAV; challenge ZA. The analyzed ranged from 147.6 kb (strain MAV) to 161.8 3207). All sequences affected by several mutations, covering 24 93 open reading...
Abstract Motivation: Existing coalescent models and phylogenetic tools based on them are not designed for studying the genealogy of sequences like those HIV, since in HIV recombinants with multiple cross-over points between parental strains frequently arise. Hence, ambiguous cases classification into subtypes circulating recombinant forms (CRFs) have been treated ad hoc methods lack a comprehensive model accounting complex recombination patterns. Results: We developed program ARGUS that...
Amphidiploid fungal Verticillium longisporum strains Vl43 and Vl32 colonize the plant host Brassica napus but differ in their ability to cause disease symptoms. These represent two V. lineages derived from different hybridization events of haploid parental strains. carry same-sex mating-type genes both lineages. similarly penetrate roots, asymptomatic proliferation planta is lower than virulent Vl43. The highly conserved genomes include less 1% unique genes, karyotypes 15 or 16 chromosomes...