A5001373612- Genomics and Phylogenetic Studies
- Hepatitis C virus research
- HIV/AIDS drug development and treatment
- Hepatitis B Virus Studies
- Evolution and Genetic Dynamics
- HIV Research and Treatment
- Genetic diversity and population structure
- Liver Disease Diagnosis and Treatment
- Fractal and DNA sequence analysis
- Neuroblastoma Research and Treatments
- Bioinformatics and Genomic Networks
- Escherichia coli research studies
- Bacteriophages and microbial interactions
- Biochemical and Molecular Research
- Data-Driven Disease Surveillance
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Plant Virus Research Studies
- Bacterial Genetics and Biotechnology
- Biomedical Text Mining and Ontologies
- Data Analysis with R
- Enzyme Production and Characterization
- Chromosomal and Genetic Variations
- Yersinia bacterium, plague, ectoparasites research
- HIV/AIDS Research and Interventions
Max Planck Institute for Molecular Genetics
2020-2023
Max Planck Institute for Informatics
2012-2018
German Center for Infection Research
2016-2018
Max Planck Society
2012-2017
Saarland University
2012-2016
University of Southern Denmark
2012
Universidade Federal de Minas Gerais
2012
Heidelberg University
2010
The face of hepatitis C virus (HCV) therapy is changing dramatically. Direct-acting antiviral agents (DAAs) specifically targeting HCV proteins have been developed and entered clinical practice in 2011. However, despite high sustained viral response (SVR) rates more than 90%, a fraction patients do not eliminate the these cases treatment failure has associated with selection drug resistance mutations (RAMs). RAMs may be prevalent prior to start treatment, or can selected under therapy,...
Abstract Phylogenetics has a crucial role in genomic epidemiology. Enabled by unparalleled volumes of genome sequence data generated to study and help contain the COVID-19 pandemic, phylogenetic analyses SARS-CoV-2 genomes have shed light on virus’s origins, spread, emergence reproductive success new variants. However, most approaches, including maximum likelihood Bayesian methods, cannot scale size datasets from current pandemic. We present ‘MAximum Parsimonious Likelihood Estimation’...
Abstract For neuroblastoma, the most common extracranial tumour of childhood, identification new biomarkers and potential therapeutic targets is mandatory to improve risk stratification survival rates. MicroRNAs are deregulated in cancers, including neuroblastoma. In this study, we analysed 430 miRNAs 69 neuroblastomas by stem‐loop RT‐qPCR. Prediction event‐free (EFS) with support vector machines (SVM) actual times Cox regression‐based models (CASPAR) were highly accurate independently...
Identifying resistance to antiretroviral drugs is crucial for ensuring the successful treatment of patients infected with viruses such as human immunodeficiency virus (HIV) or hepatitis C (HCV). In contrast Sanger sequencing, next-generation sequencing (NGS) can detect mutations in minority populations. Thus, genotypic testing based on NGS data offer novel, treatment-relevant insights. Since existing web services analyzing samples are subject long processing times and follow strictly...
Phylogenetics plays a crucial role in the interpretation of genomic data1. Phylogenetic analyses SARS-CoV-2 genomes have allowed detailed study virus's origins2, its international3,4 and local4-9 spread, emergence10 reproductive success11 new variants, among many applications. These been enabled by unparalleled volumes genome sequence data generated employed to help contain pandemic12. However, preferred model-based phylogenetic approaches including maximum likelihood Bayesian methods,...
Homology detection is a long-standing challenge in computational biology. To tackle this problem, typically all-versus-all BLAST results are coupled with data partitioning approaches resulting clusters of putative homologous proteins. One the main problems, however, has been widely neglected: all clustering tools need density parameter that adjusts number and size clusters. This crucial but hard to estimate without gold standard at hand. Developing standard, difficult time consuming task....
Background HCV infections can now be completely cured, thanks to the currently marketed direct-acting antivirals (DAAs). It is known that patients carry viral populations with baseline polymorphisms and/or mutations make them resistant against some of these DAAs, which negatively impact patient's treatment outcome. Using complete coding sequences isolated from 1,306 treatment-naive genotypes (GTs) 1, 2, 3, 4 and 6 around globe, we studied prevalence resistance-associated (RAPs) resistance...
A temporal increase in non-B subtypes has earlier been described Sweden by us and we hypothesized that this increased viral heterogeneity may become a hotspot for the development of more complex unique recombinant forms (URFs) if epidemics converge. In present study, performed subtyping using four automated tools phylogenetic analysis RAxML pol gene sequences (n = 5246) HIV-1 near full-length genome (HIV-NFLG) 104). CD4+ T-cell decline trajectory algorithm was used to estimate time HIV...
Hepatitis C virus (HCV) causes a major health burden and can be effectively treated by direct-acting antivirals (DAAs). The non-structural protein 5A (NS5A), which plays role in the viral genome replication, is one of DAAs’ targets. Resistance-associated viruses (RAVs) harbouring NS5A resistance-associated mutations (RAMs) have been described at baseline after therapy failure. A mutation from glutamine to arginine position 30 (Q30R) characteristic RAM for HCV sub/genotype (GT) 1a, but...
Journal Article On the trail of EHEC/EAEC—unraveling gene regulatory networks human pathogenic Escherichia coli bacteria Get access Josch Pauling, Pauling Computational Systems Biology, Max Planck Institute for Informatics, GermanyCenter Bioinformatics, Saarland University, Saarbrücken, GermanyCluster Excellence Multimodal Computing and Interaction, Germany Search other works by this author on: Oxford Academic Google Scholar Richard Röttger, Röttger Andreas Neuner, Neuner Biochemical...
Abstract The widely used model for evolutionary relationships is a bifurcating tree with all taxa/observations placed at the leaves. This not appropriate if taxa have been densely sampled across time and may be in direct ancestral relationship, or there enough information to fully resolve branching points tree. In this article, we present fast distance-based agglomeration method called family-joining (FJ) constructing so-called generally labeled trees which internal vertices contain...
Choi et al.(Choi al. JMLR, 2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, statistical framework that is commonly used inferring phylogenetic trees. While CLGrouping works correctly if there unique MST, we observe an indeterminacy in the case are multiple MSTs. We demonstrate of using synthetic quartet and over primate genera. The can be removed input MST shares topological relationship with...
Abstract Motivation Phylogeny inference via maximum likelihood is NP-hard. Current methods make simplifying assumptions such as stationarity, homogeneity, and time-reversibility for computational ease. The stationarity assumption violated by empirical observations of GC content evolution, might systematically bias phylogeny inference. general Markov model (GM) a suitable alternative to stationary models because it allows the evolution content. Related work on GM has predominantly focused...
Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, statistical framework that is commonly used inferring phylogenetic trees. While CLGrouping works correctly if there unique MST, we observe an indeterminacy in the case are multiple MSTs. In this work remove by introducing so-called vertex-ranked We note effectiveness of inversely related to number leaves MST. This motivates problem...