A5038053340- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Bacteriophages and microbial interactions
- Hepatitis C virus research
- Microbial infections and disease research
- Plant Pathogenic Bacteria Studies
- Hepatitis B Virus Studies
- RNA regulation and disease
- Plant Virus Research Studies
Friedrich Schiller University Jena
2023-2025
Schiller International University
2023
The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion Rfamseq to 26 106 genomes, 76% increase, incorporating latest UniProt reference proteomes and additional viral genomes. Sixty-five families were enhanced using experimentally determined 3D structures, improving accuracy consensus secondary structures annotations. R-scape covariation analysis was refine...
Motivation: Multiple sequence alignment of full viral genomes can be challenging due to factors such as long sequences, large insertions/deletions (spanning several 100 nucleotides), high number divergence, and computational complexity, e.g., in the context secondary structure prediction. Standard methods often face these issues, especially when processing highly variable sequences or specific phylogenetic analysis is required on selected subsequences. We present AnchoRNA, a Python-based...
Abstract Hepatitis C virus (HCV) is a plus-stranded RNA that often chronically infects liver hepatocytes and causes cirrhosis cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate large ‘cloud’ of (quasispecies) which—by trial error—comprehensively explore the sequence space available for functional maintain ability efficient replication immune escape. In this context, it important to identify which secondary structures in HCV genome...
Abstract The Rfam database, a widely-used repository of non-coding RNA (ncRNA) families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion Rfamseq to 26, 106 genomes, 76% increase, incorporating latest UniProt reference proteomes and additional viral genomes. Sixty-five families were enhanced using experimentally determined 3D structures, improving accuracy consensus secondary structures annotations. R-scape covariation...
Abstract Oxford Nanopore Technologies (ONT) allows direct sequencing of ribonucleic acids (RNA) and, in addition, detection possible RNA modifications due to deviations from the expected ONT signal. The software available so far for this purpose can only detect a small number modifications. Alternatively, two samples be compared different We present Magnipore , novel tool search significant signal shifts between data similar or related species. classifies them into mutations and potential...
Mycoplasmopsis (M.) bovis, the agent of mastitis, pneumonia, and arthritis in cattle, harbors a small genome approximately 1 Mbp. Combining data from Illumina Nanopore technologies, we sequenced assembled genomes 35 European strains isolate DL422_88 Cuba. While high proportion repetitive structures M. bovis represent particular challenge, implementation our own pipeline Mycovista (available on GitHub www.github.com/sandraTriebel/mycovista ) hybrid approach enabled contiguous assembly and,...
The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. primary objective of the conference to establish a dynamic scientific environment conducive discussion, collaboration, and generation novel research ideas. As first in-person event following SARS-CoV-2 pandemic, meeting facilitated highly interactive exchanges among attendees. It served as pivotal gathering for gaining insights into...
Abstract Hepatitis C virus (HCV) is a plus-stranded RNA that often chronically infects liver hepatocytes and causes cirrhosis cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate large “cloud” of which - by trial error comprehensively explore the sequence space available for functional maintain ability efficient replication immune escape. In this context, it important to identify secondary structures in HCV genome are conserved,...
Mycoplasma (M . ) bovis , the agent of mastitis, pneumonia, and arthritis in cattle, harbors a small genome approximately 1 Mbp. Combining data from Illumina Nanopore technologies, we sequenced assembled genomes 35 European strains isolate DL422_88 Cuba. While high proportion repetitive structures M. represents particular challenge, implementation our own pipeline Mycovista (available on GitHub www.github.com/sandraTriebel/mycovista hybrid approach enabled contiguous assembly and,...