Publications by authors named "Anastasis Togkousidis"
Article Synopsis
- Phylogenetic inference using maximum likelihood often explores vast search spaces, with different starting trees potentially leading to a single tree topology or multiple distinct topologies depending on input data.
- Haag et al. developed a method to determine the difficulty of datasets for phylogenetic inference, showing that easier multiple sequence alignments (MSAs) tend to converge quickly to one topology, while more complex datasets present multiple optimal likelihood peaks.
- The introduction of an adaptive tree search heuristic in RAxML-NG modifies search strategies based on predicted dataset difficulty, achieving significant speedups—averaging over 10× faster—particularly for easy and difficult datasets.
The COVID-19 pandemic represents an unprecedented global crisis necessitating novel approaches for, amongst others, early detection of emerging variants relating to the evolution and spread of the virus. Recently, the detection of SARS-CoV-2 RNA in wastewater has emerged as a useful tool to monitor the prevalence of the virus in the community. Here, we propose a novel methodology, called lineagespot, for the monitoring of mutations and the detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing (NGS).
View Article and Find Full Text PDFObjective: The characterization of microRNAs (miRNA) in recent years is an important advance in the field of gene regulation. To this end, several approaches for miRNA expression analysis and various bioinformatics tools have been developed over the last few years. It is a common practice to analyze miRNA PCR Array data using the commercially available software, mostly due to its convenience and ease-of-use.
View Article and Find Full Text PDFA recent refinement in high-throughput sequencing involves the incorporation of unique molecular identifiers (UMIs), which are random oligonucleotide barcodes, on the library preparation steps. A UMI adds a unique identity to different DNA/RNA input molecules through polymerase chain reaction (PCR) amplification, thus reducing bias of this step. Here, we propose an alignment free framework serving as a preprocessing step of fastq files, called UMIc, for deduplication and correction of reads building consensus sequences from each UMI.
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