Evgeny M. Zdobnov

LEMMIv2 benchmarks metagenomic and 16S amplicon tools using diverse scenarios, sequencing data types, and taxonomies, providing a standardized catalogue for users and developers.

This paper defines human gut microbiota at subspecies resolution, identifies disease-associated subspecies, and shows that subspecies-level analysis improves CRC diagnosis compared to species-level methods.

The paper identifies an AH>GH substitution signature in mtDNA linked to aging and TSSS, showing higher frequency in species with longer generation lengths.

The paper investigates how human genetic variation influences Epstein-Barr virus (EBV) sequence diversity by analyzing paired viral and human genomic data from HIV-coinfected individuals.

The paper presents the first genome sequence for a thysanopteran insect, providing insights into its biology and evolution as a crop pest.

ATLAS is a Snakemake workflow for processing metagenome data to assemble, annotate, and bin sequences into genomes and functional annotations.

Phigaro annotates prophage regions in genome and metagenome assemblies, producing prophage genome maps and taxonomic annotations.

The paper identifies microbial contaminant sequences in recent human pan-genome studies and highlights issues with false positive novel gene predictions.

The paper analyzes gene and protein domain content changes across 76 arthropod genomes to understand evolutionary patterns and their association with phenotypic adaptations.

This paper reports the genome of Campodea augens, a dipluran hexapod, and identifies genomic features related to its regenerative abilities and sensory adaptations.

The paper identifies a novel Rhabdovirus and a nearly complete drain fly transcriptome from contaminations in clinical samples, highlighting the importance of considering non-human sources in metagenomic analyses.

This study provides insights into the biology of the stable fly by combining genome sequencing, microbiome analysis, and RNA-seq to identify genes related to reproduction, host interactions, and pest control.

The paper presents the milkweed bug genome and comparative analyses to study molecular evolution and feeding ecology in Hemiptera.

BUSCO v3 quantifies genome, gene set and transcriptome completeness via near-universal single-copy orthologs and repurposes them for gene predictor training, reference selection, and phylogenomic marker discovery.