Anne Kupczok

Identification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut Microbiome

The paper distinguishes expressed orphan genes from spurious ones and conserved genes in the human gut microbiome using metatranscriptomic data and machine learning.

RdRpCATCH: A unified resource for RNA virus discovery using viral RNA-dependent RNA polymerase profile Hidden Markov models

RdRpCATCH consolidates multiple RdRp pHMM databases into a single platform for RNA virus discovery and taxonomic annotation, improving accessibility and performance.

Genus-wide homologous recombination of tail fibers maintains tailocin diversity in Pectobacterium

The paper investigates the evolutionary dynamics of carotovoricin in Pectobacterium, finding that tail fiber gene exchange maintains diversity and influences community interactions.

Temperate versus virulent phage lifestyle impacts microdiversity in soil environments

The paper analyzes viromics datasets to compare microdiversity between temperate and virulent phages in soil environments, finding higher microdiversity in temperate phages in most datasets.

Phylogenetic support of pebS as a phage-exclusive auxiliary metabolic gene

The paper re-evaluates the presence of pebS in cyanobacterial genomes and finds it absent, suggesting it is a phage-exclusive gene.

Machine learning can identify orphans that have diverged into the ''twilight zone'' of sequence similarity

The paper uses machine learning to identify diverged orphan genes from similarity search outputs, finding that ~30% of simulated orphans are predicted to be divergent.

Pangenomics to understand prophage dynamics in the Pectobacterium genus and the radiating lineages of P. brasiliense

The paper studies prophage dynamics in Pectobacterium species using a pangenome approach, finding that prophages contribute significantly to genome evolution and lineage diversification.

Insights into diversity, host range, and evolution of iflaviruses in Lepidoptera through transcriptome mining

The paper reconstructs iflaviruses from Lepidoptera transcriptomes, identifies novel genomes and virus-host associations, and shows recombination in one virus species.

Goldfinder: Unraveling Networks of Gene Co-occurrence and Avoidance in Bacterial Pangenomes

Goldfinder infers gene co-occurrence and co-avoidance in bacterial pangenomes by considering phylogenetic relationships, reducing spurious associations compared to existing tools.