Alexander Herbig

TSSpredator-Web provides an interactive web tool for predicting and exploring transcription start sites from RNA-seq data in prokaryotes.

This study reconstructs the evolutionary history of ancient Salmonella enterica using 53 new genomes, revealing host adaptation events and convergent evolution in pathogenic lineages.

The paper presents a Yersinia pestis genome from a Bronze Age sheep, showing it belongs to a lineage previously only found in ancient humans and suggests transmission via livestock.

This paper develops ViraChron, a temporal foundation model for HBV evolution, enabling accurate sequence completion and analysis of ancient HBV genomes.

The paper presents ancient HSV-1 genomes from Europe, estimates mutation rates, and suggests lineage replacement during the Bronze Age.

This study introduces a Y-chromosome capture assay (YMCA) to improve NRY coverage and haplogroup resolution, revealing new evidence for a two-path Neolithic expansion to Western Europe.

This study compares three DNA enrichment methods for ancient pathogen DNA, finding in-solution approaches are most effective and RNA baits outperform DNA baits.

The paper analyzes a 17th-century Mycobacterium tuberculosis genome to estimate the origin of the MTBC, finding a Neolithic emergence around 3683 years before present.

HOPS automates the detection and authentication of bacterial DNA in ancient DNA samples to identify candidates for genomic analysis.

This study analyzes historical Y. pestis genomes to trace the phylogeography of the second plague pandemic, revealing patterns of genetic diversity and virulence gene loss.

The paper identifies Salmonella enterica genomes from a 16th-century epidemic cemetery in Mexico, linking them to enteric fever as a cause of population decline.

This study analyzes the genetic patterns of modern syphilis strains and identifies a globally dominant pandemic cluster with azithromycin resistance.

This study examines how X-ray irradiation affects ancient DNA in sub-fossil bones and provides guidelines to minimize DNA damage during imaging.

The paper analyzes Yersinia pestis genomes from an 18th-century plague outbreak in Marseille, revealing a historical plague focus that persisted for over three centuries.

The paper reconstructs mitochondrial genomes of giant deer from 12,000-year-old bones, showing their later survival in Central Europe and phylogenetic relationship to fallow deer.