ArticleGenome biology2019
HOPS: automated detection and authentication of pathogen DNA in archaeological remains.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- A minimal hybridization capture approach for the parallel enrichment and cost-effective detection of ancient human pathogens.iScience · 2026Article
- A prehistoric East-Asian Yersinia pestis genome and a ~5.3 ka trans-Eurasian expansion of plague.Nature communications · 2026Article
- Ancient Mycobacterium leprae genomes reveal a potential origin and dispersal of the ancestral Branch 0.Communications biology · 2026Article
- Evidence of sheeppox in seventeenth-to nineteenth-century France: a multi-disciplinary investigation of a sheep mass mortality assemblage.Royal Society open science · 2026Article
- Bioarchaeological analysis illustrates the life of a 16th-century Sámi individual from Kitka, Kuusamo, northern Finland.BMC genomics · 2026Article
- Insights into infectious diseases through ancient pathogen genomics.Nature reviews. Microbiology · 2026Review
- Probing the zooarchaeological record across time and space for ancient pathogen DNA.Nature communications · 2026Article
- Analysis of medieval burials from Ibiza reveals genetic and pathogenic diversity during the Islamic period.Nature communications · 2026Article
- Recent Microbial Evolutionary Insights From Metagenomics.Genome biology and evolution · 2026Review
- Reconstruction of the lifeways of Central European Late Bronze Age communities using ancient DNA, isotope and osteoarchaeological analyses.Nature communications · 2026Article
- Genetic affinities between the ancient Greek colony of Amvrakia and its metropolis.Genome biology · 2026Article
- How low can you go? Establishing detection limits for rare eukaryotes in Southern Ocean sedimentary ancient DNA.Bioinformatics advances · 2026Article
- Bamdam: a post-mapping authentication toolkit for ancient metagenomics.Genome biology · 2025Article
- CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.Genome biology · 2025Article
- 4,000-year-old Mycobacterium lepromatosis genomes from Chile reveal long establishment of Hansen's disease in the Americas.Nature ecology & evolution · 2025Article
- Archaeogenetics reveals fine-scale genetic continuity and patterns of kinship and health in medieval Finland.iScience · 2025Article
- AdDeam: a fast and scalable tool for estimating and clustering reference-level damage profiles.Bioinformatics (Oxford, England) · 2025Article
- Postglacial bioweathering, soil nutrient cycling, and podzolization from palaeometagenomics of plants, fungi, and bacteria.Science advances · 2025Article
- Human occupations at the Alpysbaev Cave (western Tian Shan): Bioarchaeological insights from the Iron Age burial cluster.PloS one · 2025Article
- Corroborating written history with ancient DNA: The case of the Well-man described in an Old NorseiScience · 2024Article
8 more citing papers are in PubMed but not listed here.
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from archaeological remains. Investigations of ancient microbes can provide valuable information on past bacterial commensals and pathogens, but their molecular detection remains a challenge. Here, we present HOPS (Heuristic Operations for Pathogen Screening), an automated bacterial screening pipeline for ancient DNA sequences that provides detailed information on species identification and authenticity. HOPS is a versatile tool for high-throughput screening of DNA from archaeological material to identify candidates for genome-level analyses.
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