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Cited by 141Paleopathology and ancient diseasesGenomics and Phylogenetic StudiesForensic and Genetic Research

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HOPS: automated detection and authentication of pathogen DNA in archaeological remains

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Hübler, Ron, Key, Felix M., Warinner, Christina, Bos, Kirsten I., Krause, Johannes, Herbig, Alexander·2019·Genome Biology
DOI 10.1186/s13059-019-1903-0PMC PMC6913047

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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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Cited by

Sorted by citations

  • Ancient DNA analysis

    Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411

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Metadata

Authors
Hübler, R., Key, F. M., Warinner, C., Bos, K. I., Krause, J., & Herbig, A.
Affiliations
Max Planck Institute of Geoanthropology (DE)
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2019-12
Volume
20
Issue
1
Pages
280-280
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-019-1903-0
PMC
PMC6913047
OpenAlex
W2996069160
Cited by
141
References
9
Citations by year
2026: 25 · 2025: 18 · 2024: 27 · 2023: 17 · 2022: 18 · 2021: 24 · 2020: 9 · 2019: 3
FWCI
78.67
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
  • MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
Funders
  • Max-Planck-Gesellschaft
  • Deutsche Forschungsgemeinschaft (KE 2408/1-1)
Topics
  • Social Sciences › Arts and Humanities › Archeology (arts and humanities) › Paleopathology and ancient diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Keywords
ancient DNA, pathogen detection, metagenomics, species identification, Humulus lupulus, archaeological finds
MeSH terms
Archaeology, DNA, Bacterial, Genetic Techniques, Software, Metagenomics

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