The DOI matches its Crossref record; 31 of the 32 references it cites were found in a registry or an index.
Detecting contamination in viromes using ViromeQC
Open accessOverview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Both experimental and computational accessibility of non-bacterial microbial community members remains limited.”
From Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2021) · cites this paper as Zolfo et al., 2019
In the citing paper
“StrainPhlAn 3 improves the original implementation in several aspects: (i) the integration of an improved and validated pipeline for consensus sequence generation (Zolfo et al., 2019)”
From Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2021) · cites this paper as Zolfo et al., 2019
In the citing paper
“These components of metagenomes – and, for RNA viruses, metatranscriptomes – are often measured with surprising heterogeneity during the initial generation of sequencing data themselves (Zolfo et al., 2019)”
From Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2021) · cites this paper as Zolfo et al., 2019
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Marine viruses — major players in the global ecosystem
Suttle, C. (2007) · Nature Reviews Microbiology · doi:10.1038/nrmicro1750 · Cited by 3,054
Leinonen, R., Sugawara, H., & Shumway, M. F. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1019 · Cited by 2,872
Shotgun metagenomics, from sampling to analysis
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202
Self-citationViruses in the faecal microbiota of monozygotic twins and their mothers
Reyes, A., Haynes, M. R., Hanson, N., Angly, F. E., Heath, A. C., Rohwer, F. L., & Gordon, J. I. (2010) · Nature · doi:10.1038/nature09199 · Cited by 1,230
VirSorter: mining viral signal from microbial genomic data
Roux, S., Enault, F., Hurwitz, B. L., & Sullivan, M. B. (2015) · PeerJ · doi:10.7717/peerj.985 · Cited by 1,074
The human gut virome: inter-individual variation and dynamic response to diet
Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S. A., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2011) · Genome Research · doi:10.1101/gr.122705.111 · Cited by 935
Self-citationEcogenomics and potential biogeochemical impacts of globally abundant ocean viruses
Roux, S., Brum, J. R., Dutilh, B. E., Sunagawa, S., Duhaime, M. B., Loy, A., Poulos, B. T., Solonenko, N., Lara, E., Poulain, J., et al. (2016) · Nature · doi:10.1038/nature19366 · Cited by 863
Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome
Shkoporov, A. N., & Hill, C. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.01.017 · Cited by 783
The International Nucleotide Sequence Database Collaboration
Karsch‐Mizrachi, I., Nakamura, Y., & Cochrane, G. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1006 · Cited by 717
Cryptic prophages help bacteria cope with adverse environments
Wang, X., Kim, Y., Ma, Q., Hong, S. H., Pokusaeva, K., Sturino, J. M., & Wood, T. K. (2010) · Nature Communications · doi:10.1038/ncomms1146 · Cited by 677
Cited by
Sorted by citations
Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303
Self-citationThe human virome: assembly, composition and host interactions
Liang, G., & Bushman, F. D. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00536-5 · Cited by 652
Self-citationMetagenomic compendium of 189,680 DNA viruses from the human gut microbiome
Nayfach, S., Páez-Espino, D., Call, L., Low, S. J., Sberro, H., Ivanova, N. N., Proal, A. D., Fischbach, M. A., Bhatt, A. S., Hugenholtz, P., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00928-6 · Cited by 580
Lee, K. A., Thomas, A. M., Bolte, L. A., Björk, J. R., de Ruijter, L. K., Armanini, F., Asnicar, F., Blanco-Miguez, A., Board, R., Calbet-Llopart, N., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01695-5 · Cited by 464
Self-citationA distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche
Zepeda-Rivera, M., Minot, S. S., Bouzek, H., Wu, H., Blanco-Míguez, A., Manghi, P., Jones, D. S., LaCourse, K. D., Wu, Y., McMahon, E. F., et al. (2024) · Nature · doi:10.1038/s41586-024-07182-w · Cited by 451
Self-citation
Metadata
- Authors
- Zolfo, M., Pinto, F., Asnicar, F., Manghi, P., Tett, A., Bushman, F. D., & Segata, N.
- Affiliations
- University of Trento (IT)
- University of Pennsylvania (US)
- Corresponding author
- Segata, Nicola
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2019-11-20
- Volume
- 37
- Issue
- 12
- Pages
- 1408-1412
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2990215402
- Cited by
- 103
- References
- 32
- Citations by year
- 2026: 8 · 2025: 9 · 2024: 17 · 2023: 15 · 2022: 19 · 2021: 22 · 2020: 12
- FWCI
- 8.42
- Type
- journal article
- Language
- en
- Open access
- green
- hdl.handle.net
- Licence
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Institutional Research Information System (Università degli Studi di Trento) (submittedVersion, other-oa)
- Funders
- European Commission (H2020 SC1, 716575, 825410, H2020-SFS-2018-1, 818368, H2020-SC1-BHC)
- Ministero dell’Istruzione, dell’Università e della Ricerca (H2020, RBFR13EWWI_001)
- Horizon 2020 Framework Programme (MASTER-818368, OncoBiome 825410, 818368, SC1-BHC, H2020-SC1, 825410)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Keywords
- metagenomics, virome, contamination detection
- MeSH terms
- DNA, Bacterial, RNA, Viral, Software, Virion, Virus Cultivation, Genome, Viral, Sequence Analysis, DNA, Sequence Analysis, RNA, Genes, rRNA, Metagenomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
