The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
Relating the metatranscriptome and metagenome of the human gut
Open accessAbstract
Significance: Recent years have seen incredible growth in both the scale and specificity of projects analyzing the microbial organisms living in and on the human body (the human microbiome). Such studies typically require subjects to report to clinics for sample collection, a complicated practice that is impractical for large studies. To address these issues, we developed a protocol that allows subjects to collect microbiome samples at home and ship them to laboratories for multiple different types of molecular analysis. Measurements of microbial species, gene, and gene transcript composition within self-collected samples were consistent across sampling methods. In addition, our subsequent analysis of these samples revealed interesting similarities and differences between the measured functional potential and functional activity of the human microbiome.
Overview
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.
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
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
Bacterial Community Variation in Human Body Habitats Across Space and Time
Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., & Knight, R. (2009) · Science · doi:10.1126/science.1177486 · Cited by 3,231
A framework for human microbiome research
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11209 · Cited by 2,650
Metagenomic microbial community profiling using unique clade-specific marker genes
Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., & Huttenhower, C. (2012) · Nature Methods · doi:10.1038/nmeth.2066 · Cited by 1,776
Self-citationClostridium difficile infection: new developments in epidemiology and pathogenesis
Rupnik, M., Wilcox, M. H., & Gerding, D. N. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2164 · Cited by 1,380
Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor
Smith, M. I., Yatsunenko, T., Manary, M. J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A. L., Rich, S. S., Concannon, P., Mychaleckyj, J. C., et al. (2013) · Science · doi:10.1126/science.1229000 · Cited by 1,173
Segata, N., Haake, S. K., Mannon, P., Lemon, K. P., Waldron, L., Gevers, D., Huttenhower, C., & Izard, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-6-r42 · Cited by 1,076
Self-citationXenobiotics shape the physiology and gene expression of the active human gut microbiome
Maurice, C. F., Haiser, H. J., & Turnbaugh, P. J. (2013) · Cell · doi:10.1016/j.cell.2012.10.052 · Cited by 811
Cited by
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
Lloyd-Price, J., Arze, C., Ananthakrishnan, A. N., Schirmer, M., Avila-Pacheco, J., Poon, T. W., Andrews, E., Ajami, N. J., Bonham, K. S., Brislawn, C. J., et al. (2019) · Nature · doi:10.1038/s41586-019-1237-9 · Cited by 3,143
Self-citationBest practices for analysing microbiomes
Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0029-9 · Cited by 2,030
Species-level functional profiling of metagenomes and metatranscriptomes
Franzosa, E. A., McIver, L. J., Rahnavard, G., Thompson, L. R., Schirmer, M., Weingart, G., Lipson, K. S., Knight, R., Caporaso, J. G., Segata, N., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0176-y · Cited by 1,693
Self-citationThe microbiome in early life: Implications for health outcomes
Tamburini, S., Shen, N., Wu, H. C., & Clemente, J. C. (2016) · Nature Medicine · doi:10.1038/nm.4142 · Cited by 1,213
Kelly, J. R., Kennedy, P. J., Cryan, J. F., Dinan, T. G., Clarke, G., & Hyland, N. P. (2015) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2015.00392 · Cited by 1,110
Metadata
- Authors
- Franzosa, E. A., Morgan, X. C., Segata, N., Waldron, L., Reyes, J., Earl, A. M., Giannoukos, G., Boylan, M. R., Ciulla, D., Gevers, D., Izard, J., Garrett, W. S., Chan, A. T., & Huttenhower, C.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2014-05-19
- Volume
- 111
- Issue
- 22
- Pages
- E2329-38
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2063158722
- Cited by
- 704
- References
- 13
- FWCI
- 21.54
- Type
- journal article
- Language
- en
- Open access
- bronze
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Relating the metatranscriptome and metagenome of the human gut. https://app.cochat.ai/papers/10.1073/pnas.1319284111
- The paper
- Franzosa, E. A., Morgan, X. C., Segata, N., Waldron, L., Reyes, J., Earl, A. M., Giannoukos, G., Boylan, M. R., Ciulla, D., Gevers, D., Izard, J., Garrett, W. S., Chan, A. T., & Huttenhower, C. (2014). Relating the metatranscriptome and metagenome of the human gut. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1319284111
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
