The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.
METAGENassist: a comprehensive web server for comparative metagenomics
Open accessAbstract
With recent improvements in DNA sequencing and sample extraction techniques, the quantity and quality of metagenomic data are now growing exponentially. This abundance of richly annotated metagenomic data and bacterial census information has spawned a new branch of microbiology called comparative metagenomics. Comparative metagenomics involves the comparison of bacterial populations between different environmental samples, different culture conditions or different microbial hosts. However, in order to do comparative metagenomics, one typically requires a sophisticated knowledge of multivariate statistics and/or advanced software programming skills. To make comparative metagenomics more accessible to microbiologists, we have developed a freely accessible, easy-to-use web server for comparative metagenomic analysis called METAGENassist. Users can upload their bacterial census data from a wide variety of common formats, using either amplified 16S rRNA data or shotgun metagenomic data. Metadata concerning environmental, culture, or host conditions can also be uploaded. During the data upload process, METAGENassist also performs an automated taxonomic-to-phenotypic mapping. Phenotypic information covering nearly 20 functional categories such as GC content, genome size, oxygen requirements, energy sources and preferred temperature range is automatically generated from the taxonomic input data. Using this phenotypically enriched data, users can then perform a variety of multivariate and univariate data analyses including fold change analysis, t-tests, PCA, PLS-DA, clustering and classification. To facilitate data processing, users are guided through a step-by-step analysis workflow using a variety of menus, information hyperlinks and check boxes. METAGENassist also generates colorful, publication quality tables and graphs that can be downloaded and used directly in the preparation of scientific papers. METAGENassist is available at http://www.metagenassist.ca.
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
Breiman, L. (2001) · Machine Learning · doi:10.1023/a:1010933404324 · Cited by 133,538
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 19,549
Classification and Regression by randomForest
Liaw, A. I., & Wiener, M. C. (2007) · Cited by 18,594
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,641
Enterotypes of the human gut microbiome
MetaHIT Consortium (additional members), Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., et al. (2011) · Nature · doi:10.1038/nature09944 · Cited by 7,548
Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066
What is a support vector machine?
Noble, W. S. (2006) · Nature Biotechnology · doi:10.1038/nbt1206-1565 · Cited by 4,301
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565
Cited by
Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions
Zakrzewski, M., Proietti, C., Ellis, J. J., Hasan, S., Brion, M.-J., Berger, B., & Krause, L. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btw725 · Cited by 567
Human Gut-Derived Commensal Bacteria Suppress CNS Inflammatory and Demyelinating Disease
Mangalam, A., Shahi, S. K., Luckey, D., Karau, M., Marietta, E., Luo, N., Choung, R. S., Ju, J., Sompallae, R., Gibson-Corley, K., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.07.031 · Cited by 266
“, 2011) to form operational taxonomic units (OTUs) at 97% similarity; and histograms were generated using METAGENassist (Arndt et al., 2012).”
Diet-driven microbiota dysbiosis is associated with vagal remodeling and obesity
Sen, T., Cawthon, C. R., Ihde, B. T., Hajnal, A., DiLorenzo, P. M., de La Serre, C. B., & Czaja, K. (2017) · Physiology & Behavior · doi:10.1016/j.physbeh.2017.02.027 · Cited by 239
Wu, T., Zhang, Z., Liu, B., Hou, D., Liang, Y., Zhang, J., & Shi, P. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-669 · Cited by 234
Virulence factors enhance Citrobacter rodentium expansion through aerobic respiration
Lopez, C. A., Miller, B. M., Rivera-Chávez, F., Velazquez, E. M., Byndloss, M. X., Chávez-Arroyo, A., Lokken, K. L., Tsolis, R. M., Winter, S. E., & Bäumler, A. J. (2016) · Science · doi:10.1126/science.aag3042 · Cited by 201
Metadata
- Authors
- Arndt, D., Xia, J., Liu, Y., Zhou, Y., Guo, A. C., Cruz, J. A., Sinelnikov, I., Budwill, K., Nesbo, C. L., & Wishart, D. S.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-05-29
- Volume
- 40
- Issue
- W1
- Pages
- W88-W95
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1995962575
- Cited by
- 408
- References
- 23
- FWCI
- 5.00
- Type
- journal article
- Language
- en
- Open access
- gold
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: METAGENassist: a comprehensive web server for comparative metagenomics. https://app.cochat.ai/papers/10.1093/nar/gks497
- The paper
- Arndt, D., Xia, J., Liu, Y., Zhou, Y., Guo, A. C., Cruz, J. A., Sinelnikov, I., Budwill, K., Nesbo, C. L., & Wishart, D. S. (2012). METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Research. https://doi.org/10.1093/nar/gks497
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.
