The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
Open accessAbstract
We developed a fast method for denoising pyrosequencing for community 16S rRNA analysis. We observe a 2–4 fold reduction in the number of observed OTUs (operational taxonomic units) comparing denoised with non-denoised data. ~50,000 sequences can be denoised on a laptop within an hour, two orders of magnitude faster than published techniques. We demonstrate the effects of denoising on alpha and beta diversity of large 16S rRNA datasets.
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
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
Self-citationLauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.00335-09 · Cited by 4,063
Self-citationEvolution of mammals and their gut microbes
Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R., Bircher, J. S., Schlegel, M. L., Tucker, T. A., Schrenzel, M. D., Knight, R., et al. (2008) · Science · doi:10.1126/science.1155725 · Cited by 3,747
Self-citationBacterial 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
Self-citationIroning out the wrinkles in the rare biosphere through improved OTU clustering
Huse, S. M., Welch, D. M., Morrison, H. G., & Sogin, M. L. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02193.x · Cited by 1,346
Cited by
DADA2: High–resolution sample inference from Illumina amplicon data
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
Schloss, P. D., Gevers, D., & Westcott, S. L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027310 · Cited by 2,112
Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
Muegge, B. D., Kuczynski, J., Knights, D., Clemente, J. C., González, A., Fontana, L., Henrissat, B., Knight, R., & Gordon, J. I. (2011) · Science · doi:10.1126/science.1198719 · Cited by 1,988
Self-citationA Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures
De Filippis, F., La Storia, A., Stellato, G., Gatti, M., & Ercolini, D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0089680 · Cited by 1,398
Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract
Charlson, E. S., Bittinger, K., Haas, A. R., Fitzgerald, A. S., Frank, I., Yadav, A., Bushman, F. D., & Collman, R. G. (2011) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201104-0655oc · Cited by 1,144
Goodrich, J. K., Di Rienzi, S. C., Poole, A. C., Koren, O., Walters, W. A., Caporaso, J. G., Knight, R., & Ley, R. E. (2014) · Cell · doi:10.1016/j.cell.2014.06.037 · Cited by 714
Self-citationDiversity of Bifidobacteria within the Infant Gut Microbiota
Turroni, F., Peano, C., Pass, D. A., Foroni, E., Severgnini, M., Claesson, M. J., Kerr, C., Hourihane, J., Murray, D., Fuligni, F., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036957 · Cited by 647
“The sff files were processed using QIIME [29] and 454 sequence data were subjected to ‘denoising’ using the associated Denoiser [30] as independent PUNI and BIF datasets.”
MethodZhang, X., Zhao, Y., Xu, J., Xue, Z., Zhang, M., Pang, X., Zhang, X., & Zhao, L. (2015) · Scientific Reports · doi:10.1038/srep14405 · Cited by 630
Adler, C. J., Dobney, K., Weyrich, L. S., Kaidonis, J., Walker, A. W., Haak, W., Bradshaw, C. J. A., Townsend, G., Sołtysiak, A., Alt, K. W., et al. (2013) · Nature Genetics · doi:10.1038/ng.2536 · Cited by 621
Disordered Microbial Communities in the Upper Respiratory Tract of Cigarette Smokers
Charlson, E. S., Chen, J., Custers-Allen, R., Bittinger, K., Li, H., Sinha, R., Hwang, J., Bushman, F. D., & Collman, R. G. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015216 · Cited by 437
Responses of gut microbiota to diet composition and weight loss in lean and obese mice
Ravussin, Y., Koren, O., Spor, A., LeDuc, C., Gutman, R., Stombaugh, J., Knight, R., Ley, R. E., & Leibel, R. L. (2012) · Obesity · doi:10.1038/oby.2011.111 · Cited by 406
Self-citationD’Amore, R., Ijaz, U. Z., Schirmer, M., Kenny, J. G., Gregory, R., Darby, A. C., Shakya, M., Podar, M., Quince, C., & Hall, N. (2016) · BMC Genomics · doi:10.1186/s12864-015-2194-9 · Cited by 405
Ancient and modern environmental DNA
Pedersen, M. W., Overballe-Petersen, S., Ermini, L., Sarkissian, C. D., Haile, J., Hellstrom, M., Spens, J., Thomsen, P. F., Bohmann, K., Cappellini, E., et al. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2013.0383 · Cited by 329
Lin, A., Bik, E. M., Costello, E. K., Dethlefsen, L., Haque, R., Relman, D. A., & Singh, U. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053838 · Cited by 314
Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research
Jumpstart Consortium Human Microbiome Project Data Generation Working Group (2012) · PLoS ONE · doi:10.1371/journal.pone.0039315 · Cited by 297
Exercise induction of gut microbiota modifications in obese, non-obese and hypertensive rats
Petriz, B. A., Castro, A. P., Almeida, J. A., Gomes, C. P., Fernandes, G. R., Kruger, R. H., Pereira, R. W., & Franco, O. L. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-511 · Cited by 293
Impact of next generation sequencing techniques in food microbiology.
Mayo, B., Rachid, C., Alegria, A., Leite, A., Peixoto, R., & Delgado, S. (2014) · Current Genomics · doi:10.2174/1389202915666140616233211 · Cited by 188
Ercolini, D., De Filippis, F., La Storia, A., & Iacono, M. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.02218-12 · Cited by 175
Seedorf, H., Kittelmann, S., Henderson, G., & Janssen, P. H. (2014) · PeerJ · doi:10.7717/peerj.494 · Cited by 168
Association between gut microbiota and bone health: Potential mechanisms and prospective
Chen, Y.-C., Greenbaum, J., Shen, H., & Deng, H.-W. (2017) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2017-00513 · Cited by 165
Salivary Microbiota and Metabolome Associated with Celiac Disease
Francavilla, R., Ercolini, D., Piccolo, M., Vannini, L., Siragusa, S., De Filippis, F., De Pasquale, I., Di Cagno, R., Di Toma, M., Gozzi, G., et al. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.00362-14 · Cited by 111
Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients
Paroni Sterbini, F., Palladini, A., Masucci, L., Cannistraci, C. V., Pastorino, R., Ianiro, G., Bugli, F., Martini, C., Ricciardi, W., Gasbarrini, A., et al. (2016) · Applied and Environmental Microbiology · doi:10.1128/aem.01437-16 · Cited by 108
A preliminary study of gut microbiome variation and HPA axis reactivity in healthy infants
Rosin, S., Xia, K., Azcarate-Peril, M. A., Carlson, A. L., Propper, C. B., Thompson, A. L., Grewen, K., & Knickmeyer, R. C. (2021) · Psychoneuroendocrinology · doi:10.1016/j.psyneuen.2020.105046 · Cited by 74
Caspase deficiency alters the murine gut microbiome
Brinkman, B. M., Hildebrand, F., Kubica, M., Goosens, D., Del Favero, J., Declercq, W., Raes, J., & Vandenabeele, P. (2011) · Cell Death & Disease · doi:10.1038/cddis.2011.101 · Cited by 70
Changes in microbiota during experimental human Rhinovirus infection
Hofstra, J. J., Matamoros, S., van de Pol, M. A., de Wever, B., Tanck, M. W., Wendt-Knol, H., Deijs, M., van der Hoek, L., Wolthers, K. C., Molenkamp, R., et al. (2015) · BMC Infectious Diseases · doi:10.1186/s12879-015-1081-y · Cited by 50
Pelissari, C., Guivernau, M., Viñas, M., de Souza, S. S., García, J., Sezerino, P. H., & Ávila, C. (2017) · Science of The Total Environment · doi:10.1016/j.scitotenv.2017.01.091 · Cited by 46
Metadata
- Authors
- Reeder, J., & Knight, R.
- Venue
- Nature Methods
- Published
- 2010-09
- Volume
- 7
- Issue
- 9
- Pages
- 668-669
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W1991486768
- Cited by
- 678
- References
- 5
- FWCI
- 20.56
- Type
- journal article
- Language
- en
- Open access
- green
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
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.
