The DOI matches its Crossref record; 115 of the 115 references it cites were found in a registry or an index.
Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing
Open accessAbstract
In 16S rRNA gene sequencing, certain bacterial genera were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings. Concerning the last, quality thresholds as well as bioinformatic settings (i.e., clustering approach, analysis pipeline, and specific adjustments such as truncation) are responsible for a number of observed differences between studies.
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Cites
1 retracted
Bellali, S., Lagier, J., Raoult, D., & Khalil, J. B. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01606 · Cited by 78
RetractedDADA2: 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
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
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0209-9 · Cited by 23,742
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,826
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 19,885
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
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Cited by
Zhang, Y.-W., Cao, M.-M., Li, Y.-J., Lu, P.-P., Dai, G.-C., Zhang, M., Wang, H., & Rui, Y.-F. (2022) · Journal of Orthopaedic Translation · doi:10.1016/j.jot.2022.08.003 · Cited by 184
AI in microbiome‐related healthcare
Probul, N., Huang, Z., Saak, C. C., Baumbach, J., & List, M. (2024) · Microbial Biotechnology · doi:10.1111/1751-7915.70027 · Cited by 36
Self-citationSepich‐Poore, G. D., Guccione, C., Laplane, L., Pradeu, T., Curtius, K., & Knight, R. (2022) · BioEssays · doi:10.1002/bies.202100252 · Cited by 33
Microbiome depiction through user-adapted bioinformatic pipelines and parameters
Nayman, E. I., Schwartz, B. A., Polanco, F. C., Firek, A. K., Gumabong, A. C., Hofstee, N. J., Narasimhan, G., Cickovski, T., & Mathee, K. (2023) · Journal of Medical Microbiology · doi:10.1099/jmm.0.001756 · Cited by 6
Yeo, K., Wu, F., Li, R., Smith, E., Wormald, P.-J., Valentine, R., Psaltis, A. J., Vreugde, S., & Fenix, K. (2024) · Pathogens · doi:10.3390/pathogens13100826 · Cited by 5
Metadata
- Authors
- Abellan-Schneyder, I., Matchado, M. S., Reitmeier, S., Sommer, A., Sewald, Z., Baumbach, J., List, M., & Neuhaus, K.
- Venue
- mSphere
- Publisher
- American Society for Microbiology
- Published
- 2021-02-24
- Volume
- 6
- Issue
- 1
- ISSN
- 2379-5042 (ISSN-L)
- OpenAlex
- W3132450255
- Cited by
- 498
- References
- 115
- FWCI
- 16.17
- Type
- journal article
- Language
- en
- Open access
- gold
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- Abellan-Schneyder, I., Matchado, M. S., Reitmeier, S., Sommer, A., Sewald, Z., Baumbach, J., List, M., & Neuhaus, K. (2021). Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing. mSphere. https://doi.org/10.1128/msphere.01202-20
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