The DOI matches its Crossref record; 66 of the 66 references it cites were found in a registry or an index.
Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
Open accessAbstract
The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.
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
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
KEGG: Kyoto Encyclopedia of Genes and Genomes
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232
An introduction to probability theory and its applications
(1958) · Journal of the Franklin Institute · doi:10.1016/0016-0032(58)90688-4 · Cited by 29,269
Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 16,184
ARB: a software environment for sequence data
Ludwig, W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh293 · Cited by 6,702
Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
A Genomic Perspective on Protein Families
Tatusov, R. L., Koonin, E. V., & Lipman, D. J. (1997) · Science · doi:10.1126/science.278.5338.631 · Cited by 3,590
Biological sequence analysis probabilistic models of proteins and nucleic acids
Durbin, R. M., Eddy, S. R., Krogh, A., & Mitchison, G. (1998) · Cited by 3,565
Wooding, S. (2004) · The American Journal of Human Genetics · doi:10.1086/383584 · Cited by 3,032
Improved microbial gene identification with GLIMMER
Delcher, A. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.23.4636 · Cited by 2,493
Cited by
Experimental and analytical tools for studying the human microbiome
Kuczynski, J., Lauber, C. L., Walters, W. A., Parfrey, L. W., Clemente, J. C., Gevers, D., & Knight, R. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3129 · Cited by 709
Namiki, T., Hachiya, T., Tanaka, H., & Sakakibara, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks678 · Cited by 668
PhyloSift: phylogenetic analysis of genomes and metagenomes
Darling, A. E., Jospin, G., Lowe, E., Matsen, F. A., Bik, H. M., & Eisen, J. A. (2014) · PeerJ · doi:10.7717/peerj.243 · Cited by 631
Antibiotic Resistance: One Health One World Outlook
Aslam, B., Khurshid, M., Arshad, M. I., Muzammil, S., Rasool, M., Yasmeen, N., Shah, T., Chaudhry, T. H., Rasool, M. H., Shahid, A., et al. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.771510 · Cited by 609
Chapter 12: Human Microbiome Analysis
Morgan, X. C., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002808 · Cited by 496
Metadata
- Authors
- Chen, K., & Pachter, L.
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2005
- Volume
- 1
- Issue
- 2
- Pages
- e24
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W2098290178
- Cited by
- 391
- References
- 66
- FWCI
- 5.76
- 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: Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. https://app.cochat.ai/papers/10.1371/journal.pcbi.0010024
- The paper
- Chen, K., & Pachter, L. (2005). Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.0010024
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.
