The DOI matches its Crossref record; 29 of the 29 references it cites were found in a registry or an index.
CoNet app: inference of biological association networks using Cytoscape
Open accessAbstract
Here we present the Cytoscape app version of our association network inference tool CoNet. Though CoNet was developed with microbial community data from sequencing experiments in mind, it is designed to be generic and can detect associations in any data set where biological entities (such as genes, metabolites or species) have been observed repeatedly. The CoNet app supports Cytoscape 2.x and 3.x and offers a variety of network inference approaches, which can also be combined. Here we briefly describe its main features and illustrate its use on microbial count data obtained by 16S rDNA sequencing of arctic soil samples. The CoNet app is available at: http://apps.cytoscape.org/apps/conet .
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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
Structure, function and diversity of the healthy human microbiome
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The diversity and biogeography of soil bacterial communities
Fierer, N., & Jackson, R. B. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507535103 · Cited by 5,711
Microbial interactions: from networks to models
Faust, K., & Raes, J. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2832 · Cited by 4,141
Self-citationInferring Correlation Networks from Genomic Survey Data
Friedman, J., & Alm, E. J. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002687 · Cited by 2,706
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The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11209 · Cited by 2,650
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Population-level analysis of gut microbiome variation
Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., Kurilshikov, A., Bonder, M. J., Valles-Colomer, M., Vandeputte, D., et al. (2016) · Science · doi:10.1126/science.aad3503 · Cited by 2,400
Self-citationAssembly of species communities
Diamond, J. M. (1975) · Medical Entomology and Zoology · Cited by 1,745
Microbial co-occurrence relationships in the human microbiome
Faust, K., Sathirapongsasuti, J. F., Izard, J., Segata, N., Gevers, D., Raes, J., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002606 · Cited by 1,527
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Layeghifard, M., Hwang, D. M., & Guttman, D. S. (2017) · Trends in Microbiology · doi:10.1016/j.tim.2016.11.008 · Cited by 851
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Zhang, B., Zhang, J., Liu, Y., Shi, P., & Wei, G. (2018) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2017.12.011 · Cited by 417
Network analysis methods for studying microbial communities: A mini review
Matchado, M. S., Lauber, M., Reitmeier, S., Kacprowski, T., Baumbach, J., Haller, D., & List, M. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.05.001 · Cited by 357
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Metadata
- Authors
- Faust, K., & Raes, J.
- Venue
- F1000Research
- Publisher
- F1000 Research Ltd
- Published
- 2016-06-27
- Volume
- 5
- Pages
- 1519
- ISSN
- 2046-1402 (ISSN-L)
- OpenAlex
- W4245901258
- Cited by
- 615
- References
- 29
- FWCI
- 15.20
- Type
- journal article
- Language
- en
- Update notices
- new_version (2016-10-14)
- Open access
- gold
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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