A Similarity Measure Based on Species Proportions

By J. C. Yue, Murray K. Clayton. 2005

516 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, Statistics and Probability

View Paper: https://www.semanticscholar.org/paper/01ad3bfaa8ed1c94e367738c76c9c348e74d9464

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Citations in the corpus

The Gut Microbiome Modulates Colon Tumorigenesis (2013, methodology): “To calculate -diversity, we used the YC distance metric with OTU frequency data (42), and we calculated UniFrac”
A diversity profile of the human skin microbiota. (2008, methodology): “The SONS program calculates values of , a community similarity index that takes abundance of OTUs into account (Yue and Clayton 2005; Schloss and Handelsman 2006).”
Temporal Stability of the Human Skin Microbiome (2016, unknown): “…and structure over short and long time intervals using the Yue-Clayton theta index, which calculates the distance between communities based on relative proportions of shared and non-shared species in each population (Yue and Clayton 2005). q = 0 indicates dissimilar and q = 1 identical communities.”
Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals (2015, background): “The YC distance (1 YC) between bacterial communities measures differences in community structure (44) and was selected because it weighs rare and abundant OTUs more evenly than other metrics such as Bray-Curtis or Morisita-Horn (39).”
Stool Microbiome and Metabolome Differences between Colorectal Cancer Patients and Healthy Adults (2013, methodology): “This inter-individual variation was also apparent in estimates of beta diversity, where a low degree of similarity in overall microbial community composition between individuals was observed as determined using the unweighted Jaccard distance (Jclass) to compare community membership (Figure 1A) and ”
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies (2011, methodology): “The reciprocal Simpson Index was selected because it represents the number of uniformly distributed OTUs that were required to have the same diversity as the actual community; thus giving it an easier biological interpretation compared to other indices (e.g. Shannon Index). b diversity was measured ”
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform (2013, background): “FIG 4 Principal coordinate ordination of YC values (28) relating the community structures of the fecal microbiota from 12 mice collected on days 0 through 9 (Early) and days 141 through 150 (Late) after weaning.”
Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures (2006, methodology): “variance formula for that was derived by Yue and Clayton (26).”