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A perspective on the cellular components, molecular functions and biological processes involved in the divergent gene expression between phenotypes was obtained by GO Slim classification of the set of 865 features.
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The similarities between phenotypes were obtained using the matrix introduced by van Driel et al [ 32], who used the anatomy (A) and the disease (C) sections of the medical subject headings vocabulary (MeSH) to extract terms from online Mendelian inheritance in man (OMIM) to identify similar diseases.
In the disease phenotype network, the relationship between disease phenotypes is obtained from the phenotype relationship database, which can also be replaced by the disease-disease relationship database.
First, the phenotype similarity profile, represented as a matrix of similarity scores between 5080 human disease phenotypes, is obtained from the literature (van Driel et al., 2006).
Strains exhibiting caffeine-tolerant phenotypes were obtained in multiple independent SCRaMbLE experiments with selection immediately post-SCRaMbLE on solid medium containing caffeine or in liquid YPD containing caffeine.
Phenotypes were obtained from a minimum of five parental individuals.
Functional annotations and phenotypes were obtained from WormBase build WS246.
Binary phenotypes were obtained by thresholding the Gaussian phenotype such that the case:control ratio was 50 50.
A strain with a reverted phenotype (mainly concerning the resistance phenotype) was obtained from the resistant mutant.
In medicine, high-resolution anatomic assessment of phenotype is obtained from histology.
Our phenotype data was obtained from previously published mouse phenotyping studies using transgenic or knockout mice.
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