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To train the CSIDOP method, we integrated protein-protein interaction (PPI) data from the organisms S. cerevisiae, C. elegans, and D. melanogaster, in addition to the large data set from H. sapiens.
Due to the existing limitations of this second group, the kpath database links genetic and metabolic information from Kegg, Uniprot and Reactome (3, 33, 34) databases by using Linked Data technology and all metabolic data from the organisms included in Kegg.
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Predictions were refined based on EST data from the organism of interest or related taxa when available.
However, for applications where such primers are not available (because of a lack or absence of sequence data from the organism or a related species) and must be designed de novo based on sequencing results, this present approach has major advantages.
The early-diverging alveolate lineages are still poorly studied compared with model organisms from the three main lineages, but without more data from these organisms our understanding of the evolution of the main lineages will remain incomplete.
To derive the final version of PhosTryp we used our data from L. infantum combined with recently published data from the related organisms T. cruzi and T. brucei.
Consequently, the acquisition of genomic data from these organisms has lagged other lineages.
The application of ontologies to the curation of phenotype data from the model organism literature and sharing of these annotations in community databases has promoted clarity in communication among researchers and allowed for integration of large quantities of data.
Here we combined in silico analysis of the A. aeolicus genome and dRNA-seq data from the same organism to identify novel ncRNA candidates, some of which were subsequently analyzed by Northern blot analysis.
There is a growing pool of available disease-related data, increasing interest from end users and pressure from funding agencies to make clear connections between the data from model organisms and the human diseases they reference.
In this way only the display is restricted to nodes of interest, but the accuracy undiminished since the data from all organisms is used every time; the tree topology is not recalculated using only the reduced subset of organisms.
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