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Variance stabilizing transformation function in DESEq library of expression values was plotted with the heatmap library after scaling to Z-score of the rows.
The identifier of best hit is scanned across the inbuilt library of expression data files to finally calculate the Pearson Correlation Coefficient for co-expression.
Johnson & Johnson's pharmaceutical research and development division has contributed a library of expression profiles for 100 paradigm compounds, primarily hepatotoxicants, to the Chemical Effects in Biological Systems (CEBS) knowledge base based at the National Center for Toxicogenomics, a part of the NIEHS.
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To accomplish this feat, researchers have relied on DNA and protein sequence databases and high-throughput expression analysis techniques such as microarrays to produce ever-growing libraries of expression data.
Gene expression analysis was conducted on a library of gene expression datasets from children with JIA collated from the NCBI Gene Expression Omnibus (GEO) database (Additional file 2: Table S2).
To screen for recombination-proficient ZFR mutants, DS941 cells containing a recombination substrate plasmid were transformed with a library of mutant expression plasmids.
To achieve a better understanding of the antigenic repertoire of the CD8 and CD4 T-cell responses against KSHV, we constructed a library of lentiviral expression vectors each coding for one of 31 individual KSHV open reading frames (ORFs).
Because genetic approaches suggest there are redundant HJ resolving activities, and possibly other exo- or endonucleases involved in HR, we undertook a proteomic screen making use of the movable ORF (MORF) library of yeast expression plasmids [19].
To identify novel exo- and endo-nucleases that might function in DNA repair, we undertook a proteomic screen making use of the movable ORF (MORF) library of yeast expression plasmids.
Although this study examined only a few tumors, it described a method that allows any human tumor to be matched against a library of gene expression profiles collected from normal tissues at different stages of development.
As a realistic application scenario we used our framework for inferring gene interactions in yeast Saccharomyces cerevisiae based on a library of gene expression data measured in mutants with single knockouts of transcription factors [ 35].
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