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The control (null) set for the miRNA target genes was created using homology-based bioinformatics searches to identify appropriate paralog "pseudo-target" genes from Arabidopsis.
A cDNA library of subtracted and differentially expressed genes was created for sequencing and gene annotation by transplanting a single colony of A. microphthalma from a mid-irradiance habitat at a depth of 12.7 m to near-surface solar irradiance.
A list of 177 virulence genes was created by searching published literature and available databases for Neisseria genes that are known or hypothesized to have virulence functions [4], [18], [19].
A list of WT epicardium-enriched genes was created by a parametric t-test using the Benjamini-Hochberg method to correct for multiple testing with a false discovery rate of 0.05 starting from SOM cluster 1 (from Figure 1).
A database of resistances genes was created from (1) all sequences in Antibiotic Resistance Database (ARDB) [48] and (2) sequences from known quinolone resistance genes consisting of sequences from qnrA-D, qnrS, qepA, acrA-B, norA-C and oqxA-B [29], [32], [49].
A new set of potential piRNA target genes was created.
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Using Ingenuity Pathway Analysis IPAA) software, networks for >2 fold down-regulated epigenetic genes and up-regulated autophagy genes were created.
Fusion genes are created by genetically fusing the open reading frames of two or more genes in-frame through ligation or overlap extension PCR.
Relative standard curves describing the PCR efficiency of selected genes were created and used to perform efficiency-corrected quantification with the LightCycler Relative Quantification Software (Roche Molecular Biochemicals).
A series of plasmid constructs bearing partial sequences of the viral genes were created and each construct was used as a template for in vitro transcription.
Not all genes are created equal.
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