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To determine whether Helitron insertions into genes were due to chance, a computer simulation was performed.
About 59% of these genes were due to the well-known translocations involving chromosomes 4A, 5A and 7B.
About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data.
Most parallel changes demonstrated for other genes were due to single-nucleotide mutations (Christin et al. 2007, 2008b; Christin, Petitpierre, et al. 2009).
It is particularly interesting that spontaneous mutations recovered at the homeotic genes were due to transposon insertions (Bender et al. 1983).
In the final time point, this was reversed: more differentially expressed genes were due to larger FPKM values in the low ozone samples (57 126), and more differentially expressed genes matched GO terms related to transcriptional control (5:16).
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kneri using COI or a few nuclear genes is due to sampling error.
In most cases, incomplete coverage of these genes was due to the fact that the reference cattle gene model that was used was incomplete relative to other mammals.
The difference in the gene expression breadth between gbM and unmethylated genes was due to a higher proportion of the gbM genes (82.4 vs. 72% unmethylated genes) having a maximal expression breadth.
To decipher whether the decrease in endocrine-related genes is due to decreased number of endocrine cells or a reduction of transcripts per cell, the number and percentage of endocrine progenitors (NGN3+) and their derivatives (CHGA+) were quantified at different time points during transition from D9 to D23_L (Supplementary Fig. 3b f).
Sequence swapping experiments as well as calculations of predicted mRNA secondary structure provided support for the hypothesis that differential cytoplasmic expression of the E. coli optimized versus wild-type cutinase genes is due to differences in 5′ mRNA secondary structures.
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