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We describe a microarray design based on the concept of error-correcting codes from digital communication theory.
Here we present results obtained using a five array whole-genome tiling X. tropicalis design and a promoter microarray design based on chromatin decorated with H3K4me3.
For Xenopus, a promoter microarray design based on current Joint Genome Institute gene annotation would lose valuable information regarding the TSS, since a large number of H3K4me3-enriched regions do not overlap with current JGI gene annotation within 1 kb (40%; 4,116 out of 10,179).
A microarray design based on fixed effects parameters which was applied here was originally described by Kerr and Churchill [ 34].
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Further, given that the rhesus and cynomolgus sequences were very similar, we predict that oligonucleotide microarrays designed based on rhesus sequence will work very well with cynomolgus samples.
We used species specific Agilent microarrays, designed based on the ORF annotations of each species, as collected in the Fungal Orthogroup Repository (Wapinski et al., 2007b) (http://www.broadinstitute.org/regev/orthogroups/).org/regev/orthogroups/
These findings indicate that a carrier design based on microarray analysis and the manipulation of intracellular trafficking constitutes a rational strategy for reducing the host immune response to NPs.
They can design based on instinct.
For one of these genes (i.e. lmo0265), the microarray probe (designed based on the genome of L. monocytogenes strain EGD-e) showed a low hybridization index (HI; % match between strain-specific sequence and oligonucleotide probe) to 10403S (< 80%).
Our microarray was designed based on the 2006 gene annotations, before the 2008 version was available.
Because the microarray was designed based on the reference B73 genomic sequence this observation is an expected consequence of ascertainment bias.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com