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Molecular estimates of divergence time for multiple gene data were performed using the relaxed Bayesian molecular clock approach as implemented in MULTIDISTRIBUTE package [ 36].
HGT has only recently been recognized as a potentially important force in the evolution of plant mitochondrial genomes and detecting HGT is highly dependent upon the presence of multiple gene data sets with robust taxon sampling [ 38, 39].
This effect hints at the importance of using multiple gene data on calibration exercises, both as a way to average across genes, diluting idiosyncratic behaviors of stand-alone markers, but also to help the analyses to converge into more precise estimates.
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For some disease studies, multiple gene expression data sets have been collected and the related integrative analysis of multiple data sets has been investigated [ 9].
An intriguing pattern emerged during the integration of multiple gene expression data sets on pathogen induction with the diurnal control study.
Our results indicate that integrative analysis of multiple gene expression data is essential and promising.
KM plots provides meta-analyses by combining multiple gene expression data sets.
Although the integrative analysis of multiple gene expression data sets has been well studied in recent years [ 10, 11], the genome-wide concordance has not been well considered.
Here we report the first comparative analyses of multiple gene transcription data sets obtained in parallel with different microarray technologies over several popular normalisation methods using multiple cross-platform concordance criteria.
The most commonly used approach is to study the combinatory patterns of transcription factor binding sites (TFBSs) in a set of co-expressed genes, often derived from clustering analysis of multiple gene expression data.
For example, Freishtat et al. report a 26-member lung stress network comprised of genes regulated by asthma-relevant challenges or tobacco smoke in multiple gene expression data sets [ 16].
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