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From a comparative evolutionary perspective, our results underscore the importance of looking for conservation of networks, and not just conservation at the level of individual genes.
It could be argued that the conservation of networks is warranted despite the higher costs and time investment, given the aforementioned benefits of monitoring and analysing interactions, in addition to species diversity.
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Here we investigate both the conservation of network architectural properties across methodological variation and the reproducibility of individual architecture across multiple scanning sessions.
First, we define individual p-values for the conservation of network topology and sequence homology.
A characteristic feature of these networks is the apparent conservation of network diameter even in distantly related organisms [ 167].
An analysis of conservation of network edges following gene duplications of different ages was also performed (Table 7).
Topological similarity on the other hand is a measure of the conservation of network topologies with respect to the given set of mappings in the alignment.
As with the genome, there is significant conservation of network structure between organisms (Matthews et al., 2001; Yu et al., 2004).
Using predicted orthologs, we compared networks across the three plant species based on network properties (e.g. betweenness centrality), network motifs (e.g. feed-forward loops), conservation of gene-gene co-expression links and conservation of network neighbourhoods.
A similar definition for conservation coherency has been used in [ 13], where they study evolutionary conservation of network patterns in the protein-protein interaction network of the yeast S. cerevisiae.
Using protein interaction networks, previous studies addressing this question analyzed the conservation of network motifs [ 11, 12], link numbers, interacting partners and functional modules of the network proteins [ 13- 15] and regions of network topology [ 16].
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