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In addition, only limited number of genes are allowed as input.
First, genes are allowed to be multilevel instead of binary.
Our model is based on a regulatory process in which all genes are allowed to be deregulated.
Because we do not require for each gene j, overlapping genes are allowed among different gene sets.
For this purpose, we introduce a model based on a regulatory process in which genes are allowed to be deregulated, i.e. not respond to their regulators as expected.
Furthermore, the user has to specify a tissue focus, where submitted genes are allowed to show expression in normal individuals; for example, the testis might be of interest to the user, as it is an immunologically privileged tissue (12).
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The genes were allowed to have a value of 0 or 1.
Exogenous genes were allowed to express for 24 hours at which time the cells were treated with fresh normal growth medium, 1 mM HCA or DMEM without FBS.
Gaps, i.e. intervening genes, were allowed when detecting clusters, with the optimal gap size limit determined by repeating the analysis with increasing the gap size until the clustering was no longer improved.
Initially, only interactions between selected genes were allowed; this was then extended by allowing one joining gene between two selected genes to form interactions where the genes were not interacting in the first phase.
Pathogenicity clusters were further extended if the initially defined cluster has PSEP-encoding genes downstream or upstream to it and two interruptions by nonsecreted protein-coding genes were allowed if the following gene was again a PSEP-encoding gene.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com