Instruct: Identify the main category of Biorxiv papers based on the titles and abstracts
Query: Reduced gene templates for supervisedanalysis of scale-limited CRISPR-Cas9 fitnessscreens Pooled genome-wide CRISPR-Cas9 screens are furthering our mechanistic understanding of human biology and have allowed us to identify new oncology therapeutic targets. Scale-limited CRISPR-Cas9 screens - typically employing guide RNA libraries targeting subsets of functionally related genes, individual biological pathways, or portions of the druggable genome - constitute an optimal setting for investigating narrow hypotheses and they are easier to execute on complex models, such as organoids and in-vivo models. Different supervised methods are used for the computational analysis of genome-wide CRISPR-Cas9 screens; most are not well suited for scale-limited screens as they require large sets of positive/negative control genes (gene templates) to be included among the screened ones. We have developed a computational framework identifying optimal subsets of known essential and nonessential genes (at different subsampling percentages) that can be used as templates for supervised analyses of scale-limited CRISPR-Cas9 screens, while having a reduced impact on the size of the employed library.

HighlightsO_LIScale-limited CRISPR-Cas9 screens are experimentally easier than genome-wide screens
C_LIO_LIReference gene templates (RTs) are used for supervised analyses of genome-wide screens
C_LIO_LIReduced RTs allow supervised analyses of scale-limited CRISPR-Cas9 screens
C_LIO_LIWe present optimal reduced RTs and a computational method to assemble them
C_LI

Graphical abstract

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The categories of this paper are: animal
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The categories of this paper are: cell
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The categories of this paper are: paleontology
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The categories of this paper are: pharmacology
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The categories of this paper are: genetics
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The categories of this paper are: plant
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The categories of this paper are: developmental
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The categories of this paper are: behavior
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The categories of this paper are: biochemistry
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The categories of this paper are: communication
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The categories of this paper are: biophysics
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The categories of this paper are: systems
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The categories of this paper are: physiology
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The categories of this paper are: and
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The categories of this paper are: neuroscience
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The categories of this paper are: pathology