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Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality
Genome-scale metabolic models are powerful tools for understanding cellular physiology. Flux balance analysis (FBA), in particular, is an...
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A bacterial pan-genome makes gene essentiality strain-dependent and evolvable
Many bacterial species are represented by a pan-genome, whose genetic repertoire far outstrips that of any single bacterial genome. Here we...
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ELIMINATOR: essentiality analysis using multisystem networks and integer programming
A gene is considered as essential when it is indispensable for cells to grow and replicate in a certain environment. However, gene essentiality is...
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ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens
High-throughput CRISPR-Cas9 knockout screens are widely used to evaluate gene essentiality in cancer research. Here we introduce a probabilistic...
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DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction
BackgroundThe study of gene essentiality is fundamental to understand the basic principles of life, as well as for applications in many fields. In...
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Gene Switching and Essentiality Testing
The identification of essential genes is of major importance to mycobacterial research, and a number of essential genes have been identified in...
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Genome-wide CRISPR/Cas9 deletion screen defines mitochondrial gene essentiality and identifies routes for tumour cell viability in hypoxia
Mitochondria are typically essential for the viability of eukaryotic cells, and utilize oxygen and nutrients (e.g. glucose) to perform key metabolic...
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The impact of genetic diversity on gene essentiality within the Escherichia coli species
Bacteria from the same species can differ widely in their gene content. In Escherichia coli , the set of genes shared by all strains, known as the...
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Analysis of Gene Essentiality from TnSeq Data Using Transit
TnSeq, or sequencing of transposon insertion libraries, has proven to be a valuable method for probing the functions of genes in a wide range of...
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Reproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses
BackgroundSignificant progress has been made in advancing and standardizing tools for human genomic and biomedical research. Yet, the field of...
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Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality
In vivo transposon mutagenesis, coupled with deep sequencing, enables large-scale genome-wide mutant screens for genes essential in different growth...
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A Method to Map Gene Essentiality of Human Pluripotent Stem Cells by Genome-Scale CRISPR Screens with Inducible Cas9
Human pluripotent stem cells (hPSCs) have the capacity for self-renewal and differentiation into most cell types and, in contrast to widely used cell...
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Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations
A multitude of sequencing-based and microscopy technologies provide the means to unravel the relationship between the three-dimensional organization...
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PESM: predicting the essentiality of miRNAs based on gradient boosting machines and sequences
BackgroundMicroRNAs (miRNAs) are a kind of small noncoding RNA molecules that are direct posttranscriptional regulations of mRNA targets. Studies...
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Essential genes: a cross-species perspective
Protein coding genes exhibit different degrees of intolerance to loss-of-function variation. The most intolerant genes, whose function is essential...
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Author Correction: The impact of genetic diversity on gene essentiality within the Escherichia coli species
A Correction to this paper has been published: https://doi.org/10.1038/s41564-021-00889-w.
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A Simple Evolutionary Model of Genetic Robustness After Gene Duplication
When a dispensable gene is duplicated (referred to the ancestral dispensability denoted by O + ), genetic buffering and duplicate compensation together...
