Gene essentiality and variability: What is the link? A within‐ and between‐species perspective
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DOI: 10.1002/bies.202200132
Abstract: A gene is considered essential when its loss of function results in a deleterious phenotype, hugely reducing the organism's viability or fitness. However, the link between the essentiality of a gene and its degree of… read more here.
Keywords: within species; gene essentiality; gene; essentiality variability ... See more keywords
Gene Essentiality Profiling Reveals Gene Networks and Synthetic Lethal Interactions with Oncogenic Ras
Sign Up to like & getrecommendations! Published in 2017 at "Cell"
DOI: 10.1016/j.cell.2017.01.013
Abstract: The genetic dependencies of human cancers widely vary. Here, we catalog this heterogeneity and use it to identify functional gene interactions and genotype-dependent liabilities in cancer. By using genome-wide CRISPR-based screens, we generate a gene… read more here.
Keywords: gene essentiality; gene networks; oncogenic ras; gene ... See more keywords
Putting gene essentiality into context
Sign Up to like & getrecommendations! Published in 2017 at "Nature Reviews Genetics"
DOI: 10.1038/nrg.2017.141
Abstract: been to characterize genes that are essential for cellular or organismal viability. Such sets of genes — which are deemed the most important for survival — have numerous applications, including to design and engineer streamlined… read more here.
Keywords: gene essentiality; essential genes; drug; essential gene ... See more keywords
Human gene essentiality
Sign Up to like & getrecommendations! Published in 2018 at "Nature Reviews Genetics"
DOI: 10.1038/nrg.2017.75
Abstract: A gene can be defined as essential when loss of its function compromises viability of the individual (for example, embryonic lethality) or results in profound loss of fitness. At the population level, identification of essential… read more here.
Keywords: gene essentiality; human gene; genetics; gene ... See more keywords
Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms.
Sign Up to like & getrecommendations! Published in 2022 at "Nature communications"
DOI: 10.1038/s41467-022-29228-1
Abstract: Due to epistasis, the same mutation can have drastically different phenotypic consequences in different individuals. This phenomenon is pertinent to precision medicine as well as antimicrobial drug development, but its general characteristics are largely unknown.… read more here.
Keywords: insertional mutagenesis; essentiality; transposon insertional; gene essentiality ... See more keywords
In-silico gene essentiality analysis of polyamine biosynthesis reveals APRT as a potential target in cancer
Sign Up to like & getrecommendations! Published in 2017 at "Scientific Reports"
DOI: 10.1038/s41598-017-14067-8
Abstract: Constraint-based modeling for genome-scale metabolic networks has emerged in the last years as a promising approach to elucidate drug targets in cancer. Beyond the canonical biosynthetic routes to produce biomass, it is of key importance… read more here.
Keywords: biosynthesis; gene essentiality; silico gene; cancer ... See more keywords
Gradients in gene essentiality reshape antibacterial research.
Sign Up to like & getrecommendations! Published in 2022 at "FEMS microbiology reviews"
DOI: 10.1093/femsre/fuac005
Abstract: Essential genes encode the processes that are necessary for life. Until recently, commonly applied binary classifications left no space between essential and non-essential genes. In this review, we frame bacterial gene essentiality in the context… read more here.
Keywords: reshape antibacterial; essentiality reshape; essentiality; gradients gene ... See more keywords
Revealing Causes for False-Positive and False-Negative Calling of Gene Essentiality in Escherichia coli Using Transposon Insertion Sequencing
Sign Up to like & getrecommendations! Published in 2022 at "mSystems"
DOI: 10.1128/msystems.00896-22
Abstract: Transposon mutagenesis is an efficient way to explore gene essentiality of a bacterial genome. However, there was a discrepancy between the essential gene set determined by transposon mutagenesis and that determined using single-gene knockout strains.… read more here.
Keywords: gene essentiality; gene; transposon insertion; insertion ... See more keywords
DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction
Sign Up to like & getrecommendations! Published in 2021 at "BMC Bioinformatics"
DOI: 10.1186/s12859-021-04348-5
Abstract: Background The study of gene essentiality is fundamental to understand the basic principles of life, as well as for applications in many fields. In recent decades, dozens of sets of essential genes have been determined… read more here.
Keywords: gene essentiality; bacterial genome; gene; essentiality ... See more keywords
Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier
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DOI: 10.1186/s13073-020-00809-3
Abstract: Background Identifying essential genes in genome-wide loss-of-function screens is a critical step in functional genomics and cancer target finding. We previously described the Bayesian Analysis of Gene Essentiality (BAGEL) algorithm for accurate classification of gene… read more here.
Keywords: target; analysis; crispr; gene essentiality ... See more keywords
Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes
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DOI: 10.1371/journal.pcbi.1006556
Abstract: Essential metabolic reactions are shaping constituents of metabolic networks, enabling viable and distinct phenotypes across diverse life forms. Here we analyse and compare modelling predictions of essential metabolic functions with experimental data and thereby identify… read more here.
Keywords: gene essentiality; metabolism; metabolic models; experimental data ... See more keywords