Improving target assessment in biomedical research: the GOT-IT recommendations

CH Emmerich, LM Gamboa, MCJ Hofmann… - Nature reviews Drug …, 2021 - nature.com
Academic research plays a key role in identifying new drug targets, including understanding
target biology and links between targets and disease states. To lead to new drugs, however …

Cyclic di-AMP signaling in bacteria

J Stülke, L Krüger - Annual review of microbiology, 2020 - annualreviews.org
The second messenger molecule cyclic di-AMP (c-di-AMP) is formed by many bacteria and
archaea. In many species that produce c-di-AMP, this second messenger is essential for …

A bacterial pan-genome makes gene essentiality strain-dependent and evolvable

F Rosconi, E Rudmann, J Li, D Surujon, J Anthony… - Nature …, 2022 - nature.com
Many bacterial species are represented by a pan-genome, whose genetic repertoire far
outstrips that of any single bacterial genome. Here we investigate how a bacterial pan …

CRISPR screens in physiologic medium reveal conditionally essential genes in human cells

NJ Rossiter, KS Huggler, CH Adelmann, HR Keys… - Cell metabolism, 2021 - cell.com
Forward genetic screens across hundreds of cancer cell lines have started to define the
genetic dependencies of proliferating human cells and how these vary by genotype and …

Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast

EM Teyssonniere, Y Shichino, M Mito… - Nucleic Acids …, 2024 - academic.oup.com
Gene expression is known to vary among individuals, and this variability can impact the
phenotypic diversity observed in natural populations. While the transcriptome and proteome …

The identification of essential cellular genes is critical for validating drug targets

T Xu, S Wang, T Ma, Y Dong, CR Ashby Jr, GF Hao - Drug Discovery Today, 2024 - Elsevier
Highlights•The identification of novel drug targets is a key step in drug innovation.•Essential
genes are vital for organism survival and are promising drug targets.•We describe in detail …

Synergisms of machine learning and constraint‐based modeling of metabolism for analysis and optimization of fermentation parameters

MK Khaleghi, ISP Savizi, NE Lewis… - Biotechnology …, 2021 - Wiley Online Library
Recent noteworthy advances in developing high‐performing microbial and mammalian
strains have enabled the sustainable production of bio‐economically valuable substances …

Nme8 is essential for protection against chemotherapy drug cisplatin-induced male reproductive toxicity in mice

H Zhu, H Wang, D Wang, S Liu, X Sun, Z Qu… - Cell Death & …, 2024 - nature.com
Cisplatin (CP), a chemotherapy drug commonly used in cancers treatment, causes serious
reproductive toxicity. With younger cancer patients and increasing survival rates, it is …

Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality

R Hasibi, T Michoel, DA Oyarzún - npj Systems Biology and …, 2024 - nature.com
Genome-scale metabolic models are powerful tools for understanding cellular physiology.
Flux balance analysis (FBA), in particular, is an optimization-based approach widely …

Construction and application of the conditionally essential gene knockdown library in Klebsiella pneumoniae to screen potential antimicrobial targets and virulence …

Q Zhu, Q Lin, Y Jiang, S Chen, J Tian… - Applied and …, 2023 - Am Soc Microbiol
Klebsiella pneumoniae is a ubiquitous human pathogen, and its clinical treatment faces two
major challenges: multidrug resistance and the pathogenesis of hypervirulent K …