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Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts
Protein–protein interactions (PPIs) drive cellular processes and responses to environmental cues, reflecting the cellular state. Here we develop...
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De novo genes with an lncRNA origin encode unique human brain developmental functionality
Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant in general, yet how and why this...
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Spatially activated conserved auxin-transcription factor regulatory module controls de novo root organogenesis in rice
Main conclusionThis study reveals that the process of crown root development and auxin-induced de novo root organogenesis during in vitro plantlet...
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Allosteric regulation of CAD modulates de novo pyrimidine synthesis during the cell cycle
Metabolism is a fundamental cellular process that is coordinated with cell cycle progression. Despite this association, a mechanistic understanding...
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Epstein–Barr virus tegument protein BGLF2 in exosomes released from virus-producing cells facilitates de novo infection
BackgroundViruses must adapt to the environment of their host cells to establish infection and persist. Diverse mammalian cells, including...
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De novo pyrimidine biosynthetic complexes support cancer cell proliferation and ferroptosis defence
De novo pyrimidine biosynthesis is achieved by cytosolic carbamoyl-phosphate synthetase II, aspartate transcarbamylase and dihydroorotase (CAD) and...
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Class 3 PI3K coactivates the circadian clock to promote rhythmic de novo purine synthesis
Metabolic demands fluctuate rhythmically and rely on coordination between the circadian clock and nutrient-sensing signalling pathways, yet...
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De novo Nanopore Genome Sequencing of the Clinical Diutina catenulata Type-strain CBS565
Diutina catenulata is an ascomycetous yeast, that is regularly fluconazole-resistant and increasingly reported as the cause of invasive infection in...
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De novo purine nucleotide biosynthesis mediated by MoAde4 is required for conidiation, host colonization and pathogenicity in Magnaporthe oryzae
AbstractAmidophosphoribosyltransferase catalyzes the conversion of 5-phosphoribosyl-1-pyrophosphate into 5-phosphoribosyl-1-amine in the de novo...
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Nucleus-exported CLOCK acetylates PRPS to promote de novo nucleotide synthesis and liver tumour growth
Impairment of the circadian clock is linked to cancer development. However, whether the circadian clock is modulated by oncogenic receptor tyrosine...
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Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
Haplotype-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases. Current...
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De Novo Evolution of Genes in Rice
De novo evolution of genes was used as an important approach in the rice breeding program. The identification of the novel genes in the rice genome...
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De novo assembly-based transcriptome analysis of resistant and susceptible potato varieties to Phytophthora infestans
An effective tool for discovering differentially expressed genes (DEGs) related to late blight (LB) resistance is the transcriptome sequencing of...
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Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection
BackgroundInfectious bursal disease (IBD) is an economically very important issue to the poultry industry and it is one of the major threats to the...
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De novo genome assembly and annotation of the medicinal plant Tinospora cordifolia (Willd.) Miers ex Hook. f. & Thom’s
Indian natural climbing shrub Tinospora cordifolia , often known as “Guduchi” and “Amrita,” is a highly esteemed medicinal plant in the Indian system...
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A new direction in managing avulsed teeth: stem cell-based de novo PDL regeneration
Management of avulsed teeth after replantation often leads to an unfavorable outcome. Damage to the thin and vulnerable periodontal ligament is the...
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Haploflow: strain-resolved de novo assembly of viral genomes
With viral infections, multiple related viral strains are often present due to coinfection or within-host evolution. We describe Haploflow, a...
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USP22 controls type III interferon signaling and SARS-CoV-2 infection through activation of STING
Pattern recognition receptors (PRRs) and interferons (IFNs) serve as essential antiviral defense against SARS-CoV-2, the causative agent of the...
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De novo histidine biosynthesis protects Mycobacterium tuberculosis from host IFN-γ mediated histidine starvation
Intracellular pathogens including Mycobacterium tuberculosis ( Mtb ) have evolved with strategies to uptake amino acids from host cells to fulfil their...
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De novo transcriptome profiling reveals the patterns of gene expression in plum fruits with bud mutations
Bud mutation is a common technique for plant breeding and can provide a large number of breeding materials. Through traditional breeding methods, we...
