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Proteomic and transcriptomic profiling of brainstem, cerebellum and olfactory tissues in early- and late-phase COVID-19
Neurological symptoms, including cognitive impairment and fatigue, can occur in both the acute infection phase of coronavirus disease 2019 (COVID-19) and at later stages, yet the mechanisms that contribute to ...
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Article
Open AccessPost-COVID exercise intolerance is associated with capillary alterations and immune dysregulations in skeletal muscles
The SARS-CoV-2 pandemic not only resulted in millions of acute infections worldwide, but also in many cases of post-infectious syndromes, colloquially referred to as “long COVID”. Due to the heterogeneous natu...
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Open AccessModelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids
Herpes simplex encephalitis is a life-threatening disease of the central nervous system caused by herpes simplex viruses (HSVs). Following standard of care with antiviral acyclovir treatment, most patients sti...
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Open AccessLive-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters
Vaccines play a critical role in combating the COVID-19 pandemic. Future control of the pandemic requires improved vaccines with high efficacy against newly emerging SARS-CoV-2 variants and the ability to redu...
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Open AccessThe trispecific DARPin ensovibep inhibits diverse SARS-CoV-2 variants
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with potential resistance to existing drugs emphasizes the need for new therapeutic modalities with broad variant activity...
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Article
Open AccessSingle-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury
Acute kidney injury (AKI) occurs frequently in critically ill patients and is associated with adverse outcomes. Cellular mechanisms underlying AKI and kidney cell responses to injury remain incompletely unders...
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Article
Open AccessHuman alveolar progenitors generate dual lineage bronchioalveolar organoids
Mechanisms of epithelial renewal in the alveolar compartment remain incompletely understood. To this end, we aimed to characterize alveolar progenitors. Single-cell RNA-sequencing (scRNA-seq) analysis of the H...
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Article
Virus-induced senescence is a driver and therapeutic target in COVID-19
Derailed cytokine and immune cell networks account for the organ damage and the clinical severity of COVID-19 (refs. 1–4). Here we show that SARS-CoV-2, like other viruses, evokes cellular senescence as a primary...
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Article
Open AccessAuthor Correction: Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses
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Open AccessIntegrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses
Inactivation of RB is one of the hallmarks of cancer, however gaps remain in our understanding of how RB-loss changes human cells. Here we show that pRB-depletion results in cellular reprogramming, we quantita...
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Open AccessTemporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19
In COVID-19, immune responses are key in determining disease severity. However, cellular mechanisms at the onset of inflammatory lung injury in SARS-CoV-2 infection, particularly involving endothelial cells, r...
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Open AccessSARS-CoV-2-mediated dysregulation of metabolism and autophagy uncovers host-targeting antivirals
Viruses manipulate cellular metabolism and macromolecule recycling processes like autophagy. Dysregulated metabolism might lead to excessive inflammatory and autoimmune responses as observed in severe and long...
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Article
Open AccessIntegrative functional genomics decodes herpes simplex virus 1
The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection...
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Open AccessSingle-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program
Herpesvirus infection initiates a range of perturbations in the host cell, which remain poorly understood at the level of individual cells. Here, we quantify the transcriptome of single human primary fibroblas...
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Open AccessWidespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection
Herpesviruses can infect a wide range of animal species. Herpes simplex virus 1 (HSV-1) is one of the eight herpesviruses that can infect humans and is prevalent worldwide. Herpesviruses have evolved multiple ...
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Open AccessRattus norvegicus BN/SHR liver and heart left ventricle ribosomal RNA depleted directional RNA sequencing
The spontaneously hypertensive rat strain is a frequently used disease model. In a previous study, we measured translational efficiency from this strain and BN-Lx animals. Here, we describe long RNA sequencing re...
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Open AccessJACUSA: site-specific identification of RNA editing events from replicate sequencing data
RNA editing is a co-transcriptional modification that increases the molecular diversity, alters secondary structure and protein coding sequences by changing the sequence of transcripts. The most common RNA edi...
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Article
Detecting actively translated open reading frames in ribosome profiling data
RiboTaper quantifies the three-nucleotide periodicity in Ribo-seq data to find translated open reading frames (ORFs). The de novo inferred set of ORFs comprehensively defines the cellular proteome across a wide e...
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Article
Open AccessRC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway
The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNFα mRNA decay via a 3′UTR constitutive decay element (CDE). Here we applied PAR-CLIP to human RC3H1 to identify ∼3,800 mRNA targets with >16,000 ...
