Emanuel Wyler

Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated transcriptome in human cells

This study rapidly depletes UPF1 in human cells to investigate NMD-regulated transcriptome dynamics, identifying core transcripts and biological processes affected.

Rewired type I IFN signaling is linked to age-dependent differences in COVID-19

This study identifies age-related rewiring of type I IFN signaling in immune cells linked to increased inflammation and altered antibody responses in COVID-19.

Merkel cell polyomavirus infection and persistence modelled in skin organoids

This paper demonstrates that iPSC-derived skin organoids support MCPyV infection, persistence, and tumor development, providing a model to study viral interactions with the immune system and treatment strategies.

Complex Human hear bearing Skin Organoids reveal Cell Type Specific Susceptibility and Innate Immune Responses to Herpes Simplex Virus 1

This study uses human hair-bearing skin organoids to investigate HSV-1 infection and host responses, revealing cell-type-specific susceptibility and spatially organized immune reactions.

Dissecting the role of RNA-binding proteins in early herpes simplex virus 1 transcription using acute protein depletion

The paper investigates the role of five RNA-binding proteins in HSV-1 transcription and their impact on viral replication, finding that SPT5 is essential for immediate-early gene expression while SFPQ has a different regulatory role.

Poxviruses induce a nuclear environment in the cytoplasm to promote viral replication

This study investigates the cellular response to poxvirus infection, showing that MVA activates innate immune genes, while Camelpoxvirus activates NF-kB signaling, and poxviruses induce nuclear remodeling by transporting nuclear proteins into viral factories.

Comprehensive profiling of wastewater viromes by genomic sequencing

The paper longitudinally analyzes wastewater viromes to track viral diversity and detect pathogens, identifying thousands of novel viral transcripts.

DNA virus infections shape transposable elements activity in vitro and in vivo

This study shows DNA virus infections activate transposable elements (TEs) through KAP1/TRIM28 inhibition and DUX4 expression, with in vivo correlations in cancer patients.

VoltRon: A Spatial Omics Analysis Platform for Multi-Resolution and Multi-omics Integration using Image Registration

VoltRon is an R package for spatial omics analysis that integrates multi-resolution and multi-omics data through image registration and spatial alignment.

The Cytomegalovirus M35 Protein Modulates Transcription of Ifnb1 and Other IRF3-Driven Genes by Direct Promoter Binding

This paper identifies M35 as a viral protein that binds DNA and inhibits IRF3-mediated gene expression, including Ifnb1, thereby suppressing the antiviral type I IFN response.

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19

This study links gut microbiota dysbiosis and altered tryptophan metabolism to increased inflammation in severe COVID-19 patients.

De Novo Whole Genome Assembly of the Roborovski Dwarf Hamster (Phodopus roborovskii) Genome, an Animal Model for Severe/Critical COVID-19

In vitro Kinase-to-Phosphosite database (iKiP-DB) predicts kinase activity in phosphoproteomic datasets

The paper introduces iKiP-DB, a database that predicts kinase activity from phosphoproteomic data, showing its effectiveness in analyzing both well-known and understudied kinases.

Insights into standards of care: dexamethasone and antibodies against COVID-19 in hamster models

The paper evaluates dexamethasone and anti-SARS-CoV-2 antibodies in hamster models, showing reduced viral burden with antibodies and anti-inflammatory effects with dexamethasone, with synergistic benefits when combined.

Transcriptomic responses of the human kidney to acute injury at single cell resolution

This study uses single-nuclei transcriptomics to analyze human kidney injury responses, identifying four injury-associated cell states and showing similar gene expression changes between AKI patients with and without COVID-19.

The zinc finger antiviral protein ZAP destabilises viral transcripts and restricts cytomegalovirus

This study shows that ZAP restricts HCMV infection by destabilizing viral transcripts with low CG content, revealing its role in antiviral defense against DNA viruses.

DDX3 depletion represses translation of mRNAs with complex 5' UTRs

This study identifies mRNAs regulated by DDX3 depletion using ribosome profiling and RNA-seq, showing DDX3 preferentially affects a subset of transcripts with complex 5' UTRs.

Neurodegeneration in human brain organoids infected with herpes simplex virus type 1

This study infects human brain organoids with HSV-1 and identifies molecular and cellular changes associated with neurodegeneration.

Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention

The paper uses bulk and single-cell transcriptomics to analyze SARS-CoV-2 infection in human cell lines, identifying HSP90 as a potential therapeutic target.

CRNKL1 is a highly selective regulator of intron-retaining HIV-1 and cellular mRNAs

The paper identifies CRNKL1 as a regulator that enhances nuclear retention of intron-retaining HIV-1 and cellular mRNAs, affecting their cytoplasmic levels.

Single-cell RNA-sequencing of Herpes simplex virus 1-infected cells identifies NRF2 activation as an antiviral program

The paper uses single-cell RNA-sequencing to study HSV-1 infection in human fibroblasts, identifying NRF2 activation as an antiviral response that reduces virus production.

A spectral analysis approach to detect actively translated open reading frames in high-resolution ribosome profiling data

RiboTaper identifies actively translated open reading frames using spectral analysis of Ribo-seq data, revealing novel ORFs and validating peptide products in HEK293 cells.