Markus Landthaler

Global quantification of mammalian gene expression noise

The paper quantifies gene expression noise in mammalian cells using single-cell proteomics and finds that noise is largely extrinsic and structured across cellular states.

Distinct roles for MNK1 and MNK2 in social and cognitive behavior through kinase-specific regulation of the synaptic proteome and phosphoproteome

This study shows that MNK1 and MNK2 have distinct roles in social and cognitive behaviors by regulating different aspects of the synaptic proteome and phosphoproteome in knockout mice.

Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation

The paper identifies CRISPRa-responsive enhancers and their target genes in a 2 Mb region around PHOX2B using TESLA-seq, revealing both known and novel regulatory relationships.

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.

The Establishment of Cell-Type Specific Gene Regulation in the Sea Urchin Embryo

This study creates a single-cell atlas of gene expression, transcription, and chromatin accessibility in sea urchin embryos, revealing dynamic regulatory elements and lineage-specific gene activation patterns.

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.

Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting

The paper measures mRNA flow rates between subcellular compartments in mouse embryonic stem cells and identifies nuclear retention as the rate-limiting step for many mature mRNAs.

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.

AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor

The paper presents an AI-guided pipeline for PPI drug discovery, identifying a SARS-CoV-2 inhibitor by combining experimental assays, machine learning, and virtual screening.

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.

A critical period of translational control during brain development at codon resolution

The paper measures translation dynamics in mouse neocortex neurogenesis, revealing a critical period of translational control that regulates protein expression and neuronal differentiation.

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.

Spatio-temporal mRNA dynamics in the early zebrafish embryo

The paper uses spatial transcriptomics and single-cell RNA labeling to study mRNA localization and dynamics in early zebrafish embryos, revealing transport to primordial germ cells and evolutionary conservation.

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.

The architecture of protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit

The paper reveals Ebp1's role in neuronal proteostasis by analyzing ribosomal architecture and proteomic changes in the developing mouse neocortex.

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.

Codon Bias Confers Stability to mRNAs via ILF2 in Humans

The paper shows that codon bias affects mRNA stability in humans through ILF2, with GC3 codons stabilizing and AT3 codons destabilizing mRNA.

Quantifying multi-layered expression regulation in response to stress of the endoplasmic reticulum

The paper quantifies gene expression regulation at multiple layers in response to ER stress in cervical cancer cells over time, identifying shared and stress-specific regulatory events.