Florian Erhard

Robust ORF Deconvolution from Multiple Ribo-seq Datasets with Group LASSO Penalty

PRICE 2 improves detection of short and overlapping ORFs using group LASSO regularization, outperforming existing tools and enabling discovery of more cryptic MHC-I peptides.

Glycosylated GM-CSF expands B-1b cells and B-1b plasma cells and programs them for immunosuppression

This study shows glycosylated GM-CSF expands immunosuppressive B-1b plasma cells and promotes regulatory functions, while non-glycosylated GM-CSF drives pro-inflammatory responses.

Exonuclease ISG20 inhibits human cytomegalovirus replication by inducing an innate immune defense signature

This study identifies ISG20 as an antiviral factor against HCMV by inducing an innate immune defense signature that enhances IFN production and response.

Single-cell RNA-seq using UltraMarathonRT expands the known transcriptome

This paper introduces UltraMarathonRT for scRNA-seq, revealing new transcriptomic features and demonstrating its utility in capturing additional genes and genomic elements.

tRNA modifications are required for stress granule formation and melanoma metastasis

This study shows that tRNA modification mcm5s2U34 is essential for stress granule formation and melanoma metastasis, suggesting it as a therapeutic target.

Respiratory syncytial virus load-dependent ciliated cell dedifferentiation and downregulation of immune response genes

This study shows RSV causes ciliated cell dedifferentiation and downregulates immune response genes, with IRF1 remaining expressed and reducing viral replication.

SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant tumor cells

This study uses SILAC-based quantification to analyze how MAPK inhibitors affect the immunopeptidome in melanoma cells, identifying potential targets for immunotherapy.

SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomes

The paper uses SLAM-seq and scRNA-seq to show RNA processing and stability independently influence mRNA levels in African trypanosomes.

Identifying Modulators of Cellular Responses by Heterogeneity-sequencing

Heterogeneity-seq identifies causal factors driving heterogeneous cellular responses by combining single-cell RNA-seq with metabolic labeling and double machine learning.

Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data

The paper develops computational methods to correct 4sU-induced quantification bias in nucleotide conversion RNA-seq data by addressing mappability and reverse transcription efficiency issues.

HSV-1 infection induces a downstream shift of promoter-proximal pausing for most host genes

This study shows HSV-1 infection causes a downstream shift in promoter-proximal Pol II pausing for most host genes, more pronounced than NELF depletion.

Single-cell temporal dynamics reveals the relative contributions of transcription and degradation to cell-type specific gene expression in zebrafish embryos

The paper quantifies transcription and degradation rates of mRNA in zebrafish embryos to understand their roles in cell-type specific gene expression.

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.

grandR: a comprehensive package for nucleotide conversion sequencing data analysis

grandR provides tools for analyzing nucleotide conversion sequencing data, including quality control, differential expression, and kinetic modeling, with a Bayesian approach for temporal RNA dynamics.

U1 snRNP-dependent suppression of miRNA biogenesis by alternative intronic polyadenylation in melanoma

The paper shows that U1 snRNP-dependent intronic polyadenylation suppresses miRNA biogenesis in melanoma by altering TRPM1 alternative polyadenylation signals.

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.

Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation

This study shows HSV-1 infection causes widespread changes in host mRNA alternative polyadenylation, with ICP27 playing a role in shifting polyadenylation to intronic sites and affecting mRNA export and expression.

scSLAM-seq reveals core features of transcription dynamics in single cells

scSLAM-seq measures transcription dynamics in single cells by distinguishing newly synthesized from pre-existing RNA, revealing stochastic transcription and gene-specific differences.