Samuel Marguerat

Denaturing purifications support direct interaction between PRC2 and RNA in cells

The paper reanalyzes CLAP data to show PRC2 directly interacts with RNA in cells, correcting previous findings that missed this interaction due to a scaling step.

Aging-associated long non-coding RNA boosts longevity and reduces the ribosome content of non-dividing fission yeast cells

This study identifies a lncRNA, aal1, that extends lifespan in fission yeast by reducing ribosome content and protein translation, with similar effects observed in Drosophila.

A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes

This paper develops a coarse-grained resource allocation model to explain cellular growth laws and resource allocation strategies in unicellular microbes.

Modelling capture efficiency of single cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics

The paper develops a method to model capture efficiency in scRNA-seq data to improve inference of transcriptome-wide burst kinetics.

Fission yeast obeys a linear size law under nutrient titration

This paper investigates how cell size and geometry in fission yeast vary under different growth conditions and finds that cell volume and growth rate follow a linear scaling under nitrogen and carbon titration.

Large-scale changes of molecular network states explain complex traits

The paper identifies a central state transition in yeast molecular networks linked to PKA and TOR signaling, showing how genetic variants can cause global or local molecular changes affecting multiple cellular traits.

Growth-Rate Dependent And Nutrient-Specific Gene Expression Resource Allocation In Fission Yeast

This study investigates how growth rate and nutrient-specific factors influence gene expression in fission yeast, revealing coordinated and condition-specific regulation of metabolic enzymes.

Functional profiling of long intergenic non-coding RNAs in fission yeast

The paper functionally profiles long intergenic non-coding RNAs (lincRNAs) in fission yeast by analyzing mutant phenotypes across various conditions.

R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements

The paper identifies age-related genome rearrangements in non-dividing fission yeast cells, linking them to R-loops and regulatory changes, and finds similar patterns in human brain cells.

Size-dependent increase in RNA Polymerase II initiation rates mediates gene expression scaling with cell size

The paper investigates how RNA Polymerase II initiation rates scale with cell size in fission yeast, showing that RNAPII is a limiting factor for transcriptional scaling.

bayNorm: Bayesian gene expression recovery, imputation and normalisation for single cell RNA-sequencing data

bayNorm provides a Bayesian method for normalizing, imputing, and recovering gene expression in scRNA-seq data, improving accuracy and reducing batch effects.

Single-cell phenotyping and RNA sequencing reveal novel patterns of gene expression heterogeneity and regulation during growth and stress adaptation in a unicellular eukaryote

The paper uses scRNA-seq and imaging to study gene expression heterogeneity in fission yeast under different environmental conditions, revealing how gene expression varies during growth and stress responses.

Condensin controls cellular RNA levels through the accurate segregation of chromosomes instead of directly regulating transcription

This study shows condensin affects RNA levels by causing chromosome missegregation, not by directly regulating transcription.

Long non-coding RNA repertoire and regulation by nuclear exosome, cytoplasmic exonuclease and RNAi in fission yeast

The paper identifies 5775 novel lncRNAs in fission yeast and characterizes their regulation by RNA-processing pathways.

Division rate, cell size and proteome allocation: impact on gene expression noise and implications for the dynamics of genetic circuits

The paper models stochastic gene expression in growing cells to show how division rates affect noise in mRNA and protein levels, and how cell size regulation impacts circuit robustness.

Skip and bin: pervasive alternative splicing triggers degradation by nuclear RNA surveillance in fission yeast

This study identifies pervasive alternative splicing in fission yeast, showing that exon-skipping transcripts are mostly non-functional and degraded by nuclear RNA surveillance.

Proportionality: a valid alternative to correlation for relative data

The paper introduces proportionality as an alternative to correlation for analyzing relative compositional data, demonstrating its validity using yeast gene expression data.