Mihaela Zavolan

This study identifies PAIP1 as a cofactor for mRNA export and shows it couples nuclear to cytoplasmic mRNP remodeling and poly(A) homeostasis, affecting mRNA stability and development.

The paper shows that SYBR Gold fluorescence is strongly influenced by guanosines in single-stranded nucleic acids, impacting its use in nucleic acid quantification.

The paper identifies H1 histone variants as regulators of transcriptional programs in autism with 16p11.2 deletion, showing their upregulation and link to MAZ.

This study shows Arf1 regulates TORC1 activity in yeast by both inhibiting and promoting its function under different stress conditions.

This study uses ribosome profiling to show that steatohepatitis-associated HCC has extensive translational alterations affecting hundreds of genes and revealing novel translated regions.

The paper identifies new interactors of eIF3f in human muscle cells using BioID technology, revealing both nuclear and cytoplasmic interactions relevant to muscle structure and function.

The paper shows heat shock increases silent ribosomes and reorganizes mRNA turnover in yeast by prioritizing heat-shock protein synthesis over ribosome biogenesis.

This study identifies mRNA deadenylation as a key mechanism regulating body plan formation in mouse gastruloids by affecting mesoderm and endoderm differentiation.

This study evaluates deep learning models' ability to predict mRNA translation from 5UTR sequences, finding poor generalization to endogenous mRNAs compared to reporter constructs.

The paper benchmarks eight tools for identifying and quantifying alternative polyadenylation sites from RNA-seq data using real, synthetic, and 3'-end sequencing data.

The paper identifies CCAR1 as a splicing fidelity factor that regulates alternative splicing of FANCA and other genes, impacting DNA repair processes.

RCRUNCH improves eCLIP data analysis to identify RNA-binding protein binding sites and motifs, creating a comprehensive resource of in vivo-bound RBP sequence motifs.

This study identifies RPL39L as an efficiency factor in cotranslational folding of alpha helical proteins by analyzing its expression, ribosome structure, and impact on translation dynamics.

This study uses single-cell RNA sequencing to compare gene expression variation in unstimulated macrophages from BALB/c and C57BL/6 mice, revealing intrinsic differences and polarization patterns.

The paper introduces MAPP, a method to infer RNA-binding protein impacts on pre-mRNA processing from RNA-seq data, revealing co-regulation of splicing and polyadenylation.

ZARP is an RNA-seq analysis workflow that automates data processing using Snakemake, reducing hands-on time for users by integrating best practices and generating detailed reports.

The paper develops a computational method to analyze 3' UTR length changes in tumor tissues and finds widespread shortening of 3' UTRs in LUAD, suggesting APA plays a role in protein metabolism.

The paper uses long-read sequencing to identify novel NMD-sensitive mRNAs and reveals features of their biogenesis and biological role.

This study examines how 3D extracellular matrix scaffolds affect the transcriptome of hepatoma cells, aiming to understand their growth and differentiation potential in 3D cultures.

This paper introduces a Bayesian normalization method for scRNA-seq data that improves clustering and differential expression analysis by accounting for biological and technical noise.

The paper develops PAQR and KAPAC to analyze PAS use and motif activities in RNA-seq data, identifying Polypyrimidine tract binding protein 1 as a regulator of PAS choice in glioblastoma.

This paper introduces a new model for transcription factor binding site prediction that accounts for pairwise dependencies between positions, outperforming existing methods on ChIP-seq and HT-SELEX data.

The paper develops computational methods to identify C/D box snoRNA targets using CLIP and RiboMeth-seq data, revealing new insights into snoRNA-guided 2-O-ribose methylation.

The paper uses single-cell sequencing and mathematical modeling to estimate miRNA target parameters and uncover their in vivo hierarchy.

This study shows that EWSR1 prevents DNA double-strand breaks by binding to intronic regions in its own locus and maintaining genomic stability.

The paper analyzes 3′ end sequencing data to identify novel polyadenylation signals and demonstrates HNRNPC's repressive role in poly(A) site usage and 3′ end processing.