Grzegorz R. Kudla

This study models how 3D confinement affects RNA folding and circularization in the Zika virus genome, showing increased circularization under confinement.

The paper uses deep mutational scanning to distinguish disease mechanisms in ERCC2 variants, finding that TTD variants have lower fitness than XP variants.

The paper identifies endogenous double-stranded RNAs in mammalian embryonic stem cells by developing a method combining antibody-based purification and RNase I treatment, revealing transposable elements as their main source.

The paper benchmarks splicing predictors on synthetic gene variants to assess their performance and generalization beyond natural genomes.

The paper identifies missplicing as a common issue in heterologous gene expression and develops a splice-aware optimization algorithm to improve transgene performance.

The paper benchmarks siRNA prediction methods, showing that rigorous cross-validation and z-curve representation improve performance and reliability.

CPLfold improves RNA secondary structure prediction by incorporating chimeric evidence and pseudoknots, achieving better accuracy on long sequences and benchmarks.

The paper functionally characterizes PRKN variants using a pooled assay, reclassifies variants of uncertain significance, and predicts Parkinson's disease age at onset.

The paper identifies molecular domains in the U8 snoRNA affected by LCC mutations and shows how U8 function impacts stability through a post-transcriptional mechanism.

The paper develops a method to estimate enzymatic activities from genetic variants using fitness assays and combines allele effects to predict pathogenicity in recessive diseases.

The paper introduces HiCapR, a method to map HIV-1 RNA structures, homodimers, and long-range interactions, revealing new insights into RNA organization and its role in viral processes.

This study improves sequence-to-expression models by integrating mechanistic sequence features with one-hot encodings, enhancing generalization across Escherichia coli and Saccharomyces cerevisiae datasets.

This paper demonstrates that active learning improves regulatory DNA sequence optimization for yeast promoters, outperforming one-shot methods in complex landscapes.

The paper uses deep mutational scanning to assess the functional impact of INSR variants, identifying clinically relevant function scores and potential gain-of-function variants.

The paper uses deep mutational scanning to quantify PAX6:DNA binding and predict clinical outcomes of variants, finding most pathogenic mutations affect DNA binding.

The paper maps RNA homodimers in living cells using proximity ligation methods, revealing their rarity across the transcriptome and enrichment in specific RNAs and viral genomes.

The paper identifies HAX1 RNA targets and shows its role in ribosome biogenesis and translation, linking it to disease mechanisms.

The paper investigates the structural features of the NORAD lncRNA and their role in modulating Pumilio protein activity through RNA structure and interactions.

This study maps the in vivo RNA-RNA interactome of SARS-CoV-2 during its life cycle, revealing structural features and dynamics that regulate replication, transcription, and frameshifting.

The paper systematically explores RNA-ligand interactions by analyzing mutations in an RNA aptamer, revealing complex phenotypic effects and training a model to predict RNA structure from epistasis.

The paper shows splicing enhances expression of AT-rich genes by increasing mRNA stability and cytoplasmic localization, while GC-rich genes are less affected by splicing.

The paper shows that synonymous codon usage affects bacterial fitness through translation-independent RNA toxicity, identifying mRNA sequence determinants and suppressor strains.