Ágnes Tóth-Petróczy

Pinc: a simple probabilistic AlphaFold interaction score

The paper introduces Pinc, a simple probabilistic score to assess interface confidence in AlphaFold models, showing it matches or exceeds complex methods' performance.

How are evolutionarily young and old proteins distributed in sequence space?

The paper compares the distribution of young de novo proteins, old canonical proteins, and randomized sequences in sequence space using k-mer-based distances, finding distinct patterns and potential pathways between classes.

Regulatory landscape of widespread stop codon readthrough in Drosophila

The paper identifies 1,400 stop codon readthrough genes in Drosophila, reveals sequence features associated with programmed readthrough, and shows conserved cis-elements functional in mammalian cells.

Amino acid and codon usage explain amino acid misincorporation rates across the tree of life

The paper analyzes amino acid misincorporation rates across 14 species, finding that codon and amino acid usage explain error rates, with 70% of errors due to codon-anticodon mispairing.

Ribosomal frameshifting is a carefully tuned modifier of proteins

The paper identifies and characterizes ribosomal frameshifting sites across organisms, showing their prevalence and evolutionary tuning to mitigate harmful effects.

Born to Condense: Polysomes Drive Co-Translational Condensation of Biomolecular Condensate Proteins

This paper introduces a theoretical framework for co-translational condensation (CTC), showing how polysomes drive the formation of biomolecular condensates through protein synthesis.

PICNIC accurately predicts condensate-forming proteins regardless of their structural disorder across organisms

PICNIC predicts condensate-forming proteins across organisms by analyzing sequence and structure, outperforming existing methods and showing no correlation between disorder content and predicted condensate proteome across species.

SHARK enables homology assessment in unalignable anddisordered sequences

SHARK-dive, an alignment-free method, accurately assesses homology in unalignable and disordered sequences, improving functional annotation of intrinsically disordered regions.

ENVIRONMENT MODULATES PROTEIN HETEROGENEITY THROUGH TRANSCRIPTIONAL AND TRANSLATIONAL STOP CODON MISCODING

The paper quantifies stop codon miscoding in E. coli under stress, showing up to 80% error rates and environmental regulation of protein heterogeneity.

Characterization of Alternative Splicing During Mammalian Brain Development Reveals the Magnitude of Isoform Diversity and its Effects on Protein Conformational Changes

The paper characterizes alternative splicing during mammalian brain development, revealing extensive isoform diversity and its impact on protein conformational changes.

DeMAG predicts the effects of variants in clinically actionable genes by integrating structural and evolutionary epistatic features

DeMAG improves variant classification by integrating structural and evolutionary epistatic features, reducing false positives and improving accuracy for clinically actionable genes.

Pathway-based Rare Variant Burden Analysis Identifies a Role for the Complement System in an Extreme Phenotype of Sepsis with Coagulopathy

The paper identifies rare variants in the complement system associated with severe sepsis with coagulopathy using pathway-based analysis of whole exome sequencing data.

Homozygous TRPV4 mutation causes congenital distal spinal muscular atrophy and arthrogryposis

This study identifies a homozygous TRPV4 mutation as a cause of congenital spinal muscular atrophy and arthrogryposis through whole exome sequencing and functional analysis.

The EVcouplings Python framework for coevolutionary sequence analysis

The paper introduces EVcouplings, a Python framework for coevolutionary sequence analysis that enables structure prediction and mutation effect assessment.