Jakub Wiktor Wojciechowski

This paper evaluates AlphaFold3's ability to predict amyloid structures using three datasets, finding it performs better on known fibrillar structures but struggles with non-fibrillar and short fragments.

The paper introduces metagenomic-deepFRI, a framework that integrates protein structure models into functional annotation pipelines, improving GO term prediction confidence and coverage in metagenomic datasets.

The paper identifies gut microbiome functional amyloids and links their abundance to neurodegenerative diseases like Parkinson's and Alzheimer's.

PACT predicts amyloid cross-interactions by modeling fibril stability, achieving high AUC and F1 scores on AmyloGraph data and validating interactions between CsgA and Alpha-synuclein.

The paper analyzes fungal NLR proteins to identify effector domains and amyloid signaling motifs using bioinformatics and structural prediction tools, revealing new domains and expanded amyloid motif families.

The paper reconstructs the spatiotemporal gene expression blueprint for C. elegans pharyngeal cuticle construction and identifies phase-separating proteins involved in cuticle remodeling.