Michał I. Świrski

The paper shows EWSR1::FLI1 fusion drives the production of cancer-specific neoproteins in Ewing sarcoma, revealing a reversible dark proteome with therapeutic potential.

The paper defines an extended translation initiation sequence (eTIS) and shows that a deep-learning model trained on eTIS features accurately predicts translation initiation, revealing that the Kozak sequence is not optimal and identifying conserved nucleotides that enhance initiation efficiency.

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

The paper determines the structure of the ribosome stalled by the AMD1 C-tail, revealing how it traps eRF1 and ABCE1 to block translation termination.

The paper identifies a novel RNA stimulator that enhances +1 ribosomal frameshifting in yeast by promoting P-site tRNA re-pairing, revealing two distinct frameshifting mechanisms.

The paper expands and refines a reference catalog of human non-canonical open reading frames (ncORFs) by incorporating more datasets and introducing a translation signature score framework to prioritize high-quality ncORFs.

CHOPOFF improves CRISPR off-target detection by addressing limitations in symbolic alignments and introducing efficient data structures for accurate and fast prediction.

This paper introduces Ribosome Decision Graphs (RDGs) to represent eukaryotic RNA translation complexity, enabling analysis of translation patterns and genetic variation effects.

The paper identifies a stem-loop and modified adenines in the uORF2/ATF4 overlap that regulate ATF4 translation under stress, revealing a more complex mechanism than previously thought.

The paper identifies diverse genome decoding mechanisms in yeast that generate functionally distinct proteoforms and improves genome annotation.

ORFik is an R/Bioconductor toolkit for analyzing translation data, supporting multiple high-throughput assays and providing over 30 translation-related metrics.