Pavel V. Baranov

This study introduces TISCA2 and IncepTIS to map and predict stress-responsive translation initiation sites, revealing tissue-specific patterns and enabling engineered mRNA 5' leaders.

The paper shows that reduced electron flux through complex IV leads to cytochrome c accumulation via increased stability and membrane retention, without increasing apoptosis sensitivity.

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.

This study examines early transcriptional and translational changes in human T cells within four hours of activation, revealing dynamic gene expression and translation initiation patterns.

The paper identifies essential uORFs for cell proliferation in human cell lines and shows their regulatory role through cis-elements and variant disruption.

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.

The paper assesses MS-based identifications of unannotated human microproteins, finding large variation in reported proteins and PSM quality across studies.

The paper identifies a programmed ribosomal frameshifting event in PLEKHM2 mRNA that generates a constitutively active protein domain essential for lysosome transport and cardiac function.

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 thousands of non-AUG initiated proteoforms in humans and mice, many lacking evolutionary selection evidence, using ribo-seq and phylogenetic analysis.

This paper outlines a community-driven initiative to create a consolidated catalog of human Ribo-seq ORFs, addressing the lack of standardized annotation for these features.

The paper investigates how alternative transcription start sites regulate the production of cytosolic and mitochondrial branched-chain aminotransferase proteoforms in Kluyveromyces marxianus, showing condition-specific regulation by transcription factors.

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

The paper develops a ribosome profiling protocol for Kluyveromyces marxianus and provides tools for data analysis and sharing.

The paper identifies a novel protein, POLGARF, encoded by an overlapping reading frame in POLG mRNA, showing efficient CUG initiation and evolutionary origins via MIR transposition.

The paper uses retapamulin-assisted ribosome profiling to identify alternative translation start sites in E. coli, revealing new proteins and regulatory roles.

The paper develops a computational model to explain how a single upstream open reading frame (uORF) can upregulate downstream ORF translation during the Integrated Stress Response.