Can Cenik

RiboFlow v2 improves ribosome profiling analysis by incorporating genome alignment and configurable handling of multimapping reads, revealing gene-specific differences in coverage and translation efficiency.

The paper investigates the relationship between allele-specific expression and translational efficiency in mouse embryos and stem cells, finding lower translational efficiency associated with allelic imbalance.

Ribo-ITP identifies thousands of translons from low-input samples, revealing their regulatory roles and impact on cell growth.

The paper identifies four stages of forelimb initiation in mouse embryos using scRNA-seq and other sequencing methods, revealing TBX5-target genes involved in limb development.

The paper uses deep mutational scanning to study the TRPM8 channel's pore region, revealing how structural elements coordinate gating and ion selectivity in response to menthol and cold.

The paper analyzes translational buffering across human and mouse datasets, finding conserved patterns and highlighting the role of cellular context in gene expression regulation.

The paper identifies a cytoplasmic surveillance pathway that detects and degrades faulty ribosomes during biogenesis but allows defective ribosomes to escape into translation if they bypass the pathway.

The paper identifies a ribosomal mutation conferring cycloheximide resistance in C. elegans and shows it alters translation efficiency and developmental timing without activating stress pathways.

The paper predicts translation efficiency (TE) of mRNA in mammalian cells using a deep learning model trained on ribosomal profiling data across multiple cell types.

The paper analyzes ribosome profiling data to show translation efficiency covariation (TEC) is conserved across human and mouse cells, revealing gene functions not evident from RNA or protein co-expression.

The paper measures mRNA translation in C. elegans embryos and identifies stage-specific translational regulation and the role of OMA-1 in repressing and promoting translation of target mRNAs.

The paper uses long-read RNA sequencing to detect allele-specific N6-methyladenosine modifications in human and mouse cells, revealing sequence and allelic factors influencing m6A deposition.

RiboGraph provides an interactive visualization tool for ribosome profiling data, enabling real-time analysis at read length resolution without preprocessing.

This study investigates how haploinsufficiency of ribosomal proteins affects mitochondrial morphology, respiration, and stress responses in C. elegans and human cells.

The paper integrates multiplexed assays to identify cis-regulatory variants affecting COMT gene expression across multiple layers.

The paper identifies how reduced ribosome levels in neural progenitor cells contribute to neurodevelopmental disorders and shows that mTOR activation can alleviate these defects.

The paper shows Reh1 remains on 60S subunits during early translation elongation and is displaced by the growing peptide chain.

This paper develops Ribo-ITP to measure ribosome occupancy in single cells during early mouse development, revealing differential translation efficiency and allele-specific ribosome engagement.

satmut_utils is a tool for simulating and analyzing saturation mutagenesis data, showing that single-codon variants can alter mRNA abundance and demonstrating improved variant calling performance.

The paper identifies genes with 5' terminal oligopyrimidine tracts that escape suppression by SARS-CoV-2 NSP1 through RNA-Seq and ribosome profiling, revealing a role for LARP1 in their preferential translation.

The paper analyzes RNA expression and splicing in a family with a rare Mendelian disorder, revealing disrupted coordination between mitochondrial components and RPL11 transcripts.

The paper identifies a class of human transcripts (5IM) with 5′-intron depletion, specific coding sequence features, and N1-methyladenosine modification, comprising ~20% of human transcripts.

The paper integrates RNA, translation, and protein data to show genetic variation affects translation and protein levels in humans.